surface = Surface.read_triangular('lh.white') has problem

[tanjia123456]

from freesurfer_surface import Surface surface = Surface.read_triangular('lh.white') with open('lhedges.txt', "w") as f: for triangle in surface.triangles: for edge_vertex_indices in triangle.adjacent_vertex_indices(): edge_vertices = surface.select_vertices(edge_vertex_indices) f.write("{} {}\n".format(edge_vertex_indices[0],edge_vertex_indices[1]))

Traceback (most recent call last):
File "D:/my_subject/2020.7.1-7.7/2016GCN/graph-to-spectral-coordinate/fsaverage5/test1.py", line 19, in
surface = Surface.read_triangular('lh.white')
File "D:\anaconda3.4\lib\site-packages\freesurfer_surface_init_.py", line 431, in read_triangular
surface.read_triangular(surface_file)
File "D:\anaconda3.4\lib\site-packages\freesurfer_surface_init.py", line 424, in _read_triangular
self.command_lines = list(self.read_cmdlines(stream))
File "D:\anaconda3.4\lib\site-packages\freesurfer_surface_init.py", line 381, in _read_cmdlines
assert tag == cls._TAG_CMDLINE # might be TAG_GROUP_AVG_SURFACE_AREA
AssertionError

Is there a problem with the library file?

[fphammerle]

Hi,

thanks for reporting!

Could you maybe share lh.white ?

[tanjia123456]

Hello, the lh.white was uploaded in: https://github.com/tanjia123456/Mindboggle_datasets

[tanjia123456]

hello, this bug can you solve? I am very confused about it.

[fphammerle]

sorry, I haven't found time to look into the bug yet.
I'll get back to you.
thanks for the upload!

[fphammerle]

Hi @tanjia123456,

I was able to read https://github.com/tanjia123456/Mindboggle_datasets/blob/e09c454d0a07d968bb8531d96f9a2dc8a5f4fe79/lh.white with freesurfer-stats (commit 26bdd6a):

In [1]: import freesurfer_surface

In [2]: surface = freesurfer_surface.Surface.read_triangular('lh.white')

In [3]: len(surface.vertices)
Out[3]: 130921

In [4]: surface.creator
Out[4]: b'arno'

In [5]: surface.creation_datetime
Out[5]: datetime.datetime(2012, 8, 17, 9, 39, 26)

In [6]: !sha256sum lh.white
62bfa01abd9669f2baafc81b2adb1a3d833d2df7f2dbdd91bb7f2981a0ece689  lh.white

What version of freesurfer-surface do you use?

[tanjia123456]

Hi @tanjia123456,

I was able to read https://github.com/tanjia123456/Mindboggle_datasets/blob/e09c454d0a07d968bb8531d96f9a2dc8a5f4fe79/lh.white with freesurfer-stats (commit 26bdd6a):

In [1]: import freesurfer_surface

In [2]: surface = freesurfer_surface.Surface.read_triangular('lh.white')

In [3]: len(surface.vertices)
Out[3]: 130921

In [4]: surface.creator
Out[4]: b'arno'

In [5]: surface.creation_datetime
Out[5]: datetime.datetime(2012, 8, 17, 9, 39, 26)

In [6]: !sha256sum lh.white
62bfa01abd9669f2baafc81b2adb1a3d833d2df7f2dbdd91bb7f2981a0ece689  lh.white

What version of freesurfer-surface do you use?

2.0.0

[tanjia123456]

Hello, I have met another question. when I use List Labels in Annotation File

from freesurfer_surface import Annotation

annotation = Annotation.read('**.annot')
for label in annotation.labels.values():
    print(label.index, label.hex_color_code, label.name)

the error is:

`D:\installAPP\Anaconda\python.exe D:/MySubject/My_article/Mindboggle/data_label_orig_after/orig/read_annot1.py
Traceback (most recent call last):
  File "D:/MySubject/My_article/Mindboggle/data_label_orig_after/orig/read_annot1.py", line 3, in <module>
    annotation = Annotation.read('subject1.annot')
  File "C:\Users\86177\AppData\Roaming\Python\Python36\site-packages\freesurfer_surface\__init__.py", line 349, in read
    annotation._read(annotation_file)
  File "C:\Users\86177\AppData\Roaming\Python\Python36\site-packages\freesurfer_surface\__init__.py", line 340, in _read
    for vertex_index, color_code in annotations
  File "C:\Users\86177\AppData\Roaming\Python\Python36\site-packages\freesurfer_surface\__init__.py", line 340, in <dictcomp>
    for vertex_index, color_code in annotations
KeyError: 1639705`

[tanjia123456]

[fphammerle]

Looks like either *.annot is corrupt (using color code that was not defined in its header) or freesurfer introduced a breaking change in the file format.

error occurs here:
https://github.com/fphammerle/freesurfer-surface/blob/v2.0.0/freesurfer_surface/__init__.py#L339

[tanjia123456]

Thanks, I found a project called nibabel that seems to achieve what I want.
https://github.com/nipy/nibabel

[fphammerle]

Ah great, I haven't heard of that project yet, thanks!