External Email - Use Caution Hi Yujing, thanks a lot for your reply. It worked perfectly. I used the following command:
mri_surf2surf --sd <dir> --srcsubject fsaverage --trgsubject CON01 --hemi lh --sval-annot input_atlas.gii --tval output_atlas.gii Maybe it would be good to give a hint about this e.g. in the tutorial about the "Anatomical ROI Analysis". Best regards, Peter On Tue, Nov 14, 2023 at 6:26 PM Huang, Yujing <yhuan...@mgh.harvard.edu> wrote: > Hi Peter, > > > > mri_label2label can only read MGH format label files. > > > > lh.JulichBrainAtlas_3.0.3.label.gii looks like an annotation file. I think > mri_surf2surf should be used instead > https://secure-web.cisco.com/1KlupFrku-RTBvwM0DUZAxUvepcNhKgK5fSrxbQmFrHjvii3fm6Uv0jJv91WUytYYprj3Sc_Ho9slSeeybHK3SmSbvO2AsX36OMopWtQPM-LhjGuIRi4_ZmPLOw6jQbjfBuyT_YkgbEdRXa3t48Bx9QQMus0aI7YkaWBh9efuzcWwY5zIuXRkmR197n1Sp06D0FgKK1hqWxVae6JqycAWTAn95Fwc5OWIoefp7eefyxQBdYlbLuA2VMyi_iJjxtf7jWfIXY6g5CFil7jyOU2VUoLjC43FZwXfG8njGZZGojNdgSDr6VYFKdL4lEq5_Dg7ipRKxXaz6D8KQZuJ1x_YRQ/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2Fmri_surf2surf > > > > Best, > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *P Pieperhoff > *Sent:* Tuesday, November 14, 2023 11:19 AM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]mri_label2label > with Gifti file > > > > * External Email - Use Caution * > > Hi FreeSurfer developers, > > I want to transform a label file in Gifti-format from the fsaverage space > into the native space of a subject (CON01a). > The FreeSurfer reconstruction pipeline was completely executed before for > this subject. > The label file lh.JulichBrainAtlas_3.0.3.label.gii is in freeview > correctly visualized on the surface of fsaverage. > > But when I call mri_label2label as below, it seems that the Gifti-format > is not recognized: > > mri_label2label --srcsubject fsaverage --srclabel > ../atlas/lh.JulichBrainAtlas_3.0.3.label.gii > --trgsubject CON01a --trglabel > CON01a/label/lh.JulichBrainAtlas_3.0.3.label.gii > --hemi lh --trgsurf white --regmethod surface > > > > *Output:* > > srclabel = ../atlas/lh.JulichBrainAtlas_3.0.3.label.gii > srcsubject = fsaverage > trgsubject = CON01a > trglabel = CON01a/label/lh.JulichBrainAtlas_3.0.3.label.gii > regmethod = surface > > srchemi = lh > trghemi = lh > trgsurface = white > srcsurfreg = sphere.reg > trgsurfreg = sphere.reg > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > Loading source label. > > <!DOCTYPE GIFTI SYSTEM "*MailScanner has detected a possible fraud > attempt from "secure-web.cisco.com" claiming to