External Email - Use Caution
Thank you for looking into this, Yujing! here's my stats dir:
$ ls -l /work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/stats
total 77
-rwxrwxrwx. 1 ark19 root 972 Jun 3 17:03 lh.aparc.stats
-rwxrwxrwx. 1 ark19 root 49236 Jun 3 16:22 lh.curv.stats
-rw-rw-r--. 1 ark19 root 6606 Jun 3 17:03 lh.w-g.pct.stats
FWIW I confirmed that I'm running the original version of recon-all
(freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 from 2013)
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu>
Sent: Friday, June 2, 2023 4:23 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
I followed 5.3 recon-all a little bit. rh will be processed after lh. Your
recon-all stopped while it was still processing lh.
The error
‘MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white): could
not open file’ happened when recon-all was doing Parcellation Stats lh:
mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f
../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c
../label/aparc.annot.ctab sub-0223_mprage lh white
I don’t understand why it tried to read rh.white while it was doing lh white.
I’m wondering maybe it was actually complaining about ../stats/lh.aparc.stats.
Can you do ‘ls -l’ of your stats directory?
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing
Sent: Friday, June 2, 2023 3:31 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hi Annchen,
It seems that recon-all only processed lh. By default, it should process both
lh and rh. Original recon-all have this line ‘set hemilist = (lh rh);’ at the
beginning of the script. Can you make sure the one you are running is the
original?
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Annchen Knodt
Sent: Friday, June 2, 2023 2:53 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
External Email - Use Caution
Hi Yujing,
Thanks so much for your response! I tried copying
$FREESURFER_HOME/subjects/fsaverage and
$FREESURFER_HOME/subjects/${hemi}.EC_average to $SUBJECTS dir before running,
and this time I ran with the original recon-all instead of the one that had
been edited to remove links (recon-all_noLink). I was sure this would solve
the problem, but I ended up getting the same error:
Command:
/cifs/hariri-long/Scripts/Tools/FreeSurfer_v5.3/freesurfer/bin/recon-all -all
-s sub-0223_mprage -openmp 1 -i
/cifs/hariri-long/Studies/DBIS_P52/Imaging/sourcedata/sub-0223/anat/sub-0223_T1w.nii.gz
Error:
MRISread(/work/long/freesurfer_v5.3_DBIS/sub-0223_mprage/surf/rh.white):
could not open file
Did I need to copy them somewhere besides $SUBJECTS_DIR ? I’m not seeing any
“failed to create symbolic link” messages which I interpret as the script
having found the files and not need to run the ‘ln -s’ commands.
Attaching the log file from this latest run.
Thanks!
Annchen
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu<mailto:yhuan...@mgh.harvard.edu>>
Date: Thursday, June 1, 2023 at 3:06 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3
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:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Annchen Knodt
Sent: Thursday, June 1, 2023 2:10 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
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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