Hi John
--projfrac assumes that we know the thickness at each point, which is
probably not true in your case, unless you have models of the top and
bottom of the cerebellar cortex. You can use projdist instead, which takes
a distance in mm (0 would mean you are sampling at the gray/white
boundary). Unless your data is very high resolution though you probably
won't be able to sample from a specific layer with any confidence. We do
have data around on the thickness of the various cerebellar layers if that
would be useful to you.
cheers
Bruce
On Fri, 25 Jan 2019, john Anderson wrote:
External Email - Use Caution
Hi Dr Greve, yes indeed I used the flag "projfrac" and I missed including it
in my command bellow. I greatly
apologize!
My I kindly ask, if "projfrac" is not used then at which layer of the
cerebellum the projection will take place, is
it 0.5? Also, is there any method that can help to use "projfrac".
I apologies if my questions are overwhelming. I am just trying to learn how to
it correctly. Thanks
It should only do that if you have specified a projection fraction. Is that
your full command line? Can you send
the full terminal output?
On 1/24/19 4:56 PM, john Anderson wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve, I appreciate your guidance very much.
>
> I followed your suggestion. I put lh.cerebellum in fsaverage and I ran
> mri_vol2surf.
> as follows:
> mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf
> cerebellum --mni152reg --o grf_onto_cerebellum.nii.gz
>
> Now I am getting this error
>
> ERROR: number of vertices in /FSV6.0/fsaverage/surf/lh.thickness does
> not match surface (163842,34247)
>
> Any suggestions are appreciated ;-)
> John
> ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Thursday, January 24, 2019 4:56 PM, john Anderson
<john.ande...@protonmail.com> wrote:
Hi Dr Greve, I appreciate your guidance very much.
I followed your suggestion. I put lh.cerebellum in fsaverage and I ran
mri_vol2surf.
as follows:
mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf cerebellum
--mni152reg --o
grf_onto_cerebellum.nii.gz
Now I am getting this error
ERROR: number of vertices in /FSV6.0/fsaverage/surf/lh.thickness does not match
surface (163842,34247)
Any suggestions are appreciated ;-)
John
You will have to put the cerebellar surface in fsaverage/surf/lh.cerebellum Note use
"lh" even if it is the
entire cerebellum as FS commands generally require a hemisphere.
The run mri_vol2surf specifying --hemi lh --surf cerebellum
On 1/23/19 10:04 AM, john Anderson wrote:
>
> External Email - Use Caution
>
> Dear FS experts,
> I ran surface based PET analysis on subcortical regions. Then
> corrected the results for multiple comparisons using the method --grf
> in the command mri_glmfit-sim.
>
> I can visualize the output of multiple comparisons (i.e. the file
> grf.th1.3.pos.sig.cluster.mgh) on volume using tkmedit, this
> statistical map shows difference between the groups in the
> cerebellum.... Instead of visualizing the results on volume, I want to
> move this file to the cerebellum surface. I already created the
> cerebellum surfaces from aseg.mgz file in fsaverage using the command
> mris_tesselate.
>
> How can I move the the file grf.th1.3.pos.sig.cluster.mgh from volume
> space and map it on the cerebellum surface?
>
> I tried mri_vol2surf but this command requires the flag --hemi as a
> result it will map the file "grf.th1.3.pos.sig.cluster.mgh" on
> cerebral hemispheres (lh or rh) but not the cerebellum..
> How can I map the file "grf.th1.3.pos.sig.cluster.mgh" on the
> cerebellum surface?
>
> Thanks for any suggestions,
> John
>
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