exceeds matrix dimensions when running denoise #1

annapbarnes · 2020-08-06T19:05:28Z

HI

When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs?

**Current indexing filetype: *rNEST*rsfMRI.nii

Index exceeds matrix dimensions.

Error in
brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)]
(line 413)
mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x);
mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise>check_masks (line 413)
mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x);
mask_files_tmp{3}(x); mask_files_tmp{4}(x)],...

Error in brant_run_denoise (line 71)
[mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths,
denoise_infos.space_mask, nm_pos);

Error in brant_preprocess_jobman (line 164)
end_prefix = brant_run_denoise(working_dir,
run_data.(processes_curr{m}), run_data.subjs.files, subj_ids,
data_input.is4d, output_dirs, jobman.subj.out.nmpos);

Error in brant_preprocess>run_cb (line 343)
brant_preprocess_jobman(jobman, gcf);

Error while evaluating UIControl Callback**

Anna

The text was updated successfully, but these errors were encountered:

YongLiuLab · 2020-08-07T00:34:04Z

Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. Very best Yours Yong From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant <brant@noreply.github.com> Cc: Subscribed <subscribed@noreply.github.com> Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) HI When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? Anna — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif>

annapbarnes · 2020-08-07T08:26:45Z

Yes of course Error message, screenshot and log file attached **Current indexing filetype: *rNEST*rsfMRI.nii Index exceeds matrix dimensions. Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos); Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos); Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf); Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu ***@***.***> wrote: Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. Very best Yours Yong From: ***@***.*** ***@***.*** On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant ***@***.***> Cc: Subscribed ***@***.***> Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) HI When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? Anna — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ>.

DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1*.nii ft_wm: rc2*.nii ft_csf: rc3*.nii mask_res_type: nearest neighbour ft_motion: rp*.txt Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08 Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

YongLiuLab · 2020-08-07T09:01:09Z

I think maybe you need to check “*rNEST*rsfMRI.nii see how many time points, or how many nii files in the same directory Then double-check the rp*.txt, how many time points. I guess maybe you have so many nii files be read by the brant. Very best Yours Yong From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant <brant@noreply.github.com> Cc: Yong Liu <yliu@nlpr.ia.ac.cn>; Comment <comment@noreply.github.com> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Yes of course Error message, screenshot and log file attached **Current indexing filetype: *rNEST*rsfMRI.nii Index exceeds matrix dimensions. Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos); Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos); Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf); Error while evaluating UIControl Callback**

On 7 Aug 2020, at 01:34, Yong Liu ***@***.*** ***@***.***> > wrote: Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. Very best Yours Yong From: ***@***.*** ***@***.***> ***@***.*** On Behalf Of annapbarnes Sent: Friday, August 07, 2020 3:06 AM To: YongLiuLab/brant ***@***.*** ***@***.***> > Cc: Subscribed ***@***.*** ***@***.***> > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) HI When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? Anna — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ>.

DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1*.nii ft_wm: rc2*.nii ft_csf: rc3*.nii mask_res_type: nearest neighbour ft_motion: rp*.txt Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08 Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif>

annapbarnes · 2020-08-07T09:27:09Z

Hi Yong I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file thank you - your GUI is very nice and it is great that you have put all your tools together like this. Anna

…

On 7 Aug 2020, at 10:01, Yong Liu ***@***.***> wrote: I think maybe you need to check “*rNEST*rsfMRI.nii see how many time points, or how many nii files in the same directory Then double-check the rp*.txt, how many time points. I guess maybe you have so many nii files be read by the brant. Very best Yours Yong From: ***@***.*** ***@***.*** On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant ***@***.***> Cc: Yong Liu ***@***.***>; Comment ***@***.***> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Yes of course Error message, screenshot and log file attached **Current indexing filetype: *rNEST*rsfMRI.nii Index exceeds matrix dimensions. Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos); Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos); Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf); Error while evaluating UIControl Callback** > On 7 Aug 2020, at 01:34, Yong Liu ***@***.*** ***@***.***> > wrote: > > > Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. > > > > > > > > Very best > > Yours > > Yong > > > > From: ***@***.*** ***@***.***> ***@***.*** On Behalf Of annapbarnes > Sent: Friday, August 07, 2020 3:06 AM > To: YongLiuLab/brant ***@***.*** ***@***.***> > > Cc: Subscribed ***@***.*** ***@***.***> > > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > HI > > When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? > > Anna > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub <#1> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif> > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ>. > DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1*.nii ft_wm: rc2*.nii ft_csf: rc3*.nii mask_res_type: nearest neighbour ft_motion: rp*.txt Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08 Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA7R5VC4DRHTPB3VT7LR7O7GJANCNFSM4PW4JKFQ>.

YongLiuLab · 2020-08-09T07:56:59Z

Yes, pls double-check it to make sure you have No of “*rNEST*rsfMRI.nii” = size (‘rp*.txt’,1) in the same directory. Any further question, please let me know. Very best Yours Yong From: bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com [mailto:bounces+848413-4538-yliu=nlpr.ia.ac.cn@sgmail.github.com] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant <brant@noreply.github.com> Cc: Yong Liu <yliu@nlpr.ia.ac.cn>; Comment <comment@noreply.github.com> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hi Yong I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file thank you - your GUI is very nice and it is great that you have put all your tools together like this. Anna

On 7 Aug 2020, at 10:01, Yong Liu ***@***.*** ***@***.***> > wrote: I think maybe you need to check “*rNEST*rsfMRI.nii see how many time points, or how many nii files in the same directory Then double-check the rp*.txt, how many time points. I guess maybe you have so many nii files be read by the brant. Very best Yours Yong From: ***@***.*** ***@***.***> ***@***.*** On Behalf Of annapbarnes Sent: Friday, August 07, 2020 4:27 PM To: YongLiuLab/brant ***@***.*** ***@***.***> > Cc: Yong Liu ***@***.*** ***@***.***> >; Comment ***@***.*** ***@***.***> > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Yes of course Error message, screenshot and log file attached **Current indexing filetype: *rNEST*rsfMRI.nii Index exceeds matrix dimensions. Error in brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... Error in brant_run_denoise>check_masks (line 413) mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... Error in brant_run_denoise (line 71) [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, denoise_infos.space_mask, nm_pos); Error in brant_preprocess_jobman (line 164) end_prefix = brant_run_denoise(working_dir, run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, data_input.is4d, output_dirs, jobman.subj.out.nmpos); Error in brant_preprocess>run_cb (line 343) brant_preprocess_jobman(jobman, gcf); Error while evaluating UIControl Callback** > On 7 Aug 2020, at 01:34, Yong Liu ***@***.*** ***@***.******@***.***> ***@***.***> > wrote: > > > Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. > > > > > > > > Very best > > Yours > > Yong > > > > From: ***@***.*** ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > Sent: Friday, August 07, 2020 3:06 AM > To: YongLiuLab/brant ***@***.*** ***@***.******@***.***> ***@***.***> > > Cc: Subscribed ***@***.*** ***@***.******@***.***> ***@***.***> > > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > HI > > When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? > > Anna > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub <#1> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif> > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ>. > DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: rc1*.nii ft_wm: rc2*.nii ft_csf: rc3*.nii mask_res_type: nearest neighbour ft_motion: rp*.txt Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08 Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA7R5VC4DRHTPB3VT7LR7O7GJANCNFSM4PW4JKFQ>.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUSXBLXTSBURLF6J2IDR7PCHXANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQAFZVCJXH4FOCNOZ3R7PCHXA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE7256QI.gif>

annapbarnes · 2020-08-10T09:10:11Z

Hi Yong Definitely have 260 rows in the rp*.txt file and 260 volumes in the 4D *.nii file. Attached is the log file, text file and a link to my data, in individual space https://drive.google.com/file/d/1a-WaU8w04eKMXgS3ocUNsFH1kdBSxyrI/view?usp=sharing <https://drive.google.com/file/d/1a-WaU8w04eKMXgS3ocUNsFH1kdBSxyrI/view?usp=sharing> thanks Anna

