External Email - Use Caution
Dear FS List,
My group was trying to look at the overlap between cortical labels in the longitudinal processing stream and I had a question re: use of transform files. In brief, we followed the commands for the longitudinal processing stream, creating a "subject-specific" template for each participant ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing#WorkflowSum..., using FS v.6.0). We processed T1w images multiple times and now, we wanted to transform the time 1 and time 2 (native space) scans to their subject-specific template.
We used the following commands-- mri_vol2vol --mov $INDIVIDUAL_SCAN_TIME1_DIR/sub-BNU_25864_001.long.sub-BNU_25864_template/mri/brain.mgz --o $INDIVIDUAL_SCAN_TIME1/brain_001_to_temp.mgz --lta $SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/transforms/sub-BNU_25864_001_to_sub-BNU_25864_template.lta --targ $SUBJECT_SPECIFIC_TEMPLATE_DIR/mri/brain.mgz
But when we did this for time 1 and time 2 scans, they were poorly aligned. I also used the lta file for template to 001, but again things were poorly aligned. Should we be using m3z files? Or combining different transforms? Any guidance or suggestions are deeply appreciated.
Thanks much, Jamie.
-- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org