Right, I can run recon-all for the structural run. But what about for a functional run where all I have is one nifti per subject? I meant for preprocessing etc. the functional things, if I manually create the hierarchy, is that one raw .nii per subject enough info to carry out the rest of the pipeline? Or do I need to find a way to dcmunpack the functional run, or something else?
Thanks, Steph
On Jun 2, 2018, at 8:04 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Stephanie
you shouldn't have to create the directory structure or anything. If you have nifti files you can give those to recon-all as input in the same way you would dicom (with -i <nifti volume file) and it will create the directories and do it's thing
cheers Bruce On Sat, 2 Jun 2018, DeCross, Stephanie N. wrote:
Hi,
I have scans from a Philips scanner I want to process with FreeSurfer. Previously, the scans have been downloaded in the Philips PAR/REC format and converted into niftis, and those niftis have been used as the raw inputs in other imaging pipelines.
Instead of dredging up the original dicoms and unpacking from scratch (I’ve been trying to but I’m running into a variety of problems), will the whole FreeSurfer pipeline work if I simply take the niftis I already have, manually create dirs specifying the FreeSurfer hierarchy of session/fsd/run, and stick the nifti inside the run dir? (I’ve already tried this and I’m running into problems during preprocessing, and I’m not sure if it’s because I need to unpack from scratch with dcmunpack, or if I have bugs in preprocessing.)
Thanks, Stephanie
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