On Tue, Sep 2, 2014 at 5:11 AM, Stephen Smith <[email protected]> wrote:
> Hi > > On 2 Sep 2014, at 10:28, David Hofmann <[email protected]> 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. Workbench will also read them without manual unzipping. > >> > 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. Actually, most operations you can do on cifti are also available to volume (and surface) - correlation is the main exception, as (numvoxels)^2 would make for an absurdly large file, and a lot of unneccesary computation (white matter, anything outside the brain). See this thread for a previous discussion of independently normalizing each brainordinate's timeseries using wb_command: http://www.mail-archive.com/[email protected]/msg00444.html -volume-reduce and -volume-math exist and behave similarly, but instead of the "-select 1 1 -repeat" parts in the -cifti-math command, you will need "-subvolume 1 -repeat" >> > 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) > [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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