On 9 Aug 2020, at 08:57, Yong Liu ***@***.***> wrote: Yes, pls double-check it to make sure you have No of “*rNEST*rsfMRI.nii” = size (‘rp*.txt’,1) in the same directory. Any further question, please let me know. Very best Yours Yong From: ***@***.*** ***@***.*** On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant ***@***.***> Cc: Yong Liu ***@***.***>; Comment ***@***.***> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hi Yong I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file thank you - your GUI is very nice and it is great that you have put all your tools together like this. Anna > On 7 Aug 2020, at 10:01, Yong Liu ***@***.*** ***@***.***> > wrote: > > > I think maybe you need to check > > > > “*rNEST*rsfMRI.nii see how many time points, or how many nii files in the same directory > > > > Then double-check the rp*.txt, how many time points. > > > > I guess maybe you have so many nii files be read by the brant. > > > > > > Very best > > Yours > > Yong > > > > From: ***@***.*** ***@***.***> ***@***.*** On Behalf Of annapbarnes > Sent: Friday, August 07, 2020 4:27 PM > To: YongLiuLab/brant ***@***.*** ***@***.***> > > Cc: Yong Liu ***@***.*** ***@***.***> >; Comment ***@***.*** ***@***.***> > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > Yes of course > Error message, screenshot and log file attached > > **Current indexing filetype: *rNEST*rsfMRI.nii > Index exceeds matrix dimensions. > > Error in > brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] > (line 413) > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > Error in brant_run_denoise>check_masks (line 413) > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > Error in brant_run_denoise (line 71) > [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, > denoise_infos.space_mask, nm_pos); > > Error in brant_preprocess_jobman (line 164) > end_prefix = brant_run_denoise(working_dir, > run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, > data_input.is4d, output_dirs, jobman.subj.out.nmpos); > > Error in brant_preprocess>run_cb (line 343) > brant_preprocess_jobman(jobman, gcf); > > Error while evaluating UIControl Callback** > > > > On 7 Aug 2020, at 01:34, Yong Liu ***@***.*** ***@***.******@***.***> ***@***.***> > wrote: > > > > > > Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. > > > > > > > > > > > > > > > > Very best > > > > Yours > > > > Yong > > > > > > > > From: ***@***.*** ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > > Sent: Friday, August 07, 2020 3:06 AM > > To: YongLiuLab/brant ***@***.*** ***@***.******@***.***> ***@***.***> > > > Cc: Subscribed ***@***.*** ***@***.******@***.***> ***@***.***> > > > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > HI > > > > When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? > > > > Anna > > > > — > > You are receiving this because you are subscribed to this thread. > > Reply to this email directly, view it on GitHub <#1> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif> > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ>. > > > > > DENOISE > Space & Masks > running in individual space. > selected masks' wildcards are > ft_gs: rc1*.nii > ft_wm: rc2*.nii > ft_csf: rc3*.nii > > mask_res_type: nearest neighbour > ft_motion: rp*.txt > > Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 > > Filter options: > TR(s): 2.0 > lower cutoff: 0.01 > upper cutoff: 0.08 > > Process options > Order: Regression first, then filter > save option: all selected options will have output files > gzip option: output files will be saved as input format > GSR option: regression and selected following process will be done with and without GSR > regression output prefix: d > filter output prefix: f > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif> > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA7R5VC4DRHTPB3VT7LR7O7GJANCNFSM4PW4JKFQ>. > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUSXBLXTSBURLF6J2IDR7PCHXANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQAFZVCJXH4FOCNOZ3R7PCHXA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE7256QI.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA4YAJG752ORYQKLOUTR7ZJFPANCNFSM4PW4JKFQ>.

DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: c1*.nii ft_wm: c2*.nii ft_csf: c3*.nii mask_res_type: nearest neighbour ft_motion: rp*.txt Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08 Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 3.3307993e-03 7.6357832e-02 1.7837401e-02 -5.7212151e-05 -9.1547221e-05 3.1301502e-04 1.1045703e-02 -4.8566539e-02 5.5413523e-02 5.4641878e-04 2.4185371e-04 3.8254776e-05 4.0980593e-03 8.7049996e-02 1.0105286e-01 -2.7974734e-04 1.3759804e-04 2.3560535e-04 1.0759222e-02 -7.6154145e-02 6.1559750e-02 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1.2271228e-04 -3.6150113e-03 -9.0141175e-02 -2.9519579e-02 6.1168057e-02 9.6000809e-03 3.0863778e-04 -3.2425938e-03 -8.0014958e-02 1.3701368e-01 6.8627196e-02 9.2280831e-03 4.0498730e-04 -2.7671696e-03 -6.3981071e-02 -2.4222860e-02 8.8179662e-02 1.0211860e-02 8.6134309e-04 -2.8180324e-03 -5.3803840e-02 8.3894567e-02 7.8868506e-02 9.5418829e-03 7.7348932e-04 -2.9366260e-03 -5.4238224e-02 -4.6791539e-02 9.3106381e-02 9.6780495e-03 1.0365282e-03 -3.0383204e-03 -4.9914585e-02 6.0297941e-02 7.9496752e-02 8.9079809e-03 9.2077914e-04 -3.0099493e-03 -4.7571762e-02 -3.8005786e-02 7.6928120e-02 9.4364698e-03 1.1515302e-03 -2.9595845e-03 -5.4455166e-02 1.0663712e-01 9.4289374e-02 8.5740746e-03 8.6697003e-04 -2.6712009e-03 -4.4159663e-02 -5.8517992e-02 5.2161981e-02 9.6982143e-03 1.3034092e-03 -2.9408374e-03 -5.0228471e-02 9.6189276e-03 8.4923582e-02 9.5867329e-03 1.2808920e-03 -2.9947519e-03 -5.0904516e-02 4.1347728e-02 4.9313518e-02 9.5175203e-03 1.3388032e-03 -3.0245171e-03 -5.2464572e-02 -3.0730934e-02 6.0065728e-02 9.5709181e-03 1.4187692e-03 -3.0530555e-03 -5.8464347e-02 5.1842244e-02 7.1734230e-02 9.4784346e-03 1.3682015e-03 -3.0485601e-03 -5.6486504e-02 -2.8626180e-02 5.0363106e-02 9.7707961e-03 1.6052963e-03 -3.2066207e-03 -6.1247194e-02 6.8411954e-02 5.8221844e-02 9.5307512e-03 1.4964219e-03 -2.8924018e-03 -5.2873755e-02 -3.6496147e-02 4.5312874e-02 9.8420366e-03 1.7971649e-03 -3.1184988e-03 -6.2337307e-02 2.8697504e-02 7.8454545e-02 9.9303149e-03 1.6330756e-03 -3.1732515e-03 -5.7434567e-02 2.2036561e-02 5.8094715e-02 1.0063592e-02 1.6610840e-03 -3.4093484e-03 -6.4280858e-02 -4.2757220e-02 9.0698666e-02 1.0723815e-02 1.3597731e-03 -3.7012746e-03 -8.7126539e-02 5.1528145e-02 1.0899859e-01 1.0389357e-02 4.2088635e-04 -3.9484273e-03 -8.6187946e-02 -4.3524158e-02 1.1564132e-01 1.0721588e-02 3.2674072e-04 -3.7553934e-03 -9.0142353e-02 7.8062597e-02 9.2760387e-02 9.9912936e-03 2.8159115e-04 -3.6236680e-03 -8.5454483e-02 -3.5384405e-02 9.5200060e-02 1.0388927e-02 7.8104216e-04 -3.8440345e-03 -8.4641559e-02 8.0601688e-02 9.1999785e-02 1.0389279e-02 5.4705601e-04 -3.6435536e-03 -8.1845872e-02 -1.7014589e-02 1.1595864e-01 1.0864381e-02 8.4354168e-04 -3.7177410e-03 -7.2619905e-02 4.3486199e-02 1.0312556e-01 1.0835300e-02 8.7042791e-04 -3.7413756e-03

annapbarnes · 2020-08-14T07:12:17Z

Hello Did you manage to get take a look at the data set I sent you? Any clues as to what I am doing wrong? Very best wishes Anna Anna Barnes, PhD, CSci, FIPEM IPEM Representative NHS-England National Imaging Optimisation Delivery Board Honorary Associate Professor Centre for Medical Imaging, University College London 43-45 Foley St, London, W1W 7TS

