External Email - Use Caution
Hello FreeSurfer users/developers,
I have a subcortical ROI that I want to project to the nearest cortical vertex (see screenshot). So far, I have used the command mri_vol2surf --mov subject/mri/lh.het.nii --reg subject/mri/transforms/talairach.lta --hemi lh —o subject/surf/lh.het.mgh to project these voxels to the nearest vertex on the cortex. I am not sure if this is the correct way to do this because using mris_anatomical_stats on the result does not produce any thickness file. Any help would be greatly appreciated.
[cid:1E78E0E0-0881-4508-A885-F0579F1FB3E4]
Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
Hi Ryan
I don't think projection of that kind of ROI is well-posed. Different parts of it are probably closest to wildly different parts of cortex. What are you trying to acheive?
cheers Bruce
On Wed, 15 May 2019, Nillo, Ryan Michael R wrote:
External Email - Use Caution
Hello FreeSurfer users/developers, I have a subcortical ROI that I want to project to the nearest cortical vertex (see screenshot). So far, I have used the command mri_vol2surf --mov subject/mri/lh.het.nii --reg subject/mri/transforms/talairach.lta --hemi lh —o subject/surf/lh.het.mgh to project these voxels to the nearest vertex on the cortex. I am not sure if this is the correct way to do this because using mris_anatomical_stats on the result does not produce any thickness file. Any help would be greatly appreciated.
[IMAGE]
Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
External Email - Use Caution
Hi Bruce,
We want to study whether or not presence of periventricular heterotopias affect the thickness, volume, or surface area of the nearest cortical ROI. Since the condition we are studying is caused by failure of neurons to migrate to the cortex, we hypothesized that the nearest cortical ROI would be thinner/smaller compared to those without the heterotopia.
Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
On May 15, 2019, at 3:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Ryan
I don't think projection of that kind of ROI is well-posed. Different parts of it are probably closest to wildly different parts of cortex. What are you trying to acheive?
cheers Bruce
On Wed, 15 May 2019, Nillo, Ryan Michael R wrote:
External Email - Use Caution Hello FreeSurfer users/developers, I have a subcortical ROI that I want to project to the nearest cortical vertex (see screenshot). So far, I have used the command mri_vol2surf --mov subject/mri/lh.het.nii --reg subject/mri/transforms/talairach.lta --hemi lh —o subject/surf/lh.het.mgh to project these voxels to the nearest vertex on the cortex. I am not sure if this is the correct way to do this because using mris_anatomical_stats on the result does not produce any thickness file. Any help would be greatly appreciated. [IMAGE] Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
Hi Ryan
do you have diffusion data? You could use tracula and find the cortical ROI(s) that are most likely the end points of that bit of white matter.
cheers Bruce
On Wed, 15 May 2019, Nillo, Ryan Michael R wrote:
External Email - Use Caution
Hi Bruce, We want to study whether or not presence of periventricular heterotopias affect the thickness, volume, or surface area of the nearest cortical ROI. Since the condition we are studying is caused by failure of neurons to migrate to the cortex, we hypothesized that the nearest cortical ROI would be thinner/smaller compared to those without the heterotopia.
Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
On May 15, 2019, at 3:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:Hi Ryan
I don't think projection of that kind of ROI is well-posed. Different parts of it are probably closest to wildly different parts of cortex. What are you trying to acheive?
cheers Bruce
On Wed, 15 May 2019, Nillo, Ryan Michael R wrote:
External Email - Use Caution Hello FreeSurfer users/developers, I have a subcortical ROI that I want to project to the nearest cortical vertex (see screenshot). So far, I have used the command mri_vol2surf --mov subject/mri/lh.het.nii --reg subject/mri/transforms/talairach.lta --hemi lh —o subject/surf/lh.het.mgh to project these voxels to the nearest vertex on the cortex. I am not sure if this is the correct way to do this because using mris_anatomical_stats on the result does not produce any thickness file. Any help would be greatly appreciated. [IMAGE] Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed... surfer&d=DwICAg&c=iORugZls2LlYyCAZRB3XLg&r=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U&m=70PkXR7pfo OtgUn0p3XVxYSvqoKz7NOM0ksGg_OyUmg&s=4-bL_WUolc7CdEE6RovlOGA5oFWwlecwJNlG57CXOR0&e=
You can convert the ROI into a label (mri_vol2label), then "paint" the label onto the nearest cortex using mri_label2label with the --paint option. dmax controls the maximum distance, so you'll need to set that pretty large. You can then load the label onto the surface to see where it landed.
On 5/15/19 6:19 PM, Nillo, Ryan Michael R wrote:
External Email - Use Caution
Hi Bruce,
We want to study whether or not presence of periventricular heterotopias affect the thickness, volume, or surface area of the nearest cortical ROI. Since the condition we are studying is caused by failure of neurons to migrate to the cortex, we hypothesized that the nearest cortical ROI would be thinner/smaller compared to those without the heterotopia.
Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
On May 15, 2019, at 3:10 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Ryan
I don't think projection of that kind of ROI is well-posed. Different parts of it are probably closest to wildly different parts of cortex. What are you trying to acheive?
cheers Bruce
On Wed, 15 May 2019, Nillo, Ryan Michael R wrote:
External Email - Use Caution Hello FreeSurfer users/developers, I have a subcortical ROI that I want to project to the nearest cortical vertex (see screenshot). So far, I have used the command mri_vol2surf --mov subject/mri/lh.het.nii --reg subject/mri/transforms/talairach.lta --hemi lh —o subject/surf/lh.het.mgh to project these voxels to the nearest vertex on the cortex. I am not sure if this is the correct way to do this because using mris_anatomical_stats on the result does not produce any thickness file. Any help would be greatly appreciated. [IMAGE] Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.ed...
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. -
Nillo, Ryan Michael R