Thanks Matt/Donna - Matt-
I presume I should calculate the curvature of the WM surface right? and rename whatever the caret output is to ?h.curv and with the thickness file, load in matlab, divide the appropriate column by 4, save. simple as that? Donna - I just need a set of voxels that represent the hidbrain, or everything except the hindbrain. There is a file hindbrain* but it is "Hindbrain.TestFlood.Limits" and it's only 76 bytes. I'll see what I can do with it, and see if there are command line options that might give me a segmentation vol of hindbarin or related. I can do it by hand ultimately. It does miss a bit of hidbrain, but it's not bad best, Colin On 2 July 2012 18:17, Colin Reveley <reve...@gmail.com> wrote: > Thanks Matt - > > I presume I should calculate the curvature of the WM surface right? and > rename whatever the caret output is to ?h.curv > > and with the thickness file, load in matlab, divide the appropriate column > by 4, save. simple as that? > > Thanks Donna - > > I just need a set of voxels that represent the hidbrain, or everything > except the hindbrain. There is a file hindbrain* but it is > "Hindbrain.TestFlood.Limits" and it's only 76 bytes. > > I'll see what I can do with it, and see if there are command line options > that might give me a segmentation vol. > > It does miss a bit of hidbrain, but it's not bad > > best, > > Colin > > On 2 July 2012 18:00, <caret-users-requ...@brainvis.wustl.edu> wrote: > >> Send caret-users mailing list submissions to >> caret-users@brainvis.wustl.edu >> >> To subscribe or unsubscribe via the World Wide Web, visit >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> or, via email, send a message with subject or body 'help' to >> caret-users-requ...@brainvis.wustl.edu >> >> You can reach the person managing the list at >> caret-users-ow...@brainvis.wustl.edu >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of caret-users digest..." >> >> Today's Topics: >> >> 1. more marmoset (Colin Reveley) >> 2. myelin mapping (Colin Reveley) >> 3. Re: myelin mapping (Matt Glasser) >> 4. Re: more marmoset (Donna Dierker) >> >> >> ---------- Forwarded message ---------- >> From: Colin Reveley <cm...@sussex.ac.uk> >> To: <caret-users@brainvis.wustl.edu> >> Cc: >> Date: Sun, 1 Jul 2012 18:20:08 +0100 >> Subject: [caret-users] more marmoset >> I agree that a WM and PIAL from freesurfer is the way to go with marmoset. >> >> For what it's worth, if you calls it a galago (in caret) and uses a 300um >> MTR you can get a halfway decent surface (not really that good, but it >> works). >> >> at 300um caret successfully get's rid of the hindbrain. >> >> If I could get access to a volume either of the hidbrain, or of >> everything else with hindbrain removed, that would save me a huge amount of >> work. First, experience tells me that with no hidbrain caret will make a >> surface from 150um data. >> >> second, I'll need to remove the hindbrain by hand before I try to do this >> with Freesurfer. >> >> Caret spits out many volumes as it runs segmentation and surface >> construction. >> >> are any of these a sturctural volume with hindbrain removed? I could >> upsample that and use as a mask for hindbrain removal. >> >> best, >> >> Colin >> >> >> ---------- Forwarded message ---------- >> From: Colin Reveley <cm...@sussex.ac.uk> >> To: <caret-users@brainvis.wustl.edu> >> Cc: >> Date: Sun, 1 Jul 2012 22:13:26 +0100 >> Subject: [caret-users] myelin mapping >> Hi - >> >> I had a data accident a while ago. I lost a freesurfer dir. >> >> But, since I was importing to caret I have lh and rh white and pial from >> freesurfer, and I have the thickness files for each. And I have the >> appropriate MRIs. >> >> These files took a LONG time to get right, and then it took quite a while >> to register them to F99 in a way I found acceptable. So I'm not sure about >> doing it again, for this animal anyway. >> >> I can get a ribbon volume using mri_ribbon. It's one file for each >> hemisphere. I presume I can just merge them, and call it ribbon,mgz >> >> what I'm missinng, for myelin mapping, are the rh.curv and lh.curv. >> >> there are two programs: >> >> mris_curvature >> mris_curvature_stats >> >> the former outputs a mean and gaussian curvature file (I think these >> files are an intermediate in making "rh.curv"; mris_make_surfaces does >> generate them I think anyway) >> >> then the other program makes this stuff >> >> rh.smoothwm.K.crv >> rh.smoothwm.H.crv >> rh.smoothwm.k1.crv >> rh.smoothwm.k2.crv >> rh.smoothwm.S.crv >> rh.smoothwm.C.crv >> rh.smoothwm.BE.crv >> >> >> can I make the curv file that you want for myelin mapping from any of the >> above files? >> >> maybe just renaming the mean curvature file or gaussian curvature file to >> "rh.curv" would be fine? >> >> Also, my voxels are 1mm in freesurfer, but 0.25 in reality. >> >> is that going to be a problem for this (curvature, thickness)? Probably >> not. but making sure. >> >> cheers, >> >> Colin >> >> >> ---------- Forwarded message ---------- >> From: Matt Glasser <m...