[HCP-Users] Problem with wb_command -volume-parcel-resampling? dimension mismatch?

Hi HCPers I'm running into an error when running SubcorticalProcessing.sh in the fMRISurface pipeline. Specifically, when it tries to run: wb_command -volume-parcel-resampling fmri_timecourse.nii.gz ROIs/ROIs.voxres.nii.gz ROIs/Atlas_ROIs.voxres.nii.gz I get an error saying volume spacing

Re: [HCP-Users] Problem with wb_command -volume-parcel-resampling? dimension mismatch?

be happening. Tim C. might need you to upload that data somewhere so that he can debug. There isn’t any downside to using the generic command, but in your situation it should not be necessary. Peace, Matt. From: Keith Jamison kjami...@umn.edu Date: Thursday, April 23, 2015 at 3:21 PM

[HCP-Users] S900 group average high res?

Is there a 164k version of the S900 group average surfaces and spec file? I only see 32k on ConnectomeDB. Thanks! -Keith ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] 7T retinotopy task script

Hi Ely, We haven't distributed that code yet, but we probably should include that in the next 7T data release. The 7T tasks were written in matlab (psychtoolbox), not eprime, and it may take some work to get them into a distributable state. -Keith On Thu, Jul 21, 2016 at 5:28 PM, Ely,

Re: [HCP-Users] Reading gifti into matlab

Have you tried "which gifti" in matlab to see if some other gifti package is overriding yours? I have a few neuroimaging toolboxes (SPM, for example) that include their own gifti wrappers that don't seem compatible with HCP gifti. -Keith On Fri, Feb 10, 2017 at 1:31 PM, Lauren N

Re: [HCP-Users] unpacking 7T data

There are indeed identical redundant files in the different packages, for the reason you suggest. You can safely overwrite common files from one package with another, provided you are in the same root directory when you unzip. -Keith On Thu, Feb 16, 2017 at 3:32 PM, Ely, Benjamin

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

Steve, Have you found an obvious downside to a shorter HPF cutoff of, say, 200 seconds? Would the HCP FIX training data still apply or would the classifier need to be retrained? -Keith On Thu, Oct 6, 2016 at 12:43 PM, Xu, Junqian wrote: > > > On Oct 4, 2016, at 9:03 PM,

Re: [HCP-Users] gradient nonlinearity correction question

FYI, when available, you can enable it on the scanner in the "Resolution->Filter" tab with the "Distortion Correction" checkbox. It's often used for structural scans like MPRAGE, where you will see two DICOM folders in the output: and _ND. ND means "No Distortion [Correction]".. .A very

Re: [HCP-Users] 7T structural data

There are 1.6mm downsampled versions of the T1 and T2, which I believe are distributed with the 7T data. These are just for correspondence with the 7T functional data, which was 1.6mm isotropic. -Keith On Tue, Nov 22, 2016 at 4:40 PM, Timothy Coalson wrote: > When we say

Re: [HCP-Users] gradunwarp - "array index out of bounds" error in coef_file_parse routine

That is the correct fix for this problem. It has no side-effects. Some scanners (eg: Siemens 7T) have coefficients of even higher orders, so you can actually increase the siemens_cas to 100 or so to accommodate the full range. That value just determines the preallocation, and the matrix is

Re: [HCP-Users] 7T retinotopy MRI scanning sequence

The files that Jenn pointed to are the stimulus MASKS, which of course is the most important aspect of the retinotopy stimulus, but it is worth noting that the stimulus itself is not a standard checkerboard, but a rapidly changing collage of real-world objects, faces, etc. You can find more

Re: [HCP-Users] Behavioral performance data

I wasn't involved in these specific experiments, but I THINK the info you're looking for is in the TAB files: ${StudyFolder}/${SubjectID}/MNINonLinear/Results/tfMRI_{ TASK}_{RUN}/{TASK}_run*_TAB.txt There's a row for each event (along with rows for other things you'll have to ignore), and

[HCP-Users] removing cross-hairs, slice labels when using wb_command -show-scene?

