Hi Yujing

I figured it out – it turns out the R package shifts vertex indices by 1 by default, I was able to fix the problem by changing the option to stop the index adjustment because I was merging information from two recon-all outputs so the vertices matched and did not need adjustment. It all works well now !

Best

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Huang, Yujing <YHUANG43@mgh.harvard.edu>
Date: Wednesday, March 8, 2023 at 10:36
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] freesurfer could not parse freeview-loadable surface label

You don't often get email from yhuang43@mgh.harvard.edu. Learn why this is important

Hi Yigu,

I’m trying to understand how you obtained the label file with R package functions. What is your R command to generate the label file, and how did you view it in freeview?

Here is some information about the label file - MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles

Besides the first two lines in the file, it needs 5 columns on each row. The error message suggested your label file doesn’t follow the format on that line.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Yigu Zhou
Sent: Tuesday, March 7, 2023 1:22 PM
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] freesurfer could not parse freeview-loadable surface label

External Email - Use Caution

Hello Freesurfer community

I am trying to transform a label file obtained in subject native surface space to subject native volume space.

This label file was obtained through binarizing the subject lh.sulc morphological data through the function write.fs.label from R package freesurferformats, in the left hemisphere, resulting in a binary label for all sulci in the subject. Visual quality control of the label file through Freeview was adequate: I can load the surface label file with any surface of the subject.

Now, I would like to map the corresponding voxels that belong to sulci in the left hemisphere of this subject.

I tried to convert the label to volume using mri_label2vol first, but got the following error message

could not parse 48510th line '1e+05 -37.5524826049805 -5.55967617034912 18.56817436218261' in label file

I then tried to first convert the file to annot format using mris_label2annot and then convert to volume using mri_aseg2aparc. Similarly, mris_label2annot threw the error

could not parse 48510th line '1e+05 -37.5524826049805 -5.55967617034912 18.56817436218261' in label file

The list described similar errors but no obvious solution that I can access right now e.g. having a developer inspect the label file.

I would love to get any pointer as to why the label file may have been unparse-able to Freesurfer tools.

Sincerely

Yigu