bash-3.2$ pwd /Users/MarjaCaverle/Desktop/MRI (this means that I am in the right one right?)
Not really someone near, furthermore, almost no one uses mac. I did some analysis a few months back, and it worked just fine, but now I get these errors. I intentionally did not update to Sierra yet, because I was afraid that it might give problems with Freesurfer. Do you think I should update? On Thu, Oct 20, 2016 at 11:59 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > you probably aren't in the MRI dir. What does the command: > > pwd > > > return? And are there any mac-savvy users that can help you out nearby? > > cheers > Bruce > > > > On Thu, 20 Oct 2016, Marja Caverlé wrote: > > 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.e >> du/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/compli >> anceline . 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.e >> du/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 >> >> >> 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 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.
