Thanks for the quick answer! See my replies inline:
2014-09-02 8:10 GMT+02:00 Stephen Smith <[email protected]>: > 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. > I'm sorry, I made a mistake with the names of the dataset. I used the fix extended dataset (*100307_3T_rfMRI_REST1_fixextended*). So, just to be sure, the nifti-files are in: - ...fixextended\MNINonLinear\Results\rfMRI_REST1_RL\rfMRI_REST1_RL_hp2000_clean.nii.gz - ...fixextended\MNINonLinear\Results\rfMRI_REST1_LR\rfMRI_REST1_LR_hp2000_clean.nii.gz After unzipping the above files: -rfMRI_REST1_RL_hp2000_clean.nii -rfMRI_REST1_LR_hp2000_clean.nii I assume this have to be the correct NIFTI-files for the first session. > > > 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). > Ok, I will wait :). > > > 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. > Until then, I understand I have to normalize (demean) and then combine the LR,RL-files and this can be done for example with Matlab by extracting the voxel time courses and concatenating them. Is this the correct way or is there an easier way by using the workbench tool? > > > 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. > That's great, so I can just extract the voxel time course data from the rfMRI_REST1_RL_hp2000_clean.nii files. > > > 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... > For example like the file: *brainmask_fs.2.nii.gz* provided in the preproc-dataset in order to localize the cortical and subcortical voxel coordinates. I can't find such a file provied in the fix extended dataset. > > 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 again! > > > > > > > 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
