[Freesurfer] newbie, white matter volumes
Hi all, I would like to compare two groups of human subjects on volumetric measures of cerebral white matter. Does anyone know how to get more detailed information on white matter volumes ? (per brain region, or per white matter structure). Thanks! Romke ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] transform back to original coordinates ?
You cannot always rely on tkmedit to show you differences between two volumes if their underlying geometry is the same. eg, if you simply reorient coronals into sagitals and make the appropriate changes to the geometry info, then they will show up identically in tkmedit (as they should). Try this instead: tkregister2 --mov brainmask.mgz --targ rawavg.mgz --regheader --reg reg.dat --noedit mri_vol2vol --mov brainmask.mgz --targ rawavg.mgz --o brain-in-rawavg.mgz --reg reg.dat --interp nearest I might need to give you a new version of mri_vol2vol, let me know doug Bruce Fischl wrote: hmm, that should put them into the same voxel coords I thought. You can always use the vox2ras given by mri_info to go from one voxel coords to the other. Bruce On Sat, 2 Sep 2006, Frederick Klauschen wrote: Hi Bruce, visualizing with tkmedit works fine for me as well, but when I am loading the backtransformed file brainmask_xformed.mgz with Matlab or plain C I still get the shifted image. Doing the same with the original (pre-FS) image works fine (no coordinate shift). Thanks, Frederick --- Bruce Fischl [EMAIL PROTECTED] wrote: p.s. how are you visualizing it? This works fine for me: mri_convert -rl rawavg.mgz brainmask.mgz brainmask_xformed.mgz tkmedit -f rawavg.mgz -aux brainmask_xformed.mgz then use alt-c to switch back and forth Bruce On Fri, 1 Sep 2006, Frederick Klauschen wrote: Hi Bruce, (aim: transform fs format back to original file format) when I run the commands you suggested: mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz the backtransformed image is in the original coordinate boundaries, but it is not a the same position as the original data (see attached example). Frederick --- Bruce Fischl [EMAIL PROTECTED] wrote: if your orig volume is in orig/001.mgz, then you can do: mri_convert -rl orig/001.mgz brainmask.mgz brainmask_transformed.mgz cheers, Bruce On Thu, 31 Aug 2006, tulu wrote: __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com __ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] newbie, white matter volumes
We are in the process of fine-tuning our white matter parcellation. I hate to try to give a date on it as it always gets pushed back, but should not be more than 2 mo. You can do whole-hemisphere (both cortical and cerebellar) measures now. doug Romke Rouw wrote: Hi all, I would like to compare two groups of human subjects on volumetric measures of cerebral white matter. Does anyone know how to get more detailed information on white matter volumes ? (per brain region, or per white matter structure). Thanks! Romke ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] tkmedit problem, crash on loading aseg
Hi everyone, I have a rather obscure problem. There are some subjects whose aseg subcortical parcellations will not load up in tkmedit, causing it to crash. This happens when using a Mac with X11 to view them, not on my Linux machine. Interestingly though, this does not happen for all subjects, some do get displayed correctly on the Mac, too. Here's what I do: tkmedit mysubj T1.mgz Then, use tkmedit's File-Load Segmentation There, select aseg.mgz and tkmeditColorsCMA tkmedit then crashes, producing the following log: tkmedit started: Tue Sep 5 17:26:20 2006 tkmedit PAT_ T1.mgz lh.white -aux-surface rh.white $Id: tkmedit.c,v 1.274.2.1 2006/03/06 19:52:48 kteich Exp $ $Name: stable3 $ Set user home dir to /Volumes/JalapenoSAN/Scratch/XX/fs Set subject home dir to /Scratch/XX/fs/PAT_ Using interface file /usr/local/freesurfer/lib/tcl/tkmedit.tcl Tcl: Successfully parsed tkmedit.tcl Tcl: Successfully parsed tkm_functional.tcl Error 1 in CLUT_GetLabel: Invalid pointer to object. I wonder if this is a known problem for Macs? Thanks, Johannes ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
