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 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

 

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