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/1ipCoc76p1Py8Q7ItL5tFg7Mt0w5AJQ7F0ZIrDYhkWgtW8is9qw_a5tqW4UCqZSaQ-tteYOPi5jDM30nE3pnA6_9yY0XToBBGW1Sg7nWHevGpUvi9A4_mGZn27a6-pWVm9Di8bnV_v48QaPCQiVgE_p57HmEdzEVUVCd2yh20eWrmVL4IiQwBlYG3kW8emQlZcyXx6-AVbX3jwmZym-GHgGvTjCizqypNqTSIlUezGBExK89U0gI8otHaGwN1Y0rS16h_uItiAG29HaIbHaJA61cUhYWf6XvlbG1eUrcezYDnsYJmgzyCeIRT0I_XQGnkKZvTo59JrCi-6_egr-kxvA/https%3A%2F%2Fwww.mathworks.com%2Fsupport<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/1ePBoZGZpVu8T0goQaBhTg4I6kMEncKG4nh7KI0SVfRejodZsTKdav1NcBnDA5Ih7nVNcUvfG3tS57OG7APMy6__f1FYRDgDQII_KCw85sjbG1IeyYCloTvsesojg2-jX1uPvHSHeeRD1_0rB7FrRRVFNrwi3f2l7wewTmYKHtR4OkBB97oUawsZZi8qOneMU6vTgVVNzuCmrBp65TFcH-elHfps4q9BPNbx5cXkVgeYWFcDx2-0GXClcLJonC7Hq1VBJLBcCxjAN2UsOadSw7xRTz7WCjcFnHTjViLgHh_2bL_Dp13eotoeNERhHP30bsd1WPY7ZZQTqSnO4VwzEyg/http%3A%2F%2Fwww.mathworks.com<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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@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-9lqpgU3wZ3CKpKkpmxKauCoUHs79JC7iiFYA5lqiAXvEgka0JZaJZfH3lLJqzsVZU5MO98Nj1pBD7zeUFsRoyrKd5EYWFW3Pa-r-MMGIp0ueicZS-nWjrNt5AQBAqAZtXHLMrnSCfs1RcIRsgdgiKLU-aAJ_h08MxztCXuUOj8zx-45fKIhwaa38jYaNBoq2LQPuLbJvkTAefMZZRpNnnEQFPr9WB9ByMgHn-TWLup4lFr0B7UxJoryfwO3zSQOuF7hRkHJV4aHZybSSZ_wyiA1sdOk11hwvztol8iMGzauOL0g/https%3A%2F%2Ffreesurfer.net%2Ffswiki%2Fmri_surf2surf<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-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<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-rc30bu4QrMQyWFwk4nzzqoGKiuPIkWkpWkCAmQjGwdRHVIe5aOkTr9vQNtWnBQwQURLFFdeDg12y8ZdB3731gZmd8VGxroFdmtx7zeYYNm7sDw8pqzCBCJNtcT2lllVJvLqJYZMf5z5AODhyHkLSEgJNmgbgJKIlbqu31px2ZDrgp6IbkGeuzaJm8iCMlAO7rn-WpA19kg7EX_CJuRiNA__STM11bYNMmT4u_vy2HqTa4Dczir_a9iDf-_3eU-fDJnFzOCBw6dY4DEeKuHMnWwbHO5V2skr5lrT8dVpXEWT0X27Gz6_OiFvXpN-lzAzQ/http%3A%2F%2Fgifti.projects.nitrc.org%2Fgifti.dtd<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
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