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

Hi Ely - one additoinal point - if you are wanting to apply these pipelines to your own data, you may want to change the (very unaggressive, basically just detrending as you said) approach to highpass filtering (both in general and for use pre-FIX). I haven't seen many datasets where the "slow"

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

Hi Greg, Thank you very much for your detailed response! I have now generated a Movement_Regressors.mat file with the correct 24 parameters (6 rigid body, 6 derivatives, 6 rigid body squared, 6 derivatives squared). As I didn't have code handy to run highpass filtering on the movement regresso

Re: [HCP-Users] Custom parcellation for HCP data

Hi Tim, Thanks for your email. To clarify, when I said voxels on the medial wall, I was referring to voxels near the sagittal midline of the brain (i.e., I wasn't referring to voxels that have been labelled as medial wall). As such, these voxels have been labelled as part of a structure in the lef

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

Hi Michael, As you proposed, running a modified hcp_fix script that uses the HCP-supplied .fix list of bad components yielded results identical to the denoised data released by the HCP. I'm glad to have such a clear confirmation that my local implementation of ICA-FIX is working correctly! Full

Re: [HCP-Users] A question about twins' zygosity

Yes, that is the plan. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110

[HCP-Users] A question about twins' zygosity

Dear HCP experts, I have a question about twins' zygosity. I saw the HCP manual mentioned that the zygosity information in ConnectomeDB is self-reported. Will the genetic confirmed zygosity information be released sometime this year or later? Thank you. ___

Re: [HCP-Users] Custom parcellation for HCP data

Note that this command just makes the left hemisphere take precedence - you said the overlap was in medial wall, which is more of an artifact of processing than a structure of importance, so this should be fine. The surfaces shouldn't have any overlap on real structures, so ribbon constrained surf

Re: [HCP-Users] Custom parcellation for HCP data

Assuming that your label values don't have any overlap (each integer uniquely identifies not only the area but also the hemisphere), you can do the math part with wb_command -volume-math: wb_command -volume-math 'L + (L == 0) * R' ${Subject}.custom_raw.nii.gz -var L ${Subject}.L.custom.nii -var R

[HCP-Users] Custom parcellation for HCP data

Hi all, We want to use our own custom parcellation with the connectome project data. Ultimately the parcellation needs to be a NIFTI volume. We mapped our own custom parcellation from fsaverage (.annot file in FreeSurfer space) onto an HCP subject (GIFTI surface .label.gii file in ${Subject}/MNIN

Re: [HCP-Users] HCP question. Data not shelled

http://fsl.fmrib.ox.ac.uk/fsldownloads/patches/eddy-patch-fsl-5.0.9/ -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Eucli

Re: [HCP-Users] HCP question. Data not shelled

Hi Michael, Do we download it from FSL website? We searched but couldn't find it On Mon, Oct 3, 2016 at 6:22 PM, Harms, Michael wrote: > > I think you need the ‘eddy’ patch to get the --data_is_shelled option in > ‘eddy’ itself (or wait until the next FSL release). > > Then we need to modify the

[HCP-Users] Converting legacy data to CIFTI format

Hello, I would like to convert a legacy dataset into CIFTI format. The legacy dataset lacks T2-weighted images or field maps. How does the HCP advise that investigators go about converting legacy data into CIFTI format? I assume this must be possible, as we can use FreeSurfer to convert to flat

Re: [HCP-Users] HCP question. Data not shelled

I think you need the ‘eddy’ patch to get the --data_is_shelled option in ‘eddy’ itself (or wait until the next FSL release). Then we need to modify the HCP Pipelines to support passing in of the --data_is_shelled option in a convenient fashion. Tim Brown can comment, but I believe that will b

Re: [HCP-Users] Dicom for the 7T data

Hi Michael, Thank you so much for your reply. Because we want to know the 7T fMRI scanning protocols. Similar to your release reference manual for 3T , if you could provide us with some parameters like Sequence, TR, TE, flip angle, FOV, Matrix, Slice thickness, Multiband factor, Echo spacing,

Re: [HCP-Users] Dicom for the 7T data

Hi, We don’t release the original DICOMs because they contain potentially identifying information (e.g., scan date). Could you please clarify why you would need/want them? cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neur

[HCP-Users] Dicom for the 7T data

Dear HCP experts, I am downloading your newly released initial 7T dataset. When I look at the first few cases, it looks that you only release the nifti data? I am wondering if it is possible for me to download the corresponding original data in dicom format. Thanks and best regards, Xiao Da

Re: [HCP-Users] HCP question. Data not shelled

eddy_openmp nor eddy_cuda command from fsl5.0.9 doesn't have --data_is_shelled option. --data_is_shelled: Option doesn't exist! do we have to wait for the next Pipeline release? thanks, Sung >>> "Harms, Michael" 9/29/2016 10:38 AM >>> See the wiki page for ‘eddy’: http://fsl.fmrib.ox.ac.uk/f

Re: [HCP-Users] Segmentations

Not yet, though it is on the feature request list. Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Rachel Woodall mailto:rachel.wood...@york.ac.uk>> Date: Monday, October 3, 2016 at 10:02 AM To: "hcp-users@humanconnectome.org

[HCP-Users] Segmentations

Dear all, Do you know the best method for amending human brain segmentations following the processing stream? The pipeline has done a pretty good job however, there are areas which need adjustments, particularly in visual cortex. Any help would be appreciated. Many thanks, Rachel __