ps - my email program "cleaned up" (!) a sentence missing here: The volumetric NIFTI files are: rfMRI_REST1_LR_hp2000_clean.nii.gz etc.
On 2 Sep 2014, at 07:10, Stephen Smith <[email protected]> wrote: > Hi > > On 1 Sep 2014, at 19:22, David Hofmann <[email protected]> wrote: > >> Hello HCP-team, >> >> after taking a look into the HCP related papers, I decided to download the >> FIX/pre-processed rfMRI-data for 1 subject (100307_3T_rfMRI_REST_fix). I >> want the "ready-to-analyze"-pre-processed data for the first session and >> assume the volumetric data is provided via the fix dataset and the following >> nifti-files (only first rfMRI-session): >> >> -rfMRI_REST1_LR_hp2000_clean.nii >> -rfMRI_REST1_RL_hp2000_clean.nii > > no - these are the "grayordinate" CIFTI files combining cortical vertices and > noncortical voxels. > rfMRI_REST1_LR_hp2000_clean.nii.gz > etc. > >> My aim is >> >> 1. to extract the timecourse from every (greymatter) voxel, i.e. creating a >> 4D-Matrix (x,y,z, Volume) >> >> 2. to extract data from ROIs created by HCP (parcellated connectome?) > > The HCP hasn't yet released a parcellation - but it is about to very soon. > It will also provide, along with the ICA-based parcellations, node-timeseries > (timeseries associated with the parcels), and estimated nodeXnode network > matrices (as part of the same release). > >> in short, I want to handle the data like a pre-processed nii-file ready to >> extract the voxel/ROI time course data. >> >> since I'm still a little uncertain about how to proceed and if I have the >> correct dataset the following questions arise: >> >> 1. Is it necessary to combine/concatenate LR and RL - data? If so, is there >> a way to combine them via the workbench? > > One way or another you will want to combine them, yes. In the upcoming > release the 4 runs for a subject are already concatenated inside the > node-timeseries files. > >> 2. Can I handle the nii-files like a "normal" nii-file for example in Matlab >> (e.g. read voxel time courses via spm) or are still some pre-processing >> steps necessary (I understand that only "non-agressive" filtering was >> applied)? > > There is no *need* to apply further processing to the CIFTI / NIFTI files. > The highpass already applied is quite unaggressive, and no lowpass has been > applied, so some people may apply further highpass or lowpass, and other > people may apply global signal removal, but personally I don't do any of > those further options. > >> 3. Are white matter and csf-signals already regressed out of the FIX data? > > Not explicitly - but the whitematter and CSF timecourses are used to help > classify ICA components inside FIX. In general ICA+FIX does a good job of > removing such components. > >> 4. Is there a mask-file for the localization of voxels? I only found a >> mask-file in the 100307_3T_rfMRI_REST1_preproc dataset in which there seems >> to be no correction of motion and physiologic artefacts(?) > > Not sure what you mean by a mask file... > >> 5. How to get the data for the parcellation in order to extract ROI means? > > Watch this space.... > >> 6. Is it possible to extract also the voxel time courses (4D Matrix) from >> subcortical regions? > > They are present in both forms of the data mentioned at the top of this > email, yes, > > Cheers, Steve. > > >> >> >> Thanks in advance for your time & keep up the good work! >> >> David >> >> >> >> >> -- >> David Hofmann (M.Sc.) >> Institute of Medical Psychology and Systems Neuroscience >> University of Muenster >> Von-Esmarch-Str. 52 >> D-48149 Muenster, Germany >> Phone: +49 (0) 251 - 83 52794 >> Mobile: +49 (0) 152 - 09822352 >> E-Mail: [email protected] >> >> http://campus.uni-muenster.de/medpsych.html >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [email protected] http://www.fmrib.ox.ac.uk/~steve > --------------------------------------------------------------------------- > > Stop the cultural destruction of Tibet > > > > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [email protected] http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
