External Email - Use Caution
Dear Freesurfer team:
We are working with a medium-large dataset.
All brain scans have been processed on Freesurfer 7.1.0., but we are encountering problems in running LGI using Freesurfer 7.1.0. We are using MATLAB R2021b
The error appears after MATLAB opens. I have also attached the full recon-all.log with this email.
MATLAB is selecting SOFTWARE OPENGL rendering.
< M A T L A B (R) > Copyright 1984-2021 The MathWorks, Inc. R2021b (9.11.0.1769968) 64-bit (glnxa64) September 17, 2021
For online documentation, see https://secure-web.cisco.com/1ipCoc76p1Py8Q7ItL5tFg7Mt0w5AJQ7F0ZIrDYhkWgtW8i...https://secure-web.cisco.com/1hamuVtiQzQaht-XuuuYtXaEVPWbnPJU5lzNqy6FhpF5skK8imsVPhqbc0GwMwx3n-CR2MkedN5l7rpvuicuwpMJv8qncwjAt3ojo-emEqDkBp6DgIO4nao54HV7bP-4mW6yT4hcQopLvK8i8nE7BSb1VXHYiSmzLY7QgextcM-BYb23JGz0x6GRKFz9HenKtN0bBBB7UAzvJ02j3OuYtRw9HV1zcR9NV84cLWbGiXh22h-ggELFTBtRjoluhwBKUCSUol84JFivDwJgVjErbehEk8_1jZHiUCZlJcmKWKTFrNSqxxxs1AvrBqGoiQeykqFf6BEJmkvxP4NzP2Kgw-A/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__www.mathworks.com_support%26d%3DDwMFaQ%26c%3DWO-RGvefibhHBZq3fL85hQ%26r%3DKlJbht4h1i6aPJHMk7qSgoiYID4UiBhKWpU1g8jq1jGYs1J8DNn5OCC8GTgoNIpL%26m%3DZ3cbPyM90NScP1aXUWmTyMWngvh1BEnJ7EzcsBG9Mb8XMIMXNcIjDAo702op_TEs%26s%3DYjMs6iOer82IeTnes65E2IF1ZN6Yv9TP2_XtAfftr7c%26e%3D For product information, visit http://secure-web.cisco.com/1ePBoZGZpVu8T0goQaBhTg4I6kMEncKG4nh7KI0SVfRejodZ...https://secure-web.cisco.com/1EiZzOyqEnJ5UmkIiH6iTOXY79lMrJaqe68pgBge8gY7PmvCKSH2NLp5A9PCgkCf79gDz6avCcEhR0uIa5Rs7bWAGP_tIKl-qtUW0h-t4zVmrwcOQoXb1kXLDwEK9VUItmQNO5ap_85wJTmvhs0QFsKlWjz8oFNw08wBQ7XSjIEFlPy6k-O4KdBzftWUpqudgh_Thc_ye0A6Qt6tRy2kvmE3T9fDKHit2ReippQ9p4jLzIs1nGSXf_W6f1CWMg_PYQHAQmqwo8RW3r744Hpa8aGeV2QhZqGnSfzS2WL7_sBBNYaIk9Rn3RcyWlJwMtNtve6tLTowVbyxW0qUPXOsbcQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__www.mathworks.com%26d%3DDwMFaQ%26c%3DWO-RGvefibhHBZq3fL85hQ%26r%3DKlJbht4h1i6aPJHMk7qSgoiYID4UiBhKWpU1g8jq1jGYs1J8DNn5OCC8GTgoNIpL%26m%3DZ3cbPyM90NScP1aXUWmTyMWngvh1BEnJ7EzcsBG9Mb8XMIMXNcIjDAo702op_TEs%26s%3DBqkl6oe628-zn51ieRhS6rzh3UhOdWs-NhI2l97FCuM%26e%3D.
[ Warning: Argument must be a string scalar or character vector.]
[ > In ver (line 45) In freesurfer_read_surf (line 70) In find_corresponding_center_FSformat (line 26)] { Error using fprintf Function is not defined for 'struct' inputs.
Error in freesurfer_read_surf (line 70) fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); }
ERROR: find_corresponding_center_FSformat did not complete successfully!
Thank you for your time, best, Elisabetta
Elisabetta C. del Re, Ph.D.
