XCP-D processing generated Pearson coefficients but showed an error during generation of Connectivity plot for custom atlas

Software Support
1

Summary of what happened:

A custom atlas with 36 ROI regions was constructed using the in house segmentation technique. The XCP-D processing was carried with the aid of flag setting option –atlases to indicate the custom atlas utilization.

Command used (and if a helper script was used, a link to the helper script or the command generated):

apptainer run \
--cleanenv \
--bind /home/homesp/Projects \
--bind ${atlas} \
--bind ${DATA}:/data \
--bind ${APP_DERIV_DIR}:/outputs \
--bind ${WORK_DIR}:/work \
${APP} \
/data /outputs participant \
--participant-label ${Subject} \
--fs-license-file ${LIC}/license.txt \
-w /work \
--file-format nifti \
--mode linc \
--datasets thomascort8=${atlas}/thomascort8 \
--atlases THOMASCORT8

Version:

0.10.5

Environment (Docker, Singularity / Apptainer, custom installation):

Apptainer

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

One or more execution steps failed (4). Error details are attached below.

Node Name: xcp_d_0_10_wf.sub_188_wf.postprocess_3_wf.connectivity_wf.connectivity_plot

Node Name: xcp_d_0_10_wf.sub_188_wf.postprocess_1_wf.connectivity_wf.connectivity_plot

Node Name: xcp_d_0_10_wf.sub_188_wf.postprocess_0_wf.connectivity_wf.connectivity_plot

Node Name: xcp_d_0_10_wf.sub_188_wf.postprocess_2_wf.connectivity_wf.connectivity_plot

Traceback (most recent call last):

File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 66, in run_node

result["result"] = node.run(updatehash=updatehash)

File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run

result = self._run_interface(execute=True)

File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface

return self._run_command(execute)

File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command

raise NodeExecutionError(msg)

nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node connectivity_plot.

Traceback:

Traceback (most recent call last):

File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 401, in run

runtime = self._run_interface(runtime)

File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/interfaces/connectivity.py", line 479, in _run_interface

ax = self.plot_matrix(

File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/interfaces/connectivity.py", line 350, in plot_matrix

assert corr_mat.shape[0] == len(network_labels)

AssertionError

Screenshots / relevant information:

Parcellation Labels

image
image117×538 1.77 KB

Hi Tsalo,

Thank you.
We were able to generate the Connectivity plots after removing the background label.
But, we don't see the x-labels and y-labels in the plot.
I tried to upload the connectivity plots for reference, but .svg file was not supported here.
As such the x-labels and y-labels depict none.

Suhail
2

Hi @suhail and welcome to neurostars!

In the future please use the Software Support post category and post template. You can see I edited your post for you this time.

Please provide the full command with the full apptainer run preamble.

Also please provide the tree directory structure of your custom atlas folder.

It looks like your labels TSV file has a dimension mismatch with your parcellation size. Read more about external atlas requirements here: Running XCP-D — xcp_d 0.10.7.dev2+gd43d167 documentation

Best,
Steven

1 Like
3

Hi Steven,

Thank you for quick reply and editing in Software Support.
I was able to insert one image containing parcellations in the Software Support, whereas for new user it is not allowing to insert second image which is the tree structure.

Thank you

4

XCP-D’s parcellation and connectivity code will automatically drop that background label, but it looks like the ConnectPlot interface does not, so there’s a mismatch in the number of labels in the TSV (which includes “background”) with those in the correlation matrix (which does not). This is a bug in XCP-D, but an easy fix would be to drop the background row from your dseg TSV before running XCP-D.

1 Like