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 -123.0 -75.0*) were the reason I was getting error. Should I use these numbers for any data? As you mentioned, since my dataset includes sheep brains, computed cerebral hull may not be as convex as it should be. However, if I can compute an accurate segmentation volume with Caret, I can compute the hull with more adjusted tuning parameters in Matlable. The problem is that the brains are smaller than human brain and and I think volume spacing 1 1 1 is quite big for them. I tried to use a smaller volume spacing (e.g. caret_command *-volume-set-spacing* hull_vol.nii hull_vol.nii *0.2 0.2 0.2*) but it is giving me errors. Do you think there would be any way to use volume spacing smaller than 1 for this caret command. Cheers, Rosita On Sat, Jan 9, 2016 at 10:16 AM, <do...@brainvis.wustl.edu> wrote: > Hi Rosita, > > This is a sheep brain, so I don't know that the hull Caret generates will > be suitable for your purposes, because this was designed for human brains. > > Still, I tried these steps after converting to caret coord/topo: > > caret_command -volume-create 176 208 176 hull_vol.nii > caret_command -volume-set-origin hull_vol.nii hull_vol.nii -88.0 -123.0 > -75.0 > caret_command -volume-set-spacing hull_vol.nii hull_vol.nii 1 1 1 > caret_command -surface-to-segmentation-volume sheep_90_rh.pial.surf.coord > sheep_90_rh.pial.surf.topo hull_vol.nii > caret_command -surface-identify-sulci Other.sheep.R.1002.spec right > hull_vol.nii sheep_90_rh.pial.surf.topo sheep_90_rh.pial.surf.coord > sheep_90_rh.pial.surf.coord NIFTI_GZIP > > And I got a cerebral hull volume, but it probably isn't as convex as you'd > like. How are you using this? > > Donna > > > > 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 > >> > > caret-users@brainvis.wustl.edu > >> > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > > >> > > >> > _______________________________________________ > >> > caret-users mailing list > >> > caret-users@brainvis.wustl.edu > >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > > >> > > >> > > >> > -- > >> > Rosita Shishegar > >> > PhD Candidate > >> > Neuroimaging Group > >> > University of Melbourne > >> > Parkville, VIC 3010 > >> > _______________________________________________ > >> > caret-users mailing list > >> > caret-users@brainvis.wustl.edu > >> > http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > >> > >> _______________________________________________ > >> caret-users mailing list > >> caret-users@brainvis.wustl.edu > >> http://brainvis.wustl.edu/mailman/listinfo/caret-users > >> > > > > > > > > -- > > Rosita Shishegar > > PhD Candidate > > Neuroimaging Group > > University of Melbourne > > Parkville, VIC 3010 > > _______________________________________________ > > caret-users mailing list > > caret-users@brainvis.wustl.edu > > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > > -- Rosita Shishegar PhD Candidate Neuroimaging Group University of Melbourne Parkville, VIC 3010
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