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Dear all, I want to identify differential expressed genes (DEGs) between ROIs (for example, PFC versus the rest of brain) using limma R package, after parcellation through the `abagen.get_expression_data` function....

[https://github.com/rmarkello/abagen/blob/6f5542522247b9a7fb00ded198c34f4dc25957f3/abagen/samples_.py#L220C1-L224C46](url) Line 220-224 in samples_.py ``` annot = annotation.assign(hemisphere=hemisphere, structure=structure) \ .query('(hemisphere == "L" & mni_x < 0) ' '| (hemisphere == "R" & mni_x > 0) ' '| (hemisphere...

[FIX] Refactor design matrix and contrast formula for the two-sample T-test example

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Closes #4400 Changes proposed in this pull request: - Simplify the design matrix for paired and unpaired design from [1 -1] to [1 0]. - Fix the uncorrect design matrix...

Is there an error in the design matrix from the second level two sample test example?

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Hello, I'm trying to follow the tutorial to deal with two-sample t-test using nilearn, but I'm finding something a bit confused. In the code: https://github.com/nilearn/nilearn/blob/3559d80643bbc44f1408664447d552181bd7845d/examples/05_glm_second_level/plot_second_level_two_sample_test.py#L66-L78 and the document page: https://nilearn.github.io/dev/auto_examples/05_glm_second_level/plot_second_level_two_sample_test.html#sphx-glr-auto-examples-05-glm-second-level-plot-second-level-two-sample-test-py...

Hello @takuya-hayashi , In `FreeSurfer/scripts/RescaleVolumeAndSurface.sh` line 56-57, the `?h.sulc` files were simply copied to the 0.5mm subject when rescaling the 1mm surface to 0.5mm surface. Since the `?h.sulc` were calculated...

Question about the MATLAB style correlation function in genes.py

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https://github.com/alegiac95/Imaging-transcriptomics/blob/46adb1df85c37123c77226d023b6d763edae8aca/imaging_transcriptomics/genes.py#L116C1-L125C36 Hi, I am wondering if there is some thing wrong with the correlation here. ``` def correlate(c1, c2): """Return the MATLAB style correlation between two vectors.""" return np.corrcoef(np.hstack((c1, c2)),...

* **What is the current behavior?** When running the following code: `histology_profiles = read_histology_profile(template="fslr32k")`, the error will occur: ``` "File /opt/miniconda3/envs/imagingwork/lib/python3.8/site-packages/brainstat/context/histology.py:159, in read_histology_profile(data_dir, template, overwrite) [154](https://file+.vscode-resource.vscode-cdn.net/opt/miniconda3/envs/imagingwork/lib/python3.8/site-packages/brainstat/context/histology.py:154) download_histology_profiles( [155](https://file+.vscode-resource.vscode-cdn.net/opt/miniconda3/envs/imagingwork/lib/python3.8/site-packages/brainstat/context/histology.py:155) data_dir=data_dir, template=template,...