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That worked, thanks Doug.
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: Monday, 17 October 2022 8:15 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL]Re: [Freesurfer] mris_transform with flirt transformation
wrong result
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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)
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.adam...@mcri.edu.au<mailto:chris.adam...@mcri.edu.au>
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