External Email - Use Caution I'm a Philips user as well. Creating a hierarchical directory tree is sufficient enough, but for one thing. Nifti files do not carry the information normally stored in DICOM header, and FS-Fast requires the f.nii to have embeded info about the repetition time. So you have to manually use mri_convert on each file to update the TR. Apart from that - the fMRI pipline works fine (at least on Achieva TX data).
Best regards, Patrycja 2018-06-03 1:28 GMT+02:00 DeCross, Stephanie N. <sdecr...@mgh.harvard.edu>: > 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 <fis...@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 > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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