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tasklist for aa_demo_v1? #81

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giuseppecabras opened this issue Mar 15, 2015 · 15 comments

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@giuseppecabras
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commented Mar 15, 2015

Dear aa developers,
after have read your interesting paper, I've installed the last git distribution (current devel-share branch) on my linux with Matlab2012b and tried to run the demo downloaded from http://cusacklab.org/downloads/aa_demo_v1.tar.gz, which I assume it works out-of-box.
Unfortunately the demo is looking for the aap_tasklist_fmri_noslicetiming_withmodel_firstlevelonly.xml tasklist, which is not in the aa_recipes_and_parametersets directory. Where can I get it? Can I replace it with another existing recipe? (probably commenting out second level modelling)?
Of course, my next step will be to use/modify your examples with my datasets,... have you any long write-up tutorial/manual for a quick start with aa?
Thanks and regards,
Giuseppe

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commented Mar 17, 2015

Giuseppe,
I've added the two missing tasklists to the devel-share branch. Can you check if there is anything else missing? Very best
Rhodri

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commented Mar 17, 2015

Dear Rhodri,
I have tried the aa_demo and now it works partially... at the end I get this error:

[...]
MODULE aamod_convert_structural RUNNING: Convert T1 image from DICOMs for /home/gc/aa_demo/src/../analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001
retrieve stream dicom_structural from /home/gc/aa_demo/src/../analysis_v1/auditory/aamod_get_dicom_structural_00001/2014_03_29_9001 to /home/gc/aa_demo/src/../analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001
executing
Sequence has a TR of 2300.0 ms

**** automatic analysis failed - see reason and line numbers below
Cannot open input file /home/gc/aa_demo/src/../analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii
for help, see the aa wiki
Error using aas_log (line 63)
aa error

Error in aas_md5 (line 32)
aas_log(aap,true,sprintf('Cannot open input file %s',pth));

Error in aas_desc_outputs (line 89)
[aap md5_base64]=aas_md5(aap,trimmedoutputs,localroot);

Error in aamod_convert_structural (line 51)
aap = aas_desc_outputs(aap, subjInd, outStreamImg, convertedfns(structVols, :));

Error in aa_feval (line 18)
[a b]=feval(funcname,varargin{:});

Error in aa_feval_withindices (line 6)
[aap,resp]=aa_feval(mfile_alias,aap,task,indices(1));

Error in aa_doprocessing_onetask (line 151)
[aap,resp]=aa_feval_withindices(mfile_alias,aap,task,indices);

Error in aaq_localsingle/runall (line 16)
aa_doprocessing_onetask(obj.aap,job.task,job.k,job.indices);

Error in aa_doprocessing (line 385)
taskqueue.runall(dontcloseexistingworkers, false);

Error in aa_user_demo_v1 (line 52)
aap = aa_doprocessing(aap);

as you can see, the path after
**** automatic analysis failed - see reason and line numbers below
is constructed wrong (see /home/gc/ again in the middle of the path).

If you need the full output or other info I'll send you all.

Thanks and best,
Giuseppe

@giuseppecabras

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commented Mar 21, 2015

Dear Rhodri,
I continue to have the problem in the aa_demo_v1, and current devel-share (just cloned again).
The recipe do correctly to aamod_convert_structural, I have the correct input in:
/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii
but aamod_convert_structural use the wrong path to read it:
/home/gc/aa_demo/src/../analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii

I am using Matlab R2102b and SPM12, but I guess this is an aa4 devel-share problem or aa_demo_v1 specification error that I don't know how to investigate.
Any suggestion?
Cheers,
Giuseppe

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commented Mar 21, 2015

Giuseppe
Can you post your user script exactly as you ran it? And, what OS are you
running on?
Thank you-
Rhodri

On 21 March 2015 at 10:56, giuseppecabras notifications@github.com wrote:

Dear Rhodri,
I continue to have the problem in the aa_demo_v1, and current devel-share
(just cloned again).
The recipe do correctly to aamod_convert_structural, I have the correct
input in:

/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii
but aamod_convert_structural use the wrong path to read it:

/home/gc/aa_demo/src/../analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii

I am using Matlab R2102b and SPM12, but I guess this is an aa4 devel-share
problem or aa_demo_v1 specification error that I don't know how to
investigate.
Any suggestion?
Cheers,
Giuseppe


Reply to this email directly or view it on GitHub
#81 (comment)
.

