Sorry for the delay
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.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.analyst@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>
Cc:
where perfusion_calib is the CBF map in the same space asldata_mc_even_brain.asldata_mc_even_brain is the mean of the control imagesHi, 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
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
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, 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)
Second, Do i have to pass --surf argument pial or white in step 3? What is the correct way to do this?
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.
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.
Thank you for your suggestions. I will really appreciate your thoughts.
Regards
-VM
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