Re: [HCP-Users] CIFTI tools in the Python

I worked on several higher-level tools as well at the recent NeuroHackWeek (based partly on Dr. Cottaar’s tools). I’m working with the NiBabel and NiWidgets groups to get some of these incorporated into future releases, but for now the provisional scripts are available at

Re: [HCP-Users] CIFTI tools in the Python

I worked on several higher-level tools as well at the recent NeuroHackWeek (based partly on Dr. Cottaar’s tools). I’m working with the NiBabel and NiWidgets groups to get some of these incorporated into future releases, but for now the provisional scripts are available at

Re: [HCP-Users] Subjects with less than 1200 time points

Scanner error is another possibility. Matt. From: "Elam, Jennifer" > Date: Thursday, October 12, 2017 at 2:47 PM To: Reinder Vos de Wael >, Matt Glasser

Re: [HCP-Users] Subjects with less than 1200 time points

Hi Reinder, We have not released notes on each case a scan was incomplete. Generally, scans were stopped early because the subject asked to end the scan due to comfort or anxiety issues. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University

Re: [HCP-Users] Subjects with less than 1200 time points

Hi, Is there any documentation of what the reason was for stopping the scan early in each case? If not, what were generally the reasons for stopping early? Reinder > On Oct 12, 2017, at 9:52 AM, Glasser, Matthew wrote: > > That just means that the scan did not complete

Re: [HCP-Users] CIFTI tools in the Python

I will note that CIFTI support is pre-release, so you'll need to install from GitHub. Releasing is taking some time... From: hcp-users-boun...@humanconnectome.org on behalf of Yaroslav Halchenko

Re: [HCP-Users] surf2surf

Hi Rogier, Do you have a spherical registration between the surfaces? You can use wb_command -metric-resample if you do. If you want to use FreeSurfer tools for this, probably better to ask on the FreeSurfer list, as I am not as familiar with their tools that overlap with Connectome

[HCP-Users] surf2surf

Hello, I’m trying to place the data from a results.func.gii associated with a particular surface (say, OLD.surf.gii, created from OLD_T1w.nii.gz) into the space of another surface (say, NEW.surf.gii, created from NEW_T1w.nii.gz). The surfaces do not necessarily have the number of vertices. Is

Re: [HCP-Users] Subjects with less than 1200 time points

That just means that the scan did not complete for some reason. You can use them so long as your code does not assume all subjects have 1200 time points. Peace, Matt. From: > on behalf of Ruby Kong

Re: [HCP-Users] CIFTI tools in the Python

http://nipy.org/nibabel/reference/nibabel.cifti2.html ? On October 12, 2017 12:18:32 AM EDT, Aaron Crank wrote: >Dear HCP experts, > > >I have a question about loading CIFTI files in the Python. Would you >please suggest if there are any well-established tools in the

[HCP-Users] Error to compute a MEG Wrkmem eravg difference contrast

Hi, I encountered an error when computing a contrast (difference between conditions) for subject 102816 (it worked fine, at least without error, for other subjects {'100307'} ;  {'104012'} ; {'105923'} and {'106521'} ; The error comes from a mismatch in buffer dimensions : ( cf attached

Re: [HCP-Users] CIFTI tools in the Python

I've written a higher-level library for the reading and writing of CIFTI files in python based on the lower-level I/O from nibabel. You can find it at https://github.com/MichielCottaar/cifti . However, if you are looking for a well-established tool you might want to stick with nibabel. Best

[HCP-Users] Subjects with less than 1200 time points

Dear HCP experts, We found several subjects with less than 1200 time points. May we know why this happens? Are these subjects problematic and should we exclude them or can they be used? Here are the subjects with less than 1200 time points: 119732 rfMRI_REST2_LR 119732 rfMRI_REST2_RL 119833