Re: [Freesurfer] surface area of outer smoothed hull

2015-09-07 Thread Marie Schaer
Hi Christiane, You can use mris_info lh.pial-outer-smoothed Best, Marie On Sep 7, 2015, at 10:57 PM, "Jockwitz, Christiane" mailto:c.jockw...@fz-juelich.de>> wrote: Dear all, I would like to extract the surface area from the outer smoothed hull of a particular region of interest that is

[Freesurfer] surface area of outer smoothed hull

2015-09-07 Thread Jockwitz, Christiane
Dear all, I would like to extract the surface area from the outer smoothed hull of a particular region of interest that is created during the local gyrification process. Using mri_segstats I got the error message: couldn't determine type of file lh.pial-outer-smoothed Is there any other way to

[Freesurfer] Research Assistant Position

2015-09-07 Thread Benson Mwangi
The Neuroimaging Lab, Department of Psychiatry and Behavioral Sciences, University of Texas Health Science Center at Houston is looking for a Research Assistant with the following job specifications. - Conducts research data activities, under general direction of a Principal Investigator and/or S

Re: [Freesurfer] Segmenting deep and outer white matter

2015-09-07 Thread Bruce Fischl
Those labels are for gray matter structures Cheers Bruce > On Sep 7, 2015, at 6:48 PM, John Anderson wrote: > > Hi Doug, > Thank you for your response. > When we open "wmparc.mgz" in freeview we can see clearly that we have labels > for cortical parcellations and it is white matter parcella

[Freesurfer] Cortical parcellation and mri_annotation2label

2015-09-07 Thread Jacek Manko
Dear All, In your entry on corical parcellation: https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation You enumerate a certain list of cortical labels obtained in that procedure. If I run aparcstats2table I got the measures for exactly these labels. However, when I run mri_annotation2

Re: [Freesurfer] Segmenting deep and outer white matter

2015-09-07 Thread John Anderson
Hi Doug, Thank you for your response. When we open "wmparc.mgz" in freeview we can see clearly  that we have labels for cortical parcellations and it is white matter parcellations as well as the unsegmented white matter What is really confusing me is that deep structures like the thalamus, amygd

Re: [Freesurfer] Segmenting deep and outer white matter

2015-09-07 Thread Douglas Greve
The best thing is to take a look at the wmparc. It was not really designed to be deep and superficial. There is only one "deep" WM seg which is called "Unsgemented White Matter" or something like that. doug On 9/5/15 5:54 PM, Bruce Fischl wrote: Hi John I defer to Doug. Not sure he ever publ

[Freesurfer] Basic questions regarding of layers

2015-09-07 Thread Yun Wang
> > > Hi All, > > > I have some basic questions regarding of layers surface in freesurfer. The > main idea is to extract the time series between different layers. > > 1 After recon -all, I got white surface and pial surface, then I use > mri_expand to get 3 additional layers’ surface betwe

[Freesurfer] Postdoc position in multisensory and foreign language learning

2015-09-07 Thread Katharina von Kriegstein
Applications are welcomed for a postdoctoral research position at the Max Planck Institute for Human Cognitive and Brain Sciences (MPI-CBS) in Leipzig, Germany. The objective of the postdoctoral research project is to use neurostimulation (TMS, tDCS) and neuroimaging to understand the role of se