Hi On 2 Sep 2014, at 10:28, David Hofmann <davidhofma...@gmail.com> wrote:
> > 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. apologies for the confusion - yes, these are the volumetric files. The grayordinate files are differently named - e.g. rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii Btw - there's no need to unzip these volumetric NIFTI files - at least for FSL usage. >> > 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? Doing that in matlab is fine, yes. I suspect that you can do it with the workbench tool, but I'm not so familiar with that. Workbench command line tool is more oriented towards CIFTI/grayordinate representations than volumetric. >> > 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. The volumetric datasets are already in 2mm MNI152 standard space, so (e.g.) atlases provided with FSL may be helpful depending on exactly what you're wanting to do. All subjects' volumetric datasets should be in the same space. Cheers. --------------------------------------------------------------------------- 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) st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve --------------------------------------------------------------------------- Stop the cultural destruction of Tibet _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
