From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Annchen Knodt
Sent: Sunday, June 4, 2023 9:22 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Troubleshooting "could not open file" errors in FS 5.3

 

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

 

 

 

 

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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

 

 

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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

 

 

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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

 

 

 

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