cortex.quickshow IndexError

[mingxue1204]

I'm trying to plot a flatmap and can't get past quickshow. I've processed a subject's data with freesurfer and goyt the transform files and the surfaces, then put them in the subject file below the database. After that I'm trying to start a quickshow to see the map but encounter the following error:

Traceback (most recent call last):  File "/run/user/1003/gvfs/smb-hare:server=172.22.124.104,share=mingxue/Project/code/make_mapper.py", line 23, in <module>
    cortex.quickshow(voxel_vol)

  File "/home/mingxue/.local/lib/python3.8/site-packages/cortex/quickflat/view.py", line 142, in make_figure
    data_im, extents = composite.add_data(ax, dataview, pixelwise=pixelwise, thick=thick, sampler=sampler,
  File "/home/mingxue/.local/lib/python3.8/site-packages/cortex/quickflat/composite.py", line 162, in add_data
    im, extents = make_flatmap_image(dataview, recache=recache, pixelwise=pixelwise, sampler=sampler,
  File "/home/mingxue/.local/lib/python3.8/site-packages/cortex/quickflat/utils.py", line 44, in make_flatmap_image
    mask, extents = get_flatmask(braindata.subject, height=height, recache=recache)
  File "/home/mingxue/.local/lib/python3.8/site-packages/cortex/quickflat/utils.py", line 137, in get_flatmask
    mask, extents = _make_flatmask(subject, height=height)
  File "/home/mingxue/.local/lib/python3.8/site-packages/cortex/quickflat/utils.py", line 362, in _make_flatmask
    left, right = polyutils.trace_poly(polyutils.boundary_edges(polys))
  File "/home/mingxue/.local/lib/python3.8/site-packages/cortex/polyutils/misc.py", line 136, in trace_poly
    hemisphere_0, hemisphere_1 = components[order[-1]], components[order[-2]]
IndexError: index -1 is out of bounds for axis 0 with size 0

Can anyone help me with this? Thanks a lot~~~

[mvdoc]

Hi @mingxue1204, have you manually flattened the surfaces and imported them with cortex.freesurfer.import_subj? cortex.quickshow requires flattened surfaces. If you don't have flattened surfaces, you can use the webgl viewer with cortex.webgl.show, but you'll need to have access to a physical display.

You can check this tutorial by @tknapen's lab on how to do the cutting and flattening.

[mingxue1204]

Thank you for your kindly reply~ I'll have a try! ^_^

[mingxue1204]

Hi @mingxue1204, have you manually flattened the surfaces and imported them with cortex.freesurfer.import_subj? cortex.quickshow requires flattened surfaces. If you don't have flattened surfaces, you can use the webgl viewer with cortex.webgl.show, but you'll need to have access to a physical display.

You can check this tutorial by @tknapen's lab on how to do the cutting and flattening.

Sorry to bother again. I encounter an error when I'm trying to import a subject by using the command' cortex.freesurfer.import_subj("subj01")', the error is as follows:

----> 1 cortex.freesurfer.import_subj("subj01")

File ~/.local/lib/python3.8/site-packages/cortex/freesurfer.py:206, in import_subj(fs_subject, cx_subject, freesurfer_subject_dir, whitematter_surf)
    204         pts, polys, _ = get_surf(fs_subject, hemi, fsname, freesurfer_subject_dir=freesurfer_subject_dir)
    205         fname = str(surfs.format(subj=cx_subject, name=name, hemi=hemi))
--> 206         formats.write_gii(fname, pts=pts + surfmove, polys=polys)
    208 for curv, info in dict(sulc="sulcaldepth", thickness="thickness", curv="curvature").items():
    209     lh, rh = [parse_curv(curvs.format(hemi=hemi, name=curv)) for hemi in ['lh', 'rh']]

File ~/.local/lib/python3.8/site-packages/cortex/formats.pyx:193, in cortex.formats.write_gii()

File ~/.local/lib/python3.8/site-packages/nibabel/deprecator.py:181, in Deprecator.__call__.<locals>.deprecator.<locals>.deprecated_func(*args, **kwargs)
    178 @functools.wraps(func)
    179 def deprecated_func(*args, **kwargs):
    180     if until and self.is_bad_version(until):
--> 181         raise error_class(message)
    182     warnings.warn(message, warn_class, stacklevel=2)
    183     return func(*args, **kwargs)

ExpiredDeprecationError: from_array method is deprecated. Please use GiftiDataArray constructor instead.

* deprecated from version: 2.1
* Raises <class 'nibabel.deprecator.ExpiredDeprecationError'> as of version: 4.0

what should I do next to fix this? thank you so much for your great patience~

[mvdoc]

Oh, thanks for sharing that. We need to fix our code to adapt to Nibabel's new version. In the meanwhile, you could downgrade nibabel to < 4.0 (python -m pip install "nibabel<4")

[mingxue1204]

Oh, thanks for sharing that. We need to fix our code to adapt to Nibabel's new version. In the meanwhile, you could downgrade nibabel to < 4.0 (python -m pip install "nibabel<4")

Thank you so much for your reply! That problem has been solved by downgrading the nibabel ^_^.

However, I seem to have another problem ... Sorry to bother again...
I've used the tksurfer to cut the surface and got the file named like 'lh.full.patch.3d'. Then I tried to flatten the surface by using the command 'mris_flatten lh.full.patch.3d lh.full.flat.patch.3d'. Then followed by the command 'mris_convert lh.full.flat.patch.3d flat_lh.gii' to get the gifti file.
After that I put the file into the surfaces file under subject's database and use the following code to check my experimental results:

import cortex
import cortex.polyutils
import numpy as np
import matplotlib.pyplot as plt
from voxelwise_tutorials.viz import plot_flatmap_from_mapper

subject = "subj01"
xfm = 'fullhead'

voxel_vol = cortex.Volume(array_scores, subject, xfm)  #'array_scores' stands for the volumn data
mapper = cortex.get_mapper(subject, xfm, 'line_nearest', recache=True)
vertex_map = mapper(voxel_vol)
cortex.quickshow(vertex_map)
plt.show()

The results is really weird! It only shows the part that I tend to remove during the surface cutting process. Is there anything wrong with my operation? Thank you so much for your great patience!