Rhodri Cusack
www.cusacklab.org

Associate Professor
Brain and Mind Institute
Natural Sciences Centre, Room 203
The University of Western Ontario
London, Ontario N6A 5B7
CANADA
+1 519 661 2111 ext 86381

@giuseppecabras

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commented Mar 21, 2015

Hi Rhodri,
I use Scientific Linux release 6.6 (Carbon), which is like RHEL6.6
In attach the aa_user_demo I run.
Thanks,
Giuseppe

On 21/03/2015 16:17, rhodricusack wrote:

Giuseppe
Can you post your user script exactly as you ran it? And, what OS are you
running on?
Thank you-
Rhodri

On 21 March 2015 at 10:56, giuseppecabras notifications@github.com
wrote:

Dear Rhodri,
I continue to have the problem in the aa_demo_v1, and current
devel-share
(just cloned again).
The recipe do correctly to aamod_convert_structural, I have the correct
input in:

/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii
but aamod_convert_structural use the wrong path to read it:

/home/gc/aa_demo/src/../analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii

I am using Matlab R2102b and SPM12, but I guess this is an aa4
devel-share
problem or aa_demo_v1 specification error that I don't know how to
investigate.
Any suggestion?
Cheers,
Giuseppe


Reply to this email directly or view it on GitHub

#81 (comment)
.

Rhodri Cusack
www.cusacklab.org

Associate Professor
Brain and Mind Institute
Natural Sciences Centre, Room 203
The University of Western Ontario
London, Ontario N6A 5B7
CANADA
+1 519 661 2111 ext 86381


Reply to this email directly or view it on GitHub
#81 (comment).

Giuseppe Cabras, PhD - Chemistry, Physics and Environment Dept.
InterUniversity Center for Behavioral Neurosciences http://icbn.uniud.it
University of Udine - via delle Scienze, 206 - 33100 UDINE
Phone: +39-043255-8212 - Fax: +39-043255-8222
URL: http://people.uniud.it/page/giuseppe.cabras
BOOK:http://www.amazon.com/Advanced-component-analysis-techniques-decomposition/dp/3639873149

% Automatic analysis (aa) - user master script
% This example runs one session of one subject through a standard SPM-based
% fMRI analysis. After running, look at the results using SPM in
% ../analysis_v1/auditory/aamod_firstlevel_contrasts_00001/2014_03_29_9001/stats
% Prerequistes are aa and spm 8 or 12, I'm using Matlab 2014a.
% v1: Rhodri Cusack Brain and Mind Institute, Western University, 2014-12-15

aa_ver4_nocloud

% Add the directory of this script to the top of the matlab path
addpath(fileparts(mfilename('fullpath')),'-begin');

% Load the recipe tasklist
aap = aarecipe('aap_tasklist_fmri_noslicetiming_withmodel_firstlevelonly.xml');
% aap = aarecipe('aap_tasklist_typical_fmri.xml');
% You might want to later set up a configuration for your local site
% aap=aas_localconfig(aap);
% I just have this one thing
aap.directory_conventions.dicomfilter='*.IMA';

% DEFINE STUDY SPECIFIC PARAMETERS
aap.options.aa_minver = 4.0; % designed for aa version 4.0 or above

% Define following paths relative to this script. You might not always want
% to do this, but it is good for this example
thisfilespath=fileparts(mfilename('fullpath'));

% Location of raw DICOM data
aap.directory_conventions.rawdatadir = fullfile(thisfilespath,'../rawdata');

% Where to put the analyzed data
aap.acq_details.root = fullfile(thisfilespath,'../analysis_v1');
aap.directory_conventions.analysisid = 'auditory';

% This is name of the structural protocol, as typed into the scanner. If
% you're consistent with this, it can be found automatically in each new
% subject
aap.directory_conventions.protocol_structural = 'MPRAGE iPAT2_sag';

% Number of dummy scans at start of EPI runs
aap.acq_details.numdummies = 10;

% Just one session
aap = aas_addsession(aap,'lullaby_task');

% Just one subject
aap = aas_addsubject(aap,'2014_03_29_9001',[6]);

% Specify model - just one regressor here ('Sound')
% block onsets 0, 26, 52... 390 secs and duration 15 secs
%aap = aas_addevent(aap,'aamod_firstlevel_model','','','Sound',0:26:390, 15);

% Specify contrast - just sound minus silence
%aap = aas_addcontrast(aap, 'aamod_firstlevel_contrasts', '*', 'sameforallsessions', 1, 'sound-silence', 'T');

% DO PROCESSING
aap = aa_doprocessing(aap);

@rhodricusack

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commented Mar 21, 2015

I can't see the attachment, can you paste it into the message body? Thanks!
On Mar 21, 2015 11:45 AM, "giuseppecabras" notifications@github.com wrote:

Hi Rhodri,
I use Scientific Linux release 6.6 (Carbon), which is like RHEL6.6
In attach the aa_user_demo I run.
Thanks,
Giuseppe

On 21/03/2015 16:17, rhodricusack wrote:

Giuseppe
Can you post your user script exactly as you ran it? And, what OS are you
running on?
Thank you-
Rhodri

On 21 March 2015 at 10:56, giuseppecabras notifications@github.com
wrote:

Dear Rhodri,
I continue to have the problem in the aa_demo_v1, and current
devel-share
(just cloned again).
The recipe do correctly to aamod_convert_structural, I have the correct
input in:

/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii

but aamod_convert_structural use the wrong path to read it:

/home/gc/aa_demo/src/../analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii

I am using Matlab R2102b and SPM12, but I guess this is an aa4
devel-share
problem or aa_demo_v1 specification error that I don't know how to
investigate.
Any suggestion?
Cheers,
Giuseppe


Reply to this email directly or view it on GitHub

<
#81 (comment)

.

