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. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>> _______________________________________________ >>> 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. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender and >>> properly >>> dispose of the e-mail. >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > 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. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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