Hi, Thank you for your quick response!
I have already copied the dicoms to my cluster space: /cluster/guptagp/Emad/Epilepsy/temp/slices and the permissions of this folder seem right to me: drwxrwsr-x 2 emad guptagp 32768 Oct 30 10:30 slices The permissions on the dicom files are the same: -bash-4.1$ ls -l MR1.3.12.2.1107.5.2.32.35006.2009021913370421213012700 -rwxrwxr-x 1 emad guptagp 2219694 Oct 30 10:30 MR1.3.12.2.1107.5.2.32.35006.2009021913370421213012700 Any thoughts? Best, Emad > On Oct 30, 2015, at 10:43 AM, dgw <dgwake...@gmail.com> wrote: > > Hi Emad, > > The only problems, which I have run into is major weaknesses in dcm2nii: > 1. You must have write permissions on the directory the files are > located in. > 2. dcm2nii cannot work on symbolically linked files. > > Therefore, first copy the files to your own analysis workspace: e.g. > /cluster/<whatever-your space is>/ > then run dcm2nii. > With that I have no problems. > > hth > d > > On 10/30/15 10:28 AM, Emad Ahmadi wrote: >> Hi Freesurfer experts, >> >> I hope you’re all enjoying your day! >> >> Working in Launchpad, I want to extract the bvals/bvecs from DTI dicoms >> obtained at Martinos Center. The dicoms have the following format: >> >> MR1.3.12.2.1107.5.2.32.35006.2010052613553219211129919 >> MR1.3.12.2.1107.5.2.32.35006.2010052613553736471330196 >> MR1.3.12.2.1107.5.2.32.35006.201005261355429098330464 >> ... >> >> I receive error when I run dcm2niix (to extract the b values and b >> vectors): >> >> Command: >> dcm2niix -f dti <folder of dicoms> >> >> The error I receive: >> >> Warning: output folder invalid >> MR1.3.12.2.1107.5.2.32.35006.2010052614044051320551992 will try >> Error: unable to find any DICOM images in >> Conversion required 0.000000 seconds. >> >> When I do the following steps to generate “treatable” dicoms, dcm2niix >> recognizes these dicoms: >> >> 1. copy Martinos Center dicoms to my local Mac >> 2. import dicoms into OsiriX >> 3. Export them as dicoms >> 4. copy the OsiriX-exported dicoms back to Launchpad >> 5. Run dcm2niix on the new dicoms >> >> Since this copying back and forth takes a lot of time, I need a better >> way to convert the “crazy” Martinos Center dicoms into the “treatable” ones! >> >> I would really appreciate your help. >> >> Best, >> Emad >> >> >> Emad Ahmadi, MD >> ----------------------------------------------- >> Research Fellow >> Department of Radiology >> Massachusetts General Hospital >> Harvard Medical School >> >> 25 New Chardon Street, Suite 400 >> Boston, MA 02114 >> Tel: 617 726 5237 >> Email: e...@nmr.mgh.harvard.edu <mailto:e...@nmr.mgh.harvard.edu> >> <mailto:e...@nmr.mgh.harvard.edu <mailto:e...@nmr.mgh.harvard.edu>>
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