what does: ls -l /Documents/MRI/L001.nii.gz
show? On Wed, 19 Oct 2016, Marja Caverlé wrote:
Dear Bruce, Thanks for your reply. I tried that, but it does not change anything (at least if I did correctly what you suggested): bash-3.2$ recon-all -i /Documents/MRI/L001.nii.gz -sd MRI -subjid L1 -all ERROR: cannot find /Documents/MRI/L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 15:39:16 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On Wed, Oct 19, 2016 at 3:34 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: You need to provide the full path to it with the -i command. Then you can use -sd <SUBJECTS_DIR> and -s <SUBJECT ID> to specify where the output should go. Make sure that the directory <SUBJECTS_DIR> exists and is writeable by you, as recon-all will create a subtree called <SUBJECT_ID> under it cheers Bruce On Wed, 19 Oct 2016, Marja Caverle wrote: I changed it multiple times because I thought it would solve the problem (applications, desktop, documents). Currently it is in Documents/MRI. Marja Caverlé On 19 Oct 2016, at 15:29, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: what directory is the file L001.nii.gz in? cheers Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Hi Bruce, I tried a lot of different commands, trying to figure it out, with .nii and .nii.gz, and changing the SUBJECTS_DIR to different folders, but it did not really matter, it keeps on saying that the inputfile does not exist, or that the subject folder does not exist. ---bash-3.2$ recon-all -i L001.nii -subjid L1 -all ERROR: cannot find L001.nii Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:11:01 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --- bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Desktop/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: SUBJECTS_DIR /Documents/MRI does not exist. bash-3.2$ export SUBJECTS_DIR=/Documents/MRI/L1 bash-3.2$ recon-all -i L001.nii.gz -subjid L1 -all ERROR: cannot find L001.nii.gz Darwin Marjas-MacBook-Pro.local 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Wed Oct 19 14:16:52 CEST 2016 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --- Where can I find the log? I have been looking for it, hoping to give me some insight in the problem, but I could not find it. It has been a while since I used Freesurfer, so probably I am doing something wrong, but I cannot figure it out. Thank you! Best, Marja On Wed, Oct 19, 2016 at 3:01 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: Hi Marja can you send us the command you ran and the full screen output and the recon-all.log file? thanks Bruce On Wed, 19 Oct 2016, Marja Caverlé wrote: Dear all, When I want to run a recon-all -all, I keep getting the error saying that the input file cannot be found. Any idea what is going wrong? Best, Marja _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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