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HCP-Users

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Welcome to the HCP-Users Google group, which is the primary forum for discussions of topics relevant to the Human Connectome Project (HCP) and Connectome Coordination Facility (CCF). Topics covered include the HCP-Young Adult (HCP-YA) original dataset of 1200 healthy adults ages 22-35, the Lifespan HCP projects (HCP-Development, ages 5-21, and HCP-Aging, ages 35-100+), the Connectomes Related to Human Disease projects (CRHD, see humanconnectome.org), all processing and analysis methods/pipelines developed by HCP including the HCP Pipelines, HCP-Style MRI acquisition, T1w/T2w myelin mapping, sICA+FIX, temporal ICA, MSM surface registration, CIFTI and grayordinates, the fs_LR standard surface space, the HCP’s multi-modal parcellation, Connectome Workbench visualization and analysis software (wb_view and wb_command), and the Brain Analysis Library of Spatial maps and Atlases (BALSA) database (balsa.wustl.edu).

The QuNex container is best discussed at https://forum.qunex.yale.edu/. FreeSurfer and FSL non-HCP specific topics are best discussed on those mailing lists (https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport , https://fsl.fmrib.ox.ac.uk/fsl/docs/#/support). The PALM software is best discussed on the FSL mailing list.

Post here or by sending messages to hcp-users@humanconnectome.org

0 selected

Johanne, Glasser, Matthew2

12:23 PM

Drawing neighboring surface ROIs, getting overlapping areas

I would zero out overlapping vertices and then use surface dilation to fill in the gaps

unread,

Drawing neighboring surface ROIs, getting overlapping areas

I would zero out overlapping vertices and then use surface dilation to fill in the gaps

12:23 PM

Evgenii Shvedovskii, Elam, Jennifer2

Sep 25

Inquiry about SSAGA (Section F: Cannabis) variables in HCP-Y restricted data

Hi Evgenii, You and your PI need to (in this order) register for an account on BALSA, sign the HCP-YA

unread,

Inquiry about SSAGA (Section F: Cannabis) variables in HCP-Y restricted data

Hi Evgenii, You and your PI need to (in this order) register for an account on BALSA, sign the HCP-YA

Sep 25

Otero Ospina, Andrea

Sep 25

Postdoctoral Associate Position in Human Neuroimaging

Department of Psychiatry and Behavioral Sciences Postdoctoral Associate Position in Human

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Postdoctoral Associate Position in Human Neuroimaging

Department of Psychiatry and Behavioral Sciences Postdoctoral Associate Position in Human

Sep 25

yi yang, … Tim Coalson3

Sep 24

Efficient download & decompression of HCP rfMRI datasets

Most zip utilities have a way to specify extraction of only a subset of files, which may save a bit

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Efficient download & decompression of HCP rfMRI datasets

Most zip utilities have a way to specify extraction of only a subset of files, which may save a bit

Sep 24

Katherine Farber, Harms, Michael2

Sep 24

BALSA Structural Preprocessed Extended

Yes, those are available. Make sure that you've set the toggles appropriately to see ALL

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BALSA Structural Preprocessed Extended

Yes, those are available. Make sure that you've set the toggles appropriately to see ALL

Sep 24

Yiwen Xiao, Glasser, Matthew2

Sep 24

Any experience extracting cortical thickness from HCP annot (fsaverage) in FreeSurfer 7.4.1?

I would ask this on the FreeSurfer list. We can tell you how to do this with Connectome Workbench

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Any experience extracting cortical thickness from HCP annot (fsaverage) in FreeSurfer 7.4.1?

I would ask this on the FreeSurfer list. We can tell you how to do this with Connectome Workbench

Sep 24

Matthieu Vanhoutte, … Ignacio Martin8

Sep 24

fMRIVolume pipeline: steps after minimal preprocessing

Hi, Just to make things clear, the file you refer: The recommended file to use is ${StudyFolder}/${

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fMRIVolume pipeline: steps after minimal preprocessing

Hi, Just to make things clear, the file you refer: The recommended file to use is ${StudyFolder}/${

Sep 24

Kandace Kimball, Elam, Jennifer3

Sep 23

BALSA restricted data access

Hi Jenn, Yes I was recently granted access! I see my issue was missing the "Export CSV"

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BALSA restricted data access

Hi Jenn, Yes I was recently granted access! I see my issue was missing the "Export CSV"

Sep 23

Matthieu Vanhoutte, … Elam, Jennifer7

Sep 23

AWS S3 "hcp-openaccess/HCP"