Rhodri Cusack
www.cusacklab.org

Associate Professor
Brain and Mind Institute
Natural Sciences Centre, Room 203
The University of Western Ontario
London, Ontario N6A 5B7
CANADA
+1 519 661 2111 ext 86381


Reply to this email directly or view it on GitHub
<
#81 (comment)
.

Giuseppe Cabras, PhD - Chemistry, Physics and Environment Dept.
InterUniversity Center for Behavioral Neurosciences http://icbn.uniud.it
University of Udine - via delle Scienze, 206 - 33100 UDINE
Phone: +39-043255-8212 - Fax: +39-043255-8222
URL: http://people.uniud.it/page/giuseppe.cabras
BOOK:
http://www.amazon.com/Advanced-component-analysis-techniques-decomposition/dp/3639873149

% Automatic analysis (aa) - user master script
% This example runs one session of one subject through a standard SPM-based
% fMRI analysis. After running, look at the results using SPM in
%
../analysis_v1/auditory/aamod_firstlevel_contrasts_00001/2014_03_29_9001/stats
% Prerequistes are aa and spm 8 or 12, I'm using Matlab 2014a.
% v1: Rhodri Cusack Brain and Mind Institute, Western University,
2014-12-15

aa_ver4_nocloud

% Add the directory of this script to the top of the matlab path
addpath(fileparts(mfilename('fullpath')),'-begin');

% Load the recipe tasklist
aap =
aarecipe('aap_tasklist_fmri_noslicetiming_withmodel_firstlevelonly.xml');
% aap = aarecipe('aap_tasklist_typical_fmri.xml');
% You might want to later set up a configuration for your local site
% aap=aas_localconfig(aap);
% I just have this one thing
aap.directory_conventions.dicomfilter='*.IMA';

% DEFINE STUDY SPECIFIC PARAMETERS
aap.options.aa_minver = 4.0; % designed for aa version 4.0 or above

% Define following paths relative to this script. You might not always want
% to do this, but it is good for this example
thisfilespath=fileparts(mfilename('fullpath'));

% Location of raw DICOM data
aap.directory_conventions.rawdatadir =
fullfile(thisfilespath,'../rawdata');

% Where to put the analyzed data
aap.acq_details.root = fullfile(thisfilespath,'../analysis_v1');
aap.directory_conventions.analysisid = 'auditory';

% This is name of the structural protocol, as typed into the scanner. If
% you're consistent with this, it can be found automatically in each new
% subject
aap.directory_conventions.protocol_structural = 'MPRAGE iPAT2_sag';

% Number of dummy scans at start of EPI runs
aap.acq_details.numdummies = 10;

% Just one session
aap = aas_addsession(aap,'lullaby_task');

% Just one subject
aap = aas_addsubject(aap,'2014_03_29_9001',[6]);

% Specify model - just one regressor here ('Sound')
% block onsets 0, 26, 52... 390 secs and duration 15 secs
%aap = aas_addevent(aap,'aamod_firstlevel_model','','','Sound',0:26:390,
15);

% Specify contrast - just sound minus silence
%aap = aas_addcontrast(aap, 'aamod_firstlevel_contrasts', '*',
'sameforallsessions', 1, 'sound-silence', 'T');

% DO PROCESSING
aap = aa_doprocessing(aap);


Reply to this email directly or view it on GitHub
#81 (comment)
.

@giuseppecabras

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commented Mar 21, 2015

Sorry, scrip follows:
% Automatic analysis (aa) - user master script
% This example runs one session of one subject through a standard SPM-based
% fMRI analysis. After running, look at the results using SPM in
%
../analysis_v1/auditory/aamod_firstlevel_contrasts_00001/2014_03_29_9001/stats
% Prerequistes are aa and spm 8 or 12, I'm using Matlab 2014a.
% v1: Rhodri Cusack Brain and Mind Institute, Western University, 2014-12-15

aa_ver4_nocloud

% Add the directory of this script to the top of the matlab path
addpath(fileparts(mfilename('fullpath')),'-begin');

