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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.mathworks.com/support
For product information, visit MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be www.mathworks.com.
 
>> [ 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://freesurfer.net/fswiki/mri_surf2surf.

 

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 beMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be  http://gifti.projects.nitrc.org/gifti.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