Hi David,
The conditions are coded in the TAB.txt files in the public data release.
BILLIARD-A.AVI Random
BILLIARD-B.AVI Random
COAXING-B.AVI Mental
Dancing.AVI Mental
DRIFTING-A.AVI Random
DRIFTING-B.AVI Random
Fishing.AVI Mental
MOCKING-A.AVI Mental
MOCKING-B.AVI Mental
Random mechanical.AVI Ra
I believe that the Open Access Data Use terms
(https://www.humanconnectome.org/study/hcp-young-adult/document/wu-minn-hcp-consortium-open-access-data-use-terms)
require that anyone receiving the data must have first agreed to the Open
Access Data Use Terms. If my understanding is correct, that w
PALM does provide an option to do spatial cluster correction using TFCE.
Currently, that is the only cluster-based multiple correction method available
in CIFTI grayordinate space. Otherwise, you could use conduct parcellated
analyses and correct for the number of parcels, or conduct vertex-wise
Hello Xinyang,
Most likely, you haven’t accounted for “NLR”, which stands for “no logged
responses”. If the response period timed out without an overt response, we
can’t be sure whether the participant would have made a correct response or an
error response. Since NLRs are neither correct or er
Hi Daniel,
I agree with Matt that it’s probably not a good idea to ‘cut’ the data into
Language-only pieces. FMRI data are always relative, meaning that they only
have meaning in comparison to other conditions.
There is additional information about the task design in the Barch et al (2013)
Neu
Hello Iris,
If you’re interested in individual subject estimates of the face-tool contrast,
I don’t believe that you can create new contrasts without running your own GLM.
(Perhaps other users will be familiar with a different method.)
However, if you are interested in the average difference be
Hi Daniel,
The Language task and Emotion tasks were designed with no blocks of resting
fixation. The intention was to directly contrast STORY vs. MATH in the Language
task, and FACES vs. SHAPES in the Emotion task. If possible, you should
consider using only the STORY-MATH and FACES-SHAPES cont
Hi Manasij,
We’ve discussed this in some detail with the folks at FMRIB. They have long
known that the cost function in FLIRT (and MCFLIRT) is biased toward zero for
very small motions. However, when the movement regressors have long series of
zeroes, the motion corrected time series does not a
Medicine
Department of Psychiatry
Phone: 314-362-7864
Email: gburg...@wustl.edu<mailto:gburg...@wustl.edu>
On Nov 12, 2018, at 4:25 PM, Burgess, Gregory
mailto:gburg...@wustl.edu>> wrote:
If you want to review the stimuli used in the Relational task, you can always
download th
If you want to review the stimuli used in the Relational task, you can always
download the 3T E-Prime scripts from the ConnectomeDB.
https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources&resource=Scripts&filePath=HCP_TFMRI_scripts.zip
--Greg
___
The rationale for using a blocked design versus event-related design is
discussed in Barch et al. 2013. In general, blocked designs have higher
sensitivity than event-related designs. The event-related design showed the
same pattern of activation, but was less sensitive. Therefore, the blocked
Hello Katerina,
- The first row in the SyncSlide.OnsetTime column reflects the onset of the
first TR in E-Prime clock (i.e., the first trigger). This time must be
subtracted from all other timestamps in the TAB.txt to determine the amount of
time since the first trigger / first BOLD volume.
-
Hi Yann,
In a GLM, the baseline / intercept / B0 reflects the mean of the residual BOLD
time series after removing variance explained by all other regressors. Beta
weights for other conditions can be conceptualized as BOLD differences between
those conditions and the baseline.
When the task in
That’s correct. There is no need to adjust the timing of any of the EV files.
--Greg
Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Psychiatry
Phone: 314-362-
The scripts are currently available for download at:
https://www.humanconnectome.org/study/hcp-lifespan-aging/project-protocol/task-protocols-hcp-aging
https://www.humanconnectome.org/study/hcp-lifespan-development/project-protocol/task-protocols-hcp-development
Currently, there is not a single-sc
Department of Psychiatry
Phone: 314-362-7864
Email: gburg...@wustl.edu<mailto:gburg...@wustl.edu>
[X]
--
Meizhen Han
PhD Candidate
Center for MRI Research
Peking University
Beijing, China
At 2018-02-24 01:57:49, "Burgess, Gregory"
mailto:gburg...@wustl.edu>> wrote:
There
There is no difference between the duration of the E-Prime tasks and the
duration of the BOLD time series from the scan. There is likely a
misunderstanding of what the duration should be, but I can’t help without
knowing specifically what doesn’t line up in your opinion.
