Hi HCP folks,
I had a similar issue with 7T data collected locally but preprocessed via
the HCP pipeline - assuming FSL doesn¹t release a fix, you might want to
include a warning about this when the HCP 7T data is released. Will
probably be disconcerting for your Mac users.
Best,
-Ely
Icahn
Hi HCP leaders,
I’m interested in examining some subclinical psychiatric features in the HCP
dataset, and it would be helpful to have access to subjects’ specific answers
to behavioral assessment questions in addition to the composite scores for each
measure (e.g. responses on the NIH Toolbox
Oh okay, still using the 500 Subjects Release data and didn’t think to look for
hidden files. I see it now. Thanks to both of you!
-Ely
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Hi all,
I’m interested in running some analyses (particularly smoothness estimations)
on the noise components identified by ICA-FIX. I’ve looked through several
subjects’ ICA folders (e.g.,
rfMRI_REST1_LR_hp2000.ica/filtered_func_data.ica/), which contain a number of
output stats and nifti
Hi HCP team,
I'd like to download the retinotopy eprime scripts used for the 7T HCP release.
I was previously able to download the 3T scripts, but I can't find where the 7T
scripts are hosted. Could you please advise?
Many thanks,
-Ely
___
HCP-Users
Hi team HCP,
I have two semi-related questions about generating resting-state gradients:
1) What is the theoretical motivation behind using cifti-correlation-gradient
rather than cifti-gradient to generate a resting-state gradient .dscalar.nii
from a .dconn.nii file, per this thread (
Ah okay; remeaning as you suggested works well (restores the expected
Tmean/Tsd). Thanks!
From: Glasser, Matthew [glass...@wustl.edu]
Sent: Tuesday, February 21, 2017 8:40 PM
To: Ely, Benjamin; HCP-Users@humanconnectome.org
Cc: Brown, Tim
Subject: Re: [HCP-Users
Great, thank you!
From: Keith Jamison [kjami...@umn.edu]
Sent: Thursday, February 16, 2017 4:42 PM
To: Ely, Benjamin
Cc: HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] unpacking 7T data
There are indeed identical redundant files in the different packages
Hi HCP team,
The FIX-denoised 7T data released by the HCP appear to have a mean intensity of
~0, versus 10,000 for the pre-FIX 7T data due to intensity normalization. By
contrast, the most recently released 3T data from the HCP retain a mean value
of ~10,000 following the ICA-FIX step. Is this
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 gives us a similar
temporal profile. Sounds like I should compare our temporal
Hi Michael,
My initial interest was in comparing aggressive vs. soft regression of the
noise ICs. When I tried simply regressing them out using fsl_regfilt with and
without the -a flag, though, I realized that my soft denoised file didn't match
the HCP denoised file, so this became more of an
Hi all,
I ran a test recently comparing "aggressive" vs. "soft" denoising in MELODIC on
an HCP resting-state run, regressing out the "bad" components found in the
rfMRI_REST1_LR_hp2000.ica/.fix file (I believe the location of this info is
different in the newer release but I'm working off
...@wustl.edu]
Sent: Wednesday, August 17, 2016 1:16 PM
To: Ely, Benjamin; HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] cifti-gradient vs. cifti-correlation-gradient, also
volume-based dense connectomes
Hi Ely,
1. The idea is to look for differences in connectivity patterns, rather than
Hi Matt and Greg,
Thanks for the feedback! I've looked at the various fix .m files from the
current release; based on fix_3_clean.m, I tried the following for a single
resting-state run:
# highpass filter; sigma of 1000.08 = FWHM of 2355 per Smith et al 2013
NeuroImage, also consistent with
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
Hi HCP team,
I'm interested in comparing the performance of ICA-FIX using a 200s vs. 2000s
highpass filter cutoff for some locally-acquired HCP-like resting-state data,
as suggested in a previous thread. The HCP wrapper for ICA-FIX includes a
reference to a 200s training file, HCP_hp200.RData,
Great, thank you!