@ma-tea.com> >> To: "'Caret, SureFit, and SuMS software users'" < >> caret-users@brainvis.wustl.edu> >> Cc: >> Date: Sun, 1 Jul 2012 18:43:29 -0500 >> Subject: Re: [caret-users] myelin mapping >> ** >> >> lh.curv and rh.curv are made by mris_make_surfaces normally. You might >> as well use caret to remake the curvature files:**** >> >> ** ** >> >> caret_command -surface-curvature**** >> >> ** ** >> >> and then use mean curvature.**** >> >> ** ** >> >> You will want to make sure that the thickness matches your volumes, >> because it is used as a part of the mapping. If you have 1mm volumes in >> Caret, then it is fine. If you have 0.25mm volumes, you should divide the >> thickness by 4.**** >> >> ** ** >> >> Peace,**** >> >> >> Matt.**** >> >> ** ** >> ------------------------------ >> >> *From:* **caret-users-boun...@brainvis.wustl.edu** [mailto:** >> caret-users-boun...@brainvis.wustl.edu**] *On Behalf Of *Colin Reveley >> *Sent:* Sunday, July 01, 2012 4:13 PM >> *To:* caret-users@brainvis.wustl.edu >> *Subject:* [caret-users] myelin mapping**** >> >> ** ** >> >> Hi - >> >> I had a data accident a while ago. I lost a freesurfer dir. >> >> But, since I was importing to caret I have lh and rh white and pial from >> freesurfer, and I have the thickness files for each. And I have the >> appropriate MRIs. >> >> These files took a LONG time to get right, and then it took quite a while >> to register them to F99 in a way I found acceptable. So I'm not sure about >> doing it again, for this animal anyway. >> >> I can get a ribbon volume using mri_ribbon. It's one file for each >> hemisphere. I presume I can just merge them, and call it ribbon,mgz >> >> what I'm missinng, for myelin mapping, are the rh.curv and lh.curv. >> >> there are two programs: >> >> mris_curvature >> mris_curvature_stats >> >> the former outputs a mean and gaussian curvature file (I think these >> files are an intermediate in making "rh.curv"; mris_make_surfaces does >> generate them I think anyway) >> >> then the other program makes this stuff >> >> rh.smoothwm.K.crv >> rh.smoothwm.H.crv >> rh.smoothwm.k1.crv >> rh.smoothwm.k2.crv >> rh.smoothwm.S.crv >> rh.smoothwm.C.crv >> rh.smoothwm.BE.crv >> >> >> can I make the curv file that you want for myelin mapping from any of the >> above files? >> >> maybe just renaming the mean curvature file or gaussian curvature file to >> "rh.curv" would be fine? >> >> Also, my voxels are 1mm in freesurfer, but 0.25 in reality. >> >> is that going to be a problem for this (curvature, thickness)? Probably >> not. but making sure. >> >> cheers, >> >> Colin**** >> >> >> ---------- Forwarded message ---------- >> From: Donna Dierker <do...@brainvis.wustl.edu> >> To: "Caret, SureFit, and SuMS software users" < >> caret-users@brainvis.wustl.edu> >> Cc: >> Date: Mon, 2 Jul 2012 09:29:33 -0500 >> Subject: Re: [caret-users] more marmoset >> All of the volumes, except the inner and outer boundaries, are >> segmentations, rather than structural volumes (as far as I know). >> >> But you could find one of those intermediate volumes -- possibly named >> like hindbrain* -- and subtract that volume from the anatomical volume, and >> then use the volume math features to set the floor to 0. There are lots of >> caret_command tools for this sort of thing, not to mention FSL/AFNI tools >> (e.g., 3dcalc). >> >> I'm surprised Caret gets rid of the marmoset hindbrain at any resolution >> -- cool. >> >> >> On Jul 1, 2012, at 12:20 PM, Colin Reveley wrote: >> >> > I agree that a WM and PIAL from freesurfer is the way to go with >> marmoset. >> > >> > For what it's worth, if you calls it a galago (in caret) and uses a >> 300um MTR you can get a halfway decent surface (not really that good, but >> it works). >> > >> > at 300um caret successfully get's rid of the hindbrain. >> > >> > If I could get access to a volume either of the hidbrain, or of >> everything else with hindbrain removed, that would save me a huge amount of >> work. First, experience tells me that with no hidbrain caret will make a >> surface from 150um data. >> > >> > second, I'll need to remove the hindbrain by hand before I try to do >> this with Freesurfer. >> > >> > Caret spits out many volumes as it runs segmentation and surface >> construction. >> > >> > are any of these a sturctural volume with hindbrain removed? I could >> upsample that and use as a mask for hindbrain removal. >> > >> > best, >> > >> > Colin >> > _______________________________________________ >> > 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 >> >> >
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