There have been two thi
Hi Manasij,
Sorry for the delay in responding. I missed this message to the mailing list.
I understand your confusion here. The cue was included in the onset and
duration of the EVs in our analyses of the earlier data release for the 2013
paper. However, the timing of the EVs in the publicly re
Hi Xinyang,
The accuracy and RT for individual stimuli within a scan are in the
preprocessed directory for that scan (i.e., preproc resources). The files end
with “TAB.txt”, and are tab-delimited E-Prime outputs. If you need detail about
the variables contained in those TAB.txt outputs, you ca
The Language task was not designed to be an alternating (ABAB) blocked design.
The _first_ run had alternating blocks (ABAB) simply by chance.
--Greg
Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington Univ
o the surface, but as this requires quite a bit more work I was hoping to
> avoid this.
>
> Reinder
>
> On Thu, Mar 23, 2017 at 2:00 PM, Burgess, Gregory wrote:
> When we called this a “fake” NIFTI, that was a misnomer. It is a real NIFTI
> file. The issue is that the voxels
When we called this a “fake” NIFTI, that was a misnomer. It is a real NIFTI
file. The issue is that the voxels are not ordered in space as you would expect
from a real brain. So, your software should work with it, as long as you’re not
trying to do processing along a spatial dimension (e.g., smo
Hi Yann,
Thanks for looking into this. We will take some time to review the data files
and processing scripts. If there’s need for an update, we’ll announce that to
this list, and post the information on the known issues wiki page.
Thanks,
--Greg
___
That code is technically maintained by CMRR. Visit
https://github.com/CMRR-C2P/MB and http://www.cmrr.umn.edu/multiband/ for info.
I’m hoping that they will update that code for DICOM-formatted files soon.
--Greg
Greg Burgess,
Hi Andrew,
To be clear, ICA-FIX may not improve task fMRI data when it is run separately
on each tfMRI scan. MELODIC separates signal from noise better when there are
tons of time points going into the ICA, which isn’t always the case with single
tfMRI scans. Also, the confound regression will
MINUSCUE.dtseries.nii STDEV
> /stdevcopeMOTORTMINUSCUE.dscalar.nii;
> -cifti-math '(mean) / stdev' /cohendmapMOTORTMINUSCUE.dscalar.nii -var mean
> /meancopeMOTORTMINUSCUE.dscalar.nii -var stdev
> /stdevcopeMOTORTMINUSCUE.dscalar.nii
>
> Thank you very much,
> Xavier.
> ___
I thought that contrasting each effector against the average of the others
(e.g., RH-AVG) was a more-effective control to isolate motor-specific regions.
If you are still interested in contrasting each effector versus the cue
(controlling for visual activation without controlling for other task-
The error may be referring to the location specified in Aspera Connect >
Preferences > Transfers > Save downloaded files to:
[cid:4A4CB0FE-ED27-4CD2-A866-FFEE544CC7FB@wucon.wustl.edu]
Does that location in your preferences exist?
--Greg
__
Hello Bo-yong,
We did not directly measure the size of stimuli for the working memory
paradigm. Unfortunately, the same scanner environment is no longer available,
so we can’t really measure it in retrospect.
--Greg
Greg Burg
That’s correct. There is no TTL trigger pulse during the multiband calibration
scans or SBRef image. The first TTL trigger comes at the onset of the first
volume in the BOLD timeseries.
--Greg
Greg Burgess, Ph.D.
Staff Scienti
HCP processing does not conduct low-pass filtering for either minimally
preprocessed or FIX-cleaned data. However, low pass temporal filtering is
probably not necessary, and is not recommended by the HCP consortium.
One goal of FIX is to selectively remove high frequency noise, but keep other
h
_IM options for
> 3dDeconvovle. Does something comparable exist for FEAT or do I have to code
> each time point for each individual as a separate regressor in the subject's
> fsf file before running feat_model?
>
> Thanks,
> Michael
> From: Burgess, Gregory
> Sent: Wednesday, Oc
In general, if you do a conversion from CIFTI to (fake) NIFTI, you can conduct
any timeseries analyses using any tools you would desire, and then convert back
to CIFTI. Spatial processing (spatial smoothing, defining clusters, etc.) needs
to happen in CIFTI space using wb_command.
--Greg
_
Hi Ferdaus,
It doesn’t appear that you’re using FIX data, but I think you should seriously
consider doing so. To be clear, we believe that using FIX-denoised timeseries
data is a replacement for / better alternative to: 1) regression of head motion
estimates, 2) frame censoring / scrubbing of h
or if
> this is specific to our site.