From: Stephen Smith [st...@fmrib.ox.ac.uk]
Sent: Monday, November 07, 2016 2:36 PM
To: Ely, Benjamin
Cc: HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] ICA-FIX HP200 training data
Hi - try the following:
www.fmrib.ox.ac.uk/~steve/ftp
Hi everyone,
I'm running some connectivity analyses following the procedure outlined in this
thread
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg04403.html. Since
my ROIs are fairly small, I'd like to calculate the correlation between the
mean unsmoothed timeseries of each
: Benjamin Risk [bb...@cornell.edu]
Sent: Thursday, May 04, 2017 2:34 PM
To: Harms, Michael
Cc: Ely, Benjamin
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
That's true, but the sample correlation coefficient is asymptotically normal. I
agree with Benjamin based on some
:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ely, Benjamin"
<benjamin@mssm.edu<mailto:benjamin@mssm.edu>>
Date: Wednesday, May 3, 2017 at 11:46 PM
To: "Glasser, Matthew" <glass...@wus
_
From: Glasser, Matthew [glass...@wustl.edu]
Sent: Wednesday, May 03, 2017 11:32 PM
To: Ely, Benjamin; HCP-Users@humanconnectome.org
Subject: Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation
Hi Ely,
We don’t have a function like this yet, but have been discussing making one.
I worked on several higher-level tools as well at the recent NeuroHackWeek
(based partly on Dr. Cottaar’s tools). I’m working with the NiBabel and
NiWidgets groups to get some of these incorporated into future releases, but
for now the provisional scripts are available at
I worked on several higher-level tools as well at the recent NeuroHackWeek
(based partly on Dr. Cottaar’s tools). I’m working with the NiBabel and
NiWidgets groups to get some of these incorporated into future releases, but
for now the provisional scripts are available at
Oh great, that was fast – thank you!
From: "Elam, Jennifer" <e...@wustl.edu<mailto:e...@wustl.edu>>
Date: Tuesday, January 30, 2018 at 12:37 PM
To: Benjamin Ely <benjamin@mssm.edu<mailto:benjamin@mssm.edu>>,
"hcp-users@humanconnectome.org<ma
Dear HCP team,
I’m interested in the NIH Toolbox Pain Intensity measure (PainIntens_RawScore).
However, the 500 Subject Release data dictionary states that it was “Excluded
currently due to glitch in the Toolbox data download”, and it doesn’t seem to
be mentioned in the updated 1200 Subject
Hi Claude,
Are you using workbench viewer? If so, you should be able to identify
particular thalamus or other subcortical MNI coordinates in the Volume tab
(brainordinate subcortical coordinates = MNI coordinates). You can also
split the thalamus structure out from subject¹s CIFTI file, if you
Hi Greg and co,
What’s the status on the planned release of PSQI component scores? Also, are
there plans to release the MMSE (aka Mini) component scores?
Thank you!
-Ely
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HCP-Users@humanconnectome.org
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Ely, Benjamin"
mailto:benjamin@mssm.edu>>
Date: Thursday, December 27, 2018 at 5:17 PM
To: HCP User List
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] export workbench scenes as vector graphics
Hi
Hi everyone,
I’ve created a number of figure panels using workbench viewer and would like to
export them to vector-format graphics files (e.g. EPS or PDF) for use in a
manuscript. Is there a way to do this? While there are many file-type options
in the wb_view Capture Image menu and the
Hi Matt,
MSMAll didn't work very well the first time we tried using 10 min (600 vol) of
resting-state data only, but we re-ran it after concatenating the resting-state
run with some task runs and that seems to have mostly fixed the issue. Dropbox
links to screenshots below in case anyone is
Hi Matt,
Thanks for getting back to me so quickly! That's okay, it's not critical; will
submit as a feature request through the HCP website.
-Ely
From: Glasser, Matthew
Sent: Friday, December 14, 2018 10:18 PM
To: Ely, Benjamin; hcp-users@humanconnectome.org
Hi all,
I currently have a scene file where I created a separate scene for each panel
of a figure. I'd like to combine the tabs from these scenes into a single scene
and display them using the tile tab feature. Is there a way to do this?
Whenever I load a second scene, it closes all tabs
Hi Matt,
I’ve been using a matlab command similar to the one you gave to regress/remove
timeseries values from our data, based on code from the ICAFIX script
fix_3_clean.m. Glad to hear that’s what you suggest! Quick question though:
before regressing out ICA component timeseries values, the
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