be* > http://secure-web.cisco.com/1bh5BILxlXO2-2u_rICDwh_PxQJMa3W_GIDLy9626BeX4BmkcASMPREIERA56dvB2CFwo-RdVIQ1899denf9hWyHKS2L-Ny59rCnPZ1zGYCCjNGcQMKI9cligpYZB7SUr1g10g95mOVXKMjGKiz_lbzzVxls0CoyvsEZt-j7Syr69mjOiYJtuvDqICsqmKkR_icuggj0wA096conjiWI1g_C5WLZUPxUeeFnmwzl3r7AU0OnFOPc91_L__xiJHLo0oBTu8q9n_3rgZjIK4PK3uLBnV-oKG_AhDxvqeQ5PTJjc6yiwHncHdgtmZNAxEKZgn3cqLEN2UVpA_MOBDQexeA/http%3A%2F%2Fgifti.projects.nitrc.org%2Fgifti.dtd > <http://secure-web.cisco.com/10pJypOCaxCr0cVxOqUZEEwUWnA-a8JBJInZZrsmFvbBpZc5VeJKOP7gLhQ1SmX0dDXn_JrEuwDnXsXCgYbucJ6Zt55yeYSZaXS7RcQ-zmSplQhIanXs83UHpvi7aPZ47je5_XAgbMekrym-5sfhTz1Q7l7H3-5yWH9jnTYY8IOcMMxUK_UyTbIS8X1zsXA0dQHmVoAc1_wHJSoInnKzw7RSqIhMcqc78nv5SHDXgrYNh_v-YDkmYaVWQBfdGsqZECbPP7RXwbKi1ebJSd1nEvw4gEd992keTTGgWegeDvHuM2IQnqR-kBkHRTG_IODfJ/http%3A%2F%2Fgifti.projects.nitrc.org%2Fgifti.dtd>"> > > error: mri_label2label: could not scan # of lines from label file > > > > The Gifti-file contains a LabelTable (including a RGB-color for each > label), and a DataArray of Labels (for each vertex), but not the vertex > coordinates. > > Please, could you tell me how I can transform this file into the native > space of each subject? > I have attached the compressed label file to this mail. > > Best regards, > Peter > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1ffWEhog-0nw-gd8FQTw3_r7bTJMx-QmCTLwGAvEn26vGHlZZQaSAYeV0AeOWjslq_o9rO-vzLb59HzIpG09SU4HE-2QyftftErC4jGzRAWgmY5kCwNePec456baPjvV8RqLfJcmLj_WKIz2ESXjHG4ymfZsFiZrrxeP_HkvbFZ6cNIv4kgLox6y8KeEbaGNR2wxrRrv30hQVMl1eSdLaEPVenNe3J6cVQqHBU_U4iWmxH-h3OK7Jvvd1a2s-eHtL05SBQi7umUrYb9hKH8-3xC2iWXr7SOWfo2f01ier0qU1SasNyy1FyZhaayUYiuIzWu56N_w7F_VFIPjoNBtYpA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > 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 Mass General > Brigham Compliance HelpLine at > https://secure-web.cisco.com/1U6Da9K785PAmsYpqkis7FtZt6aQUrBWyS_9sLqkFKoUszLbAKZjCYCPzqStu8vS-8BIlurURN0d0IjyVo8TG11QKCIY3-EIrr8O2a3us35vIM0_QUuYhN7qnDN2V-_KY1To6-4ypxiOxUY2ImwR70OEwJP1P0klRrDDiZde0M4uW7BmXA_mxUYu5hw6QLD_8ychC-YTg2IBSoRtoSg-FxxVQhmAxixzmYM8JF56dLU_d7wlO1Z9yHo3q3EwlmUYspbM4f5C9kKr4AZ-HchyXFIRonZ968qcw7UoO-KEh7UGfWjeUdLbV3sTdCjoOkydEg82Xx_ObaISQFW8xtNJ48w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > < > https://secure-web.cisco.com/1U6Da9K785PAmsYpqkis7FtZt6aQUrBWyS_9sLqkFKoUszLbAKZjCYCPzqStu8vS-8BIlurURN0d0IjyVo8TG11QKCIY3-EIrr8O2a3us35vIM0_QUuYhN7qnDN2V-_KY1To6-4ypxiOxUY2ImwR70OEwJP1P0klRrDDiZde0M4uW7BmXA_mxUYu5hw6QLD_8ychC-YTg2IBSoRtoSg-FxxVQhmAxixzmYM8JF56dLU_d7wlO1Z9yHo3q3EwlmUYspbM4f5C9kKr4AZ-HchyXFIRonZ968qcw7UoO-KEh7UGfWjeUdLbV3sTdCjoOkydEg82Xx_ObaISQFW8xtNJ48w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > . >
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