Hi Anastasia -

 I'm hoping to convert these *trk files to nifti files. Can you help with the command to convert the file format?

Thanks,
Judith
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu>
Sent: Tuesday, November 23, 2021 5:46 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Converting .trk files in mini space to nifti using dorm_trk2trk
 
Hi Judith - The files under hcp/mni/ are in the space of the actual MNI template. The files under hcp/syn/ are in the space of MGH35_HCP_FA_template.nii.gz.

Also, there is no need to use version 7.2.0-beta any more, the official 7.2.0 is out.

Hope this helps,
Anastasia.

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Schaechter, Judith D. <JSCHAECHTER@mgh.harvard.edu>
Sent: Monday, November 22, 2021 7:46 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Converting .trk files in mini space to nifti using dorm_trk2trk
 
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