On Oct 30, 2015, at 10:43 AM, dgw <dgwakeman@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: emad@nmr.mgh.harvard.edu <mailto:emad@nmr.mgh.harvard.edu>