[HCP-Users] FNIRT for HCP diffusion data

Hi all, I am trying to run probtrackx using HCP preprocessed diffusion data and MMP1.0 ROIs. To my understanding the corresponding T1w image of MMP1.0 ROIs is: HCP_PhaseTwo / Q1-Q6_RelatedParcellation210 / MNINonLinear / Q1-Q6_RelatedParcellation210_AverageT1w_restore.nii.gz Is this a right

Re: [HCP-Users] FoV phase for fMRI

We are interested in small structures of the midbrain and would therefore like to maximize our spatial resolution, at least go smaller than 2mm isotropic. Any suggestions? cheers seb From: Glasser, Matthew [glass...@wustl.edu] Sent: Monday, October 31, 2016

Re: [HCP-Users] surface label to 3D mask

There aren’t any surfaces specified either… Matt. From: Timothy Coalson > Date: Monday, October 31, 2016 at 5:29 PM To: Matt Glasser > Cc: "Burgess, Gregory" >,

Re: [HCP-Users] FreeSurferPipeline.sh with FreeSurfer dev version (-hires option)

We will need to update the pipelines to work with FreeSurfer 6.0 when it is released. Earlier versions of FreeSurfer did required the current approach to get highres surface placement. Your approach is probably fine if it is producing nice results for you. If you wish, you could send us the

Re: [HCP-Users] Extracting time series in grayordinates from any brain parcellation

The parcellation I mentioned below is CIFTI, so it will work without issue with CIFTI fMRI data. Peace, Matt. From: Timothy Coalson > Date: Monday, October 31, 2016 at 3:17 PM To: "PALLARES PICAZO, VICENTE"

Re: [HCP-Users] HCP to FreeSurfer Resampling

The instructions in part D of the pdf result in data that is already on the fsaverage standard mesh. If what you are trying to do with mris_preproc is just resample to fsaverage from subject native mesh, you can skip that step entirely. This step looks suspicious: wb_command

Re: [HCP-Users] Extracting time series in grayordinates from any brain parcellation

The CIFTI fMRI data does not contain subcortical information outside those defined ROIs. If you need to redefine them, you would need to get the data from the volume fMRI files, and the resulting cifti files would be challenging to compare/use with the released cifti data. You can incorporate

Re: [HCP-Users] FreeSurferPipeline.sh with FreeSurfer dev version (-hires option)

Hi, The current HCP structural pipeline was developed well before the forthcoming FS version that will have improved support/processing of “hires” structurals. In fact, parts of the HCP structural pipeline are there basically so that we could refine the positioning of the surfaces to take full

[HCP-Users] FreeSurferPipeline.sh with FreeSurfer dev version (-hires option)

Dear experts, I was wondering, why do you run in FreeSurferPipeline the recon-all with downsampled 1mm3 data? It is due to the fact that you do not want to rely on development version of FreeSurfer which only enables reconstruction of high resolution data (via -cm or -hires option)? Isn't it

[HCP-Users] FoV phase for fMRI

Hi, We are trying to run a fMRI sequence on our PRISMA similar to the one used in the HCP–lifespan but with 1.5mm isotropic voxels and a AP phase encoding direction. In the HCP sequence documents, it is mentioned that if we use AP phase encoding we should use a FoV phase of 100%. We seem to be

Re: [HCP-Users] Extracting time series in grayordinates from any brain parcellation

Ok, but is it possible then to use another NIFTI parcellation, for instance, a functional parcellation, with the CIFTI fMRI data? Or, since the subcortical regions are already defined in the CIFTI file, is not possible to re-define these ROI? Thank you again, Vicente On 29 October 2016 at

Re: [HCP-Users] Question about the multi-modal parcellation brain map (Glasser et al., 2016)

Hi David, Here you go: https://balsa.wustl.edu/study/show/RVVG Robert From: hcp-users-boun...@humanconnectome.org on behalf of David Hofmann Sent: 31 October 2016 10:23:51 To: Glasser, Matthew

Re: [HCP-Users] Question about the multi-modal parcellation brain map (Glasser et al., 2016)

Thank you Matthew, can you tell me, where can I download the map? Thanks David 2016-10-29 22:04 GMT+02:00 Glasser, Matthew : > Matlab can read CIFTI, see option B here: https://wiki.humanconnectome. > org/display/PublicData/HCP+Users+FAQ > > Peace, > > Matt. > > From: