Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

External Email - Use Caution The annot file loaded successfully and without any branches. Thanks a lot. Ting > On Oct 15, 2018, at 2:22 PM, Greve, Douglas N.,Ph.D. > wrote: > > Click on the surface file name in the upper left corner of FreeView, > then load the Annotation from

[Freesurfer] Nonsensical Vertex Coordinates, please help with interpretation

External Email - Use Caution I'm trying to make a surface file from a subject's head and to map coordinates to that surface. If I run: mri_seghead --invol $SUBJECTS_DIR/$sub/mri/T1.mgz --outvol $SUBJECTS_DIR/$sub/mri/seghead.mgz --fill 255 --thresh1 20 --thresh2 20 --nhitsmin

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

Click on the surface file name in the upper left corner of FreeView, then load the Annotation from the panel just below it. It does not make sense that you would see the branches on the folded surface but not on the inflated. On 10/15/2018 03:06 PM, Ting Li wrote: > > External Email - U

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

Hi Amanda mris_convert -c lh.thickness.asc lh.white lh.thickness.mgz should do the trick cheers Bruce On Mon, 15 Oct 2018, Worker, Amanda wrote: External Email - Use Caution How would I do that? mris_convert doesn't seem to take .asc as an input?

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

External Email - Use Caution How would I do that? mris_convert doesn't seem to take .asc as an input? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: 15 October 2018 16:25:51 To: freesurfer@nmr.mgh.harv

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

Not sure. Can you use mris_convert to convert the asc back to a curv file? On 10/15/2018 11:20 AM, Worker, Amanda wrote: > > External Email - Use Caution > > Hello, > > > I am trying to overlay a .asc file in either freeview or tksurfer, but > so far having no luck. > > > As practice and

[Freesurfer] Using a .asc file as overlay in freeview/tksurfer

External Email - Use Caution Hello, I am trying to overlay a .asc file in either freeview or tksurfer, but so far having no luck. As practice and to determine the right format, I am simply using lh.thickness, which I've converted to .asc using the following command: % mris_

Re: [Freesurfer] fMRI mask for hippocampal subfields

Hi Chanelle you can segment hippocampal subfields directly for individual subjects with the FreeSurfer tools written by Eugenio Iglesias: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields cheers Bruce On Mon, 15 Oct 2018, Buckle, Chanelle [cbuc...@sun.ac.za] wrote:

Re: [Freesurfer] qdec analysis with more than 2 covariates

You cannot use QDEC. For this case you'll need to use the "command line" stream. You'll need to start by creating an FSGD file https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples On 10/15/18 10:15 AM, vittal korann wrote: External Email - Use Caution Hi Doug, Recently I started work

[Freesurfer] qdec analysis with more than 2 covariates

External Email - Use Caution Hi Doug, Recently I started working on freesurfer for volume based analysis. For QDEC, I need to include more than 2 variables. For example if I include patients who hail from different places like statutory town, census town and rural. In present scen

[Freesurfer] fMRI mask for hippocampal subfields

External Email - Use Caution Good day I have fMRI data and would like to look at BOLD activation in the hippocampal subfields (particularly the subiculum). I was wondering if there is currently an AAL mask available for the hippocampal subfields or if there is some way to creat