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.
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer