# Using mne\_annot2labels

**URL:** <https://mne.discourse.group/t/using-mne-annot2labels/92>\
**Category:** Mailing List Archive (read-only)\
**Tags:** list-archive\
**Created:** [February 18, 2009, 2:01am UTC](https://mne.discourse.group/t/using-mne-annot2labels/92 "2009-02-18T02:01:05Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [February 18, 2009, 2:01am UTC](https://mne.discourse.group/t/using-mne-annot2labels/92/1 "2009-02-18T02:01:05Z")

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Hi folks,

&nbsp;&nbsp;&nbsp;&nbsp;I am trying to convert freesurfer parcellation data into labels using  
mne\_annot2labels(Page 241 of Manual) command. The command ran, however  
the  
converted label files when opened in text editor showed a row of 4 zeros  
next to each vertex (meaning it did not look like a typical label file  
which has the 3 coordinates corresponding to the vertex). Any help on  
successful use of this command will be appreciated.

Our aim is to load these converted labels using mne\_analyze and also to  
compute the lead field matrices for each of these labels using  
mne\_forward\_solution script. My expectation was that converted labels  
using this command could be viewed in the same way as manually created  
labels (described in 7.13.4 of manual). Is this correct?

I ran the command from the directory labels which had the  
following files  
lh.aparc.a2005s.annot lh.test\_aparc.annot rh.aparc.annot  
lh.aparc.annot rh.aparc.a2005s.annot  
The command was used after correctly setting the SUBJECTS\_DIR and SUBJECT  
env variables was  
mne\_annot2labels --parc aparc

Here is what it returned

---

<div class="post-metadata">

**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [February 18, 2009, 2:13am UTC](https://mne.discourse.group/t/using-mne-annot2labels/92/2 "2009-02-18T02:13:24Z")

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Do not worry about the zeros, they are immaterial to MNE, only the  
vertex numbers (first column) count. It is normal that  
mne\_annot2labels writes these zeros.

Incidentally, the FreeSurfer parcellation most probably too coarse to  
be used as parcels of the source space.

- Matti