…

On 9 Aug 2020, at 08:57, Yong Liu ***@***.***> wrote: Yes, pls double-check it to make sure you have No of “*rNEST*rsfMRI.nii” = size (‘rp*.txt’,1) in the same directory. Any further question, please let me know. Very best Yours Yong From: ***@***.*** ***@***.*** On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant ***@***.***> Cc: Yong Liu ***@***.***>; Comment ***@***.***> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hi Yong I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file thank you - your GUI is very nice and it is great that you have put all your tools together like this. Anna > On 7 Aug 2020, at 10:01, Yong Liu ***@***.*** ***@***.***> > wrote: > > > I think maybe you need to check > > > > “*rNEST*rsfMRI.nii see how many time points, or how many nii files in the same directory > > > > Then double-check the rp*.txt, how many time points. > > > > I guess maybe you have so many nii files be read by the brant. > > > > > > Very best > > Yours > > Yong > > > > From: ***@***.*** ***@***.***> ***@***.*** On Behalf Of annapbarnes > Sent: Friday, August 07, 2020 4:27 PM > To: YongLiuLab/brant ***@***.*** ***@***.***> > > Cc: Yong Liu ***@***.*** ***@***.***> >; Comment ***@***.*** ***@***.***> > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > Yes of course > Error message, screenshot and log file attached > > **Current indexing filetype: *rNEST*rsfMRI.nii > Index exceeds matrix dimensions. > > Error in > brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] > (line 413) > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > Error in brant_run_denoise>check_masks (line 413) > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > Error in brant_run_denoise (line 71) > [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, > denoise_infos.space_mask, nm_pos); > > Error in brant_preprocess_jobman (line 164) > end_prefix = brant_run_denoise(working_dir, > run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, > data_input.is4d, output_dirs, jobman.subj.out.nmpos); > > Error in brant_preprocess>run_cb (line 343) > brant_preprocess_jobman(jobman, gcf); > > Error while evaluating UIControl Callback** > > > > On 7 Aug 2020, at 01:34, Yong Liu ***@***.*** ***@***.******@***.***> ***@***.***> > wrote: > > > > > > Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. > > > > > > > > > > > > > > > > Very best > > > > Yours > > > > Yong > > > > > > > > From: ***@***.*** ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > > Sent: Friday, August 07, 2020 3:06 AM > > To: YongLiuLab/brant ***@***.*** ***@***.******@***.***> ***@***.***> > > > Cc: Subscribed ***@***.*** ***@***.******@***.***> ***@***.***> > > > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > HI > > > > When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? > > > > Anna > > > > — > > You are receiving this because you are subscribed to this thread. > > Reply to this email directly, view it on GitHub <#1> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif> > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ>. > > > > > DENOISE > Space & Masks > running in individual space. > selected masks' wildcards are > ft_gs: rc1*.nii > ft_wm: rc2*.nii > ft_csf: rc3*.nii > > mask_res_type: nearest neighbour > ft_motion: rp*.txt > > Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 > > Filter options: > TR(s): 2.0 > lower cutoff: 0.01 > upper cutoff: 0.08 > > Process options > Order: Regression first, then filter > save option: all selected options will have output files > gzip option: output files will be saved as input format > GSR option: regression and selected following process will be done with and without GSR > regression output prefix: d > filter output prefix: f > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif> > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA7R5VC4DRHTPB3VT7LR7O7GJANCNFSM4PW4JKFQ>. > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUSXBLXTSBURLF6J2IDR7PCHXANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQAFZVCJXH4FOCNOZ3R7PCHXA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE7256QI.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA4YAJG752ORYQKLOUTR7ZJFPANCNFSM4PW4JKFQ>.

YongLiuLab · 2020-08-14T07:17:20Z

Hi, Anna, Could you please send me a link of your data so that I can try to proprecess it. Very best Yours Yong From: noreply@github.com [mailto:noreply@github.com] On Behalf Of annapbarnes Sent: Friday, August 14, 2020 3:13 PM To: YongLiuLab/brant <brant@noreply.github.com> Cc: Yong Liu <yliu@nlpr.ia.ac.cn>; Comment <comment@noreply.github.com> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hello Did you manage to get take a look at the data set I sent you? Any clues as to what I am doing wrong? Very best wishes Anna Anna Barnes, PhD, CSci, FIPEM IPEM Representative NHS-England National Imaging Optimisation Delivery Board Honorary Associate Professor Centre for Medical Imaging, University College London 43-45 Foley St, London, W1W 7TS

On 9 Aug 2020, at 08:57, Yong Liu ***@***.*** ***@***.***> > wrote: Yes, pls double-check it to make sure you have No of “*rNEST*rsfMRI.nii” = size (‘rp*.txt’,1) in the same directory. Any further question, please let me know. Very best Yours Yong From: ***@***.*** ***@***.***> ***@***.*** On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant ***@***.*** ***@***.***> > Cc: Yong Liu ***@***.*** ***@***.***> >; Comment ***@***.*** ***@***.***> > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hi Yong I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file thank you - your GUI is very nice and it is great that you have put all your tools together like this. Anna > On 7 Aug 2020, at 10:01, Yong Liu ***@***.*** ***@***.******@***.***> ***@***.***> > wrote: > > > I think maybe you need to check > > > > “*rNEST*rsfMRI.nii see how many time points, or how many nii files in the same directory > > > > Then double-check the rp*.txt, how many time points. > > > > I guess maybe you have so many nii files be read by the brant. > > > > > > Very best > > Yours > > Yong > > > > From: ***@***.*** ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > Sent: Friday, August 07, 2020 4:27 PM > To: YongLiuLab/brant ***@***.*** ***@***.******@***.***> ***@***.***> > > Cc: Yong Liu ***@***.*** ***@***.******@***.***> ***@***.***> >; Comment ***@***.*** ***@***.******@***.***> ***@***.***> > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > Yes of course > Error message, screenshot and log file attached > > **Current indexing filetype: *rNEST*rsfMRI.nii > Index exceeds matrix dimensions. > > Error in > brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] > (line 413) > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > Error in brant_run_denoise>check_masks (line 413) > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > Error in brant_run_denoise (line 71) > [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, > denoise_infos.space_mask, nm_pos); > > Error in brant_preprocess_jobman (line 164) > end_prefix = brant_run_denoise(working_dir, > run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, > data_input.is4d, output_dirs, jobman.subj.out.nmpos); > > Error in brant_preprocess>run_cb (line 343) > brant_preprocess_jobman(jobman, gcf); > > Error while evaluating UIControl Callback** > > > > On 7 Aug 2020, at 01:34, Yong Liu ***@***.*** ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> > wrote: > > > > > > Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. > > > > > > > > > > > > > > > > Very best > > > > Yours > > > > Yong > > > > > > > > From: ***@***.*** ***@***.***> ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > > Sent: Friday, August 07, 2020 3:06 AM > > To: YongLiuLab/brant ***@***.*** ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> > > > Cc: Subscribed ***@***.*** ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> > > > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > HI > > > > When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? > > > > Anna > > > > — > > You are receiving this because you are subscribed to this thread. > > Reply to this email directly, view it on GitHub <#1> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif> > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ>. > > > > > DENOISE > Space & Masks > running in individual space. > selected masks' wildcards are > ft_gs: rc1*.nii > ft_wm: rc2*.nii > ft_csf: rc3*.nii > > mask_res_type: nearest neighbour > ft_motion: rp*.txt > > Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 > > Filter options: > TR(s): 2.0 > lower cutoff: 0.01 > upper cutoff: 0.08 > > Process options > Order: Regression first, then filter > save option: all selected options will have output files > gzip option: output files will be saved as input format > GSR option: regression and selected following process will be done with and without GSR > regression output prefix: d > filter output prefix: f > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif> > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA7R5VC4DRHTPB3VT7LR7O7GJANCNFSM4PW4JKFQ>. > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUSXBLXTSBURLF6J2IDR7PCHXANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQAFZVCJXH4FOCNOZ3R7PCHXA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE7256QI.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA4YAJG752ORYQKLOUTR7ZJFPANCNFSM4PW4JKFQ>.

