The problem was solved. I typed the wrong name. mris_fill had generated wm.mgz correctly, with the problem that a significant portion of white matter was cutted off. The problem I believe is that the resolution or the matrix size of wm.mgz is limited to 256 X 256 X 256, but the high resolution data has dimension larger than that. Is it possible to have a wm.mgz larger than 256^3? Or some kind of trick to make it happen?
Thanks,Xiaomin Date: Wed, 10 Dec 2014 11:37:29 -0500 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] thickness from pial and white what version of FS do you have? You can try runing it with -pial pial but I wouldn't think that is needed. Is the lh.pial in /misc/data41/yuex/recon_test/test_DB48/surf/ and is it readable? On Wed, 10 Dec 2014, Xiaomin Yue wrote: > 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 > > > _______________________________________________ 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.
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