Hi Bruce, After downloading, I have put the files in those folders, and I can see them. Furthermore, when I go to the folder and then do the ls command, they are listed as being there. however the command looking for all files with the .nii extension says there are no files there. I don't understand how this is possible, do you?
Thanks for helping out. ls: /Desktop/MRI/L001.nii.gz: No such file or directory bash-3.2$ ls -l /Desktop/MRI/*.nii* ls: /Desktop/MRI/*.nii*: No such file or directory bash-3.2$ ls L001.nii.gz S1 S13 S4 S8 L1 S1.nii S13.nii S4.nii S8.nii bash-3.2$ cd .. bash-3.2$ cd .. bash-3.2$ ls 20151020volunteer Library Applications Movies Desktop Music oasys.log Desktop.feat OneDrive simdir Desktop.ica Pictures simdir- Documents Public simdir-- Downloads ibt_application.log simdir--- Dropbox ibtsa.log summary.txt Google Drive matlab bash-3.2$ cd Desktop bash-3.2$ ls ARCsleep TIMID printscreens MRI Uren.xlsx bash-3.2$ cd MRI bash-3.2$ ls L001.nii.gz S1 S13 S4 S8 L1 S1.nii S13.nii S4.nii S8.nii bash-3.2$ On Thu, Oct 20, 2016 at 3:52 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Marja > > you need to figure out where the input files are! How do you know they are > there? Can you run: > > ls -l /Desktop/MRI/*.nii* > > > > cheers > Bruce > On Wed, 19 Oct 2016, Marja Caverlé wrote: > > Hi Bruce, >> >> that command also says there is no file or directory: >> >> bash-3.2$ ls -l /Documents/MRI/L001.nii.gz >> ls: /Documents/MRI/L001.nii.gz: No such file or directory >> bash-3.2$ ls -l /Desktop/MRI/L001.nii.gz >> ls: /Desktop/MRI/L001.nii.gz: No such file or directory >> >> Even though, the niftis are really there. >> >> Best, >> >> Marja >> >> >> On Wed, Oct 19, 2016 at 3:44 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> 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. 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/compli >> anceline . 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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 > > > 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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