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. So, I wrote the name of the used command and their inputs as well as the complete command. Thanks again! Cheers, Rosita On Wed, Jan 6, 2016 at 4:01 AM, Donna Dierker <do...@brainvis.wustl.edu> wrote: > 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 < > r.shishe...@student.unimelb.edu.au> wrote: > > > 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 sulcal depth. Later, I ran > caret command SURFACE IDENTIFY SULCI using the previous step output but I > get an error saying cerebral hull VTK file has no points. > > > > I think I do not create segmentation volume properly because when > visualizing the volume (output_volume.nii file created using SURFACE TO > SEGMENTATION VOLUME), it includes just few voxels in a raw. > > > > Any help would be greatly appreciated. > > > > Thanks, > > Rosita > > > > > > On Thu, Sep 3, 2015 at 12:36 PM, Donna Dierker < > donna.dier...@sbcglobal.net> wrote: > > Hi Rosita, > > > > This zip archive has a script named gen_depth.sh: > > > > brainmap.wustl.edu/pub/donna/US/UCDAVIS/cwn.zip > > login pub > > password download > > > > You'll need to adapt it to your data, but it will give you a head start. > > > > Donna > > > > > > On Sep 2, 2015, at 7:01 PM, Rosita Shishegar < > r.shishe...@student.unimelb.edu.au> wrote: > > > > > 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 any way to compute the > Cerebral Hull using Caret from cortical surface rather than the volume? > > > > > > > > > Thanks, > > > > > > Rosita > > > > > > > > > > > > > > > _______________________________________________ > > > caret-users mailing list > > > email@example.com > > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > _______________________________________________ > > caret-users mailing list > > firstname.lastname@example.org > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > > > > > -- > > Rosita Shishegar > > PhD Candidate > > Neuroimaging Group > > University of Melbourne > > Parkville, VIC 3010 > > _______________________________________________ > > caret-users mailing list > > email@example.com > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > _______________________________________________ > caret-users mailing list > firstname.lastname@example.org > http://brainvis.wustl.edu/mailman/listinfo/caret-users > -- Rosita Shishegar PhD Candidate Neuroimaging Group University of Melbourne Parkville, VIC 3010
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