search

ramp-kits / autism

Data Challenge on Autism Spectrum Disorder detection
https://paris-saclay-cds.github.io/autism_challenge/
67 stars 43 forks source link

Regarding preprocessing #46

Closed joc19008 closed 5 years ago

joc19008 commented 5 years ago

Hi,

I am working on the competition data after attended the challenge. May I ask a quick question regarding preprocessing? Do you mind specify what kind of preprocessing you did for rs-fMRI and T1 (especially for rs-fMRI)? For example, specific parameters for slice timing, realignment, registration, smoothing, frequency band, etc.

Looking forward to hearing from you. Thanks a lot!

Best, Jongwoo Choi

glemaitre commented 5 years ago

The script of the fMRI extraction is available there: https://github.com/ramp-kits/autism/blob/master/preprocessing/extract_time_series.py

You can refer to the nilearn documentation for the internal of the functions used.

joc19008 commented 5 years ago

Hi,

Thanks for the reply. We checked the code In extract_time_series.py, and found that input image is 'session_1/rest_1/rest_res2standard.nii.gz', which means you already preprocessed the data (normalized to MNI space). What kind of procedure did you include (e.g., slice timing, realignment, registration, smoothing) when you preprocess this data, i.e., how did you generate PATH_TO_RESTING_STATE = 'session_1/rest_1/rest_res2standard.nii.gz' ?

Best, Jongwoo Choi

glemaitre commented 5 years ago

You are right. We did not make the scripts available. We are going to do that soon. You can check the progress of #47.

glemaitre commented 5 years ago

The PR with the scripts have been merged.