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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)

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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 

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