Pial-outer-smoothed was a surface created from recon-all -localGI. Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
> On Jul 1, 2019, at 11:41 AM, Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> > wrote: > > how was pial-outer-smoothed create? > > On 7/1/2019 2:33 PM, Nillo, Ryan Michael R wrote: >> Hi Doug, >> >> lh.test.nii was created with: >> >> mri_vol2surf --mov ./misc/lh.probability.nii --trgsubject fsaverage_1 >> --regheader fsaverage_1 --hemi lh --fwhm 30 --surf pial-outer-smoothed --o >> ./lh.test.nii >> >> Where lh.probability.nii is a probability mask created from about 63 >> subjects. >> >> Thanks in advance for the help, >> >> Ryan Michael Nillo >> Staff Research Associate I >> University of California San Francisco >> Department of Radiology and Biomedical Imaging >> >>> On Jul 1, 2019, at 11:13 AM, Greve, Douglas N.,Ph.D. >>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: >>> >>> Who did you create lh.test.nii? >>> >>> On 7/1/2019 1:47 PM, Nillo, Ryan Michael R wrote: >>>> Hi Bruce, >>>> >>>> We wanted to map values from a previous analysis to a representation of >>>> the brain with the sulci filled — something that resembles the output >>>> lh.pial-outer-smoothed from the recon-all -localGI. I tried using >>>> mri_surf2surf, but I get the error: >>>> >>>> ERROR: dimension inconsistency in source data >>>> Number of surface vertices = 163842 >>>> Number of value vertices = 73466 >>>> >>>> My command: mri_surf2surf --srcsubject fsaverage_1 --trgsubject fsaverage >>>> --sval ./lh.test.nii --tval lh.pial-outer-smoothed2white.nii --hemi lh >>>> >>>> fsaverage_1 is a copy of fsaverage that I ran recon-all -localGI on to get >>>> the pial-outer-smoothed surface. >>>> Ryan Michael Nillo >>>> Staff Research Associate I >>>> University of California San Francisco >>>> Department of Radiology and Biomedical Imaging >>>> >>>>> On Jul 1, 2019, at 10:27 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu >>>>> <mailto:fis...@nmr.mgh.harvard.edu>> wrote: >>>>> >>>>> Hi Ryan >>>>> >>>>> I'm not sure why you would have a surface with 73K vertices on fsaverage. >>>>> Why not use one of the ico representations (40K or 160K vertices)? In any >>>>> case, mri_surf2surf should do the trick, although you will probably need >>>>> to create a new subject with a set of 73K vertex surfaces >>>>> >>>>> cheers >>>>> Bruce >>>>> On Mon, 1 Jul 2019, Nillo, Ryan Michael R wrote: >>>>> >>>>>> Hello Freesurfer users/developers, >>>>>> I have surface with ~73,400 vertices generated from the Freesurfer >>>>>> version 6 >>>>>> fsaverage brain, left hemisphere. I have a surface map that was created >>>>>> by >>>>>> mapping a volume to the fsaverage white surface. Is there a way to map >>>>>> the >>>>>> surface map to the new surface with less vertices? Is there a way to map >>>>>> values from the 73,000 vertices-map to the standard fsaverage pal >>>>>> surface? >>>>>> Thanks in advance, >>>>>> Ryan Michael Nillo >>>>>> Staff Research Associate I >>>>>> University of California San Francisco >>>>>> Department of Radiology and Biomedical Imaging >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=iORugZls2LlYyCAZRB3XLg&r=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U&m=aI3KHyWjwZdI30RWj_f9dSUns7AMWcCrba9ZabJNI7w&s=Dl9keiwCh5CkYL34O0rnLQUOtm3qH01lSoG5FGod7Ow&e= >>>>> >>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=iORugZls2LlYyCAZRB3XLg&r=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U&m=aI3KHyWjwZdI30RWj_f9dSUns7AMWcCrba9ZabJNI7w&s=Dl9keiwCh5CkYL34O0rnLQUOtm3qH01lSoG5FGod7Ow&e=> >>>> >>>> >>>> External Email - Use Caution >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> MailScanner has detected a possible fraud attempt from >>>> "urldefense.proofpoint.com" claiming to be >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMGaQ&c=iORugZls2LlYyCAZRB3XLg&r=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U&m=KZafiDpWfd1AKhGg8N3guW90iGbHCnKbiayUEjeKvhg&s=EA1H4VuXjUSeBglZfSe-BxQKIubSYpJUk6ZYumGjoo8&e=> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=iORugZls2LlYyCAZRB3XLg&r=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U&m=KZafiDpWfd1AKhGg8N3guW90iGbHCnKbiayUEjeKvhg&s=EA1H4VuXjUSeBglZfSe-BxQKIubSYpJUk6ZYumGjoo8&e= >>> >>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=iORugZls2LlYyCAZRB3XLg&r=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U&m=KZafiDpWfd1AKhGg8N3guW90iGbHCnKbiayUEjeKvhg&s=EA1H4VuXjUSeBglZfSe-BxQKIubSYpJUk6ZYumGjoo8&e=> >> >> >> External Email - Use Caution >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMGaQ&c=iORugZls2LlYyCAZRB3XLg&r=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U&m=UJsdK96psr1iv5MMLwa_aB1gM2qmIaqI0bCFu-MlcmE&s=fOpFD-iBSUn1tsCdj_PQ2_HqcKHUpZ1ADhtto4eX428&e=> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=iORugZls2LlYyCAZRB3XLg&r=-dSNp2WfY7DySdV4_Sqc4m6hoXOmD3OskcWVyhGbe1U&m=UJsdK96psr1iv5MMLwa_aB1gM2qmIaqI0bCFu-MlcmE&s=fOpFD-iBSUn1tsCdj_PQ2_HqcKHUpZ1ADhtto4eX428&e=
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