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.Clem@utsouthwestern.edu ________________________________

UT Southwestern Medical Center The future of medicine, today.

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From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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.Clem@utsouthwestern.edu

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UT Southwestern Medical Center The future of medicine, today.

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