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
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:
- copy Martinos Center dicoms to my local Mac
- import dicoms into OsiriX
- Export them as dicoms
- copy the OsiriX-exported dicoms back to Launchpad
- 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
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.
you can also try mri_convert from the dev env. It should recognize the diffusion scan and write out the bval/bvecs
On 10/30/15 10:43 AM, dgw wrote:
Hi Emad,
The only problems, which I have run into is major weaknesses in dcm2nii:
- 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:
- copy Martinos Center dicoms to my local Mac
- import dicoms into OsiriX
- Export them as dicoms
- copy the OsiriX-exported dicoms back to Launchpad
- 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
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
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 dgwakeman@gmail.com wrote:
Hi Emad,
The only problems, which I have run into is major weaknesses in dcm2nii:
- 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:
- copy Martinos Center dicoms to my local Mac
- import dicoms into OsiriX
- Export them as dicoms
- copy the OsiriX-exported dicoms back to Launchpad
- 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 <mailto:emad@nmr.mgh.harvard.edu mailto:emad@nmr.mgh.harvard.edu>
freesurfer@nmr.mgh.harvard.edu
-
dgw -
Douglas Greve -
Emad Ahmadi