% Load the recipe tasklist
aap =
aarecipe('aap_tasklist_fmri_noslicetiming_withmodel_firstlevelonly.xml');
% aap = aarecipe('aap_tasklist_typical_fmri.xml');
% You might want to later set up a configuration for your local site
% aap=aas_localconfig(aap);
% I just have this one thing
aap.directory_conventions.dicomfilter='*.IMA';

% DEFINE STUDY SPECIFIC PARAMETERS
aap.options.aa_minver = 4.0; % designed for aa version 4.0 or above

% Define following paths relative to this script. You might not always want
% to do this, but it is good for this example
thisfilespath=fileparts(mfilename('fullpath'));

% Location of raw DICOM data
aap.directory_conventions.rawdatadir = fullfile(thisfilespath,'../rawdata');

% Where to put the analyzed data
aap.acq_details.root = fullfile(thisfilespath,'../analysis_v1');
aap.directory_conventions.analysisid = 'auditory';

% This is name of the structural protocol, as typed into the scanner. If
% you're consistent with this, it can be found automatically in each new
% subject
aap.directory_conventions.protocol_structural = 'MPRAGE iPAT2_sag';

% Number of dummy scans at start of EPI runs
aap.acq_details.numdummies = 10;

% Just one session
aap = aas_addsession(aap,'lullaby_task');

% Just one subject
aap = aas_addsubject(aap,'2014_03_29_9001',[6]);

% Specify model - just one regressor here ('Sound')
% block onsets 0, 26, 52... 390 secs and duration 15 secs
%aap =
aas_addevent(aap,'aamod_firstlevel_model','','','Sound',0:26:390, 15);

% Specify contrast - just sound minus silence
%aap = aas_addcontrast(aap, 'aamod_firstlevel_contrasts', '*',
'sameforallsessions', 1, 'sound-silence', 'T');

% DO PROCESSING
aap = aa_doprocessing(aap);

On 21/03/2015 18:56, rhodricusack wrote:

I can't see the attachment, can you paste it into the message body?
Thanks!
On Mar 21, 2015 11:45 AM, "giuseppecabras" notifications@github.com
wrote:

Hi Rhodri,
I use Scientific Linux release 6.6 (Carbon), which is like RHEL6.6
In attach the aa_user_demo I run.
Thanks,
Giuseppe

On 21/03/2015 16:17, rhodricusack wrote:

Giuseppe
Can you post your user script exactly as you ran it? And, what OS
are you
running on?
Thank you-
Rhodri

On 21 March 2015 at 10:56, giuseppecabras notifications@github.com
wrote:

Dear Rhodri,
I continue to have the problem in the aa_demo_v1, and current
devel-share
(just cloned again).
The recipe do correctly to aamod_convert_structural, I have the
correct
input in:

/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii

but aamod_convert_structural use the wrong path to read it:

/home/gc/aa_demo/src/../analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii

I am using Matlab R2102b and SPM12, but I guess this is an aa4
devel-share
problem or aa_demo_v1 specification error that I don't know how to
investigate.
Any suggestion?
Cheers,
Giuseppe


Reply to this email directly or view it on GitHub

<

#81 (comment)

.

Rhodri Cusack
www.cusacklab.org

Associate Professor
Brain and Mind Institute
Natural Sciences Centre, Room 203
The University of Western Ontario
London, Ontario N6A 5B7
CANADA
+1 519 661 2111 ext 86381


Reply to this email directly or view it on GitHub
<

#81 (comment)

.

Giuseppe Cabras, PhD - Chemistry, Physics and Environment Dept.
InterUniversity Center for Behavioral Neurosciences http://icbn.uniud.it
University of Udine - via delle Scienze, 206 - 33100 UDINE
Phone: +39-043255-8212 - Fax: +39-043255-8222
URL: http://people.uniud.it/page/giuseppe.cabras
BOOK:

http://www.amazon.com/Advanced-component-analysis-techniques-decomposition/dp/3639873149

% Automatic analysis (aa) - user master script
% This example runs one session of one subject through a standard
SPM-based
% fMRI analysis. After running, look at the results using SPM in
%

../analysis_v1/auditory/aamod_firstlevel_contrasts_00001/2014_03_29_9001/stats
% Prerequistes are aa and spm 8 or 12, I'm using Matlab 2014a.
% v1: Rhodri Cusack Brain and Mind Institute, Western University,
2014-12-15

aa_ver4_nocloud

% Add the directory of this script to the top of the matlab path
addpath(fileparts(mfilename('fullpath')),'-begin');

% Load the recipe tasklist
aap =

aarecipe('aap_tasklist_fmri_noslicetiming_withmodel_firstlevelonly.xml');
% aap = aarecipe('aap_tasklist_typical_fmri.xml');
% You might want to later set up a configuration for your local site
% aap=aas_localconfig(aap);
% I just have this one thing
aap.directory_conventions.dicomfilter='*.IMA';

