Von: Rühr, Livia
Gesendet: Donnerstag, 12. Januar 2023 17:25
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Problem with recon-all --> nii.gz file not found

Dear Sir or Madame,

for my thesis I am running recon-all on my subjects' nii.gz T1-weighted scans. I use Freesurfer 7.0 on a Linux Mint 21"Vanessa".

I am using the following layout:

recon-all -s sub-03 -i sub-03-ses-01_T1w.nii.gz -all

This worked for me in december, whereby all my subjects were processed successfully and freesurfer created the directories. However, today I wanted to continue my work, but now it says that the file "sub-03-ses-01_T1w.nii.gz" ist not found (error message):

ERROR: cannot find sub-03-ses-01_T1w.nii.gz
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-03 exited with ERRORS at Thu Jan 12 16:59:42 CET 2023

For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

This applies not only to one file, but for all of them. I have also tried to rerun recon-all of another file that had been successful in december, I have also copied and renamed it to not overwrite it.. but none of the data sets were found!

For Setup, I have defined my $FREESURFER_HOME, my $SUBJECTS_DIR and also the source (SetUpFreeSurfer.sh).

After typing the following: source $FREESURFER_HOME/SetUpFreeSurfer.sh

... I can now clearly see, that I am in the correct SUBJECTS_DIR
-------- freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /freesurfer
FSFAST_HOME       /freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /home/lirh717c/Desktop/V5LGN
MNI_DIR           /freesurfer/mni

After navigating to this directory (cd $SUBJECTS_DIR) I can also see all my files. Additionally, I can open freesurfer now and open 
the scans within freeview, so that the following appears to me:
- my data are okay and I can open them
- freesurfer is generally running (only thing is one warning: (process:3965): Gtk-WARNING **: 17:07:37.677: Locale not supported by C library.
    Using the fallback 'C' locale.)
- even if setting subjects directory to another directory, it is not working, the problem is neither the data nor the directory
- the subjects directory has correctly been set and I can access it --> my files are seen here

To this reason, I have no ideas anymore.
I am looking forward to your reply!

Kind regards
Livia Rühr