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> > > > > _______________________________________________ > 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
