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 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.