I'm trying to save some images using wb_command -show-scene, and I can't figure out how to change settings for things like cross-hairs or slice labels. I know I can change these in the wb_view Preferences window in the Volume tab, but I'm hoping to script the whole process and get consistent

Re: [HCP-Users] removing cross-hairs, slice labels when using wb_command -show-scene?

m. On Mac, the name is > ~/Library/Preferences/edu.wustl.brainvis.Caret7.plist. > On our Ubuntu Linux, I found the preferences in ~/.config/ > brainvis.wustl.edu/Caret7.conf. > > John Harwell > > On May 2, 2017, at 8:58 AM, Keith Jamison <kjami...@umn.edu> wrote: > > I'm trying to save

Re: [HCP-Users] FIX error in fix_3_clean.m

Try changing line #381 in ReApplyFix/ReApplyFixPipeline.sh from: ML_PATHS="addpath('${FSL_MATLAB_PATH}'); addpath('${FSL_FIX_CIFTIRW}');" to ML_PATHS="restoredefaultpath; addpath('${FSL_MATLAB_PATH}'); addpath(' ${FSL_FIX_CIFTIRW}');" -Keith On Mon, Sep 11, 2017 at 5:54 PM, Sang-Young Kim

Re: [HCP-Users] FIX error in fix_3_clean.m

dify the script in order for working FIX? > > Thanks. > > Sang-Young > > > On Sep 11, 2017, at 6:28 PM, Keith Jamison <kjami...@umn.edu> wrote: > > Try changing line #381 in ReApplyFix/ReApplyFixPipeline.sh from: > > ML_PATHS="addpath('${FSL_MATLAB_P

Re: [HCP-Users] DWI in CCF Prisma protocol

gt; Newark, DE 19716 > > Office: 307 McKinly Laboratory > Lab:Suite 405 Wolf Hall > Phone:302.831.7078 > Email: j...@udel.edu<mailto:j...@udel.edu> > Website: http://sites.udel.edu/jmsp/ > > On Sep 27, 2017, at 3:37 PM, Keith Jamison <kjami...@um

Re: [HCP-Users] DWI in CCF Prisma protocol

We essentially split the ~197 direction in half, and the two halves can't have the exact same number of directions due to how they are stored on the scanner, so "part 1" is 98 directions and "part 2 is 99. each is then collected both AP and PA. FYI, each scan is actually 92 diffusion volumes

[HCP-Users] existing datasets for fmri+diffusion in children through young adults?

Hi HCP-ers, Does anybody know of any existing publicly available datasets with fMRI and diffusion that include ages, say, 8-25? There are the 27 subjects from the HCP Lifespan Pilot (12 of which are in this range), and I know there are a number of large studies currently in the acquisition stage

Re: [HCP-Users] Myelin Maps

wb_command -file-information -only-map-names So something like [~,result]=system('wb_command -file-information S1200.All.MyelinMap_BC_MSMAll.32k_fs_LR.dscalar.nii -only-map-names'); result=textscan(result,'%s'); subjects=regexprep(result{1},'_MyelinMap',''); -Keith On Fri, Oct 27, 2017 at

Re: [HCP-Users] Cleaning up intermediate files from the minimal pre-processing pipelines

This is not an official HCP answer, but I always delete the following after functional preprocessing: $subj/rfMRI_REST1_LR/MotionMatrices/MAT*.nii.gz $subj/rfMRI_REST1_LR/OneStepResampling/prevols/ $subj/rfMRI_REST1_LR/OneStepResampling/postvols/ MotionMatrices/*.nii.gz alone accounts for nearly

Re: [HCP-Users] Movie stimulus question

The movie lengths are: MOVIE1: 921 seconds MOVIE2: 918 seconds MOVIE3: 915 seconds MOVIE4: 901 seconds These are the entire movie scan stimulus, including "REST". Each subject's nifti/cifti data, as well as the other resources associated with it (WordNet, Motion Energy) matches these lengths as

[HCP-Users] HCP tractography pipeline?

