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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Schaechter, Judith D. <jschaech...@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 jschaech...@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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