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annapbarnes · 2020-08-14T07:52:02Z

Please let me know if there is a problem with the link Hi Yong Definitely have 260 rows in the rp*.txt file and 260 volumes in the 4D *.nii file. Attached is the log file, text file and a link to my data, in individual space https://drive.google.com/file/d/1a-WaU8w04eKMXgS3ocUNsFH1kdBSxyrI/view?usp=sharing <https://drive.google.com/file/d/1a-WaU8w04eKMXgS3ocUNsFH1kdBSxyrI/view?usp=sharing> thanks Anna

On 9 Aug 2020, at 08:57, Yong Liu ***@***.*** ***@***.***>> wrote: Yes, pls double-check it to make sure you have No of “*rNEST*rsfMRI.nii” = size (‘rp*.txt’,1) in the same directory. Any further question, please let me know. Very best Yours Yong From: ***@***.*** ***@***.***> ***@***.*** ***@***.***>] On Behalf Of annapbarnes Sent: Friday, August 07, 2020 5:27 PM To: YongLiuLab/brant ***@***.*** ***@***.***>> Cc: Yong Liu ***@***.*** ***@***.***>>; Comment ***@***.*** ***@***.***>> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hi Yong I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file thank you - your GUI is very nice and it is great that you have put all your tools together like this. Anna > On 7 Aug 2020, at 10:01, Yong Liu ***@***.*** ***@***.***> ***@***.*** ***@***.***>> > wrote: > > > I think maybe you need to check > > > > “*rNEST*rsfMRI.nii see how many time points, or how many nii files in the same directory > > > > Then double-check the rp*.txt, how many time points. > > > > I guess maybe you have so many nii files be read by the brant. > > > > > > Very best > > Yours > > Yong > > > > From: ***@***.*** ***@***.***> ***@***.*** ***@***.***>> ***@***.*** ***@***.***>] On Behalf Of annapbarnes > Sent: Friday, August 07, 2020 4:27 PM > To: YongLiuLab/brant ***@***.*** ***@***.***> ***@***.*** ***@***.***>> > > Cc: Yong Liu ***@***.*** ***@***.***> ***@***.*** ***@***.***>> >; Comment ***@***.*** ***@***.***> ***@***.*** ***@***.***>> > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > Yes of course > Error message, screenshot and log file attached > > **Current indexing filetype: *rNEST*rsfMRI.nii > Index exceeds matrix dimensions. > > Error in > brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] > (line 413) > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > Error in brant_run_denoise>check_masks (line 413) > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > Error in brant_run_denoise (line 71) > [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, > denoise_infos.space_mask, nm_pos); > > Error in brant_preprocess_jobman (line 164) > end_prefix = brant_run_denoise(working_dir, > run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, > data_input.is4d, output_dirs, jobman.subj.out.nmpos); > > Error in brant_preprocess>run_cb (line 343) > brant_preprocess_jobman(jobman, gcf); > > Error while evaluating UIControl Callback** > > > > On 7 Aug 2020, at 01:34, Yong Liu ***@***.*** ***@***.******@***.*** ***@***.******@***.*** ***@***.***>> ***@***.*** ***@***.***>> > wrote: > > > > > > Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. > > > > > > > > > > > > > > > > Very best > > > > Yours > > > > Yong > > > > > > > > From: ***@***.*** ***@***.***> ***@***.*** ***@***.***>> ***@***.*** ***@***.***>> ***@***.*** ***@***.***>] On Behalf Of annapbarnes > > Sent: Friday, August 07, 2020 3:06 AM > > To: YongLiuLab/brant ***@***.*** ***@***.***> ***@***.*** ***@***.******@***.*** ***@***.***>> ***@***.*** ***@***.***>> > > > Cc: Subscribed ***@***.*** ***@***.******@***.*** ***@***.******@***.*** ***@***.***>> ***@***.*** ***@***.***>> > > > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > HI > > > > When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? > > > > Anna > > > > — > > You are receiving this because you are subscribed to this thread. > > Reply to this email directly, view it on GitHub <#1 <#1>> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ>> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif>> > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub <#1 (comment) <#1 (comment)>>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ>>. > > > > > DENOISE > Space & Masks > running in individual space. > selected masks' wildcards are > ft_gs: rc1*.nii > ft_wm: rc2*.nii > ft_csf: rc3*.nii > > mask_res_type: nearest neighbour > ft_motion: rp*.txt > > Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 > > Filter options: > TR(s): 2.0 > lower cutoff: 0.01 > upper cutoff: 0.08 > > Process options > Order: Regression first, then filter > save option: all selected options will have output files > gzip option: output files will be saved as input format > GSR option: regression and selected following process will be done with and without GSR > regression output prefix: d > filter output prefix: f > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub <#1 (comment) <#1 (comment)>> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ <https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ>> . <https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif <https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif>> > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub <#1 (comment) <#1 (comment)>>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA7R5VC4DRHTPB3VT7LR7O7GJANCNFSM4PW4JKFQ <https://github.com/notifications/unsubscribe-auth/ABUFWA7R5VC4DRHTPB3VT7LR7O7GJANCNFSM4PW4JKFQ>>. > — You are receiving this because you commented. 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DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: c1*.nii ft_wm: c2*.nii ft_csf: c3*.nii mask_res_type: nearest neighbour ft_motion: rp*.txt Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08 Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 3.3307993e-03 7.6357832e-02 1.7837401e-02 -5.7212151e-05 -9.1547221e-05 3.1301502e-04 1.1045703e-02 -4.8566539e-02 5.5413523e-02 5.4641878e-04 2.4185371e-04 3.8254776e-05 4.0980593e-03 8.7049996e-02 1.0105286e-01 -2.7974734e-04 1.3759804e-04 2.3560535e-04 1.0759222e-02 -7.6154145e-02 6.1559750e-02 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1.7907791e-02 8.7581200e-02 9.1268972e-03 8.4185824e-04 -4.1879861e-03 -8.1361613e-02 -1.6889287e-02 6.9669758e-02 9.0907509e-03 9.2336646e-04 -4.2419008e-03 -9.0094511e-02 1.6876415e-02 1.0640062e-01 9.3362819e-03 6.6273093e-04 -3.9296509e-03 -9.9024175e-02 -3.1643092e-02 7.2252510e-02 9.7701225e-03 1.9612778e-04 -4.3717014e-03 -1.1187359e-01 -3.3781543e-02 1.4675184e-01 9.8732035e-03 -1.9512427e-04 -4.2403431e-03 -1.1866340e-01 1.3168846e-02 7.7978455e-02 9.9233164e-03 -6.9945735e-04 -4.1192319e-03 -1.1177945e-01 -2.8262260e-02 1.2569399e-01 1.0024181e-02 -3.5112587e-04 -3.7349342e-03 -1.2249137e-01 6.1054324e-03 6.4465330e-02 1.0361227e-02 -7.0414103e-04 -4.1862403e-03 -1.2257925e-01 -3.7396623e-02 1.3451627e-01 1.0552847e-02 -6.4483757e-04 -4.2028068e-03 -1.2044991e-01 1.6280418e-02 7.9556347e-02 1.0525331e-02 -8.6953567e-04 -4.3368924e-03 -1.0926393e-01 -4.2976488e-02 7.8891866e-02 1.0522318e-02 -2.5211097e-04 -4.0977243e-03 -1.0556261e-01 8.3328859e-02 5.4410014e-02 9.2856133e-03 1.2271228e-04 -3.6150113e-03 -9.0141175e-02 -2.9519579e-02 6.1168057e-02 9.6000809e-03 3.0863778e-04 -3.2425938e-03 -8.0014958e-02 1.3701368e-01 6.8627196e-02 9.2280831e-03 4.0498730e-04 -2.7671696e-03 -6.3981071e-02 -2.4222860e-02 8.8179662e-02 1.0211860e-02 8.6134309e-04 -2.8180324e-03 -5.3803840e-02 8.3894567e-02 7.8868506e-02 9.5418829e-03 7.7348932e-04 -2.9366260e-03 -5.4238224e-02 -4.6791539e-02 9.3106381e-02 9.6780495e-03 1.0365282e-03 -3.0383204e-03 -4.9914585e-02 6.0297941e-02 7.9496752e-02 8.9079809e-03 9.2077914e-04 -3.0099493e-03 -4.7571762e-02 -3.8005786e-02 7.6928120e-02 9.4364698e-03 1.1515302e-03 -2.9595845e-03 -5.4455166e-02 1.0663712e-01 9.4289374e-02 8.5740746e-03 8.6697003e-04 -2.6712009e-03 -4.4159663e-02 -5.8517992e-02 5.2161981e-02 9.6982143e-03 1.3034092e-03 -2.9408374e-03 -5.0228471e-02 9.6189276e-03 8.4923582e-02 9.5867329e-03 1.2808920e-03 -2.9947519e-03 -5.0904516e-02 4.1347728e-02 4.9313518e-02 9.5175203e-03 1.3388032e-03 -3.0245171e-03 -5.2464572e-02 -3.0730934e-02 6.0065728e-02 9.5709181e-03 1.4187692e-03 -3.0530555e-03 -5.8464347e-02 5.1842244e-02 7.1734230e-02 9.4784346e-03 1.3682015e-03 -3.0485601e-03 -5.6486504e-02 -2.8626180e-02 5.0363106e-02 9.7707961e-03 1.6052963e-03 -3.2066207e-03 -6.1247194e-02 6.8411954e-02 5.8221844e-02 9.5307512e-03 1.4964219e-03 -2.8924018e-03 -5.2873755e-02 -3.6496147e-02 4.5312874e-02 9.8420366e-03 1.7971649e-03 -3.1184988e-03 -6.2337307e-02 2.8697504e-02 7.8454545e-02 9.9303149e-03 1.6330756e-03 -3.1732515e-03 -5.7434567e-02 2.2036561e-02 5.8094715e-02 1.0063592e-02 1.6610840e-03 -3.4093484e-03 -6.4280858e-02 -4.2757220e-02 9.0698666e-02 1.0723815e-02 1.3597731e-03 -3.7012746e-03 -8.7126539e-02 5.1528145e-02 1.0899859e-01 1.0389357e-02 4.2088635e-04 -3.9484273e-03 -8.6187946e-02 -4.3524158e-02 1.1564132e-01 1.0721588e-02 3.2674072e-04 -3.7553934e-03 -9.0142353e-02 7.8062597e-02 9.2760387e-02 9.9912936e-03 2.8159115e-04 -3.6236680e-03 -8.5454483e-02 -3.5384405e-02 9.5200060e-02 1.0388927e-02 7.8104216e-04 -3.8440345e-03 -8.4641559e-02 8.0601688e-02 9.1999785e-02 1.0389279e-02 5.4705601e-04 -3.6435536e-03 -8.1845872e-02 -1.7014589e-02 1.1595864e-01 1.0864381e-02 8.4354168e-04 -3.7177410e-03 -7.2619905e-02 4.3486199e-02 1.0312556e-01 1.0835300e-02 8.7042791e-04 -3.7413756e-03

