Is any method to extract white matter tract profile of a group of subjects and draw a curve?

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1

Hi,

I have tracked some white matter tracts in two groups of subjects, and I want to draw a curve graph of to show the diffusion properties (such as MD, FA) of each group with mean +/- SD. The x axis represents the position of the tract and the y axis represents the MD value.

Up to now, I have only found the way to show the curve of only graph by DIPY or AFQ. But how to do it for a group?

Thanks

2

Hi @Roger1219,

If you used AFQ you should also have a csv with tract profile values. You’ll need to aggregate them to a dataframe like this:

node   tract    sub    value
0     Left_AF sub-001  0.2 (or whatever the value was)
1     Left_AF sub-001  0.3 (or whatever the value was)
....
n     Left_AF sub-001  X
0     Left_AF sub-002  X
.... (REPEAT FOR ALL SUBS AND TRACTS)

Name that dataframe something like df_tract you can do

import seaborn as sns
tract_vals = df_tract.query("tract == 'Left_AF'") # or whatever tract you want
sns.lineplot(data=tract_vals, x="node", y="value", orient="y")

For documentation on this seaborn command, see seaborn.lineplot — seaborn 0.12.2 documentation

Best,
Steven

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3

You might also be interested to check out our AFQ Insight software that deals with group level data processes with pyAFQ. Here’s an example that includes some group level plots: Harmonize HBN data using ComBat — AFQ-Insight 0.3.4 documentation

Another option is the BUAN framework which includes group level comparisons: DIPY : Docs 1.5.0 - BUndle ANalytics (BUAN) framework

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4

Thanks for your reply, My tracts were generated by mrtrix3, so I don’t have the css file with the node information. Is there some functions to generate this file manually?

5

Hi @Roger1219,

Mrtrix3 doesn’t have a tract bundle segmentation algorithm as far as I know. In either case, if you have .tck files for your bundles, you can use tcksample (tcksample — MRtrix 3.0 documentation) or use DIPY to generate AFQ-like profiles (DIPY : Docs 1.7.0 - Extracting AFQ tract profiles from segmented bundles).

Best,
Steven

6

Thank you all.
I have solved this problem with the following method.

  1. extract the profile of each tract (.tck) generated from mrtrix3 before (thanks @Steven )
  2. instead of illustrating the single profile directly as examples in DIPY, I saved the profile into a data frame and used seaborn to show it in group level. (thanks @Steven again!)
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