I have all of the dicoms - what is the best way to run mri_convert on all of the dicoms in the t1 directory?

Thank you,

Jesse

On Sun, Nov 29, 2009 at 5:29 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Yes, though you may need to be careful about the orientation. I'm not sure if BRIKs have orientation info, but I'm sure that mri_convert does not read it. If you can go back to the dicoms, that is best.

doug

Jesse Bledsoe wrote:
I have T1volume+org.BRIK  - should I use those with mri_convert?

Thanks again,

Jesse

On Tue, Nov 24, 2009 at 4:23 PM, Saad, Ziad S. (NIH/NIMH) [E] <saadz@mail.nih.gov <mailto:saadz@mail.nih.gov>> wrote:

   mri_convert usually work with BRIK files.

   Alternately, 3dAFNItoNIFTI  could turn BRIK files to nifti format
   which FreeSurfer can read fine.

   cheers,
   ziad

   On Nov 24, 2009, at 3:28 PM, Bruce Fischl wrote:

   > These are not the standard .BRIK files? Ziad (ccd) will know.
   >
   > Bruce
   >
   >
   > On Tue, 24 Nov 2009, Jesse Bledsoe wrote:
   >
   >> Hello,
   >>
   >> So far I have had no problems running recon-all with .mnc files but
   >> could
   >> use some guidance converting/reconstructing brains processed with
   >> AFNI
   >> (MRDC).
   >>
   >> There are 120 MRDC files in the T1 directory.
   >>
   >> I believe I need to run mri_convert on these MRDC files but am
   >> unsure of
   >> what the correct command would be?
   >>
   >> Thanks in advance,
   >>
   >> Jesse
   >>




--
Jesse Bledsoe, M.A.
Clinical Psychology
Assistant Director, Center for Neurodevelopmental Study
Department of Psychiatry
Michigan State University
321 W. Fee Hall
East Lansing, MI 48824
______________________________________

Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.
------------------------------------------------------------------------

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



--
Jesse Bledsoe, M.A.
Clinical Psychology
Assistant Director, Center for Neurodevelopmental Study
Department of Psychiatry
Michigan State University
321 W. Fee Hall
East Lansing, MI 48824
______________________________________

Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.