annapbarnes · 2020-08-17T08:53:57Z

Hi Yong Did you manage to download the data ok? I expect I was just doing something a bit silly. Much thanks Anna

…

On 14 Aug 2020, at 08:17, Yong Liu ***@***.***> wrote: Hi, Anna, Could you please send me a link of your data so that I can try to proprecess it. Very best Yours Yong From: ***@***.*** ***@***.*** On Behalf Of annapbarnes Sent: Friday, August 14, 2020 3:13 PM To: YongLiuLab/brant ***@***.***> Cc: Yong Liu ***@***.***>; Comment ***@***.***> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hello Did you manage to get take a look at the data set I sent you? Any clues as to what I am doing wrong? Very best wishes Anna Anna Barnes, PhD, CSci, FIPEM IPEM Representative NHS-England National Imaging Optimisation Delivery Board Honorary Associate Professor Centre for Medical Imaging, University College London 43-45 Foley St, London, W1W 7TS > On 9 Aug 2020, at 08:57, Yong Liu ***@***.*** ***@***.***> > wrote: > > > Yes, pls double-check it to make sure you have No of “*rNEST*rsfMRI.nii” = size (‘rp*.txt’,1) in the same directory. > > > > Any further question, please let me know. > > > > > > Very best > > Yours > > Yong > > > > From: ***@***.*** ***@***.***> ***@***.*** On Behalf Of annapbarnes > Sent: Friday, August 07, 2020 5:27 PM > To: YongLiuLab/brant ***@***.*** ***@***.***> > > Cc: Yong Liu ***@***.*** ***@***.***> >; Comment ***@***.*** ***@***.***> > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > Hi Yong > > I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file > > thank you - your GUI is very nice and it is great that you have put all your tools together like this. > > Anna > > > On 7 Aug 2020, at 10:01, Yong Liu ***@***.*** ***@***.******@***.***> ***@***.***> > wrote: > > > > > > I think maybe you need to check > > > > > > > > “*rNEST*rsfMRI.nii see how many time points, or how many nii files in the same directory > > > > > > > > Then double-check the rp*.txt, how many time points. > > > > > > > > I guess maybe you have so many nii files be read by the brant. > > > > > > > > > > > > Very best > > > > Yours > > > > Yong > > > > > > > > From: ***@***.*** ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > > Sent: Friday, August 07, 2020 4:27 PM > > To: YongLiuLab/brant ***@***.*** ***@***.******@***.***> ***@***.***> > > > Cc: Yong Liu ***@***.*** ***@***.******@***.***> ***@***.***> >; Comment ***@***.*** ***@***.******@***.***> ***@***.***> > > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > > > > > Yes of course > > Error message, screenshot and log file attached > > > > **Current indexing filetype: *rNEST*rsfMRI.nii > > Index exceeds matrix dimensions. > > > > Error in > > brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] > > (line 413) > > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > > > Error in brant_run_denoise>check_masks (line 413) > > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > > > Error in brant_run_denoise (line 71) > > [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, > > denoise_infos.space_mask, nm_pos); > > > > Error in brant_preprocess_jobman (line 164) > > end_prefix = brant_run_denoise(working_dir, > > run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, > > data_input.is4d, output_dirs, jobman.subj.out.nmpos); > > > > Error in brant_preprocess>run_cb (line 343) > > brant_preprocess_jobman(jobman, gcf); > > > > Error while evaluating UIControl Callback** > > > > > > > On 7 Aug 2020, at 01:34, Yong Liu ***@***.*** ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> > wrote: > > > > > > > > > Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. > > > > > > > > > > > > > > > > > > > > > > > > Very best > > > > > > Yours > > > > > > Yong > > > > > > > > > > > > From: ***@***.*** ***@***.***> ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > > > Sent: Friday, August 07, 2020 3:06 AM > > > To: YongLiuLab/brant ***@***.*** ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> > > > > Cc: Subscribed ***@***.*** ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> > > > > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > > > > > HI > > > > > > When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? > > > > > > Anna > > > > > > — > > > You are receiving this because you are subscribed to this thread. > > > Reply to this email directly, view it on GitHub <#1> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif> > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ>. > > > > > > > > > DENOISE > > Space & Masks > > running in individual space. > > selected masks' wildcards are > > ft_gs: rc1*.nii > > ft_wm: rc2*.nii > > ft_csf: rc3*.nii > > > > mask_res_type: nearest neighbour > > ft_motion: rp*.txt > > > > Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 > > > > Filter options: > > TR(s): 2.0 > > lower cutoff: 0.01 > > upper cutoff: 0.08 > > > > Process options > > Order: Regression first, then filter > > save option: all selected options will have output files > > gzip option: output files will be saved as input format > > GSR option: regression and selected following process will be done with and without GSR > > regression output prefix: d > > filter output prefix: f > > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif> > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA7R5VC4DRHTPB3VT7LR7O7GJANCNFSM4PW4JKFQ>. > > > > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUSXBLXTSBURLF6J2IDR7PCHXANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQAFZVCJXH4FOCNOZ3R7PCHXA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE7256QI.gif> > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA4YAJG752ORYQKLOUTR7ZJFPANCNFSM4PW4JKFQ>. > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUTVZM3I2XCSR4Y7HPTSATPV7ANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQJZMOOSLVFRMDGCALSATPV7A5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOFAVUZNQ.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA5JQ67SG7I25FDAARTSATQI5ANCNFSM4PW4JKFQ>.

