Not sure about mris_transform, but you can use mris_applyreg --lta source-surf ltafile output-surf You will have to convert your flirt reg to lta (lta_convert --infsl flirt.mtx --outlta flirt.lta --src flirtinput.nii --trg flirtoutput.nii)
On 10/13/2022 9:40 PM, Chris Adamson wrote:
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Freesurfer experts,
I’m trying to put some subject surfaces into a template space. I have performed the following flirt registration per subject:
flirt -in $SUBJECTS_DIR/$CURSUBJECT/mri/T2.nii.gz -ref template0.nii.gz -omat $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.fslmat -out $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.nii.gz -dof 12 -searchrx -$D $D -searchry -$D $D -searchrz -$D $D
Then apply the flirt transform
mris_transform --trx-src $SUBJECTS_DIR/$CURSUBJECT/mri/T2.nii.gz --trx-dst template0.nii.gz $SUBJECTS_DIR/$CURSUBJECT/surf/${CURHEMI}.${CURSURFTYPE} $SUBJECTS_DIR/$CURSUBJECT/mri/transforms/talairach.fslmat $SUBJECTS_DIR/$CURSUBJECT/surf/${CURHEMI}.${CURSURFTYPE}.flirt
When I overlay the output surface $SUBJECTS_DIR/$CURSUBJECT/surf/${CURHEMI}.${CURSURFTYPE}.flirt over the template template0.nii.gz the surface is in the wrong orientation and in the wrong position, i.e. not correct.
I have tried using lta_convert to make a lta transform and I get the same result.
Any thoughts?
Thanks,
Chris.
*Dr Chris Adamson*
Senior Research Officer, Developmental Imaging, Clinical Sciences (0.3 EFT)
Software Engineer, Cardiovascular Research (0.7 EFT)
*Murdoch Childrens Research Institute*
The Royal Children’s Hospital
Flemington Road, Parkville, VIC 3052 Australia
E chris.adamson@mcri.edu.au mailto:chris.adamson@mcri.edu.au
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