% DEFINE STUDY SPECIFIC PARAMETERS
aap.options.aa_minver = 4.0; % designed for aa version 4.0 or above

% Define following paths relative to this script. You might not
always want
% to do this, but it is good for this example
thisfilespath=fileparts(mfilename('fullpath'));

% Location of raw DICOM data
aap.directory_conventions.rawdatadir =
fullfile(thisfilespath,'../rawdata');

% Where to put the analyzed data
aap.acq_details.root = fullfile(thisfilespath,'../analysis_v1');
aap.directory_conventions.analysisid = 'auditory';

% This is name of the structural protocol, as typed into the scanner. If
% you're consistent with this, it can be found automatically in each new
% subject
aap.directory_conventions.protocol_structural = 'MPRAGE iPAT2_sag';

% Number of dummy scans at start of EPI runs
aap.acq_details.numdummies = 10;

% Just one session
aap = aas_addsession(aap,'lullaby_task');

% Just one subject
aap = aas_addsubject(aap,'2014_03_29_9001',[6]);

% Specify model - just one regressor here ('Sound')
% block onsets 0, 26, 52... 390 secs and duration 15 secs
%aap =
aas_addevent(aap,'aamod_firstlevel_model','','','Sound',0:26:390,
15);

% Specify contrast - just sound minus silence
%aap = aas_addcontrast(aap, 'aamod_firstlevel_contrasts', '*',
'sameforallsessions', 1, 'sound-silence', 'T');

% DO PROCESSING
aap = aa_doprocessing(aap);


Reply to this email directly or view it on GitHub

#81 (comment)
.


Reply to this email directly or view it on GitHub
#81 (comment).

Giuseppe Cabras, PhD - Chemistry, Physics and Environment Dept.
InterUniversity Center for Behavioral Neurosciences http://icbn.uniud.it
University of Udine - via delle Scienze, 206 - 33100 UDINE
Phone: +39-043255-8212 - Fax: +39-043255-8222
URL: http://people.uniud.it/page/giuseppe.cabras
BOOK:http://www.amazon.com/Advanced-component-analysis-techniques-decomposition/dp/3639873149

@rhodricusack

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commented Mar 22, 2015

Giuseppe
I've just checked the code at my end, by synchronizing with github and
rerunning the demo from the beginning, and it runs through without a
problem. So it must be some difference between our configurations. I'm
using a similar matlab (2013a) and Ubuntu, but we've used 2012b and a
RedHat derivative (CentOS) lots, so I don't think those will be the problem.

Lets try some debugging. What happens if after running the user script you
do

aap=aas_setcurrenttask(aap,1);
aas_getstudy_path(aap)
What is the output?

Do you have FSL installed? There are some FSL based diagnostics, which
should fail elegantly if you don't have it, but it is another potential
source of difference. What happens if you type

[s w]=aas_runfslcommand(aap,'fslmaths --help');
Do you see the FSL help, or an error with the environment variables dumped?

Finally, lets just check we're on the same release/branch of aa - what
happens if you type aa_ver4_nocloud

We'll get there - my apologies for these difficulties
Best
Rhodri

On 21 March 2015 at 14:26, giuseppecabras notifications@github.com wrote:

Sorry, scrip follows:

% Automatic analysis (aa) - user master script
% This example runs one session of one subject through a standard SPM-based
% fMRI analysis. After running, look at the results using SPM in
%

../analysis_v1/auditory/aamod_firstlevel_contrasts_00001/2014_03_29_9001/stats
% Prerequistes are aa and spm 8 or 12, I'm using Matlab 2014a.
% v1: Rhodri Cusack Brain and Mind Institute, Western University,
2014-12-15

aa_ver4_nocloud

% Add the directory of this script to the top of the matlab path
addpath(fileparts(mfilename('fullpath')),'-begin');

% Load the recipe tasklist
aap =
aarecipe('aap_tasklist_fmri_noslicetiming_withmodel_firstlevelonly.xml');
% aap = aarecipe('aap_tasklist_typical_fmri.xml');
% You might want to later set up a configuration for your local site
% aap=aas_localconfig(aap);
% I just have this one thing
aap.directory_conventions.dicomfilter='*.IMA';

% DEFINE STUDY SPECIFIC PARAMETERS
aap.options.aa_minver = 4.0; % designed for aa version 4.0 or above

% Define following paths relative to this script. You might not always want
% to do this, but it is good for this example
thisfilespath=fileparts(mfilename('fullpath'));

% Location of raw DICOM data
aap.directory_conventions.rawdatadir =
fullfile(thisfilespath,'../rawdata');

% Where to put the analyzed data
aap.acq_details.root = fullfile(thisfilespath,'../analysis_v1');
aap.directory_conventions.analysisid = 'auditory';

