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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
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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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
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.anderso@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 CautionDear 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
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.anderso@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
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Greve, Douglas N.,Ph.D. -
john Anderson