help > RE: missing BATCH.Setup.preprocessing.sliceorder in conn_batch_humanconnectomeproject.m?
Dec 18, 2017  01:12 PM | Alfonso Nieto-Castanon - McGovern Institute for Brain Research. MIT
RE: missing BATCH.Setup.preprocessing.sliceorder in conn_batch_humanconnectomeproject.m?
Hi Walter,

That is a good point, but if I recall correctly the HCP dataset used a multiband sequence rather than the default interleaved-Siemens order and they do not recommend using slice timing correction in their data (mostly due to their very short TR). The data fetched by the conn_batch_humanconnectomeproject.m script into CONN is already preprocessed, and the only additional preprocessing steps performed by CONN are structural segmentation, ART outlier identification, and functional spatial smoothing (which explains why no additional information about slice-order is required by this script). 

Best
Alfonso
Originally posted by Walter Hugo Lopez Pinaya:
Hello,

Concerning the sample script "conn_batch_humanconnectomeproject.m", is it missing the line that defines slice order?

Based on the Human Connectome Project Sessions Protocol (https://humanconnectome.org/storage/app/... page 40), should the code have the following line?
batch.Setup.preprocessing.sliceorder = 'interleaved (Siemens)'

Cheers,
Walter
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RE: missing BATCH.Setup.preprocessing.sliceorder in conn_batch_humanconnectomeproject.m?
Dec 18, 2017