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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
Hi Jamie,
looks like your command is wrong (reverse).
Here are spaces: tp1 original space tp2 original space base = tp1.long.base = tp2.long.base space
so the longitudinals and the base are in the same space (rigidly aligned and resliced to that space).
The lta files map between tp1 original and the base space.
Your command uses as mov the tp1.long.base brain.mgz file, which is already in base space. No need to map it to the template=base space again. In fact applying that transform will move it away. If you want to go from base back to original tp1 space, you need to invert the transform.
Best, Martin
On 16. Oct 2019, at 20:10, Jamie Hanson jamielarshanson@gmail.com wrote:
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... https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing#WorkflowSummary, 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 http://jamiehanson.org/
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Jamie Hanson -
Martin Reuter