Re: [HCP-Users] contrast in human connectome 3T structural MRI

Hi Jamila, These variable bright arteries in the T1w MPRAGE images are probably due to the time-of-flight (TOF) effects of those “fresh" arterial blood flowing into the brain after the inverse pulse. http://mriquestions.com/time-of-flight-effects.html Regards Gordon > On Mar 5, 2018, at

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

Tim, Just FYI (may not be the cause of this particular case) for completeness of your documentation, this old ticket is still open (after 6 years) for guest OS in VirtualBox. https://www.virtualbox.org/ticket/10085 Gordon On Jun 29, 2017, at 11:29 AM, Timothy B. Brown

Re: [HCP-Users] Question about unprocessed fMRI data

Hi Ben, Yes, the CMRR multiband sequence incorporates "dynamic off-resonance in k-space” (DORK)” method as in Pfeuffer et al., MRM 2002, which has already been implemented in the Siemens product EPI sequence ICE recon. Gordon > On Jun 8, 2017, at 12:05 PM, Benjamin Risk

Re: [HCP-Users] MELODIC denoising vs. released ICA-FIX datasets

> On Oct 4, 2016, at 9:03 PM, Ely, Benjamin wrote: > > Thanks Steve, that's good to keep in mind. Our acquisition is a single > "HCP-like" 15 minute run at MB6, 2.1mm isotropic resolution, TR=1s, AP phase > encoding, 32-channel head coil on a 3T Skyra; hopefully that

Re: [HCP-Users] MELODIC denoising vs. released ICA-FIX datasets

> On Oct 4, 2016, at 9:03 PM, Ely, Benjamin wrote: > > Thanks Steve, that's good to keep in mind. Our acquisition is a single > "HCP-like" 15 minute run at MB6, 2.1mm isotropic resolution, TR=1s, AP phase > encoding, 32-channel head coil on a 3T Skyra; hopefully that

Re: [HCP-Users] fat suppression and diffusion scans

Siemens strong fat suppression” = fat sat pulse + gradient reversal On Jul 9, 2015, at 2:37 PM, Mark A. Pinsk mpi...@gmail.com wrote: Hi Michael Thanks for that information, very helpful. I forgot to mention that we haven't requested the HCP sequences at this point since we have the

Re: [HCP-Users] Myelin mapping with FLAIR

You can take a look at the UK Biobank project FLAIR protocol first and start your site-specific piloting from there. http://users.fmrib.ox.ac.uk/~steve/BiobankPiloting/ On Jun 18, 2015, at 10:56 AM, Michael Dwyer mgdw...@bnac.netmailto:mgdw...@bnac.net wrote: Dear HCP experts, First, I would

Re: [HCP-Users] rsfMRI at 7 Tesla

Matt, Please keep in mind Marta is using a 24ch coil, instead of a 32ch coil at 7T. I would recommend keeping 1.6 mm and evaluate IPAT2+MB3 or IPAT2+MB4 with the 24ch coil. Gordon On Mar 24, 2015, at 11:07 AM, Glasser, Matthew glass...@wusm.wustl.edumailto:glass...@wusm.wustl.edu wrote: I

Re: [HCP-Users] error when processing more than 2 tasks with GenericfMRIVolume script

Tim, A patch here to use array instead of space delimited string might be helpful for error detection: e.g. Tasklist=(domino0 domino1 domino2 domino3) PhaseEncodinglist=(y y- y y-) nTasklist=${#Tasklist[@]} nPhaseEncodinglist=${#PhaseEncodinglist[@]} if [ $nTasklist -ne $nPhaseEncodinglist

Re: [HCP-Users] error when processing more than 2 tasks with GenericfMRIVolume script

, 3:03 PM, Xu, Junqian junqian...@mssm.edu wrote: Tim, A patch here to use array instead of space delimited string might be helpful for error detection: e.g. Tasklist=(domino0 domino1 domino2 domino3) PhaseEncodinglist=(y y- y y-) nTasklist=${#Tasklist[@]} nPhaseEncodinglist

Re: [HCP-Users] T1UnwarpDir

- Structural - re-shim - wrong Fieldmap, to evaluate. Gordon Peace, Matt. On 10/24/14, 10:33 PM, Xu, Junqian junqian...@mssm.edumailto:junqian...@mssm.edu wrote: As for importance, it depends on your application but readout distortion is typically quite small. Btw, weąve observed

Re: [HCP-Users] T1UnwarpDir

'Unwarp Dir’ should correspond to the Readout (frequency encoding) direction for the ‘PreFreeSurferPipeline', in which case is the Z direction (Head - Foot) for the sagittal T1w/T2w HCP structural acquisitions. Not sure what you mean by The only comment is that z appears best.” Below is what’s

Re: [HCP-Users] T1UnwarpDir

-shimming. In such cases, I think it is better to disable the readout distortion correction in the PreFreeSurferPipeline. Gordon On Oct 24, 2014, at 11:18 PM, Xu, Junqian junqian...@mssm.edu wrote: 'Unwarp Dir’ should correspond to the Readout (frequency encoding) direction

Re: [HCP-Users] Diffusion data b values

Ariel, We recommend people to use these calculated b-values (including cross-terms) instead of the input b-values. This was explained explicitly at page 137, 2nd paragraph in http://www.ncbi.nlm.nih.gov/pubmed/23702418 Small b value variations due to the cross-terms between diffusion and