YongLiuLab · 2020-08-17T10:35:54Z

Hi Anna I do not get any link or attached about the data, could you please zip that file and then send me a link so that I can download it Very best Yours Yong From: noreply@github.com [mailto:noreply@github.com] On Behalf Of annapbarnes Sent: Monday, August 17, 2020 4:54 PM To: YongLiuLab/brant <brant@noreply.github.com> Cc: Yong Liu <yliu@nlpr.ia.ac.cn>; Comment <comment@noreply.github.com> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hi Yong Did you manage to download the data ok? I expect I was just doing something a bit silly. Much thanks Anna

On 14 Aug 2020, at 08:17, Yong Liu ***@***.*** ***@***.***> > wrote: Hi, Anna, Could you please send me a link of your data so that I can try to proprecess it. Very best Yours Yong From: ***@***.*** ***@***.***> ***@***.*** On Behalf Of annapbarnes Sent: Friday, August 14, 2020 3:13 PM To: YongLiuLab/brant ***@***.*** ***@***.***> > Cc: Yong Liu ***@***.*** ***@***.***> >; Comment ***@***.*** ***@***.***> > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hello Did you manage to get take a look at the data set I sent you? Any clues as to what I am doing wrong? Very best wishes Anna Anna Barnes, PhD, CSci, FIPEM IPEM Representative NHS-England National Imaging Optimisation Delivery Board Honorary Associate Professor Centre for Medical Imaging, University College London 43-45 Foley St, London, W1W 7TS > On 9 Aug 2020, at 08:57, Yong Liu ***@***.*** ***@***.******@***.***> ***@***.***> > wrote: > > > Yes, pls double-check it to make sure you have No of “*rNEST*rsfMRI.nii” = size (‘rp*.txt’,1) in the same directory. > > > > Any further question, please let me know. > > > > > > Very best > > Yours > > Yong > > > > From: ***@***.*** ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > Sent: Friday, August 07, 2020 5:27 PM > To: YongLiuLab/brant ***@***.*** ***@***.******@***.***> ***@***.***> > > Cc: Yong Liu ***@***.*** ***@***.******@***.***> ***@***.***> >; Comment ***@***.*** ***@***.******@***.***> ***@***.***> > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > Hi Yong > > I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file > > thank you - your GUI is very nice and it is great that you have put all your tools together like this. > > Anna > > > On 7 Aug 2020, at 10:01, Yong Liu ***@***.*** ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> > wrote: > > > > > > I think maybe you need to check > > > > > > > > “*rNEST*rsfMRI.nii see how many time points, or how many nii files in the same directory > > > > > > > > Then double-check the rp*.txt, how many time points. > > > > > > > > I guess maybe you have so many nii files be read by the brant. > > > > > > > > > > > > Very best > > > > Yours > > > > Yong > > > > > > > > From: ***@***.*** ***@***.***> ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > > Sent: Friday, August 07, 2020 4:27 PM > > To: YongLiuLab/brant ***@***.*** ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> > > > Cc: Yong Liu ***@***.*** ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> >; Comment ***@***.*** ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> > > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > > > > > Yes of course > > Error message, screenshot and log file attached > > > > **Current indexing filetype: *rNEST*rsfMRI.nii > > Index exceeds matrix dimensions. > > > > Error in > > brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] > > (line 413) > > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > > > Error in brant_run_denoise>check_masks (line 413) > > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > > > Error in brant_run_denoise (line 71) > > [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, > > denoise_infos.space_mask, nm_pos); > > > > Error in brant_preprocess_jobman (line 164) > > end_prefix = brant_run_denoise(working_dir, > > run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, > > data_input.is4d, output_dirs, jobman.subj.out.nmpos); > > > > Error in brant_preprocess>run_cb (line 343) > > brant_preprocess_jobman(jobman, gcf); > > > > Error while evaluating UIControl Callback** > > > > > > > On 7 Aug 2020, at 01:34, Yong Liu ***@***.*** ***@***.******@***.******@***.******@***.***> ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> > wrote: > > > > > > > > > Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. > > > > > > > > > > > > > > > > > > > > > > > > Very best > > > > > > Yours > > > > > > Yong > > > > > > > > > > > > From: ***@***.*** ***@***.***> ***@***.***> ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > > > Sent: Friday, August 07, 2020 3:06 AM > > > To: YongLiuLab/brant ***@***.*** ***@***.******@***.******@***.******@***.***> ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> > > > > Cc: Subscribed ***@***.*** ***@***.******@***.******@***.******@***.***> ***@***.******@***.******@***.***> ***@***.******@***.***> ***@***.***> > > > > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > > > > > HI > > > > > > When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? > > > > > > Anna > > > > > > — > > > You are receiving this because you are subscribed to this thread. > > > Reply to this email directly, view it on GitHub <#1> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif> > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ>. > > > > > > > > > DENOISE > > Space & Masks > > running in individual space. > > selected masks' wildcards are > > ft_gs: rc1*.nii > > ft_wm: rc2*.nii > > ft_csf: rc3*.nii > > > > mask_res_type: nearest neighbour > > ft_motion: rp*.txt > > > > Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 > > > > Filter options: > > TR(s): 2.0 > > lower cutoff: 0.01 > > upper cutoff: 0.08 > > > > Process options > > Order: Regression first, then filter > > save option: all selected options will have output files > > gzip option: output files will be saved as input format > > GSR option: regression and selected following process will be done with and without GSR > > regression output prefix: d > > filter output prefix: f > > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif> > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA7R5VC4DRHTPB3VT7LR7O7GJANCNFSM4PW4JKFQ>. > > > > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUSXBLXTSBURLF6J2IDR7PCHXANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQAFZVCJXH4FOCNOZ3R7PCHXA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE7256QI.gif> > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA4YAJG752ORYQKLOUTR7ZJFPANCNFSM4PW4JKFQ>. > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUTVZM3I2XCSR4Y7HPTSATPV7ANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQJZMOOSLVFRMDGCALSATPV7A5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOFAVUZNQ.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA5JQ67SG7I25FDAARTSATQI5ANCNFSM4PW4JKFQ>.

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annapbarnes · 2020-08-17T11:16:51Z

please could you click on this link and let me know if you can see the data https://drive.google.com/drive/folders/1KjhssjmW4dAPXKmP7E4XwgDIjV2BGPxw?usp=sharing ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in relation to its contents. To do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services. For more information and to find out how you can switch, https://portal.nhs.net/help/joiningnhsmail 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 0.0000000e+00 3.3307993e-03 7.6357832e-02 1.7837401e-02 -5.7212151e-05 -9.1547221e-05 3.1301502e-04 1.1045703e-02 -4.8566539e-02 5.5413523e-02 5.4641878e-04 2.4185371e-04 3.8254776e-05 4.0980593e-03 8.7049996e-02 1.0105286e-01 -2.7974734e-04 1.3759804e-04 2.3560535e-04 1.0759222e-02 -7.6154145e-02 6.1559750e-02 7.8099839e-04 3.2107491e-04 1.1398264e-04 3.9933509e-03 5.6641275e-02 1.1100836e-01 4.3179485e-04 3.2500407e-04 4.1196128e-04 1.1026180e-02 -5.4313580e-02 6.8301063e-02 1.7886331e-03 6.9689813e-04 2.3084203e-04 8.9221013e-03 4.5564678e-02 1.1214351e-01 1.5546312e-03 7.9475567e-04 4.8282913e-04 1.5056796e-02 -4.5147521e-02 8.6086866e-02 2.3726663e-03 1.1437559e-03 -3.3900531e-05 1.7188667e-02 2.1131851e-02 1.1550300e-01 2.2338689e-03 9.8264240e-04 6.2381435e-05 2.2465154e-02 -2.5434334e-02 1.0038872e-01 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-3.1732515e-03 -5.7434567e-02 2.2036561e-02 5.8094715e-02 1.0063592e-02 1.6610840e-03 -3.4093484e-03 -6.4280858e-02 -4.2757220e-02 9.0698666e-02 1.0723815e-02 1.3597731e-03 -3.7012746e-03 -8.7126539e-02 5.1528145e-02 1.0899859e-01 1.0389357e-02 4.2088635e-04 -3.9484273e-03 -8.6187946e-02 -4.3524158e-02 1.1564132e-01 1.0721588e-02 3.2674072e-04 -3.7553934e-03 -9.0142353e-02 7.8062597e-02 9.2760387e-02 9.9912936e-03 2.8159115e-04 -3.6236680e-03 -8.5454483e-02 -3.5384405e-02 9.5200060e-02 1.0388927e-02 7.8104216e-04 -3.8440345e-03 -8.4641559e-02 8.0601688e-02 9.1999785e-02 1.0389279e-02 5.4705601e-04 -3.6435536e-03 -8.1845872e-02 -1.7014589e-02 1.1595864e-01 1.0864381e-02 8.4354168e-04 -3.7177410e-03 -7.2619905e-02 4.3486199e-02 1.0312556e-01 1.0835300e-02 8.7042791e-04 -3.7413756e-03 DENOISE Space & Masks running in individual space. selected masks' wildcards are ft_gs: c1*.nii ft_wm: c2*.nii ft_csf: c3*.nii mask_res_type: nearest neighbour ft_motion: rp*.txt Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 Filter options: TR(s): 2.0 lower cutoff: 0.01 upper cutoff: 0.08 Process options Order: Regression first, then filter save option: all selected options will have output files gzip option: output files will be saved as input format GSR option: regression and selected following process will be done with and without GSR regression output prefix: d filter output prefix: f