Assistant Professor of Psychiatry,
Harvard Medical School
Associate Editor,
Journal of Clinical and Health Psychology
Schizophrenia Research
Department of Psychiatry Harvard Medical School
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Huang, Yujing YHUANG43@mgh.harvard.edu Sent: Tuesday, November 14, 2023 12:26 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [WARNING: ATTACHMENT UNSCANNED]mri_label2label with Gifti file
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/1Atc93M-NIQAK10cgWyzYj-89T-H87V-2ISLRNQ-9lqpgU3...https://secure-web.cisco.com/1RXX6PylPB-SVxxtglGkGdtjYOqYMWoG6G5hH1Nj6FmoO3uNhT0e9DWEkkCnAJFFWoVbpEfKTu0xXSLfJq8aKbN-W_3fDr3lrVTCrAqcEBgQJITHooCqTJhm8WHikJ3mFjMPa1K2ErIm88jktlFH87PJslRZFwRN8EpnSVTzLfrweuwZs4vjA33-46pQvXdnRYXDgHKL_wXfF4SZSg2cGXTZ1oKdCruCZ9vNGLuu7PwHQ426fNtxaI7KNkRFSRrqr6Qx4ZjnPkMRxCyuE0oMSIpT4deUAS7qSnpDaHGStNoUO8LfN0EICgKj4Xw4-aJH49LKEBPLKVDzazT6eCNchFQ/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__freesurfer.net_fswiki_mri-5Fsurf2surf%26d%3DDwMGaQ%26c%3DWO-RGvefibhHBZq3fL85hQ%26r%3DKlJbht4h1i6aPJHMk7qSgoiYID4UiBhKWpU1g8jq1jGYs1J8DNn5OCC8GTgoNIpL%26m%3DtHd6lzvKxAetwl50fBngNaLk2Xbhic469HgIcEax9n6EMnX_2dl5RvumT2v5XIpo%26s%3DAUtLJb08rbRJni36OHu9h95Lv2vbf2-yT1UT76v4JhQ%26e%3D.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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<https://secure-web.cisco.com/1UAafK_T1_LBix1W7E36d_IY5S14peeOklv59CJJKlgS5B4yLLp9N-kjqLnpXdCVIcetNfSBA7hx4hevVY-LiThALjXdR9Ya64r691UIiQXC8DAPaOPEQBOTCVaKka_wVGpEcifs_OP5QYybEBtltVd4DkuwcaGB99zNrQlxL0YfpIdwHDUioIreowxCb1GJEoWrrcscA1cMh5NzDhWjqlhwiXuepJQLKGNKiSmutoZOW_wbxIM8vd-fNIFb_BWtME_xLJyfT_WamasOQoL_ofpxQBKMCvcviCXQzrjKNbIIejkjLA8HnbdD_SDNkgsBRiTC-3M-opFiQDgi28cgS2Q/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__secure-2Dweb.cisco.com_10pJypOCaxCr0cVxOqUZEEwUWnA-2Da8JBJInZZrsmFvbBpZc5VeJKOP7gLhQ1SmX0dDXn-5FJrEuwDnXsXCgYbucJ6Zt55yeYSZaXS7RcQ-2DzmSplQhIanXs83UHpvi7aPZ47je5-5FXAgbMekrym-2D5sfhTz1Q7l7H3-2D5yWH9jnTYY8IOcMMxUK-5FUyTbIS8X1zsXA0dQHmVoAc1-5FwHJSoInnKzw7RSqIhMcqc78nv5SHDXgrYNh-5Fv-2DYDkmYaVWQBfdGsqZECbPP7RXwbKi1ebJSd1nEvw4gEd992keTTGgWegeDvHuM2IQnqR-2DkBkHRTG-5FIODfJ_http-253A-252F-252Fgifti.projects.nitrc.org-252Fgifti.dtd%26d%3DDwMGaQ%26c%3DWO-RGvefibhHBZq3fL85hQ%26r%3DKlJbht4h1i6aPJHMk7qSgoiYID4UiBhKWpU1g8jq1jGYs1J8DNn5OCC8GTgoNIpL%26m%3DtHd6lzvKxAetwl50fBngNaLk2Xbhic469HgIcEax9n6EMnX_2dl5RvumT2v5XIpo%26s%3DXVIOSJtnWHup0Nf0_C0KlpbKsVDlqnAtaUxuSZ4mYHU%26e%3D> http://secure-web.cisco.com/1C4Sh_pY9FSBfG0fwrA5x6-rc30bu4QrMQyWFwk4nzzqoGKi...https://secure-web.cisco.com/1UAafK_T1_LBix1W7E36d_IY5S14peeOklv59CJJKlgS5B4yLLp9N-kjqLnpXdCVIcetNfSBA7hx4hevVY-LiThALjXdR9Ya64r691UIiQXC8DAPaOPEQBOTCVaKka_wVGpEcifs_OP5QYybEBtltVd4DkuwcaGB99zNrQlxL0YfpIdwHDUioIreowxCb1GJEoWrrcscA1cMh5NzDhWjqlhwiXuepJQLKGNKiSmutoZOW_wbxIM8vd-fNIFb_BWtME_xLJyfT_WamasOQoL_ofpxQBKMCvcviCXQzrjKNbIIejkjLA8HnbdD_SDNkgsBRiTC-3M-opFiQDgi28cgS2Q/https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttp-3A__secure-2Dweb.cisco.com_10pJypOCaxCr0cVxOqUZEEwUWnA-2Da8JBJInZZrsmFvbBpZc5VeJKOP7gLhQ1SmX0dDXn-5FJrEuwDnXsXCgYbucJ6Zt55yeYSZaXS7RcQ-2DzmSplQhIanXs83UHpvi7aPZ47je5-5FXAgbMekrym-2D5sfhTz1Q7l7H3-2D5yWH9jnTYY8IOcMMxUK-5FUyTbIS8X1zsXA0dQHmVoAc1-5FwHJSoInnKzw7RSqIhMcqc78nv5SHDXgrYNh-5Fv-2DYDkmYaVWQBfdGsqZECbPP7RXwbKi1ebJSd1nEvw4gEd992keTTGgWegeDvHuM2IQnqR-2DkBkHRTG-5FIODfJ_http-253A-252F-252Fgifti.projects.nitrc.org-252Fgifti.dtd%26d%3DDwMGaQ%26c%3DWO-RGvefibhHBZq3fL85hQ%26r%3DKlJbht4h1i6aPJHMk7qSgoiYID4UiBhKWpU1g8jq1jGYs1J8DNn5OCC8GTgoNIpL%26m%3DtHd6lzvKxAetwl50fBngNaLk2Xbhic469HgIcEax9n6EMnX_2dl5RvumT2v5XIpo%26s%3DXVIOSJtnWHup0Nf0_C0KlpbKsVDlqnAtaUxuSZ4mYHU%26e%3D"> 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