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________________________________ 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://secure-web.cisco.com/1z5XiLDbECZb1gv8wAZoV7fS7G_v-k4oqEkA6DCAbe1thCcFIbS8GrQ0rS8w87N0NvMiViBC0YdMwaSaNISpucIX_cXOR8Hlw_ctEC62zngdG7q65p1DvP0YEfI9NnWKw3M1gYslcsl2tUv-Rh3BP6QxrO1ymv8XqcmTbQMCeUWdSmpHoqxpNSBXWaMEYy7Zw-bi64zh_PeVMokZOpHriW3PchKqGpcU17Ubb_PerNQC-SYxuU-kUQ9F4W3ZBf55XZHT1fIDZpu3-5LlWFR5Y_0U_yCJUhW1Rb0WBZTbevTwP5zB5jEA72GyH4WJIzFT0DQk0ZNw8naeHaqRV0BVCKA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting 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
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