annapbarnes · 2020-08-17T11:26:17Z

Hi Yong Hope this worked. I think it went wrong because I invited you directly from the account which has a different email address from my own as was called inmpod@gmail.com<mailto:inmpod@gmail.com> and probably went to you junk mail Very sorry Anna On 17 Aug 2020, at 12:16, BARNES, Anna (UNIVERSITY COLLEGE LONDON HOSPITALS NHS FOUNDATION TRUST) <anna.barnes1@nhs.net<mailto:anna.barnes1@nhs.net>> wrote: please could you click on this link and let me know if you can see the data https://drive.google.com/drive/folders/1KjhssjmW4dAPXKmP7E4XwgDIjV2BGPxw?usp=sharing <rp_NEST_001_rsfMRI.txt> <brant_log_2020_8_10_9_53_20.txt> On 17 Aug 2020, at 11:36, Yong Liu <notifications@github.com<mailto:notifications@github.com>> wrote: Hi Anna I do not get any link or attached about the data, could you please zip that file and then send me a link so that I can download it Very best Yours Yong From: noreply@github.com<mailto:noreply@github.com> [mailto:noreply@github.com] On Behalf Of annapbarnes Sent: Monday, August 17, 2020 4:54 PM To: YongLiuLab/brant <brant@noreply.github.com<mailto:brant@noreply.github.com>> Cc: Yong Liu <yliu@nlpr.ia.ac.cn<mailto:yliu@nlpr.ia.ac.cn>>; Comment <comment@noreply.github.com<mailto:comment@noreply.github.com>> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hi Yong Did you manage to download the data ok? I expect I was just doing something a bit silly. Much thanks Anna

On 14 Aug 2020, at 08:17, Yong Liu ***@***.******@***.***> ***@***.***> > wrote: Hi, Anna, Could you please send me a link of your data so that I can try to proprecess it. Very best Yours Yong From: ***@***.******@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes Sent: Friday, August 14, 2020 3:13 PM To: YongLiuLab/brant ***@***.******@***.***> ***@***.***> > Cc: Yong Liu ***@***.******@***.***> ***@***.***> >; Comment ***@***.******@***.***> ***@***.***> > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hello Did you manage to get take a look at the data set I sent you? Any clues as to what I am doing wrong? Very best wishes Anna Anna Barnes, PhD, CSci, FIPEM IPEM Representative NHS-England National Imaging Optimisation Delivery Board Honorary Associate Professor Centre for Medical Imaging, University College London 43-45 Foley St, London, W1W 7TS > On 9 Aug 2020, at 08:57, Yong Liu ***@***.******@***.***> ***@***.******@***.******@***.***>> ***@***.***> > wrote: > > > Yes, pls double-check it to make sure you have No of “*rNEST*rsfMRI.nii” = size (‘rp*.txt’,1) in the same directory. > > > > Any further question, please let me know. > > > > > > Very best > > Yours > > Yong > > > > From: ***@***.******@***.***> ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > Sent: Friday, August 07, 2020 5:27 PM > To: YongLiuLab/brant ***@***.******@***.***> ***@***.******@***.******@***.***>> ***@***.***> > > Cc: Yong Liu ***@***.******@***.***> ***@***.******@***.******@***.***>> ***@***.***> >; Comment ***@***.******@***.***> ***@***.******@***.******@***.***>> ***@***.***> > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > Hi Yong > > I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file > > thank you - your GUI is very nice and it is great that you have put all your tools together like this. > > Anna > > > On 7 Aug 2020, at 10:01, Yong Liu ***@***.******@***.***> ***@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.******@***.***>> ***@***.***> > wrote: > > > > > > I think maybe you need to check > > > > > > > > “*rNEST*rsfMRI.nii see how many time points, or how many nii files in the same directory > > > > > > > > Then double-check the rp*.txt, how many time points. > > > > > > > > I guess maybe you have so many nii files be read by the brant. > > > > > > > > > > > > Very best > > > > Yours > > > > Yong > > > > > > > > From: ***@***.******@***.***> ***@***.***> ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > > Sent: Friday, August 07, 2020 4:27 PM > > To: YongLiuLab/brant ***@***.******@***.***> ***@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.******@***.***>> ***@***.***> > > > Cc: Yong Liu ***@***.******@***.***> ***@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.******@***.***>> ***@***.***> >; Comment ***@***.******@***.***> ***@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.******@***.***>> ***@***.***> > > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > > > > > Yes of course > > Error message, screenshot and log file attached > > > > **Current indexing filetype: *rNEST*rsfMRI.nii > > Index exceeds matrix dimensions. > > > > Error in > > brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] > > (line 413) > > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > > > Error in brant_run_denoise>check_masks (line 413) > > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > > > Error in brant_run_denoise (line 71) > > [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, > > denoise_infos.space_mask, nm_pos); > > > > Error in brant_preprocess_jobman (line 164) > > end_prefix = brant_run_denoise(working_dir, > > run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, > > data_input.is4d, output_dirs, jobman.subj.out.nmpos); > > > > Error in brant_preprocess>run_cb (line 343) > > brant_preprocess_jobman(jobman, gcf); > > > > Error while evaluating UIControl Callback** > > > > > > > On 7 Aug 2020, at 01:34, Yong Liu ***@***.******@***.***> ***@***.******@***.******@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.******@***.***>> ***@***.***> > wrote: > > > > > > > > > Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. > > > > > > > > > > > > > > > > > > > > > > > > Very best > > > > > > Yours > > > > > > Yong > > > > > > > > > > > > From: ***@***.******@***.***> ***@***.***> ***@***.***> ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > > > Sent: Friday, August 07, 2020 3:06 AM > > > To: YongLiuLab/brant ***@***.******@***.***> ***@***.******@***.******@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.******@***.***>> ***@***.***> > > > > Cc: Subscribed ***@***.******@***.***> ***@***.******@***.******@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.******@***.***>> ***@***.***> > > > > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > > > > > HI > > > > > > When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? > > > > > > Anna > > > > > > — > > > You are receiving this because you are subscribed to this thread. > > > Reply to this email directly, view it on GitHub <#1> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif> > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ>. > > > > > > > > > DENOISE > > Space & Masks > > running in individual space. > > selected masks' wildcards are > > ft_gs: rc1*.nii > > ft_wm: rc2*.nii > > ft_csf: rc3*.nii > > > > mask_res_type: nearest neighbour > > ft_motion: rp*.txt > > > > Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 > > > > Filter options: > > TR(s): 2.0 > > lower cutoff: 0.01 > > upper cutoff: 0.08 > > > > Process options > > Order: Regression first, then filter > > save option: all selected options will have output files > > gzip option: output files will be saved as input format > > GSR option: regression and selected following process will be done with and without GSR > > regression output prefix: d > > filter output prefix: f > > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif> > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA7R5VC4DRHTPB3VT7LR7O7GJANCNFSM4PW4JKFQ>. > > > > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUSXBLXTSBURLF6J2IDR7PCHXANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQAFZVCJXH4FOCNOZ3R7PCHXA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE7256QI.gif> > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA4YAJG752ORYQKLOUTR7ZJFPANCNFSM4PW4JKFQ>. > — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUTVZM3I2XCSR4Y7HPTSATPV7ANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQJZMOOSLVFRMDGCALSATPV7A5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOFAVUZNQ.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA5JQ67SG7I25FDAARTSATQI5ANCNFSM4PW4JKFQ>.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTURFVKWJJEWZ34RESFLSBDV3JANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUSGG6HG3PY7UZ7XBRDSBDV3JA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOFA36PMQ.gif> — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#1 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABUFWA6HGTF5GG6V4PLZ4P3SBEBZTANCNFSM4PW4JKFQ>. ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in relation to its contents. To do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland. NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and other accredited email services. For more information and to find out how you can switch, https://portal.nhs.net/help/joiningnhsmail

