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


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