Hi Andrew,
Use the -m (mask) option for the ROI, where it labels good vertices 1, excluded
0, e.g.:
palm -i ${MetricIn} -m ${AtlasROI} -s ${SurfaceGii} ${VertexAreas} …
This repository has atlas roi shape.gii for multiple resolutions:
https://github.com/Washington-University/Pipelines/tree/master/global/templates/standard_mesh_atlases
… unless the course practicals list something later/greater.
Donna
> On Sep 29, 2016, at 2:25 PM, Andrew Poppe <poppe...@gmail.com> wrote:
>
> Hello gurus,
>
> I have successfully run first- and second-level stats on a data set that was
> collected with HCP-compliant parameters, and I am ready to run group stats.
>
> I have looked at the HCP workshop materials (practicals) regarding using PALM
> for group stats on dense data, and it does not mention masking anything that
> I can see (I'm looking at practical 8 from the 2016 Course). However, I was
> told that it would be better to mask out vertices on the medial wall of both
> hemispheres as they will increase the number of tests being conducted but do
> not actually contain useful data.
>
> Is this true? Should I be masking out zero voxels from cope images prior to
> entering them into PALM?
>
>
> Thanks for your help,
>
> Andrew Poppe, Ph.D.
> Postdoctoral Researcher
> Olin Neuropsychiatry Research Center
> Institute of Living
> Hartford Hospital
> _______________________________________________
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
________________________________
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
