Sorry for the delay
On 12/21/16 12:15 AM, neuroimage analyst wrote:
Hi,
I am attaching this message again and I wI'll appreciate if somebody
could kindly comment on the approach.
Thanks
Regards
-VM
---------- Forwarded message ----------
From: "neuroimage analyst" <neuroimage.anal...@gmail.com
<mailto:neuroimage.anal...@gmail.com>>
Date: Dec 18, 2016 2:22 PM
Subject: Registering ASL-CBF maps to fsaverage
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc:
Hi, all.
I want to register CBF maps derived using pCASL to freesurfer's
surface and derive CBF values in the same regions where I report
my cortical thickness, and volumes. Hence, I did the following:
1) bbregister --s T1_data --mov asldata_mc_even_brain.nii.gz --reg
mean_asl_to_fs_T1 --bold --init-fsl
asldata_mc_even_brain is the mean of the control images
2) mri_vol2vol --mov perfusion_calib.nii.gz --targ
T1_data/mri/T1.mgz --interp nearest --o perfusion_CBF_to_T1.nii.gz
--reg register.dat --no-save-reg
where perfusion_calib is the CBF map in the same space
asldata_mc_even_brain.
3) mri_vol2surf --mov perfusion_CBF_to_T1.nii.gz --ref orig.mgz
--regheader T1_data/ --hemi lh --projfrac 0.5 --interp trilinear
--o perfusion_CBF_to_T1_surf_gray.mgh --reg register.dat
--noreshape --cortex --surfreg sphere.reg
Step (3) takes the CBF map to cortical ribbon and hopefully now I
can run mri_segstats and extract CBF values and thickness + do a
group comparison using mri_glmfit. In order to do the latter, I
have to map the perfusion maps to fsaverage. Can I then simply set
--ref to fsaverage in step 3 or what is the correct call to take
CBF maps to fsaverage in (3) ?
No, but you can set --trgsubject fsaverage and it will do what you need.
If you want to run mri_segstats to get segmentation statistics, you
should run mri_vol2vol to map the CBF to the native anatomical space,
then run mri_segstats --seg aparc+aesg.mgz --i cbf-in-anat.nii.gz ...
This will give you segstats that are specific to the segmentation of a
particular subject; if you use mri_segstats in fsaverage space, then
you lose that specificity (not sure if it really matters). You can use
asegstats2table to merge the segstats from different subjects together
into one file, then use mri_glmfit --table to get the stats.
Second, Do i have to pass --surf argument pial or white in step 3?
What is the correct way to do this?
No, it will use white by default (which is what you want). You don't
need to set --surfreg either (will use sphere.reg by default)
Third, The statistical comparisons on thickness were done using 10
mm smoothing using -qcache argument in recon-all.I want to
generate several smoothing of CBF maps (5-25 in steps of 5 mm)
In the call to mri_vol2surf I can set --surf-fwhm 5 and my
understanding is it will smooth the output surface 5 mm. Is that
right? or should I call mri_fwhm on the output returned from step 3.
You can do it like that. It is a little more computationally efficient
to do them in separate steps, but probably not a big deal unless you
have a lot of data.
Thank you for your suggestions. I will really appreciate your
thoughts.
Regards
-VM
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