YongLiuLab · 2020-08-24T10:11:40Z

Hi Yong Did the data come through yet? I sent it via UCL dropbox and also a link to the data on my Google drive? Best wishes Anna From: Yong Liu <yliu@nlpr.ia.ac.cn> Date: Monday, 17 August 2020 at 11:35 To: 'YongLiuLab/brant' <reply@reply.github.com> Cc: "anna.p.barnes@ucl.ac.uk" <anna.p.barnes@ucl.ac.uk> Subject: RE: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Resent from: <anna.p.barnes@ucl.ac.uk> Resent date: Monday, 17 August 2020 at 11:35 Hi Anna I do not get any link or attached about the data, could you please zip that file and then send me a link so that I can download it Very best Yours Yong From: noreply@github.com [mailto:noreply@github.com] On Behalf Of annapbarnes Sent: Monday, August 17, 2020 4:54 PM To: YongLiuLab/brant <brant@noreply.github.com> Cc: Yong Liu <yliu@nlpr.ia.ac.cn>; Comment <comment@noreply.github.com> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hi Yong Did you manage to download the data ok? I expect I was just doing something a bit silly. Much thanks Anna

On 14 Aug 2020, at 08:17, Yong Liu ***@***.******@***.***>> wrote: Hi, Anna, Could you please send me a link of your data so that I can try to proprecess it. Very best Yours Yong From: ***@***.******@***.***> ***@***.*** On Behalf Of annapbarnes Sent: Friday, August 14, 2020 3:13 PM To: YongLiuLab/brant ***@***.******@***.***>> Cc: Yong Liu ***@***.******@***.***>>; Comment ***@***.******@***.***>> Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) Hello Did you manage to get take a look at the data set I sent you? Any clues as to what I am doing wrong? Very best wishes Anna Anna Barnes, PhD, CSci, FIPEM IPEM Representative NHS-England National Imaging Optimisation Delivery Board Honorary Associate Professor Centre for Medical Imaging, University College London 43-45 Foley St, London, W1W 7TS > On 9 Aug 2020, at 08:57, Yong Liu ***@***.*** ***@***.******@***.******@***.***>> > wrote: > > > Yes, pls double-check it to make sure you have No of “*rNEST*rsfMRI.nii” = size (‘rp*.txt’,1) in the same directory. > > > > Any further question, please let me know. > > > > > > Very best > > Yours > > Yong > > > > From: ***@***.******@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > Sent: Friday, August 07, 2020 5:27 PM > To: YongLiuLab/brant ***@***.*** ***@***.******@***.******@***.***>> > > Cc: Yong Liu ***@***.*** ***@***.******@***.******@***.***>> >; Comment ***@***.*** ***@***.******@***.******@***.***>> > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > Hi Yong > > I have 260 volumes in the 4D files - so should I check that there are 260 time points in rp file > > thank you - your GUI is very nice and it is great that you have put all your tools together like this. > > Anna > > > On 7 Aug 2020, at 10:01, Yong Liu ***@***.*** ***@***.******@***.******@***.******@***.******@***.***>> ***@***.***> > wrote: > > > > > > I think maybe you need to check > > > > > > > > “*rNEST*rsfMRI.nii see how many time points, or how many nii files in the same directory > > > > > > > > Then double-check the rp*.txt, how many time points. > > > > > > > > I guess maybe you have so many nii files be read by the brant. > > > > > > > > > > > > Very best > > > > Yours > > > > Yong > > > > > > > > From: ***@***.******@***.***> ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > > Sent: Friday, August 07, 2020 4:27 PM > > To: YongLiuLab/brant ***@***.*** ***@***.******@***.******@***.******@***.******@***.***>> ***@***.***> > > > Cc: Yong Liu ***@***.*** ***@***.******@***.******@***.******@***.******@***.***>> ***@***.***> >; Comment ***@***.*** ***@***.******@***.******@***.******@***.******@***.***>> ***@***.***> > > > Subject: Re: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > > > > > Yes of course > > Error message, screenshot and log file attached > > > > **Current indexing filetype: *rNEST*rsfMRI.nii > > Index exceeds matrix dimensions. > > > > Error in > > brant_run_denoise>@(x)[mask_files_tmp{1}(x);mask_files_tmp{2}(x);mask_files_tmp{3}(x);mask_files_tmp{4}(x)] > > (line 413) > > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > > > Error in brant_run_denoise>check_masks (line 413) > > mask_files = arrayfun(@(x) [mask_files_tmp{1}(x); mask_files_tmp{2}(x); > > mask_files_tmp{3}(x); mask_files_tmp{4}(x)],... > > > > Error in brant_run_denoise (line 71) > > [mask_files, mask_info, mask_thrs] = check_masks(wk_dir, subj_paths, > > denoise_infos.space_mask, nm_pos); > > > > Error in brant_preprocess_jobman (line 164) > > end_prefix = brant_run_denoise(working_dir, > > run_data.(processes_curr{m}), run_data.subjs.files, subj_ids, > > data_input.is4d, output_dirs, jobman.subj.out.nmpos); > > > > Error in brant_preprocess>run_cb (line 343) > > brant_preprocess_jobman(jobman, gcf); > > > > Error while evaluating UIControl Callback** > > > > > > > On 7 Aug 2020, at 01:34, Yong Liu ***@***.*** ***@***.******@***.******@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.***> ***@***.***> > wrote: > > > > > > > > > Hi, thank you for your email. Could you please kindly send me the error information, also with the selections on the gui to me so that I can have a basic idea about your selections. > > > > > > > > > > > > > > > > > > > > > > > > Very best > > > > > > Yours > > > > > > Yong > > > > > > > > > > > > From: ***@***.******@***.***> ***@***.***> ***@***.***> ***@***.***> ***@***.*** On Behalf Of annapbarnes > > > Sent: Friday, August 07, 2020 3:06 AM > > > To: YongLiuLab/brant ***@***.*** ***@***.******@***.******@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.***> ***@***.***> > > > > Cc: Subscribed ***@***.*** ***@***.******@***.******@***.******@***.******@***.******@***.******@***.***>> ***@***.******@***.***> ***@***.***> > > > > Subject: [YongLiuLab/brant] exceeds matrix dimensions when running denoise (#1) > > > > > > > > > > > > HI > > > > > > When I run the denoise script I get an error saying exceeds matrix dimensions. Is this because the native space c1, c2, c3 images need to have the same matrix dimensions as the fMRI data before it runs? > > > > > > Anna > > > > > > — > > > You are receiving this because you are subscribed to this thread. > > > Reply to this email directly, view it on GitHub <#1> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUWBRD7WI64FBOULWNLR7L5INANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTURCF2P34EYKUMZPSXTR7L5INA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4KBUUCEA.gif> > > > > > > — > > > You are receiving this because you authored the thread. > > > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWAZGDJCNF5FGEMTT5U3R7NDYTANCNFSM4PW4JKFQ>. > > > > > > > > > DENOISE > > Space & Masks > > running in individual space. > > selected masks' wildcards are > > ft_gs: rc1*.nii > > ft_wm: rc2*.nii > > ft_csf: rc3*.nii > > > > mask_res_type: nearest neighbour > > ft_motion: rp*.txt > > > > Regressors: linear,quadratic,T,T^2,T',T'^2,R,R^2,R_prep,R_prep^2 > > > > Filter options: > > TR(s): 2.0 > > lower cutoff: 0.01 > > upper cutoff: 0.08 > > > > Process options > > Order: Regression first, then filter > > save option: all selected options will have output files > > gzip option: output files will be saved as input format > > GSR option: regression and selected following process will be done with and without GSR > > regression output prefix: d > > filter output prefix: f > > > > > > > > — > > You are receiving this because you commented. > > Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUT7VNIRPAEOJ3UVM2TR7O3FJANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQHSVNXQFN5FG52SYLR7O3FJA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE72XN5Y.gif> > > > > — > > You are receiving this because you authored the thread. > > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA7R5VC4DRHTPB3VT7LR7O7GJANCNFSM4PW4JKFQ>. > > > > > > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub <#1 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYVTUSXBLXTSBURLF6J2IDR7PCHXANCNFSM4PW4JKFQ> . <https://github.com/notifications/beacon/AEYVTUQAFZVCJXH4FOCNOZ3R7PCHXA5CNFSM4PW4JKF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOE7256QI.gif> > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub <#1 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUFWA4YAJG752ORYQKLOUTR7ZJFPANCNFSM4PW4JKFQ>. > — You are receiving this because you commented. 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