The first command line is correct, you just need to use the MNI template, not MGH35_HCP_FA_template.nii.gz, as the reference volume. ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Schaechter, Judith D. JSCHAECHTER@mgh.harvard.edu Sent: Tuesday, November 23, 2021 6:25 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Converting .trk files in mini space to nifti using dorm_trk2trk

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