>
> Cheers,
>
> Andrew
>
> On Thu, Oct 6, 2016 at 11:37 AM, Burgess, Gregory wrote:
> I haven’t had a chance to look at those new files, so I’d be interested to
> hear more about your experience.
>
> If you’re not familiar with
I haven’t had a chance to look at those new files, so I’d be interested to hear
more about your experience.
If you’re not familiar with it, you should check out
https://github.com/CMRR-C2P/MB/blob/master/readCMRRPhysio.m .
One thing to note, at least with the legacy files, the time stamp in the
We’ve reviewed the scores that we received from NIH Toolbox. These are the
scores for quinine, which are called the “primary” scores by NIH Toolbox.
--Greg
Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washingto
I think there are two problems, either of which could certainly cause large
differences in the outputs.
> # format movement parameters (manually corrected header after paste step, not
> shown)
> Text2Vest Movement_Regressors.txt Movement_Regressors.mat
> Text2Vest Movement_Regressors.txt Movemen
HCP did not have a task that was geared toward response inhibition.
Furthermore, although it’s alluring to believe that a single parcel will
encapsulate all of response inhibition, it’s doubtful.
Why not select a set of parcels in and near IFG, and correct for multiple
comparisons? Use a meta-a
ssuming I can just modify the fsf files before feat_model.
Thank you,
Michael
On Thu, Sep 22, 2016 at 3:35 PM, Burgess, Gregory
<gburg...@wustl.edu> wrote:
If you’re referring to what is sometimes called a “state-item” design (cf.
http://www.nil.wustl.edu/labs/schlaggar/Publication
ng double gamma (and there is a cost to estimating the basis
> function everywhere too).
>
> I will continue to look into these other options...
>
> Thanks again,
> Michael
>
> On Thu, Sep 22, 2016 at 2:31 PM, Burgess, Gregory
> wrote:
> Hi Michael,
>
> A few th
Hi Michael,
A few things:
1) Matt’s point about the increased activation estimates in visual cortex is a
good one. There is increased signal in occipital cortex in functional
connectivity analyses that do not assume a response shape. In part, this may
result from the back of the head being clos
The precise process in the FIX pipelines is hopefully clear upon reviewing
https://github.com/Washington-University/Pipelines/blob/master/ICAFIX/hcp_fix.for_fix1.06a
(including the FIX subfunctions that it calls).
If you started from a different starting point than the hcp_fix script, there
are
Hi Mike,
It should be noted that _not_ all families were perfect sets containing a twin
pair and two non-twin siblings. The families that participated in HCP reflect
variation that exists in families in general: some half siblings, some twins
who choose not to participate with their co-twin, an
Human Connectome Project
Washington University School of Medicine
Department of Neuroscience
Phone: 314-362-7864
Email: gburg...@wustl.edu<mailto:gburg...@wustl.edu>
On Sep 12, 2016, at 1:50 PM, Burgess, Gregory
mailto:gburg...@wustl.edu>> wrote:
Hi Michael,
I just want to verify that you are
Hi Michael,
I just want to verify that you are trying to use PALM for “higher-level” group
analyses. PALM is not currently able to conduct “lower-level” timeseries
analyses. You currently need to use the HCP task fMRI pipelines for that.
If you are attempting group analyses, it might be helpful
nd this year, but I look forward to
> seeing those examples afterward.
>
> Thank you,
> Michael
> From: Burgess, Gregory
> Sent: Thursday, August 4, 2016 10:05:47 AM
> To: Michael F.W. Dreyfuss
> Cc: hcp-users@humanconnectome.org
> Subject: Re: [HCP-Users] PALM for Cifti
pike-like ICA components as noise.
--Greg
Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Psychiatry
Phone: 314-362-7864
Email: gburg...@wustl.edu
>
> Thank you,
&g
PALM isn’t intended to replace the level 1 (timeseries) analysis. Permutation
testing doesn’t handle the autocorrelated timeseries appropriately, because
time points are not truly exchangeable.
It should be possible to do a repeated measures analysis in PALM (treating
acitvation estimates from
The FIX code includes a hcp_fix wrapper script, which you could run on the task
fMRI time series data. It should be pretty straightforward.
However, the fact is that the 3T task data was not denoised by FIX because the
zstat maps generally _decrease_ in statistical significance after FIX in
reg
> On Aug 2, 2016, at 10:17 AM, Michael F.W. Dreyfuss
> wrote:
>
> Hi, I have some basic questions about the movement parameters that are put
> out by the HCP preprocessing scripts.
>
> 1) What is the difference between Movement_Regressors_dt.txt and
> Movement_Regressors.txt? I would like to us
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