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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 YHUANG43@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-RTBvwM0DUZAxUvepcNhKgK5fSrxbQmFrHjvii...
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://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
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