Dear Freesurfer users,
I had a question regarding how to combine multiple register.dat files
into one file. Essentially, I have a T1 image which I created masks for in
native space. I then import the T1 image into freesurfer and run through
the recon-all pipeline. Subsequently, I use bbregister in order to
register my last EPI timepoint to the T1 image and generate the
register.dat file and when viewing the files the overlap looked great.
1) mri_convert -i m${sub}.T1.nii --in_type nii -o ${sub}.T1.FS.mgz
--out_type mgz
2) bbregister --s ${sub}_FS --mov $bbrest_file --reg ${sub}_RS_register.dat
--init-header --bold --frame $NP_last --nearest --template-out
${sub}.RS.template.nii
3) tkregister2 --mov EP_001.RS.template.nii --reg EP_001_RS_register.dat
--surf
I wanted to take my brain (freesurfer) and masks(native space
pre-freesurfer) and the aseg file and then register this to the EPI scan
and used the following commands:
4) Convert mask to freesurfer format
mri_convert -i ${loc_dir}/spm/c1${sub}.T1.nii --in_type nii -o
${out_dir}/__c1${sub}.T1.mgz --out_type mgz
5) Take mask to brain freesurfer formatted space
mri_vol2vol --mov ${out_dir}/__c1${sub}.T1.mgz --targ
$SUBJECTS_DIR/${sub}_FS/mri/brainmask.mgz --regheader --o
${out_dir}/__c1${sub}.T1.FS.mgz --no-save-reg --nearest
6) Apply the inverse transforms of EPI to Anatomical so that the anatomical
scans and masks are now registered with the EPI scan in native space
(pre-freesurfer file).
mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ
$SUBJECTS_DIR/${sub}_FS/mri/brain.mgz --o $out_dir/__brain_FS2spm.nii --inv
--no-save-reg --reg $out_dir/${sub}_RS_register.dat
mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ
$SUBJECTS_DIR/${sub}_FS/mri/aseg.mgz --o $out_dir/__aseg_FS2spm.nii --inv
--reg $out_dir/${sub}_RS_register.dat --interp nearest
mri_vol2vol --mov $loc_dir/spm/m${sub}.T1.nii --targ
${out_dir}/__c1${sub}.T1.FS.mgz --o $out_dir/__c1${sub}.T1.FS2spm.nii --inv
--no-save-reg --reg $out_dir/${sub}_RS_register.dat --interp nearest
The steps above work great when the T1, generated masks and EPI were all
acquired plumb (no oblique angle). I tried using the steps for when the T1
(10.144 deg from plumb) and EPI (12.44 deg from plumb) were taken at 2
different oblique angles and the images did not register correctly when
going back to native space. I essentially would not be able to apply the
inverse register.dat directly to the aseg and mask files because when I did
they did not look oriented correctly in afni (I did also try 3dWarp
-deoblique on the resulting freesurfer files but this did not work for the
oblique images).
I wanted to see if I created two registration.dat files (One for EPI to
Freesurfer's brain.mgz and another for the masks to Freesurfers brain.mgz)
and combine these transforms into one file which I can pass to the native
space images via commands in 6) so that they transforms are correct. OR am
I wrong and there is a simpler way to achieve this. Please specify the
commands to use in either case.
Thanks,
Ajay
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