% This is name of the structural protocol, as typed into the scanner. If
% you're consistent with this, it can be found automatically in each new
% subject
aap.directory_conventions.protocol_structural = 'MPRAGE iPAT2_sag';

% Number of dummy scans at start of EPI runs
aap.acq_details.numdummies = 10;

% Just one session
aap = aas_addsession(aap,'lullaby_task');

% Just one subject
aap = aas_addsubject(aap,'2014_03_29_9001',[6]);

% Specify model - just one regressor here ('Sound')
% block onsets 0, 26, 52... 390 secs and duration 15 secs
%aap =
aas_addevent(aap,'aamod_firstlevel_model','','','Sound',0:26:390, 15);

% Specify contrast - just sound minus silence
%aap = aas_addcontrast(aap, 'aamod_firstlevel_contrasts', '*',
'sameforallsessions', 1, 'sound-silence', 'T');

% DO PROCESSING
aap = aa_doprocessing(aap);

On 21/03/2015 18:56, rhodricusack wrote:

I can't see the attachment, can you paste it into the message body?
Thanks!
On Mar 21, 2015 11:45 AM, "giuseppecabras" notifications@github.com
wrote:

Hi Rhodri,
I use Scientific Linux release 6.6 (Carbon), which is like RHEL6.6
In attach the aa_user_demo I run.
Thanks,
Giuseppe

On 21/03/2015 16:17, rhodricusack wrote:

Giuseppe
Can you post your user script exactly as you ran it? And, what OS
are you
running on?
Thank you-
Rhodri

On 21 March 2015 at 10:56, giuseppecabras notifications@github.com
wrote:

Dear Rhodri,
I continue to have the problem in the aa_demo_v1, and current
devel-share
(just cloned again).
The recipe do correctly to aamod_convert_structural, I have the
correct
input in:

/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii

but aamod_convert_structural use the wrong path to read it:

/home/gc/aa_demo/src/../analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii

I am using Matlab R2102b and SPM12, but I guess this is an aa4
devel-share
problem or aa_demo_v1 specification error that I don't know how to
investigate.
Any suggestion?
Cheers,
Giuseppe

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<

#81 (comment)

.

Rhodri Cusack
www.cusacklab.org

Associate Professor
Brain and Mind Institute
Natural Sciences Centre, Room 203
The University of Western Ontario
London, Ontario N6A 5B7
CANADA
+1 519 661 2111 ext 86381


Reply to this email directly or view it on GitHub
<

#81 (comment)

.

Giuseppe Cabras, PhD - Chemistry, Physics and Environment Dept.
InterUniversity Center for Behavioral Neurosciences
http://icbn.uniud.it
University of Udine - via delle Scienze, 206 - 33100 UDINE
Phone: +39-043255-8212 - Fax: +39-043255-8222
URL: http://people.uniud.it/page/giuseppe.cabras
BOOK:

http://www.amazon.com/Advanced-component-analysis-techniques-decomposition/dp/3639873149

% Automatic analysis (aa) - user master script
% This example runs one session of one subject through a standard
SPM-based
% fMRI analysis. After running, look at the results using SPM in
%

../analysis_v1/auditory/aamod_firstlevel_contrasts_00001/2014_03_29_9001/stats

% Prerequistes are aa and spm 8 or 12, I'm using Matlab 2014a.
% v1: Rhodri Cusack Brain and Mind Institute, Western University,
2014-12-15

aa_ver4_nocloud

% Add the directory of this script to the top of the matlab path
addpath(fileparts(mfilename('fullpath')),'-begin');

% Load the recipe tasklist
aap =

aarecipe('aap_tasklist_fmri_noslicetiming_withmodel_firstlevelonly.xml');
% aap = aarecipe('aap_tasklist_typical_fmri.xml');
% You might want to later set up a configuration for your local site
% aap=aas_localconfig(aap);
% I just have this one thing
aap.directory_conventions.dicomfilter='*.IMA';

% DEFINE STUDY SPECIFIC PARAMETERS
aap.options.aa_minver = 4.0; % designed for aa version 4.0 or above

% Define following paths relative to this script. You might not
always want
% to do this, but it is good for this example
thisfilespath=fileparts(mfilename('fullpath'));

% Location of raw DICOM data
aap.directory_conventions.rawdatadir =
fullfile(thisfilespath,'../rawdata');

% Where to put the analyzed data
aap.acq_details.root = fullfile(thisfilespath,'../analysis_v1');
aap.directory_conventions.analysisid = 'auditory';

% This is name of the structural protocol, as typed into the scanner.
If
% you're consistent with this, it can be found automatically in each
new
% subject
aap.directory_conventions.protocol_structural = 'MPRAGE iPAT2_sag';

% Number of dummy scans at start of EPI runs
aap.acq_details.numdummies = 10;

% Just one session
aap = aas_addsession(aap,'lullaby_task');

% Just one subject
aap = aas_addsubject(aap,'2014_03_29_9001',[6]);

% Specify model - just one regressor here ('Sound')
% block onsets 0, 26, 52... 390 secs and duration 15 secs
%aap =
aas_addevent(aap,'aamod_firstlevel_model','','','Sound',0:26:390,
15);

% Specify contrast - just sound minus silence
%aap = aas_addcontrast(aap, 'aamod_firstlevel_contrasts', '*',
'sameforallsessions', 1, 'sound-silence', 'T');

% DO PROCESSING
aap = aa_doprocessing(aap);


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<
#81 (comment)

.


