Hi Alfonso and everyone,
I am analysing rsfMRI data acquired interleaved and multiband (TR=1.5s (500 datapoints), MB factor=4) using 3T Siemens PRISMA scanner. I read around this forum and talked to colleagues was convinced to leave out slice timing correction. I scripted my preprocessing taking bits from the NYU and HCP scripts. Now, I suddenly have a second-guess moment and I want to check if: (1) leaving out the STC is okay in this case, and if (2) my batch processing syntax are entered correctly:
batch.Setup.nsubjects=NSUBJECTS;
batch.Setup.RT=1.5;
batch.Setup.preprocessing.art_thresholds(1:2)=[3 .5];
batch.Setup.preprocessing.steps={'functional_realign&unwarp','functional_center','functional_art','functional_segment&normalize_direct','structural_center','structural_segment&normalize','functional_smooth'};
batch.Setup.preprocessing.sliceorder='interleaved (Siemens)';
batch.Setup.preprocessing.fwhm=[8]; %defining the fwhm for later smoothing
batch.Setup.done=1;
batch.Setup.overwrite='Yes';
I am worried particularly about the sliceorder line, which was originally from the NYU script. I thought it wouldn't matter since I didn't apply STC. However am I right to assume this? As it stand, this preprocessing routine is identical to a "singleband" scan for the same TR. It occurs to me that the MB factor is implied if I enter both TR and the timepoints of each slice instead. Your help is greatly appreciated! Thanks in advance everyone.
BW,
Steve
I am analysing rsfMRI data acquired interleaved and multiband (TR=1.5s (500 datapoints), MB factor=4) using 3T Siemens PRISMA scanner. I read around this forum and talked to colleagues was convinced to leave out slice timing correction. I scripted my preprocessing taking bits from the NYU and HCP scripts. Now, I suddenly have a second-guess moment and I want to check if: (1) leaving out the STC is okay in this case, and if (2) my batch processing syntax are entered correctly:
batch.Setup.nsubjects=NSUBJECTS;
batch.Setup.RT=1.5;
batch.Setup.preprocessing.art_thresholds(1:2)=[3 .5];
batch.Setup.preprocessing.steps={'functional_realign&unwarp','functional_center','functional_art','functional_segment&normalize_direct','structural_center','structural_segment&normalize','functional_smooth'};
batch.Setup.preprocessing.sliceorder='interleaved (Siemens)';
batch.Setup.preprocessing.fwhm=[8]; %defining the fwhm for later smoothing
batch.Setup.done=1;
batch.Setup.overwrite='Yes';
I am worried particularly about the sliceorder line, which was originally from the NYU script. I thought it wouldn't matter since I didn't apply STC. However am I right to assume this? As it stand, this preprocessing routine is identical to a "singleband" scan for the same TR. It occurs to me that the MB factor is implied if I enter both TR and the timepoints of each slice instead. Your help is greatly appreciated! Thanks in advance everyone.
BW,
Steve