Hi Aly, We are planning to add the AWS keys functionality to BALSA soon, but not immediately. Please

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AWS S3 "hcp-openaccess/HCP"

Hi Aly, We are planning to add the AWS keys functionality to BALSA soon, but not immediately. Please

Sep 23

Aly Kotb, … Tim Coalson22

Sep 22

Paper: Learning Cortical Parcellations Using Graph Neural Networks

Averaging over ROIs removes a lot of random noise, so a dense map for each parcel should probably be

unread,

Paper: Learning Cortical Parcellations Using Graph Neural Networks

Averaging over ROIs removes a lot of random noise, so a dense map for each parcel should probably be

Sep 22

jean-simon fortin, Glasser, Matthew2

Sep 19

Questions about using rfMRI_REST1_AP_hp0_clean.nii.gz for (f)ALFF analysis

I would use the new data we have just released on ConnectomeDB powered by BALSA. If you need the

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Questions about using rfMRI_REST1_AP_hp0_clean.nii.gz for (f)ALFF analysis

I would use the new data we have just released on ConnectomeDB powered by BALSA. If you need the

Sep 19

Việt Lương Hoàng, … Glasser, Matthew7

Sep 18

Conversion from NIFTI (.nii.gz) to CIFTI (dtseries.nii)

Using the HCP Pipelines in QuNex is your best bet then. If you want advice on that, post the specs of

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Conversion from NIFTI (.nii.gz) to CIFTI (dtseries.nii)

Using the HCP Pipelines in QuNex is your best bet then. If you want advice on that, post the specs of

Sep 18

Namrata Tamang, … Glasser, Matthew5

Sep 17

resampling of subcortical ROI

You would need to do that in something like matlab or python. Matt. From: Namrata Tamang <

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resampling of subcortical ROI

You would need to do that in something like matlab or python. Matt. From: Namrata Tamang <

Sep 17

Yael Coldham, … Jure Demsar47

Sep 17

dMRI preprocessing

Glad we solved it! Best, Jure From: Annchen Knodt <akn...@gmail.com> Sent: 17 September 2025 15

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dMRI preprocessing

Glad we solved it! Best, Jure From: Annchen Knodt <akn...@gmail.com> Sent: 17 September 2025 15

Sep 17

Sage Andrus Bergerson, Tim Coalson2

Sep 12

CLI download for HCP-YA data

Not at the moment, sorry. Network mounting your target filesystem (hopefully from the same building,

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CLI download for HCP-YA data

Not at the moment, sorry. Network mounting your target filesystem (hopefully from the same building,

Sep 12

Joern Alexander Quent, Elam, Jennifer3

Sep 11

How to download HcpPipelinesExampleDataGDC.zip?

Hey Jenn, My apologies I was under the impression that just installing the plug-in also works. After

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How to download HcpPipelinesExampleDataGDC.zip?

Hey Jenn, My apologies I was under the impression that just installing the plug-in also works. After

Sep 11

Armin Allahverdy, Glasser, Matthew2

Sep 11

Adapting FreeSurfer (HCP pipeline) for pediatric subjects with ventriculomegaly

There is a FreeSurfer recon-all -bigventricles flag (use --extra-reconall-arg when calling the HCP

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Adapting FreeSurfer (HCP pipeline) for pediatric subjects with ventriculomegaly

There is a FreeSurfer recon-all -bigventricles flag (use --extra-reconall-arg when calling the HCP

Sep 11

Sepideh Kilani, Elam, Jennifer2

Sep 11

Questions about MEG Working Memory Task - Finger Assignment and Stimulus IDs

Hi Sepideh, In the description on pp. 72-73 the S1200 Reference manual indicates that for the working

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Questions about MEG Working Memory Task - Finger Assignment and Stimulus IDs

Hi Sepideh, In the description on pp. 72-73 the S1200 Reference manual indicates that for the working

Sep 11

Shawn D'Souza, … Ezequiel Mikulan8

Sep 11

Connectome workbench download on linux ubuntu 24.04 This application failed to start because it could not find or load the Qt platform plugin "xcb" in "".

Thanks, the output pointed to this error "/lib/x86_64-linux-gnu/libfontconfig.so.1: undefined

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Connectome workbench download on linux ubuntu 24.04 This application failed to start because it could not find or load the Qt platform plugin "xcb" in "".

