Dear Bruce,
To be honest, I'm not sure, but I think I want the average of the scalar fields over the surface. I want to have some way of putting the thickness overlays on the surfaces of all my subjects together and visualizing this (I have pre-post data so I'd like to have a visualization of pre-average/added and one for post-average/added).
Hope this makes sense, thank you!
- Rose ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of freesurfer-request@nmr.mgh.harvard.edu [freesurfer-request@nmr.mgh.harvard.edu] Sent: Tuesday, July 11, 2017 12:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 21
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Today's Topics:
1. Re: Extract smoothed cortical thickness whole-brain vertex-wise (Nicolette Schwarz) 2. Re: help with code interpretation (Leanne Hunt) 3. Re: Fwd: surface inaccuracies around the optic chiasm (Bruce Fischl) 4. Re: Extract smoothed cortical thickness whole-brain vertex-wise (Bruce Fischl) 5. error with mri_glmfit --frame-mask (Sadie Marvel) 6. Re: Extract smoothed cortical thickness whole-brain vertex-wise (Nicolette Schwarz) 7. questions mri_glmfit-sim (Van Der Deijl, Rosanne) 8. Simple math with freesurfer surfaces (Van Der Deijl, Rosanne) 9. Re: Simple math with freesurfer surfaces (Bruce Fischl) 10. Re: Extract smoothed cortical thickness whole-brain vertex-wise (Bruce Fischl) 11. 'Best practice' for dealing with lesioned brains (King, Daniel (Research Student)) 12. BBRegister + partial FoV fail (Paul Glad Mihai) 13. Re: BBRegister + partial FoV fail (Bruce Fischl) 14. Re: BBRegister + partial FoV fail (Paul Glad Mihai) 15. Re: BBRegister + partial FoV fail (Bruce Fischl) 16. freeview command error (Yagmur Ozdemir 19) 17. Re: freeview command error (Bruce Fischl) 18. Re: freeview command error (Yagmur Ozdemir 19) 19. Re: freeview command error (Bruce Fischl) 20. Re: freeview command error (Yagmur Ozdemir 19)
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Message: 1 Date: Mon, 10 Jul 2017 12:12:57 -0400 From: Nicolette Schwarz nic@u.northwestern.edu Subject: Re: [Freesurfer] Extract smoothed cortical thickness whole-brain vertex-wise To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: CAKomUUrrwL7hSpRDgdh57BC920xVfkd-vqBqXNfCH=qG6GbfFQ@mail.gmail.com Content-Type: text/plain; charset="utf-8"
Hi Bruce,
Thank you for your answer!
I have tried: mris_convert -c lh.thickness.fwhm10.fsaverage.mgh lh.sphere.reg test.asc
but get this: ERROR: number of vertices in lh.thickness.fwhm10.fsaverage.mgh does not match surface (163842,141823)
Why might that be?
Thank you in advance!
Nic
On Saturday, July 8, 2017, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Nic
the problem isn't a surface/volume one, it's that the file lh.thickness.fwhm10.fsaverage.mgh is on the fsaverage surface not on the individual subject one. If you run that command using the sphere.reg from fsaverage (or any other surface from the lh fsaverage) it should work
cheers Bruce
On Fri, 7 Jul 2017, Nicolette Schwarz wrote:
Hello everyone,
I'm pretty new to FS and can't seem to find the solution for my problem.
I am trying to write whole-brain vertex-wise cortical thickness (CT) data from each participant into ascii files. In my original analysis, each participant's average CT in clusters derived from a whole-brain GLM were extracted and used in a second analysis. I'd like to extract CT vertex-wise to perform a whole-brain version of this second analysis. I need the smoothed and "fsaveraged" (to get the same # of vertices across participants in a template space) CT values to match the cluster data and that seems to be tricky.
This works: mris_convert -c lh.thickness lh.sphere.reg test1.thickness.asc
This doesn't work: mris_convert -c lh.thickness.fwhm10.fsaverage.mgh lh.sphere.reg test2.lh.thickness.asc # ERROR: number of vertices in lh.thickness.fwhm10.fsaverage.mgh does not match surface (163842,124874)
I presume the issue is that ?h.thickness.fwhm10.fsaverage.mgh is a volume file while ?h.sphere.reg is a surface file. So I've tried to convert volume to surface (created a folder test1/surf and copied both fsaverage/surf/lh.sphere.reg and sub/surf/lh.thickness.fwhm10.f saverage.mgh there) using different combinations of mri_vol2surf, e.g.:
mri_vol2surf --srcsubject test1 --src lh.thickness.fwhm10.fsaverage.mgh --trgsubject test1 --surfreg lh.sphere.reg --regheader test1 --hemi lh --o test.surf
This doesn't work as it wants me to specify a type but I have no clue what the type for the surface is (or better, it doesn't seem to be an option going by mris_convert). Other combinations asked for --reg files and I played with tkmedit2 but none of this is working out.
Also, is ?h.sphere.reg an appropriate choice and would it have to be smoothed to FWHM=10 prior to mris_convert?
Trying to solve this has me going in all kinds of circles and I'm unsure about this approach anyway. Hence, I would truly appreciate any help.
Thank you very much in advance,
Nic
-- ?Nicolette Schwarz, Ph.D. Postdoctoral Research Fellow http://heartbrain.hms.harvard.edu
-- ? Nicolette Schwarz, Ph.D. Postdoctoral Research Fellow http://heartbrain.hms.harvard.edu