Hello, We are looking to use the the Freesurfer longitudinal pipeline automatic parcellation to assist with automatic ROI segmentation for our Myelin Water Fraction (MWF) analysis.
Typically, we use a combination of FSL commands to register the first echo of the T2 sequence to the brain anatomy in a halfway space between our timepoints and then use that matrix to register our derived Myelin Water Fraction Map into that space. This is cumbersome and then requires manual ROI drawing in that space (and only allows for two timepoints at the moment). It was our understanding that we might be able to register the MWF map to the Freesurfer Base Files created during the longitudinal pipeline and then generate ROIs automatically for all of our timepoints from this template, but the registration is causing some problems. I have been struggling on whether to use mri_robust_register or bbregister, have attached my attempts at both below. I have taken the following steps to this point: 1) Successfully registered the first echo of the T2 sequence to the Freesurfer Base template anatomy and generated a matrix to be used later. This is the code for that for both mri_robust_register and bbregister (both work successfully and look good when overlaid in freeview or tkregister). ## Register 1st echo from Extracted Brain to Freesurfer T1 Template using mri_robust_register mri_robust_register --mov WMI_J01_WIP_T2W_GRASE_scratch_SENSE_4_1x1A.nii --dst Freesurfer/Output/J01_Base/mri/brain.mgz --lta FirstEcho2Brain.lta --mapmov FirstEcho2Brain.mgz --weights FirstEcho2Brain-weights.mgz --iscale —satit ## Register 1st echo from Extracted Brain to Freesurfer T1 Template using bbregister bbregister --s J01_Base --mov WMI_J01_WIP_T2W_GRASE_scratch_SENSE_4_1x1.nii --init-fsl --o output.mgz --lta register.lta --t1 2) The next step is to register our derived MWF map into this space using the output matrix from the first step. This is where things fall apart. When the following scripts are run (either in mri_robust_register OR bbregister), the output is extremely misaligned and in the wrong orientation altogether and I’m struggling to figure out why. When using FSL, we use FLIRT to execute this command and it works well. Here are the scripts again for both methods. ## Register MWF Map to Freesurfer Base Template using mri_robust_register mri_robust_register --mov WMI_J01_MWFmap.nii --dst Freesurfer/Output/J01_Base/mri/brain.mgz --nosym --sat 8 --maxsize 380 --mapmovhdr MWF2Brain.mgz --ixform FirstEcho2Brain.lta --lta MWF2Brain.lta ## Register MWF Map to Freesurfer Base Template using bbregister bbregister --s J01_Base --mov WMI_J01_MWFmap.nii --init-reg register.lta --o MWF2Brain.mgz --lta MWF2Brain.lta --t2 If anybody is able to help us understand why this step seems to be failing when the previous one works perfectly, that would be extremely helpful. Thanks very much in advance, Bimal Lakhani University of British Columbia Bimal Lakhani, PhD | Postdoctoral Fellow Department of Physical Therapy |The University of British Columbia T142A - 2211 Wesbrook Mall, Vancouver, BC, Canada V6T 1Z3 • 604.827.3369 |• bimal.lakh...@ubc.ca<mailto:bimal.lakh...@ubc.ca> | www.brain.rehab.med.ubc.ca<http://www.brain.rehab.med.ubc.ca/>
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