Re: [Freesurfer] Is there a way to obtain the thickness of every vertex of the whole brain?
yes, you can do this in matlab with load_curv and read_annotation cheers Bruce On Wed, 16 Mar 2011, [GBK] Íô¹óºê wrote: Hi,all: Just as the title says,I wonder if there is a method to obtain the thickness of each vertex in the whole brain,and so,if we can,how do we kown which of the area is the vertex belong to? I am using the freesurfer 5.0. thanks in advance! wang___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] MCSRCH error
While processing a normal brain through fsv5.0.0, an unfamiliar message popped up in the screen output (see below). Any ideas what I should do about this message (anything in particular I should check)? Many Thanks, Jenifer IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 1145193.0 tol 0.00 final transform: 1.386 -0.067 0.094 -63.518; 0.088 1.120 -0.108 -0.481; -0.131 0.093 0.972 -2.704; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 34 minutes and 38 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] MCSRCH error
Hi Jenifer we see that sometimes too, and it's never clear why. It's from an open source minimization function and doesn't usually mean anything bad. Check the talairach_with_skull.lta visually and see if it is ok cheers Bruce On Wed, 16 Mar 2011, Juranek, Jenifer wrote: While processing a normal brain through fsv5.0.0, an unfamiliar message popped up in the screen output (see below). Any ideas what I should do about this message (anything in particular I should check)? Many Thanks, Jenifer IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = 1145193.0 tol 0.00 final transform: 1.386 -0.067 0.094 -63.518; 0.088 1.120 -0.108 -0.481; -0.131 0.093 0.972 -2.704; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 34 minutes and 38 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] corpus callosum volume in aseg.mgz...
Hi: The CC volume in aseg.mgz is computed using two slices to the left and two sagital slices to the right the midline ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tkmedit undo volume?
Hi - I'm doing manual edits in tkmedit. In the tkmedit working with data page on the wiki, it states that there are three ways to undo, one taking advantage of the undo volume. The instructions say to select View-Undoable voxels, then use the shift key and mouse button 2 with the edit voxel tool active, the voxels will be returned to their original values. I have the latest version of freesurfer, and there is no undoable voxels in the view menu. I can view edited voxels. However, nothing is undone when I hold the shift key. Under edit, however, there is an option to clear undo volume which makes me think that the undo volume still exists. Is this still an option for editing? Thanks, Allison Allison Nugent, PhD MRI Physicist Section on Neuroimaging in Mood Disorders Experimental Therapeutics and Pathophysiology Branch NIMH/NIH/DHHS Ph. 301-451-8863 nuge...@mail.nih.gov ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] corpus callosum volume in aseg.mgz...
yes, although that's configurable on the mri_cc cmdline On Wed, 16 Mar 2011, Gonzalo Rojas Costa wrote: Hi: The CC volume in aseg.mgz is computed using two slices to the left and two sagital slices to the right the midline ?... Sincerely, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
