Re: [caret-users] Generating cortical hull surface
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 bd 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 huma
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 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 bd 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! > > > > > &g
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 -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
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. 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
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 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] 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 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
