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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