Re: [HCP-Users] OneStepResample fails b/c of missing BiasField image

Line 69 of ${GitRepo}/PostFreeSurfer/scripts/CreateMyelinMaps.sh should produce ${StudyFolder}/${Subject}/MNINonLinear/BiasField.nii.gz. Matt. From: "Stevens, Michael" > Date: Thursday, March 23, 2017 at 6:10 PM To: Matt

Re: [HCP-Users] OneStepResample fails b/c of missing BiasField image

Hi Matt, Sure. Contents of ${StudyFolder}/${Subject}/T1w: ACPCAlignment analysis aparc.a2009s+aseg_1mm.nii.gz aparc.a2009s+aseg.nii.gz aparc+aseg_1mm.nii.gz aparc+aseg.nii.gz BiasField_acpc_dc.nii.gz BiasFieldCorrection_sqrtT1wXT1w BrainExtraction_FNIRTbased brainmask_fs_1mm.nii.gz

Re: [HCP-Users] Contents of processed dtseries files

Ah, I see. Thank you both for the swift and thorough answer to my question! Kelli > On Mar 23, 2017, at 4:06 PM, Timothy Coalson wrote: > > The -cifti-convert command is intended as a hack to squeeze cifti data into > formats that aren't designed for it, don't read too much

Re: [HCP-Users] OneStepResample fails b/c of missing BiasField image

Hi Michael, That indeed sounds like a bug, though I’m a bit puzzled as to how it occurs. Can you post the contents of ${StudyFolder}/${Subject}/T1w and ${StudyFolder}/${Subject}/MNINonLinear? ${StudyFolder}/${Subject}/MNINonLinear/BiasField.nii.gz should be produced by PreFreeSurfer and

Re: [HCP-Users] Contents of processed dtseries files

The -cifti-convert command is intended as a hack to squeeze cifti data into formats that aren't designed for it, don't read too much significance into the details. The first and second dimensions in this nifti file (which I have referred to as "fake" nifti, because it isn't a sane volume file,

Re: [HCP-Users] Contents of processed dtseries files

You can use our CIFTI Matlab tools to read the matrix into matlab (2B on this website): https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ It will be 91282 Grayordinates X 1200 time points. For more information on the CIFTI file format and Grayordinates, please see this

[HCP-Users] Contents of processed dtseries files

Hello, I am wanting to work with the S1200 fix-denoised resting-state data in MATLAB. I am able to get the data into matlab, but have not been able to figure out exactly what the rfMRI_REST1_RL_Atlas_MSMAll_hp2000_clean.dtseries.nii file, for example, contains. When I dump the data into nifti

Re: [HCP-Users] cifti to 'real' nifti

Take a look at wb_command -cifti-separate . It will provide the subcortical NIFTI volume (in MNI coordinates I believe), and the two cortical hemispheres as GIFTI surfaces. I think it goes something like: wb_command -cifti-separate Y_Atlas.dtseries.nii COLUMN -volume-all

Re: [HCP-Users] cifti to 'real' nifti

Hi, My software is based on MINC-tools and it expects the voxels in 'real' space; an error is returned that the dimensions aren't structured as expected. I have a sub-cortical surface and wish to extract signals from that surface, hence I'd like to bring the cifti voxels back to their original

Re: [HCP-Users] cifti to 'real' nifti

When we called this a “fake” NIFTI, that was a misnomer. It is a real NIFTI file. The issue is that the voxels are not ordered in space as you would expect from a real brain. So, your software should work with it, as long as you’re not trying to do processing along a spatial dimension (e.g.,

[HCP-Users] cifti to 'real' nifti

Hi, I would like to extract the rfMRI signal from a subcortical brain volume and correlate this signal to cortical signals. Preferably I'd use the cifti voxels for this, but the software I'm using isn't compatible with cifti or the 'fake' nifti produced by wb_command -cifti-convert. So I was

[HCP-Users] OneStepResample fails b/c of missing BiasField image

Hi folks, I've run into a small problem with HCP script-based processing of non-HCP data that I think is just something that' not yet come up for y'all (i.e., there probably hasn't yet been a need to program into the processing scripts). As context -- I have fMRI data from a few projects that