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                                            YC H

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

> Had not noticed this. > > Agree that adding `-1` in the design matrix can be confusing. > > With just `1` and `0` I remember that for 2...

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

> but for second level, SPM does not add intercept automatically, no? > > https://www.fil.ion.ucl.ac.uk/spm/docs/tutorials/fmri/group/two_sample_ttest/#viewing-the-results Yes, SPM does not add intercept when calculating two-sample t-test. As I remember, SPM uses...

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

> No, you cannot add an intercept because it would make the design matrix rank deficient. Indeed the intercept is the sum of all subjects indicators. SPM somehow handles rank-deficient...

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

> Would it clarify things if the example encoded the conditions in 2 different columns and we modified the contrast computation accordingly? > > vertical horizontal > 1 0 >...

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

> Thanks for your contribution, @YCHuang0610! Just a couple final things before we merge this. > > Since this is your first contribution to nilearn could you please: > >...

In FreeSurferPipelineNHP.sh "Image Exception : #63 :: No image files match: global/templates/MacaqueYerkes19/wmskeleton.nii.gz"

[https://github.com/Washington-University/NHPPipelines/pull/3/files](url) According to the pull requeset: `Structural pipelines updates #3` update in 2020 by Takuya Hayahsi, the wmskeleton.nii.gz was from the ./global/templates/MacaqueRIKEN21 directory. The template folder composition was different in...