it only looks for that if it can't find lh.pial. Does that exist?
On Wed, 10 Dec 2014, Xiaomin Yue wrote:
Hi Bruce, the mris_thickness was looking for ?h.gray file to run correctly. But no such file exists. The freesurfer used is 5.3. Any ideas? The command line is: mris_thickness test_DB48 lh lh.thickness The error: reading gray matter surface /misc/data41/yuex/recon_test/test_DB48/surf/lh.gray MRISread(/misc/data41/yuex/recon_test/test_DB48/surf/lh.gray): could not open file. Thanks, Xiaomin ____________________________________________________________________________ From: yu...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white Date: Wed, 10 Dec 2014 02:47:02 +0000 Thanks. I will try mris_fill. Xiaomin From: Bruce Fischl Sent: Tuesday, December 9, 2014 4:31 PM To: Freesurfer support list it creates a file in curvature format, yes. Did you try mris_fill for the wm.mgz? It won't be exactly the same as the one we would generate. You could use mris_fill to generate the interior of the ?h.white surface, then use the aseg to remove non-wm voxels I guess On Tue, 9 Dec 2014, Xiaomin Yue wrote: > Thanks very much. Does this create curvature file? Again, is it possible to generate wm.mgz from those files? > > Thanks, > Xiaomin > > >> On Dec 9, 2014, at 4:19 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: >> >> I think just the ?h.white and ?h.pial >> >> cheers >> Bruce >>> On Tue, 9 Dec 2014, Xiaomin Yue wrote: >>> >>> What I mean by inputs is the default files the mris_thickness will be >>> looking for to run correctly >>> Xiaomin >>> On Dec 9, 2014, at 1:08 PM, Xiaomin Yue <yu...@hotmail.com> wrote: >>> >>> Hi Bruce, >>> >>> Thanks for your response. What's the inputs to the >>> mris_thickness? I need the wm.mgz to generate the ratio of gray >>> vs. white matter. >>> >>> Xiaomin >>> >>> Date: Tue, 9 Dec 2014 09:55:21 -0500 >>> From: fis...@nmr.mgh.harvard.edu >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] thickness from pial and white >>> the thickness you can generate using mris_thikness. Why do you want to generate a wm.mgz? I guess you could from the wmparc >>> On Mon, 8 Dec 2014, Xiaomin Yue wrote: >>>>> Hi All, >>>>> >>>>> Cortical surface reconstructed using caret from a high resolution MRI data >>>> (0.25 mm) has been converted to freesurfer format, and viewed correctly >>>> using freeview. My questions are whether it is possible to generate 1) a >>>> ?h.thickness from the ?h.pial and ?h.white; 2) wm.mgz file using ?h.pial a >>> nd >>>> ?h.white >>>>> >>>>> Thanks very much for your inputs. >>>>>> Xiaomin >>>>>> >>> >>> _______________________________________________ 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 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 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 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
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