Yes, lh.pial exists Xiaomin
> On Dec 10, 2014, at 10:33 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > > 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 > _______________________________________________ > 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
