You definitely do not want to use mni152.register.dat for this (I'm
surprised it even got close). Instead, register the orig.mgz to the
HCP842 template space, eg, with
mri_coreg --mov orig.mgz --targ HCP842.template.nii.gz --dof 12 --reg
reg.HCP842.lta
This will print out a tkregisterfv command when it finishes, run that to
make sure the registration looks ok, then run your command below using
the above regisitration file
On 5/26/2021 7:23 PM, Milena Radoman wrote:
External Email - Use Caution
Dear FreeSurfer Team,
Hope you are doing well! I've run into an issue I hope you can help me
with. After running recon-all on my subjects, I proceeded with the
thalamic segmentation step. I'm specifically interested in extracting
the mediodorsal (MD) thalamus for a subject (by first individually
extracting mediodorsal lateral and mediodorsal medial nuclei and
combining them using fslmaths). Before doing so, I've first converted
my data from freesurfer to native space. Once I've obtained my
nucleus of interest I then loaded it into DSI Studio, which I'm using
to extract my tract of interest. Given the data in the DSI studio was
in the native space, the MD nucleus aligned perfectly.
The problem is that DSI studio tracking takes forever when I do the
registration to the native space, so instead I've decided to run a
registration of my DTI data to the HCP842 template (in order to make
my results comparable to some of my colleagues and to help the
tracking run faster). The problem is that now when I load my
dorsomedial nucleus, it doesn't appear where it should and I would
need to do a different registration (my understanding is freesurfer to
ICBM152 since apparently that's what HCP842 template is related to).
I've been able to use the script below, but the nucleus doesn't show
up quite where it should (it's showing up more anterior to the thalamus).
mri_label2vol --reg $FRESURFER_HOME/average/mni152.register.dat --seg
ThalamicNuclei.v12.T1.FSvoxelSpace.mgz --temp
icbm_avg_152_t1_tal_lin.nii --o ThalamicNuclei.v12.T1-anat.mgz
Any advice? Thank you in advance for your help!!
--
*Milena Radoman*
PhD Candidate | PECTS Fellow
Graduate Program in Neuroscience
The University of Illinois at Chicago
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