External Email - Use Caution
Hi Annchen,
Your cp commands are missing destination file operands, see the errors in
recon-all.log.
ln -s $FREESURFER_HOME/subjects/fsaverage and ln -s
$FREESURFER_HOME/subjects/${hemi}.EC_average create symbolic links to
directory. You will have to copy those two directories for your subject. I
think if you copy them before recon-all, it won’t go through the codes to
create the link.
Best,
Yujing
From: [email protected]
<[email protected]> On Behalf Of Annchen Knodt
Sent: Thursday, June 1, 2023 2:10 PM
To: [email protected]
Subject: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hello,
I'm trying to run freesurfer v5.3 recon-all and running into an error I'm not
sure how to troubleshoot. I'm using essentially the same commands that i've
successfully used to run version 6.0 recently, and that i've also successfully
run 5.3 with in the past.
On my first pass, I attempted to run this full recon-all command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink
-all -s sub-0223_mprage -openmp 1 -i
/cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white):
could not open file
Lots of lh surf files were produced as well as 3 of the lh stats files (aparc,
curv, w-g), but nothing for rh, and I could not find the rh.white file. I then
tried running rh using:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink
-all -s sub-0223_mprage -openmp 1 -hemi rh
And eventually got the error:
MRISread(/work/long/freesurfer_v5.3_DBIS/rh.EC_average/surf/rh.sphere.reg):
could not open file
One thing that seems weird about the second error is that it is looking in
$SUBJECTS_DIR instead of $SUBJECTS_DIR/<subject> for the rh.sphere file, when
the file does exist in $SUBJECTS_DIR/<subject>/surf (but not the top dir where
it's looking)
Also wanted to note that i'm running this a slightly tweaked version to remove
symlinks which aren't allowed on the cluster i'm working on (which is running
CentOS 8):
$ diff
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all_noLink
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all
3447c3447
< cp $subj1 ${diffsubj}_tmp
---
> ln -s $subj1 ${diffsubj}_tmp
3753c3753
< cp $subj1 ${diffsubj}_tmp
---
> ln -s $subj1 ${diffsubj}_tmp
3911c3911
< set cmd=(cp $FREESURFER_HOME/subjects/fsaverage)
---
> set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4028c4028
< set cmd=(cp $FREESURFER_HOME/subjects/fsaverage)
---
> set cmd=(ln -s $FREESURFER_HOME/subjects/fsaverage)
4157c4157
< set cmd=(cp $FREESURFER_HOME/subjects/${hemi}.EC_average)
---
> set cmd=(ln -s $FREESURFER_HOME/subjects/${hemi}.EC_average)
Any tips on how I can troubleshoot this? Attaching recon-all.log file.
Thanks!!
Annchen
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