Is there any movement on creating an "official" HCP tractography pipeline? The diffusion-tractography branch on github hasn't been touched in 4 years. Is there any updated thinking on what the final pipeline and options will look like? Thanks! -Keith

Re: [HCP-Users] gradient nonlinearity correction question

in the version of dcm2niix that I'm > using but I re-ran the conversion with "-x n" anyway. I also used > fslreorient2std as per your suggestion. Unfortunately, the result is still > the same. Do you have any other ideas? > > > Cheers, > > Kristian > > > Q

Re: [HCP-Users] gradient nonlinearity correction question

_AS097.grad > -n > > and > >gradient_unwarp.py T1.nii.gz T1_gdc.nii.gz siemens -g coeff_AS82.grad -n > > respectively. > > I would really appreciate any help or advice you can provide. > > Cheers, > > Kristian > > > Quoting Keith Jamison <kjami...@u

Re: [HCP-Users] Intensity Normalization 3_22

The command you ran locally is using the Jacobian as the bias field, which is incorrect, and the "-div Jacobian -mul Jacobian" is just cancelling out any effect (output has same bias as input fMRI). It should instead be "-div BiasField.2 -mul Jacobian_MNI.2". That said, your original output looks

Re: [HCP-Users] can't find age, sex, etc in megatrawl?

n M. Smith, Professor of Biomedical Engineering Head of Analysis, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford. OX3 9 DU, UK +44 (0) 1865 610470 st...@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve -- On 18 Oct 2018, at 15:04, Keith Jamison wrote: We ju

[HCP-Users] can't find age, sex, etc in megatrawl?

We just noticed that certain subject measures such as age and sex are not included in the megatrawl results. I see in the release documentation that these are among the covariates removed before regressing the other quantities. Are there also results/stats somewhere from regressing netmats against

[HCP-Users] some scans have _MSMAll_hp2000_clean.dtseries.nii but not MSMSulc cifti or _hp2000_clean.nii.gz ?

We recently noticed a couple of scans on s3://hcp-openaccess that are missing the cleaned MNI volumetric nifti and clean MSMSulc cifti, even though they have the uncleaned MNI nifti AND the cleaned MSMAll cifti. Two examples:

[HCP-Users] error when running -cifti-parcellate in RHEL but not macOS?

Whenever I try to run wb_command -cifti-parcellate on linux, it hangs for a few seconds and is then "killed": > wb_command -cifti-parcellate rfMRI_REST1_3.0mm_PA_Atlas_hp2000_clean.dtseries.nii MBtest.aparc+aseg.32k_fs_LR.dlabel.nii COLUMN

Re: [HCP-Users] error when running -cifti-parcellate in RHEL but not macOS?

? > > Tim > > > On Mon, Oct 1, 2018 at 6:59 PM, Keith Jamison wrote: > >> Whenever I try to run wb_command -cifti-parcellate on linux, it hangs for >> a few seconds and is then "killed": >> >> > wb_command -cifti-parcellate >> rfM

Re: [HCP-Users] error when running -cifti-parcellate in RHEL but not macOS?

On Mon, Oct 1, 2018 at 11:27 PM Keith Jamison wrote: > See attached output file. > > -Keith > > On Mon, Oct 1, 2018 at 8:18 PM Timothy Coalson wrote: > >> I'd probably need to see the dlabel file being used. -cifti-parcellate >> doesn't seem to have changed mu

Re: [HCP-Users] TOPUP Settings

Note: The --UnwarpDir in PreFreeSurfer is the readout direction of the T1w and T2w images themselves, which in this case is completely unrelated to the plane in which the SE fieldmaps read out (which is set in --SEUnwarpDir). fMRI and DWI are 2D and their unwarpdir are more obvious. For the 3D T1w

Re: [HCP-Users] A minor question regarding HCP 7T movie data

Hi Reza, Your interpretation of the timing is correct. The validation segment in each movie scan was shifted by 40-200ms for the "v2" version. This was done in order to make that final 83 second clip begin precisely at the start of the next TR for all 4 movie sessions. Given HRF variability,