Re: [Freesurfer] Compute cortical thickness within VOI
Dr Bruce, thank you so much! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Monday, July 2, 2018 9:59 AM To: Freesurfer support list Subject: Re: [Freesurfer] Compute cortical thickness within VOI Hi Mohamed yes, that woud work. Create a label file on the surface from your VOI and give it to mris_anatomical_stats with the -l flag cheers Bruce On Mon, 2 Jul 2018, Alshikho, Mohamad J. wrote: > > Dear FreeSurfer experts, > > I have MRS volume of interest (VOI) was placed in the motor cortex > during MRS data acquisition. In order to compute the gray and white > matter volume within the VOI, I synthesized this VOI using > “mri_volsynth”. Then I registered it to T1 Freesurfer space using > “spmregister”. Finally, I used “mri_segstats” to compute the gray and white > matter volume for all the structures within this VOI. > > My question is how can I compute cortical thickness for the cortical > structures within this VOI. By looking into “recon-all.log” I found > that the command “mris_anatomical_stats” was used to compute cortical > thickness from the surfaces. Is it a correct procedure to map this VOI > onto surface using “mri_vol2surf” then feed the output into > “mris_anatomical_stats” as an annotation file? > > > > Thank you for any guidance. > > Mohamad > > > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
Re: [Freesurfer] Compute cortical thickness within VOI
Hi Mohamed yes, that woud work. Create a label file on the surface from your VOI and give it to mris_anatomical_stats with the -l flag cheers Bruce On Mon, 2 Jul 2018, Alshikho, Mohamad J. wrote: Dear FreeSurfer experts, I have MRS volume of interest (VOI) was placed in the motor cortex during MRS data acquisition. In order to compute the gray and white matter volume within the VOI, I synthesized this VOI using “mri_volsynth”. Then I registered it to T1 Freesurfer space using “spmregister”. Finally, I used “mri_segstats” to compute the gray and white matter volume for all the structures within this VOI. My question is how can I compute cortical thickness for the cortical structures within this VOI. By looking into “recon-all.log” I found that the command “mris_anatomical_stats” was used to compute cortical thickness from the surfaces. Is it a correct procedure to map this VOI onto surface using “mri_vol2surf” then feed the output into “mris_anatomical_stats” as an annotation file? Thank you for any guidance. Mohamad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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] Compute cortical thickness within VOI
Dear FreeSurfer experts, I have MRS volume of interest (VOI) was placed in the motor cortex during MRS data acquisition. In order to compute the gray and white matter volume within the VOI, I synthesized this VOI using "mri_volsynth". Then I registered it to T1 Freesurfer space using "spmregister". Finally, I used "mri_segstats" to compute the gray and white matter volume for all the structures within this VOI. My question is how can I compute cortical thickness for the cortical structures within this VOI. By looking into "recon-all.log" I found that the command "mris_anatomical_stats" was used to compute cortical thickness from the surfaces. Is it a correct procedure to map this VOI onto surface using "mri_vol2surf" then feed the output into "mris_anatomical_stats" as an annotation file? Thank you for any guidance. Mohamad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
