Thank you!
Regards
--VM
On Wed, Dec 21, 2016 at 10:41 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
On 12/21/2016 01:02 PM, neuroimage analyst wrote:
Hi, Doug.
Thank you for your response.
_Step 1: _I think what I want to really do is perform group analysis on my CBF maps that are mapped to cortex after smoothing 10mm . In such a scenario, I have to map the CBF to fsavearge to bring all the subjects in the same space and then smooth them and perform statistics. I think to do this I will do:
*a) bbregister --s T1_data --mov asldata_mc_even_brain.nii.gz --reg mean_asl_to_fs_T1 --bold --init-fsl * *b) 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* *c) mri_vol2surf --mov perfusion_CBF_to_T1.nii.gz --trgsubject fsaverage --regheader T1_data/ --hemi lh --projfrac 0.5 --interp trilinear --o perfusion_CBF_to_T1_surf_lh.mgh --reg register.dat --noreshape --cortex * *d) mris_fwhm --s fsaverage --hemi lh --fwhm 10 --smooth-only --i perfusion_CBF_to_T1_surf_lh --o perfusion_CBF_to_T1_surf_lh_smooth_10mm --cortex *
I would not include the vol2vol. It will needlessly introduce another interpolation. You can just used vol2surf and go straight from the CBF space.
_Step 2: _Once and if I want any cluster that are different then I want to use the same cluster and extract the CBF maps in the native space of each subject. Here, I have to use mri_surfcluster and mri_segstats. But, I am not sure what to pass here. *.ocn* file has the values in the cluster but my guess is they are in the fsaverage space. How do I get these values in the native space?
If you want to make stats based on the cluster, I would not go back to native space. There will be a dat file that comes out of the clustering with the values for each subject (rows) and cluster (cols).
I will again appreciate your response as to whether my steps are right?
Thanks
Regards
--VM
On Wed, Dec 21, 2016 at 7:49 AM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
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.analyst@gmail.com <mailto: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 <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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