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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.aumailto:chris.adamson@mcri.edu.au http://secure-web.cisco.com/1xyTfBzNnFowZ_Fne30rgRiCxmIVmOJ_-BycsOHrk_XaYhtx...http://secure-web.cisco.com/1qlMpfQw8j0R3pB1zfzODqkjLHdA5pw_AMVxM9hBQD5XAjotYaYlBjvNart-72HT-nZEh4HtAifeIM2EY_ix0toYDRYtfgA6aZu-lqQ5tCuS2nLzashJLDRy50deJ1HU5B95y7d3IHpE9AXSwoRI4BW01VowAhSX44tk0hlM8aWqA-1w9M9ZXcaH6eIuXajZx3cflhbcHnDII36hPwg45W8ICUSxoc2q1TYIkkEEk9zM9aZyaHr6gTcTn60QBBeylfffgqfZdmRKHEnKu092LobeQjFRWHbfBjOsO-vMgKH5LSkvSb1gMooHK_NaT-6nJWutvBdpJaCtXZYFcJjNP6w/http%3A%2F%2Fwww.mcri.edu.au%2F
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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:
External Email - Use Caution
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
*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* www.mcri.edu.au http://secure-web.cisco.com/1qlMpfQw8j0R3pB1zfzODqkjLHdA5pw_AMVxM9hBQD5XAjotYaYlBjvNart-72HT-nZEh4HtAifeIM2EY_ix0toYDRYtfgA6aZu-lqQ5tCuS2nLzashJLDRy50deJ1HU5B95y7d3IHpE9AXSwoRI4BW01VowAhSX44tk0hlM8aWqA-1w9M9ZXcaH6eIuXajZx3cflhbcHnDII36hPwg45W8ICUSxoc2q1TYIkkEEk9zM9aZyaHr6gTcTn60QBBeylfffgqfZdmRKHEnKu092LobeQjFRWHbfBjOsO-vMgKH5LSkvSb1gMooHK_NaT-6nJWutvBdpJaCtXZYFcJjNP6w/http%3A%2F%2Fwww.mcri.edu.au%2F
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
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That worked, thanks Doug.
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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:
External Email - Use Caution 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.aumailto:chris.adamson@mcri.edu.au MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1Ibqu8R4lNWjbfjXCtTMk7_O1lQVz9GcPED4GYqChN9GQliQ...http://secure-web.cisco.com/1qlMpfQw8j0R3pB1zfzODqkjLHdA5pw_AMVxM9hBQD5XAjotYaYlBjvNart-72HT-nZEh4HtAifeIM2EY_ix0toYDRYtfgA6aZu-lqQ5tCuS2nLzashJLDRy50deJ1HU5B95y7d3IHpE9AXSwoRI4BW01VowAhSX44tk0hlM8aWqA-1w9M9ZXcaH6eIuXajZx3cflhbcHnDII36hPwg45W8ICUSxoc2q1TYIkkEEk9zM9aZyaHr6gTcTn60QBBeylfffgqfZdmRKHEnKu092LobeQjFRWHbfBjOsO-vMgKH5LSkvSb1gMooHK_NaT-6nJWutvBdpJaCtXZYFcJjNP6w/http%3A%2F%2Fwww.mcri.edu.au%2F
This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Children’s Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.
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Chris Adamson -
Douglas N. Greve