Reply to this email directly or view it on GitHub
<
#81 (comment)
.

Giuseppe Cabras, PhD - Chemistry, Physics and Environment Dept.
InterUniversity Center for Behavioral Neurosciences http://icbn.uniud.it
University of Udine - via delle Scienze, 206 - 33100 UDINE
Phone: +39-043255-8212 - Fax: +39-043255-8222
URL: http://people.uniud.it/page/giuseppe.cabras
BOOK:
http://www.amazon.com/Advanced-component-analysis-techniques-decomposition/dp/3639873149


Reply to this email directly or view it on GitHub
#81 (comment)
.

Rhodri Cusack
www.cusacklab.org

Associate Professor
Brain and Mind Institute
Natural Sciences Centre, Room 203
The University of Western Ontario
London, Ontario N6A 5B7
CANADA
+1 519 661 2111 ext 86381

@giuseppecabras

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commented Mar 22, 2015

At the beginning of the user script running, before SPM initialization, I get 2 warning saying that EEG lab and GIFT are not found.
During SPM12 v6225 initialization, 3 SPM12 GUI windows pops up... is this correct?
Also, spm12 subfolders are top added to MATLAB search path
Before parallel process starts, I get this message:
You must compile the utc_time library
After aamod_get_dicom_epi executing, I get:
WARNING: defaults.modality is not set; FMRI is assumed
In the Workspace, the variable thisfilespath is correct:
'/home/gc/aa_demo/src'

Lets try some debugging. What happens if after running the user script you
do

aap=aas_setcurrenttask(aap,1);
Reference to non-existent field 'internal'.
Error in ass_setcurrenttask (line 19)
initinternal=aap.internal;

aas_getstudy_path(aap)
Undefined function 'aas_getstudy_path' for input arguments of type 'struct'.

What is the output?

in fact, aap variable struct has not the ' internal' field struct.

Do you have FSL installed? There are some FSL based diagnostics, which
should fail elegantly if you don't have it, but it is another potential
source of difference. What happens if you type
[s w]=aas_runfslcommand(aap,'fslmaths --help');
Do you see the FSL help, or an error with the environment variables dumped?

Yes (but without ";"):

[s w]=aas_runfslcommand(aap,'fslmaths --help')
s =
0
w =
Usage: fslmaths [-dt ] <first_input> [operations and inputs] [-odt ]
[...]

Finally, lets just check we're on the same release/branch of aa - what
happens if you type aa_ver4_nocloud

I get the
Welcome to aa version 4.20 Jan 2015
message and all devel-share subfolders are added on top to MATLAB search path
At the beginning, I cloned the devel-share branch with the unix command:
git clone -b devel-share https://github.com/rhodricusack/automaticanalysis.git devel-share

Thank you for your help and time. I really hope to use your sw soon... on my data too ;)
Best,
Giuseppe

@rhodricusack

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commented Mar 22, 2015

My typo. After running your user script, what do you get from

aas_getstudypath(aap)
Thanks
Rhodri

@giuseppecabras

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commented Mar 22, 2015

aas_getstudypath(aap)

ans =
/home/gc/aa_demo/src/../analysis_v1

which sounds good!
Bye,
Giuseppe

@rhodricusack

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commented Mar 22, 2015

OK, I think we're close.
Can you do

fullfile('/home/gc/aa_demo/src','../analysis_v1')

If you get
/home/gc/aa_demo/src/../analysis_v1
and not (what I see)
/home/gc/aa_demo/analysis_v1

Then can you try changing the line in the user script that currently says
aap.acq_details.root = fullfile(thisfilespath,'../analysis_v1');
to
aap.acq_details.root = '/home/gc/aa_demo/analysis_v1';
and see if it runs through?
Thanks

On 17 March 2015 at 14:45, giuseppecabras notifications@github.com wrote:

Dear Rhodri,
I have tried the aa_demo and now it works partially... at the end I get
this error:

