Hi Freesurfers,
I am using the degree of cortical atrophy between two groups. The atrophy rate had no significant difference between two groups, but the average thickness of the baseline and followup showed significant clusters in two regions between the two groups. My question is how to create the ROIs covering the clusters, and then extract the thicknesses on baseline and followup MRIs?
Thanks, Yawu
If you used mri_glmfit, then you can use mri_glmfit-sim to create significant clusters. It will create an annotation of the significant clusters, and you can pass that to mri_segstats along with the stack of thickness images to extract the mean thickness in each cluster.
On 05/12/2016 04:23 AM, Liu Y wrote:
Hi Freesurfers,
I am using the degree of cortical atrophy between two groups. The atrophy rate had no significant difference between two groups, but the average thickness of the baseline and followup showed significant clusters in two regions between the two groups. My question is how to create the ROIs covering the clusters, and then extract the thicknesses on baseline and followup MRIs?
Thanks, Yawu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Yawu,
and both baseline and follow-up surfaces (from the *.long.* directories) are in vertex correspondence, so you can use the ROI on each time point directly.
Best, Martin
On 05/12/2016 02:00 PM, Douglas N Greve wrote:
If you used mri_glmfit, then you can use mri_glmfit-sim to create significant clusters. It will create an annotation of the significant clusters, and you can pass that to mri_segstats along with the stack of thickness images to extract the mean thickness in each cluster.
On 05/12/2016 04:23 AM, Liu Y wrote:
Hi Freesurfers,
I am using the degree of cortical atrophy between two groups. The atrophy rate had no significant difference between two groups, but the average thickness of the baseline and followup showed significant clusters in two regions between the two groups. My question is how to create the ROIs covering the clusters, and then extract the thicknesses on baseline and followup MRIs?
Thanks, Yawu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Martin and Douglas,
I created the cluster ROIs (mc-zabs.the13sig.ocn.annot) for the two groups. What is the detailed command line to calculate the baseline and followup cortical thicknesses from the *.long.* directories?
Thanks, Yawu
On Thu, May 12, 2016 at 9:07 PM, Martin Reuter mreuter@nmr.mgh.harvard.edu wrote:
Hi Yawu,
and both baseline and follow-up surfaces (from the *.long.* directories) are in vertex correspondence, so you can use the ROI on each time point directly.
Best, Martin
On 05/12/2016 02:00 PM, Douglas N Greve wrote:
If you used mri_glmfit, then you can use mri_glmfit-sim to create significant clusters. It will create an annotation of the significant clusters, and you can pass that to mri_segstats along with the stack of thickness images to extract the mean thickness in each cluster.
On 05/12/2016 04:23 AM, Liu Y wrote:
Hi Freesurfers,
I am using the degree of cortical atrophy between two groups. The atrophy rate had no significant difference between two groups, but the average thickness of the baseline and followup showed significant clusters in two regions between the two groups. My question is how to create the ROIs covering the clusters, and then extract the thicknesses on baseline and followup MRIs?
Thanks, Yawu
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
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.
Is the mc-zabs annot based on thickness differences? If so, you can run mri_segstats on the stack from each time point, eg,
mri_segstats ---annot fsaverage lh /path/to/mc-zabs.the13sig.ocn.annot --i timepoint1.lh.stack.mgh --avgwf timepoint1.lh.stack.dat --excludeid 0
this will create the .dat file with a row for each input in the stack and a column for each cluster
On 05/16/2016 09:43 AM, Liu Y wrote:
Dear Martin and Douglas,
I created the cluster ROIs (mc-zabs.the13sig.ocn.annot) for the two groups. What is the detailed command line to calculate the baseline and followup cortical thicknesses from the *.long.* directories?
Thanks, Yawu
On Thu, May 12, 2016 at 9:07 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Yawu, and both baseline and follow-up surfaces (from the *.long.* directories) are in vertex correspondence, so you can use the ROI on each time point directly. Best, Martin On 05/12/2016 02:00 PM, Douglas N Greve wrote: > If you used mri_glmfit, then you can use mri_glmfit-sim to create > significant clusters. It will create an annotation of the significant > clusters, and you can pass that to mri_segstats along with the stack of > thickness images to extract the mean thickness in each cluster. > > On 05/12/2016 04:23 AM, Liu Y wrote: >> Hi Freesurfers, >> >> I am using the degree of cortical atrophy between two groups. The >> atrophy rate had no significant difference between two groups, but the >> average thickness of the baseline and followup showed significant >> clusters in two regions between the two groups. My question is how to >> create the ROIs covering the clusters, and then extract the >> thicknesses on baseline and followup MRIs? >> >> Thanks, >> Yawu >> >> >> _______________________________________________ >> 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Liu Y -
Martin Reuter