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Dear FS experts, I have a statistical map from the output of a surface based analysis in subcortical regions. This statistical map shows significant difference between the groups in the cerebellum cortex.
I reconstructed the cerebellar surfaces using the command "mri_tessalte). Now, I would like to map the volumetric statistical map to the constructed cerebellum surfaces. How can I do that? I tried the command "mri_vol2surf" in many different wants but it didn't work!
Thanks for any guidance! John
Can you be more specific about how mri_vol2surf failed? Eg, command line, terminal output, reason you think it did not work
On 1/21/19 10:47 AM, john Anderson wrote:
External Email - Use Caution
Dear FS experts, I have a statistical map from the output of a surface based analysis in subcortical regions. This statistical map shows significant difference between the groups in the cerebellum cortex.
I reconstructed the cerebellar surfaces using the command "mri_tessalte). Now, I would like to map the volumetric statistical map to the constructed cerebellum surfaces. How can I do that? I tried the command "mri_vol2surf" in many different wants but it didn't work!
Thanks for any guidance! John
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Dr Greve,
Thanks for the comment: I ran vertex wise analysis on subcortical regions, I corrected the analysis for multiple comparison using "mri_glmfit-sim". One of the created files after correction for multiple comparison is "grf.th1.3.pos.sig.cluster.mgh" I would like to move this file to the cerebellum surface? I used the command
mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf white --projfrac 0 --mni152reg --o lh.grf.th1.3.pos.sig.cluster.mgh
I want to project "grf.th1.3.pos.sig.cluster.mgh" on the cerebellum surface (I already created surfaces to the cerebellum using the command mri_tesselate), but it seems that he command mri_vol2surf is designed to move files to the cerebral surfaces not to the cerebellum surfaces. How can I modify the command to project statistical maps on specific structural surfaces such as cerebellum and brain stem?
Thanks John
Can you be more specific about how mri_vol2surf failed? Eg, command line, terminal output, reason you think it did not work
On 1/21/19 10:47 AM, john Anderson wrote:
External Email - Use Caution
Dear FS experts,
I have a statistical map from the output of a surface based analysis
in subcortical regions. This statistical map shows significant
difference between the groups in the cerebellum cortex.
I reconstructed the cerebellar surfaces using the command
"mri_tessalte). Now, I would like to map the volumetric statistical
map to the constructed cerebellum surfaces. How can I do that? I tried
the command "mri_vol2surf" in many different wants but it didn't work!
Thanks for any guidance!
John
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Monday, January 21, 2019 10:47 AM, john Anderson John.anderso@protonmail.com wrote:
Dear FS experts, I have a statistical map from the output of a surface based analysis in subcortical regions. This statistical map shows significant difference between the groups in the cerebellum cortex.
I reconstructed the cerebellar surfaces using the command "mri_tessalte). Now, I would like to map the volumetric statistical map to the constructed cerebellum surfaces. How can I do that? I tried the command "mri_vol2surf" in many different wants but it didn't work!
Thanks for any guidance! John
Is grf.th1.3.pos.sig.cluster.mgh in the mni152 2mm space? You should check the registration with tkregister2 --mov grf.th1.3.pos.sig.cluster.mgh --reg $FREESURFER_HOME/average/mni152.register.dat --surfs It looks like you projected it to the white surface of fsaverage
On 1/22/19 2:08 PM, john Anderson wrote:
External Email - Use Caution
Hi Dr Greve,
Thanks for the comment: I ran vertex wise analysis on subcortical regions, I corrected the analysis for multiple comparison using "mri_glmfit-sim". One of the created files after correction for multiple comparison is "grf.th1.3.pos.sig.cluster.mgh" I would like to move this file to the cerebellum surface? I used the command
mri_vol2surf --mov grf.th1.3.pos.sig.cluster.mgh --hemi lh --surf white --projfrac 0 --mni152reg --o lh.grf.th1.3.pos.sig.cluster.mgh
I want to project "grf.th1.3.pos.sig.cluster.mgh" on the cerebellum surface (I already created surfaces to the cerebellum using the command mri_tesselate), but it seems that he command mri_vol2surf is designed to move files to the cerebral surfaces not to the cerebellum surfaces. How can I modify the command to project statistical maps on specific structural surfaces such as cerebellum and brain stem?
Thanks John
Can you be more specific about how mri_vol2surf failed? Eg, command line, terminal output, reason you think it did not work
On 1/21/19 10:47 AM, john Anderson wrote:
External Email - Use Caution
Dear FS experts,
I have a statistical map from the output of a surface based analysis
in subcortical regions. This statistical map shows significant
difference between the groups in the cerebellum cortex.
I reconstructed the cerebellar surfaces using the command
"mri_tessalte). Now, I would like to map the volumetric statistical
map to the constructed cerebellum surfaces. How can I do that? I tried
the command "mri_vol2surf" in many different wants but it didn't work!
Thanks for any guidance!
John
‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐ On Monday, January 21, 2019 10:47 AM, john Anderson John.anderso@protonmail.com wrote:
Dear FS experts, I have a statistical map from the output of a surface based analysis in subcortical regions. This statistical map shows significant difference between the groups in the cerebellum cortex.
I reconstructed the cerebellar surfaces using the command "mri_tessalte). Now, I would like to map the volumetric statistical map to the constructed cerebellum surfaces. How can I do that? I tried the command "mri_vol2surf" in many different wants but it didn't work!
Thanks for any guidance! John
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Greve, Douglas N.,Ph.D. -
john Anderson