Thanks Donna! On Fri, Jan 15, 2016 at 3:07 AM, Donna Dierker <do...@brainvis.wustl.edu> 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: > > http://brainmap.wustl.edu/pub/donna/IN/JOHN/align.html > login pub > password download > > > Donna > > > On Jan 13, 2016, at 10:09 PM, Rosita Shishegar < > r.shishe...@student.unimelb.edu.au> wrote: > > > 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 depth. However, computing the > segmentation volume from the surface would serve the purpose for me > because I have written the codes for the rest of the steps. As you > suggested, I would try to see what else may work for my sheep brains. > > > > Thanks again for all the help. > > > > Cheers, > > Rosita > > > > On Tue, Jan 12, 2016 at 3:41 AM, Donna Dierker <do...@brainvis.wustl.edu> > wrote: > > 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 hull_vol.nii 1 1 1 > > voxel dimensions > > > > How did you get that surface? Typically, you start off with a T1 or T2 > volume and segment it using some software. Then the binary segmentation > volume is tesselated into a surface. You already had the surface, so did a > volume give rise to that? If so, its dimensions, origin, and voxdims give > clues to what these should be. In particular, if there is some volume you > want this surface to align with, that might be a good one to use for these > parameters. > > > > > caret_command -surface-to-segmentation-volume > sheep_90_rh.pial.surf.coord > > > sheep_90_rh.pial.surf.topo hull_vol.nii > > > > The above command generates a ribbon of voxels along the surface, and > I'm not sure exactly how thick. You can specify inner/outer thickness in > the Caret GUI (Surface: Region of Interest: Select all nodes: Create Volume > Region of Interest). This is more or less what the above caret_command > does, but it uses a default inner/outer thickness that might be too thick > for your sheep. > > > > Again, not sure what the end game is here (e.g., do you want sulcal > depth? hull? registration?). I fear there will be other showstopper steps > down the road that are more sheep-proof. ;-) > > > > (Sorry, Tim, I'm having trouble thinking of baaaad puns here.) > > > > Donna > > > > > > On Jan 10, 2016, at 9:31 PM, Rosita Shishegar < > r.shishe...@student.unimelb.edu.au> wrote: > > > > > 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 > > > _______________________________________________ > > > 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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