general-discussion > moving between NIAK and freesurfer?
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Feb 17, 2015  07:02 PM | John Griffiths - Rotman Research Institute
moving between NIAK and freesurfer?
Dear NIAKers,

I would like to take some of the processed data from the ADHD200 dataset and do some further work with freesurfer. I am not an expert on niak, civet, or freesurfer, so apologize if I have missed anything blindingly obvious.

I believe the best way to do this is to run recon-all on individuals' T1 images after distortion correction (and any other 'early' preprocessing stages), and then move any (niak) standard space images of interest (fMRI time series, parcellations, etc.) into native space, and then back to (freesurfer) standard space again using the freesurfer registrations. A less convoluted alternative would seem to be to run recon-all on the niak standard space template, thereby obtaining a transform from niak standard space to freesurfer standard space. Perhaps there are some useful CIVET outputs/functions for achieving this? However, I will ultimately want access to the various freesurfer files for individual subjects, and I'm not sure if that would really be compatible with the latter option.

Could you please advise on the following:
  • Does you agree that the (first) above suggestion sounds like the best way to proceed with this?
  • What is the name of the native T1 image that should I should be running recon-all on? ('X...nuc_nativet1.nii.gz'?) At present I am looking at the preprocessed-connectome KKI samples, and have download the 'test', 'intermediate', 'anat', 'fmri', and 'rois' folders. Is the correct T1 image to use here in one of these folders?


Thanks very much,


john