Hi Livia,
SUBJECTS_DIR is the root directory for recon-all processed data. Each individual subject will have a separate subdirectory under SUBJECTS_DIR.
You need to specify full path to your images in recon-all command line.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Livia Ruehr Sent: Thursday, January 12, 2023 11:31 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] WG: Problem with recon-all --> nii.gz file not found
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________________________________ Von: Rühr, Livia Gesendet: Donnerstag, 12. Januar 2023 17:25 An: freesurfer@nmr.mgh.harvard.edumailto: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