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Good evening Doug,
Thank you for the clarification.
All the best,
Jacob
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Wednesday, June 1, 2022 8:22 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] samseg2recon error / missing files
Currently, you'll have to run recon-all to the end in order to run the hippo
subfield seg
On 5/30/2022 5:55 AM, Jacob Levenstein wrote:
External Email - Use Caution
Hello Freesurfer team + users,
I am looking to run segmentHA_T1.sh following samseg + samseg2recon, and came
across this previous thread where it seemed to workout:
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Given that I am writing in, I have not yet gotten this to run properly...
Below is my samseg command:
samseg --t1w ${subject}_${ses}_T1w.nii.gz --sd . --s
${subject}_${ses}_samseg --refmode t1w --threads 16 --parallel
>From the log file, samseg seems to run correctly, but once it reaches the
>samseg2recon steps, I receive the following error:
ln -sf orig.mgz rawavg.mgz
ERROR: ln -sf orig.mgz rawavg.mgz
ERROR: samseg2recon --s ${subject}_${ses}_samseg --tmpdir
${SUBJECTS_DIR}/${subject}_${ses}_samseg/mri/samseg/tmp.pyBLVF/tmp.mergeseg
--cleanup
If I then (re)run samseg2recon on the samseg directory (see cmd below) , I can
execute the failed lines, and this script completes without error.
samseg2recon --s ${subject}_${ses}_samseg
However, when I then try to run: segmentHA_T1.sh ${subject}_${ses}_samseg, I
receive the following error:
Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject.
Has the subject been procesed with recon-all?
As the error message correctly states, within that subject's dir, I do not have
an mri/norm.mgz or mri/wmparc.mgz. I do have an
mri/samseg/transforms/samseg.talairach.xfm, but it is not in the scripts
expected location/naming convention.
If it is helpful to know:
i. Running recon-all then segmentHA_T1.sh completes without error...
ii. Copy over the mri dir from the recon-all to the samseg subject dir, then
running segmentHA_T1.sh also completes without error...
iii. I am running Ubuntu 20.04.4, freesurfer-linux-ubunu18x86_64_-7.2.0-20210721
Any idea what may be going wrong with samseg/samseg2recon? I am happy to use
the workaround listed above, but I suspect there may be a more efficient way,
and or unintended implications when mixing and matching recon-all and samseg...?
Thank you for your help and insight!
All the best,
Jacob
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