Thanks, the output pointed to this error "/lib/x86_64-linux-gnu/libfontconfig.so.1: undefined

Sep 11

Xingju Nie, … Andreas Bartsch4

Sep 11

HCP style protocol for VE11E

Thank you all! We did get a license issure recently and Siemens engineer could not figure out the

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HCP style protocol for VE11E

Thank you all! We did get a license issure recently and Siemens engineer could not figure out the

Sep 11

Zack Guo, … Elam, Jennifer5

Sep 10

Unrelated subjects

Hi Zack, Many, but not all, subjects in the Unrelated 100 that aren't listed in the S900

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Unrelated subjects

Hi Zack, Many, but not all, subjects in the Unrelated 100 that aren't listed in the S900

Sep 10

Pavithra Rajeswaran, … Glasser, Matthew3

Sep 9

Is there DWI data aligned to MNI space in HCP database?

You can use ${StudyFolder}/${Subject}/MNINonLinear/xfms/acpc_dc2standard.nii.gz to resample the

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Is there DWI data aligned to MNI space in HCP database?

You can use ${StudyFolder}/${Subject}/MNINonLinear/xfms/acpc_dc2standard.nii.gz to resample the

Sep 9

Tiago Azevedo, Glasser, Matthew2

Sep 5

ConnectomeDB closure and access to HCP-1200 PTN data

That data is out of date and no longer recommended. Some of it may persist on Amazon until we update

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ConnectomeDB closure and access to HCP-1200 PTN data

That data is out of date and no longer recommended. Some of it may persist on Amazon until we update

Sep 5

Hari Mellacheruvu, Jennifer Elam2

Sep 4

Accessing HCP-YA 2025 data from cluster: Aspera

Hi Hari, See https://groups.google.com/a/humanconnectome.org/g/hcp-users/c/jOSvL4QOCJw/m/823ZghxCAQAJ

unread,

Accessing HCP-YA 2025 data from cluster: Aspera

Hi Hari, See https://groups.google.com/a/humanconnectome.org/g/hcp-users/c/jOSvL4QOCJw/m/823ZghxCAQAJ

Sep 4

Aly Kotb, … Elam, Jennifer6

Sep 4

BALSA 2025 Release

Hi Andraz, We are working on a plan for implementing one or more alternatives to the Aspera GUI, but

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BALSA 2025 Release

Hi Andraz, We are working on a plan for implementing one or more alternatives to the Aspera GUI, but

Sep 4

Ioanna Ladopoulou, Glasser, Matthew2

Sep 3

Freesurfer recon-all sphere surface registration error

Rerunning the HCP-YA data surface generation is not recommended. We have an explicit correction for

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Freesurfer recon-all sphere surface registration error

Rerunning the HCP-YA data surface generation is not recommended. We have an explicit correction for

Sep 3

Estephan Moana, … Glasser, Matthew7

Sep 3

Recommended amount of resting BOLD for brain network estability

Thanks for the detailed advice Matt. Follow-up questions: I should have mentioned that we plan to

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Recommended amount of resting BOLD for brain network estability

Thanks for the detailed advice Matt. Follow-up questions: I should have mentioned that we plan to

Sep 3

Bokyeong Jeong, … Glasser, Matthew7

Sep 3

Regarding spatial smoothing of 7T movie-watching tfMRI data

The one I gave has major subcortical structures in it. A multi-modal parcellation of non-neocortical

unread,

Regarding spatial smoothing of 7T movie-watching tfMRI data

The one I gave has major subcortical structures in it. A multi-modal parcellation of non-neocortical

Sep 3

Ranesh Mopuru, Glasser, Matthew2

Sep 2

Gradient Deviation Correction for CSD in MRtrix3 using HCP 7T Data

I would ask the Mrtrix3 developers about this. Matt. From: Ranesh Mopuru <tur3...@temple.edu>

unread,

Gradient Deviation Correction for CSD in MRtrix3 using HCP 7T Data

I would ask the Mrtrix3 developers about this. Matt. From: Ranesh Mopuru <tur3...@temple.edu>

Sep 2

Fabio Strappazzon, Elam, Jennifer3

Sep 2

ConnectomeDB closure and MEG data

Ok, thanks! Il giorno martedì 2 settembre 2025 alle 16:02:03 UTC+2 Elam, Jennifer ha scritto: Hi

unread,

ConnectomeDB closure and MEG data

Ok, thanks! Il giorno martedì 2 settembre 2025 alle 16:02:03 UTC+2 Elam, Jennifer ha scritto: Hi

Sep 2

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