Re: [HCP-Users] coding of videos in social task?

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

Re: [HCP-Users] question about making RSFC matrices available

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

Re: [HCP-Users] task fmri group analysis

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

Re: [HCP-Users] Inconsistency in the Working Memroy tfMRI behavioral scores

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

Re: [HCP-Users] Information of HCP Data (Language Task fMRI)

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)

Re: [HCP-Users] calculate beta and t value of new contrast

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

Re: [HCP-Users] Information of HCP Data

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

Re: [HCP-Users] Some columns in the Movement_Regressors.txt are zeros

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

Re: [HCP-Users] Q about relational processing task

of 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

Re: [HCP-Users] Q about relational processing task

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=Scripts=HCP_TFMRI_scripts.zip --Greg

Re: [HCP-Users] Gambling tfMRI

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

Re: [HCP-Users] working memory task times

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.

Re: [HCP-Users] Extracting beta values from analyzed task-data

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

Re: [HCP-Users] Adjusting EV timing text files in EMO task

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:

Re: [HCP-Users] CARIT Psyexp files

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

Re: [HCP-Users] How to deal with the slight delay in 7 HCP Eprime tasks

ty School of Medicine 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" <gburg...@wustl.edu<mai

Re: [HCP-Users] How to deal with the slight delay in 7 HCP Eprime tasks

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

Re: [HCP-Users] How to find trial-level behavioral results

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

Re: [HCP-Users] task design for the language task

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

Re: [HCP-Users] cifti to 'real' nifti

ork my way back > up to 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 <gburg...@wustl.edu> wrote: > When we called this a “fake” NIFTI, that was a misnomer. It is a real NIFTI >

Re: [HCP-Users] cifti to 'real' nifti

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.,

Re: [HCP-Users] Language task variables

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

Re: [HCP-Users] Comparing ICA-FIX results to results without ICA-FIX

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

Re: [HCP-Users] Motor task contrats: no RH-cue, LH-cue, etc.?

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. > ___

Re: [HCP-Users] Motor task contrats: no RH-cue, LH-cue, etc.?

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

Re: [HCP-Users] Problem downloading data: "Destination path directory does not exist (Code: 6)"

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

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

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

Re: [HCP-Users] resting fmri processing

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

Re: [HCP-Users] Connectivity Analysis with Cifti

airly straightforward with the -stim_times_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, Greg

Re: [HCP-Users] Connectivity Analysis with Cifti

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

Re: [HCP-Users] (no subject)

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

Re: [HCP-Users] Pulse Ox - PULS.log

es, or if > this is specific to our site. > > Cheers, > > Andrew > > On Thu, Oct 6, 2016 at 11:37 AM, Burgess, Gregory <gburg...@wustl.edu> wrote: > I haven’t had a chance to look at those new files, so I’d be interested to > hear more about your experience. >

Re: [HCP-Users] Pulse Ox - PULS.log

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

Re: [HCP-Users] ROIs and Betas from Cifti Data

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

Re: [HCP-Users] Basis Function Selection

e 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/Publications_files/MIxedBlockPaper_Final.pdf), you shoul

Re: [HCP-Users] Basis Function Selection

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

Re: [HCP-Users] PALM with cifti files

n 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 <gburg...@wustl.edu<mailto:gburg...@wustl.edu>> wrote: Hi Michael, I just wan

Re: [HCP-Users] PALM with cifti files

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

Re: [HCP-Users] PALM for Cifti data

fortunately I will not be able to attend this year, but I look forward to > seeing those examples afterward. > > Thank you, > Michael > From: Burgess, Gregory <gburg...@wustl.edu> > Sent: Thursday, August 4, 2016 10:05:47 AM > To: Michael F.W. Dreyfuss > Cc: hcp-users@humanc

Re: [HCP-Users] Movement Confounds and Censoring

it would rate spike-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...@wu

Re: [HCP-Users] PALM for Cifti data

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

Re: [HCP-Users] FIX-ICA denoised task data?

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

Re: [HCP-Users] Movement Confounds and Censoring

> 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 >