Re: [HCP-Users] Questions about parameters in CCF protocols

1. TI=1000 actually separates the CSF/Grey/White peaks of the the histogram more evenly than TI=900ms (CSF and Grey too close) or TI=1100 (Grey and White too close). I don’t understand why the FreeSurfer group has recommended TI=1100 as it wouldn’t seem to make things easier for their

[HCP-Users] Questions about parameters in CCF protocols

Dear HCP team, This is Meizhen Han at Center for MRI research in Peking University. I read CCF protocol carefully and have 2 questions in my mind. I would be very appreciate it if you could share some ideas with me. 1/ Why the TI in T1w was changed from 1060ms(LS in UMN/CMRR) to 1000ms(CCF)?

[HCP-Users] S1200 Group Average Data Release

News from the Human Connectome Project (HCP) August 1, 2017 We are pleased to announce the release of group-average structural and functional MRI data for the HCP S1200 young adult subjects. The dataset includes : * group average T1w, T2w, and T1w divided by T2w volumes * group average

Re: [HCP-Users] Reading Human Connectome Project (HCP) *.dtseries.* file in Python

I don't have a code snippet for you, but there is a separate "brain model" for each subcortical structure, which contains voxel indices. The "index map" that contains that brain model has the volume space information to turn them into coordinates in mm. Note that for the cortex, the CIFTI files

Re: [HCP-Users] Reading Human Connectome Project (HCP) *.dtseries.* file in Python

Hold on, you have gone past the point. CIFTI files *DO NOT CONTAIN* coordinates for surface vertices. Do not look for them in the header, they are not there. They are in gifti surface files (.surf.gii) that we provide alongside the cifti files. What Anand has done is use the fieldtrip matlab

Re: [HCP-Users] Reading Human Connectome Project (HCP) *.dtseries.* file in Python

Thank you Demian and Matt for your fast responses. I will try these suggestions. Thank you again! best, Anand From: Demian Wassermann Sent: Tuesday, August 1, 2017 12:08:26 PM To: Glasser, Matthew Cc: Anand A Joshi; Anand

Re: [HCP-Users] fslr32k or fsaverage parcellation as seeds for probtrackx2

The diffusion data are in the subjects native (T1w) space. You just need to use surfaces that are also in that space (e.g. the surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k). I would recommend using the white surface for counting and the pial surface for stopping. As for the

[HCP-Users] Problem with files for 668361 WM task

While working on a particular volumetric task analysis, we found that a number of files are missing from subject 668361 in the tfMRI_WM_RL folder. They are missing: Movement_*.txt files WM_run1_TAB.txt tfMRI_WM_RL.nii.gz and all of the files in the EVs folder. These are missing from both

Re: [HCP-Users] Reading Human Connectome Project (HCP) *.dtseries.* file in Python

Hi Anand, as one of the guys who helped with the *first* implementation of CIFTI in nibabel I can tell you that you need to navigate the header yourself. We went for a first implementation which can effectively parse the header and we are open for help in producing helper functions that will

Re: [HCP-Users] fslr32k or fsaverage parcellation as seeds for probtrackx2

You can use wb_command -cifti-separate to get GIFTI label files out and then use https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#Using_surfaces Peace, Matt. From: > on behalf of Max Bertolero

[HCP-Users] fslr32k or fsaverage parcellation as seeds for probtrackx2

If I want to use a fslr32k (or fsaverage) parcellation as seeds for probtrackx2, does anyone know how do this on the command line? For example, I would want to use this fslr32k parcellation:

[HCP-Users] fslr32k or fsaverage parcellation as seeds for probtrackx2

If I want to use a fslr32k (or fsaverage) parcellation as seeds for probtrackx2, does anyone know how do this on the command line? For example, I would want to use this fsLR32k parcellation:

Re: [HCP-Users] Reading Human Connectome Project (HCP) *.dtseries.* file in Python

I would ask the author of the nilearn/nibabbel tools as I don’t know anything about the Python implementation of CIFTI. Peace, Matt. On 8/1/17, 1:25 PM, "Anand A Joshi" wrote: >Thanks Matt for the reply. > >I figured out how to get it in Matlab (see below), but not in Python.

Re: [HCP-Users] Reading Human Connectome Project (HCP) *.dtseries.* file in Python

Thanks Matt for the reply. I figured out how to get it in Matlab (see below), but not in Python. I can read cifti image in python. f=image.load_img(filename) But how do I get coordinates of the subcortical structures. I code snippet would be appreciated. Thank you, Best, Anand

Re: [HCP-Users] Reading Human Connectome Project (HCP) *.dtseries.* file in Python

For the volume structures these are in the CIFTI header, however for the surfaces there are no veridical xyz coordinates, it all depends on the surface model you are using. In general we recommend only using 3D coordinates of individual subject¹s midthickness surfaces (or in special circumstances

[HCP-Users] Reading Human Connectome Project (HCP) *.dtseries.* file in Python

I am trying to read .dtseries. grayordinate files from the human connectome project. I am using nilearn.image which is based on nibabel. f=image.load_img(filename) Now I want .pos filed from this file. I can get it in Matlab using: v=ft_cifti_read(filename) v.pos But nibabel does not create