Hi Matthew we don't care where they are, but you need to specificy the correct path for them to recon-all
cheers Bruce On Fri, 11 Jul 2014, Matthew Clem wrote: > Hi Bruce, > > Thanks for your quick response. Here is what comes up when I enter ls -l > /home/mclem/freesurfer/testsubjects/0000142/000001.dcm: > > ls: cannot access /home/mclem/freesurfer/testsubjects/0000142/000001.dcm: No > such file or directory > > Originally, I copied the subject's folder (0000142) from a flash drive into > the freesurfer folder - was I supposed to import them using the terminal? > > Thanks, > > > Matthew Clem, M.Ed. > Doctoral Student > Clinical Psychology > UT Southwestern Medical Center > matthew.c...@utsouthwestern.edu > ________________________________ > > UT Southwestern Medical Center > The future of medicine, today. > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Friday, July 11, 2014 3:40 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] [FreeSurfer] Importing DICOM Files > > Hi Matthew > > where are the dicoms located? Does that file exist? What happens if you > do: > > ls -l /home/mclem/freesurfer/testsubjects/0000142/000001.dcm > > cheers > Bruce > On Fri, 11 Jul > 2014, Matthew Clem wrote: > >> Hi FreeSurfers, >> >> I am very new to FreeSurfer and I'm having some issues uploading my first >> subject. I have a >> subject folder with 160 .dcm files and FreeSurfer cannot find the files. >> >> Here is the script I used: >> >> recon-all -s 0000142 \ -i $SUBJECTS_DIR/0000142/000001.dcm >> >> I even tried to type out the full path instead of using $SUBJECTS_DIR >> variable and cd to >> where the files are stored and it still didn't work. >> >> Here is my output: >> >> ERROR: cannot find /home/mclem/freesurfer/testsubjects/0000142/000001.dcm >> Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 >> x86_64 x86_64 >> x86_64 GNU/Linux >> >> recon-all -s 0000142 exited with ERRORS at Fri Jul 11 15:27:34 CDT 2014 >> >> Any thoughts on what I'm doing wrong? >> >> >> Thanks, >> >> Matthew Clem, M.Ed. >> Doctoral Student >> Clinical Psychology >> UT Southwestern Medical Center >> matthew.c...@utsouthwestern.edu >> >> _____________________________________________________________________________________________ >> >> UT Southwestern Medical Center >> The future of medicine, today. >> >> > > > _______________________________________________ > 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.
