Re: [HCP-Users] How to use TransformationMatrixVoxelIndicesIJKtoXYZ

As you said, the voxels in cifti files are stored by their integer indices as if they were in a volume file, so to get their location in space, you need a transformation matrix, similar to the nifti sform. This is exactly what the TransformationMatrixVoxelIndicesIJKtoXYZ element is. The simple

Re: [HCP-Users] create borders based on .dlabel files

The -label-to-border command requires gifti label files, as it does one surface at a time - there is not a cifti version of this command (because border files are surface only and single hemisphere, and there is no equivalent volume operation). So, first -cifti-separate to get gifti label files:

[HCP-Users] create borders based on .dlabel files

Dear HCP experts, I am trying to create borders based on HCP's .dlabel files. I am working on the FTB labels in the ICA PTN results. The reference surface I use is the R440 template, inflated surface. Here's the command I used: wb_command -label-to-border Q1-Q6_R440.L.inflated.32k_fs_LR.surf.gii

[HCP-Users] Demographic and behavioral subject data

Hello everyone, I want to pick a group of subjects from the 500 subjects +MEG2 for which I will perform (rsfMRI and dMRI) analysis. These should be young, healthy, subjects that have no abnormalities and cognitively able. Does anyone have any pointers about how I can go weeding out subjects?

Re: [HCP-Users] Demographic and behavioral subject data

All subject currently hosted in the WU-Minn HCP project on ConnectomDB were processed in a consistent manner using the "500 subject release" pipelines.  The release field refers to when they were originally released, and probably isn't of much use to you.  (Where it is relevant, is that if

Re: [HCP-Users] Demographic and behavioral subject data

Hi Joelle, All the HCP subjects are considered healthy young adults with no diagnosed cognitive abnormalities. They do, of course, have a range of abilities and scores on the behavioral tests we conduct. There is a lot of information in Chapter 1 of the current 500 Subjects Reference

Re: [HCP-Users] Demographic and behavioral subject data

Hi Michael and Jennifer, Thank you both for your help, much appreciated. One remaining question - is there currently any cutoff for cognitive scores (i.e. for the MMSE for ex) for subjects being included in the 500 release dataset? Can't find mention of it in the ref manual, so Im guessing

Re: [HCP-Users] Demographic and behavioral subject data

Hi Joelle, Here are the HCP Inclusion Criteria: Inclusion Criteria: No significant history of psychiatric disorder, substance abuse, neurological, or cardiovascular disease -No person report of diagnosis by a treating physician -No hospitalization No

Re: [HCP-Users] Demographic and behavioral subject data

One correction to the following: Again, as stated in the Ref Manual Introduction, one thing you should be aware of is that the fMRI data collected in Q1, Q2, and part of Q3 was reconstructed with a slightly different reconstruction algorithm than subsequent data. You can filter on Study

[HCP-Users] How to use TransformationMatrixVoxelIndicesIJKtoXYZ

Hi all, I have extracted the voxel to voxel connectivity correlation matrix from the 33 gb file HCP_S500_R468_MIGPd4500ROW.dconn.nii, which is a dense connectivity file. Using the wb_command - *nifti-information -print-xml* I also pulled out the xml header information within this file. And, I

Re: [HCP-Users] aliasing in diffusion images

Hi Michael Any idea on where my aliasing could be coming from? Here is a link to the data file in case it's useful to see. https://dl.dropboxusercontent.com/u/3889124/14-1-1dMRIseq1APcmrr.nii.gz thanks, Mark On Mon, Nov 23, 2015 at 9:23 PM, Mark A. Pinsk wrote: > Excite

Re: [HCP-Users] aliasing in diffusion images

Hi, The only potential "gotcha" that I see in your list of parameters is that your Excite/Refocus pulse durations seem too low, and may be resulting in clipping of your pulses.  (Those pulse durations would almost certainly max out the "MBExc 1H" and "MBRef 1H" voltages on the System:Tx/Rx

Re: [HCP-Users] create borders based on .dlabel files

When displaying them in the GUI, select the "border" input mode, select "edit" in the added toolbar, make sure "properties" is depressed, then click on a border, then you get a popup where you can edit border colors. Then, save the file from the GUI and it will have those colors. There is

Re: [HCP-Users] create borders based on .dlabel files

So I can either edit in wb_view or save a label file with the colors I want. Thanks! On Mon, Nov 30, 2015 at 4:59 PM, Timothy Coalson wrote: > When displaying them in the GUI, select the "border" input mode, select > "edit" in the added toolbar, make sure "properties" is

Re: [HCP-Users] Demographic and behavioral subject data

Hi Jennifer, Thanks a lot for your help, that's really useful. With regard to the reconstruction - I just wanted to clarify, and apologies if this is in the manual but I did not find it - When I filter by 'Study Completion' > 'Image Reconstruction' > 3T MR fMRI recon, I have 2 options - r177 and

Re: [HCP-Users] Demographic and behavioral subject data

Hi Joelle, The r227 is the newer, improved version. On the HCP Issues wiki : Image reconstruction algorithm versions Two versions of the image reconstruction algorithm applied to dMRI and fMRI data have been used in