Preprocessing Legacy style fMRI data with HCP pipelines or ciftify&fMRIprep
Ziteng Han
Hi, Dr. Tim,
I would like to process our own legacy style fMRI data (without high-res T2w and fieldmaps ) using the tools which can map the individual cortical data to surfaces.
By searching through the replies you gave on HCP public discussion mail list, I got two ways to achieve this. One is to use the command line options of the HCP pipeline scripts that are already available for the case in which I don't have field map files and T2w files. In this case, the level of data quality can not be guaranteed and the Glasser et al. (2013) paper maybe can't be used in support of this workflow.
The other one is to use the ciftify toolbox and fMRIprep toolbox you have recommended several times which can output the legacy style data in cifti format either(Fig. 1).
So Which way do you think is better and which way would be more recommended?
Thank you so much for your time and help.
Best,
Glasser, Matthew
The lack of field maps is the main issue. It is not possible to get accurate cross-modal alignment between the EPI data and structural data without distortion correcting the EPI data. Many have tried to do this without field maps, but I still have yet to see a solution that is clearly better than doing nothing (i.e. moves things in the right direction without creating more issues. Overall, you should use a tool that uses BBR for rigid alignment as this does the best job overall, even in the context of EPI distortion correction. I don’t know if ciftify or fMRIPrep use BBR.
Matt.
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Sultan YILDIZ
We saw that the registration is so well. But I dont know about mapping to surface on ciftify processing.
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