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Washington-University / HCPpipelines

Processing pipelines for the HCP
https://www.humanconnectome.org/
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Suggestion to actually change the TR in the fsf file #274

Open MoatazAssem opened 1 year ago

MoatazAssem commented 1 year ago

https://github.com/Washington-University/HCPpipelines/blob/0e220bc3e1ed1db40693377aa171d2d68c466911/TaskfMRIAnalysis/scripts/TaskfMRILevel1.sh#L279

Hi,

I was recently running an analysis for several task runs, each with a different TR. Because this line prints out the TR in the log message, I assumed it also automatically changes it in the fsf file (as is done in other steps like smoothing). However, clearly it doesn't change it. I suggest adding a line to ensure the actual TR extracted from the image file is the one used in the .fsf file.

Something like this should work: sed -i "s/fmri(tr) [0-9.]*/fmri(tr) ${TR_vol}/" ${FEATDir}/design.fsf

Thanks

Moataz

glasserm commented 1 year ago

Hi Moataz,

I thought we are already doing that, but clearly we are not. I would be happy to accept a tested pull request that does this.

Thanks,

Matt.