Re: [caret-users] Generating cortical hull surface

Thanks Donna! On Fri, Jan 15, 2016 at 3:07 AM, Donna Dierker wrote: > Hi Rosita, > > It can be so frustrating. Sounds like you have some good alternatives to > explore. > > This link details one user's alignment issues and the solution: > >

Re: [caret-users] Generating cortical hull surface

Hi Rosita, It can be so frustrating. Sounds like you have some good alternatives to explore. This link details one user's alignment issues and the solution: http://brainmap.wustl.edu/pub/donna/IN/JOHN/align.html login pub password download Donna On Jan 13, 2016, at 10:09 PM, Rosita

Re: [caret-users] Generating cortical hull surface

Hi Donna, Thanks for the explanation. Unfortunately, as a result of preprocessing steps my surfaces are transformed, resized, and they are not even aligned with the original volumes anymore and I prefer not to bother with registration with original data. The final goal was to compute sulcal

Re: [caret-users] Generating cortical hull surface

Hi Rosita, None of the parameters in these commands makes sense for sheep: > caret_command -volume-create 176 208 176 hull_vol.nii volume dimensions > caret_command -volume-set-origin hull_vol.nii hull_vol.nii -88.0 -123.0 -75.0 volume origin > caret_command -volume-set-spacing hull_vol.nii

Re: [caret-users] Generating cortical hull surface

Hi Donna, Thanks a lot for the help. I ran the commands as you suggested and now I can compute the volume and the hull. My understanding is that the inputs that you chose for creating volume (*-volume-create** 176 208 176* ) and the origin ( *-volume-set-origin* hull_vol.nii hull_vol.nii *-88.0

Re: [caret-users] Generating cortical hull surface

Thanks for offering help Donna! I uploaded the surface *.stl and its converted version to *.pial that I used as the input for Caret. The folder also include a text file containing commands that I used. For some reason I can not run caret commands in my terminal so I use caret command executor.

Re: [caret-users] Generating cortical hull surface

Upload a zip file containing the script (or just email commands used) and the inputs (surface or segmentation) here: http://brainvis.wustl.edu/cgi-bin/upload.cgi I'll have a look. On Jan 5, 2016, at 12:31 AM, Rosita Shishegar wrote: > Hi Donna and all

Re: [caret-users] Generating cortical hull surface

Hi Donna and all caret users, Happy new year! Before, I asked about computing sulcal depth from the cortical surface. Donna suggested that I use gen_depth.sh file as a guide. Using the commands, first I tried to create the volume from the surface which later I needed for computing hull and the

[caret-users] Generating cortical hull surface

Hi, I am a new Caret user and I am working on animal brain data, which are manually segmented and triangulated mesh of cortical surface is already extracted and pre-processed. I want to measure Sulcal Depth of theses brains and so I need to generate Cerebral Hull surface of them. Is there