Hi,

I'd like to convert *trk files that are in mni space to nifti files using  dmri_trk2trk.

The *trk files are here: /autofs/vast/freesurfer/centos7_x86_64/7.2.0-beta/trctrain/hcp/mni

Attempts so far (that have failed) are: 
dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.mni.nii.gz --inref ../MGH35_HCP_FA_template.nii.gz --outref ../MGH35_HCP_FA_template.nii.gz

dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.mni.nii.gz --inref ../MGH35_HCP_FA_template.nii.gz --outref ../MGH35_HCP_FA_template.nii.gz --reg MGH35_HCP_FA_template_identity.mat
 with MGH35_HCP_FA_template_identity.mat generated by: 
flirt -in MGH35_HCP_FA_template.nii.gz -ref MGH35_HCP_FA_template.nii.gz -omat MGH35_HCP_FA_template_identity.mat 

dmri_trk2trk --in TRACK_FILE.display.trk --outvol TRACK_FILE.display.mni.nii.gz --inref ../MGH35_HCP_FA_template.nii.gz --outref ../MGH35_HCP_FA_template.nii.gz --reg MGH35_HCP_FA_2_MNI152_T1_2mm_brain.mat
with MGH35_HCP_FA_2_MNI152_T1_2mm_brain.mat generated by:
flirt -in MGH35_HCP_FA_template.nii.gz -ref MNI152_T1_2mm_brain.nii.gz -omat MGH35_HCP_FA_2_MNI152_T1_2mm_brain.mat

Thanks in advance for your help!
Judith

*******************************************************

Judith D. Schaechter, Ph.D., M.S.P.T. 

Athinoula A. Martinos Center for Biomedical Imaging

Massachusetts General Hospital, Harvard Medical School

13th Street, Building 149, Room 2301 

Charlestown, MA 02129

Office 617-726-5622 | Cell 781-752-6247 | Fax 617-726-7422

Email  jschaechter@mgh.harvard.edu