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ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050 #562
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I don't think I have a login to that site. Are you able to test again on 0.4.5? Because there should have been no change in FreeSurfer between versions. The timestamps on the dist server are still January. |
I run it before on 0.4.5 and did not get that error. I can run it again. My reasoning is that the the new harmonization method must've changed something about the headers that is throwing freesurfer off. |
Oh... good call.
…-------- Original message --------
From: Chris Filo Gorgolewski <notifications@github.com>
Date: 6/16/17 12:46 (GMT-05:00)
To: poldracklab/fmriprep <fmriprep@noreply.github.com>
Cc: Christopher Markiewicz <markiewicz@stanford.edu>, Comment <comment@noreply.github.com>
Subject: Re: [poldracklab/fmriprep] ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050 (#562)
I run it before on 0.4.5 and did not get that error. I can run it again.
My reasoning is that the the new harmonization method must've changed something about the headers that is throwing freesurfer off.
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My first thought on this is we can go back to passing all T1w images to recon-all, rather than merging and then passing. It means doubling up on the But I'm grabbing these subjects so I can look at the results. If Talairach is failing, I'm guessing there's going to be a visible issue in the merged T1w images. |
Here's the change in header between the original image and the conformed image. (For sub-07, only 1c1
< filename /data/bids/ds000114/sub-07/ses-test/anat/sub-07_ses-test_T1w.nii.gz
---
> filename sub-07_ses-test_T1w_ras.nii.gz
13,14c13,14
< vox_units mm
< time_units s
---
> vox_units Unknown
> time_units Unknown
20,25c20,25
< pixdim2 1.300629
< pixdim3 1.000000
< pixdim4 0.009628
< pixdim5 0.000000
< pixdim6 0.000000
< pixdim7 0.000000
---
> pixdim2 1.300291
> pixdim3 0.999999
> pixdim4 1.000000
> pixdim5 1.000000
> pixdim6 1.000000
> pixdim7 1.000000
46,50c46,50
< qform_name Scanner Anat
< qform_code 1
< qto_xyz:1 0.999861 0.009812 0.014875 -134.640289
< qto_xyz:2 -0.008270 1.298998 0.049379 -84.381409
< qto_xyz:3 -0.014484 -0.064375 0.998669 -147.122208
---
> qform_name Unknown
> qform_code 0
> qto_xyz:1 1.000000 0.000000 0.000000 0.000000
> qto_xyz:2 0.000000 1.300291 0.000000 0.000000
> qto_xyz:3 0.000000 0.000000 0.999999 0.000000
55,56c55,56
< sform_name Scanner Anat
< sform_code 1
---
> sform_name Aligned Anat
> sform_code 2
58c58
< sto_xyz:2 -0.008271 1.298998 0.049380 -84.381409
---
> sto_xyz:2 -0.008268 1.298659 0.049367 -84.381409
66c66
< descrip FSL5.0
---
> descrip Points of concern:
In any event, I think we should set a tolerance (e.g. >0.05mm difference in zoom) to consider significant enough to rescale. But do you see any reason these header differences should cause issues? |
All of them could be problematic - it's hard to say. Might be worth passing
the header from the original file when creating the new one.
…On Fri, Jun 16, 2017 at 11:16 AM, Chris Markiewicz ***@***.*** > wrote:
Here's the change in header between the original image and the conformed
image. (For sub-07, only sub-07_ses-test_T1w.nii.gz changed.)
1c1< filename /data/bids/ds000114/sub-07/ses-test/anat/sub-07_ses-test_T1w.nii.gz---> filename sub-07_ses-test_T1w_ras.nii.gz13,14c13,14< vox_units mm< time_units s---> vox_units Unknown> time_units Unknown20,25c20,25< pixdim2 1.300629< pixdim3 1.000000< pixdim4 0.009628< pixdim5 0.000000< pixdim6 0.000000< pixdim7 0.000000---> pixdim2 1.300291> pixdim3 0.999999> pixdim4 1.000000> pixdim5 1.000000> pixdim6 1.000000> pixdim7 1.00000046,50c46,50< qform_name Scanner Anat< qform_code 1< qto_xyz:1 0.999861 0.009812 0.014875 -134.640289< qto_xyz:2 -0.008270 1.298998 0.049379 -84.381409< qto_xyz:3 -0.014484 -0.064375 0.998669 -147.122208---> qform_name Unknown> qform_code 0> qto_xyz:1 1.000000 0.000000 0.000000 0.000000> qto_xyz:2 0.000000 1.300291 0.000000 0.000000> qto_xyz:3 0.000000 0.000000 0.999999 0.00000055,56c55,56< sform_name Scanner Anat< sform_code 1---> sform_name Aligned Anat> sform_code 258c58< sto_xyz:2 -0.008271 1.298998 0.049380 -84.381409---> sto_xyz:2 -0.008268 1.298659 0.049367 -84.38140966c66< descrip FSL5.0---> descrip
Points of concern:
1. Header missing mm/s units. This should be fixable, but since this
is the assumption of pretty much all software, I doubt this is the source
of our problem.
2. qform: marked invalid, which should be fine...
3. sform: aligned? I'm not sure whether that should cause an issue.
In any event, I think we should set a tolerance (e.g. >0.05mm difference
in zoom) to consider significant enough to rescale. But do you see any
reason these header differences should cause issues?
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Also, running autorecon1 on the merged result when copying the header. Will report back. |
Update: Copying the header doesn't resolve the issue. I think the issue may be being originating within FreeSurfer's bias-field (nu) correction. Compare In which case the correct course of action is to set that threshold for resampling. I chose |
That sounds reasonable.
…On Fri, Jun 16, 2017 at 1:02 PM, Chris Markiewicz ***@***.***> wrote:
Update: Copying the header doesn't resolve the issue.
I think the issue may be being originating within FreeSurfer's bias-field
(nu) correction. Compare freesurfer/sub-07/mri/orig/001.mgz and
freesurfer/sub-07/orig.mgz (have to download because Papaya can't handle
.mgz). I *think* what might be going on is that the tiny shifts in the
image above are resulting in image statistics that are being interpreted as
a bias field effect, which then produces a weird image when "corrected".
In which case the correct course of action is to set that threshold for
resampling. I chose .05 earlier since that's the rounding distance for
.1mm, which is almost always the resolution that people are shooting for in
the scanner.
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ds114 subjects 07 and 09 only. This did not happen with 0.4.5. More info: http://openneuro.dev.sqm.io/datasets/ds000118/versions/00001?app=fmriprep&version=14&job=050a6e62-7f12-48cb-bf8d-8e3e76f739c4
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