[...]
MODULE aamod_convert_structural RUNNING: Convert T1 image from DICOMs for
/home/gc/aa_demo/src/../analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001
retrieve stream dicom_structural from
/home/gc/aa_demo/src/../analysis_v1/auditory/aamod_get_dicom_structural_00001/2014_03_29_9001
to
/home/gc/aa_demo/src/../analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001
executing
Sequence has a TR of 2300.0 ms

**** automatic analysis failed - see reason and line numbers below
Cannot open input file
/home/gc/aa_demo/src/../analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/home/gc/aa_demo/analysis_v1/auditory/aamod_convert_structural_00001/2014_03_29_9001/structurals/s140329153253DST131221107524367007-0002-00001-000192-01.nii
for help, see the aa wiki
Error using aas_log (line 63)
aa error

Error in aas_md5 (line 32)
aas_log(aap,true,sprintf('Cannot open input file %s',pth));

Error in aas_desc_outputs (line 89)
[aap md5_base64]=aas_md5(aap,trimmedoutputs,localroot);

Error in aamod_convert_structural (line 51)
aap = aas_desc_outputs(aap, subjInd, outStreamImg,
convertedfns(structVols, :));

Error in aa_feval (line 18)
[a b]=feval(funcname,varargin{:});

Error in aa_feval_withindices (line 6)
[aap,resp]=aa_feval(mfile_alias,aap,task,indices(1));

Error in aa_doprocessing_onetask (line 151)
[aap,resp]=aa_feval_withindices(mfile_alias,aap,task,indices);

Error in aaq_localsingle/runall (line 16)
aa_doprocessing_onetask(obj.aap,job.task,job.k,job.indices);

Error in aa_doprocessing (line 385)
taskqueue.runall(dontcloseexistingworkers, false);

Error in aa_user_demo_v1 (line 52)
aap = aa_doprocessing(aap);

as you can see, the path after
**** automatic analysis failed - see reason and line numbers below
is constructed wrong (see /home/gc/ again in the middle of the path).

If you need the full output or other info I'll send you all.

Thanks and best,
Giuseppe


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#81 (comment)
.

Rhodri Cusack
www.cusacklab.org

Associate Professor
Brain and Mind Institute
Natural Sciences Centre, Room 203
The University of Western Ontario
London, Ontario N6A 5B7
CANADA
+1 519 661 2111 ext 86381

@giuseppecabras

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commented Mar 22, 2015

Great Rhodri!
Now it's going on.
Just at the end I get:

Display /home/gc/aa_demo/analysis_v1/auditory/aamod_norm_noss_00001/2014_03_29_9001/structurals/mms140329153253DST131221107524367007-0002-00001-000192-01.nii,1
Error using checkfilename>validateFilename (line 166)
Function GUNZIP was unable to find file
''/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm.nii.gz''.

but I suppose I have to install it... tomorrow morning ;-)
Thank you very much for your support.
Cheers,
Giuseppe

@rhodricusack

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commented Mar 23, 2015

Hi Giuseppe
You may need to set aap.directory_conventions.fsldir correctly. You can
initially test this by putting it in your user script, but may wish to push
this setting to an aas_localconfig file (within the aa_config directory)
or by creating a version of aap_parameters_defauts with your own name,
likely which derives most of its settings from the shipped
aap_parameters_defaults and which just overrides what you need (See
aap_parameters_defaults_CBSU.xml for an example).
Best,
Rhodri

On 22 March 2015 at 19:02, Giuseppe Cabras notifications@github.com wrote:

Great Rhodri!
Now it's going on.
Just at the end I get:

Display
/home/gc/aa_demo/analysis_v1/auditory/aamod_norm_noss_00001/2014_03_29_9001/structurals/mms140329153253DST131221107524367007-0002-00001-000192-01.nii,1
Error using checkfilename>validateFilename (line 166)
Function GUNZIP was unable to find file
''/usr/share/fsl/5.0/data/standard/MNI152_T1_1mm.nii.gz''.

but I suppose I have to install it... tomorrow morning ;-)
Thank you very much for your support.
Cheers,
Giuseppe


Reply to this email directly or view it on GitHub
#81 (comment)
.

Rhodri Cusack
www.cusacklab.org

Associate Professor
Brain and Mind Institute
Natural Sciences Centre, Room 203
The University of Western Ontario
London, Ontario N6A 5B7
CANADA
+1 519 661 2111 ext 86381

@giuseppecabras

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commented Mar 23, 2015

Dear Rhodri,
I followed your suggestion and I wrote in the demo user script:
aap.directory_conventions.fsldir='/usr/local/fsl';

also I uncommented the lines that specify model and contrast, and now the demo script runs to completion!
Very impressive starting point indeed, it works in my setup just modifying few lines in the user script.
Thank you for your patience and support,
best,
Giuseppe

@tiborauer tiborauer closed this Jul 28, 2015

jooh pushed a commit to jooh/automaticanalysis that referenced this issue Feb 21, 2019

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