Re: [HCP-Users] FIRST & FAST Data

2018-07-10 Thread Harms, Michael
Sorry, no. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110

Re: [HCP-Users] Blank p-value maps after running PALM on CIFTI files

2018-07-02 Thread Harms, Michael
Hi, If you are just testing the mean activation, then you need to use the -ise option to allow sign flipping. Otherwise, by default, PALM does permutations, but permutations of your model will always generate the exact same mean, which explains your results. Cheers, -MH -- Michael Harms,

Re: [HCP-Users] Communities for MMP atlas?

2018-07-02 Thread Harms, Michael
Hi, There is something in the works: https://www.biorxiv.org/content/early/2018/01/12/206292 cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box

Re: [HCP-Users] A few specific questions about the HCP data | MNI space dedrifting & file structure

2018-07-02 Thread Harms, Michael
Hi, Re (1): If you want to work with streamlines in MNI space then you have to accept the "drift" (volume expansion) that is part of MNI space itself. Re (2): Maps may be resampled to surfaces in MNI space. But all the FreeSurfer structural quantities that we provide in the

Re: [HCP-Users] HCPID in TAB.txt

2018-06-21 Thread Harms, Michael
“functional session A” and “functional session B”. That is related to the internals of how the data was collected at the scanner. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of

Re: [HCP-Users] HCP processing with ciftify requirements

2018-06-19 Thread Harms, Michael
The issue with using FreeSurfer 6.0 in the HCP Pipelines is that some aspects of the surface generation on HCP-Young Adult data were better using the FreeSurfer 5.3.0-HCP release. We are in the process of checking the performance of a beta version of FreeSurfer 6.X on HCP-YA data. If you use

Re: [HCP-Users] Minimally preprocessed 7T files - don't see the rest

2018-06-19 Thread Harms, Michael
7T release. Ideally would include the .txt files. Thanks v much, Nina On Tue, 19 Jun 2018, Harms, Michael wrote: > > Hi, > rfMRI_REST1_7T_PA_Atlas_1.6mm_MSMAll.dtseries.nii is the CIFTI version, using > MSMAll registration, on a surface mesh with ~ 1.6 mm (average) vertex spacing. > &

Re: [HCP-Users] Minimally preprocessed 7T files - don't see the rest

2018-06-19 Thread Harms, Michael
Hi, rfMRI_REST1_7T_PA_Atlas_1.6mm_MSMAll.dtseries.nii is the CIFTI version, using MSMAll registration, on a surface mesh with ~ 1.6 mm (average) vertex spacing. Note that we've provided CIFTI data on both 1.6 mm and 2.0 mm meshes. Depending on your research question, the latter may be easier

Re: [HCP-Users] wb_command help

2018-06-12 Thread Harms, Michael
Hi, See the “HCP1200 Parcellation+Timeseries+Netmats (PTN)” packages hosted at https://db.humanconnectome.org/data/projects/HCP_1200 There are “soft parcellations” (ICA-based, and cortical only) computed at dimensionalities of 15, 25, 50, 100, 200, and 300. Cheers, -MH -- Michael Harms, Ph.D.

[HCP-Users] perceptually uniform sequential colormaps?

2018-06-05 Thread Harms, Michael
Hi guys, Which of the colormaps currently in Workbench are perceptually uniform and monotonically increasing in lightness? In the interest of supporting some of the recent colormaps with considerable thought behind them, what about including the viridis, plasma, inferno, and magma colormaps

[HCP-Users] -cifti-reduce -exclude-outliers

2018-06-04 Thread Harms, Michael
Hi Tim, I was wondering about the details of the -cifti-reduce -exclude-outliers operation. In particular, is it “iterative”? i.e., does it recompute the std without the outliers from the previous pass(es) and iterate until no further new outliers are identified? Thanks, -MH -- Michael

Re: [HCP-Users] FSL version in the HCP pipelines

2018-06-04 Thread Harms, Michael
Yes, you should be able to use the latest FSL release. In fact, due to code consolidation in the newest release, FSL 5.0.6 is no longer allowed for the task-fMRI processing. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of

Re: [HCP-Users] Exact time of measurements for task fMRI

2018-06-02 Thread Harms, Michael
Hi, The tasks are triggered by the scanner (so you can assume the start of the acquisition is at t=0) and you can assume that the spacing between frames is exactly the TR (0.720 sec for the 3T HCP-Young Adult acquisitions). Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] MSMSulc data

2018-05-14 Thread Harms, Michael
Hi, Due to the manner in which the pipeline code developed, the CIFTI files that do NOT contain “MSMAll” are by default based on “MSMSulc” registration. Perhaps at some point we will revise the pipeline code to explicitly include “MSMSulc” as part of the file names, to avoid this confusion.

Re: [HCP-Users] Volumes from dscalar.nii files?

2018-05-02 Thread Harms, Michael
Hi, Cortical thickness is purely a surface-based measure, so that particular dscalar indeed doesn’t contain any volume-based grayordinates. The task fMRI data would be one example in which volume-based grayordinates are present in the CIFTI (i.e., cerebellum and subcortical voxels) Cheers,

Re: [HCP-Users] Native space surface curvature available?

2018-04-18 Thread Harms, Michael
Hi, The entirety of the original FS output is available at ${subject}/T1w/${subject}, which you can obtain via the “Structural Extended” packages, or as part of “Connectome-in-a-Box” (no longer taking new orders, but perhaps you already have one) or available on S3. Cheers, -MH -- Michael

Re: [HCP-Users] Grand Mean Intensity Normalization

2018-04-11 Thread Harms, Michael
Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: "Glasser, Matthew" <glass...@wustl.edu> Date: Wednesday, April 11, 2018 at 5:35 PM To: erik lee <erik.lee...@gmail.com>, "Harms, Michael" &

Re: [HCP-Users] Grand Mean Intensity Normalization

2018-04-11 Thread Harms, Michael
Just to expand on this, since I think I might know why you are asking. The grand mean is computed on the brain masked volume timeseries, after bias field correction and jacobian modulation is first applied – see the end of IntensityNormalization.sh, which is called as the final step in

Re: [HCP-Users] gradient nonlinearity correction question

2018-04-11 Thread Harms, Michael
One thought: Are you sure you are using the “3D” (and not the “2D”) correction on the scanner? -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134

Re: [HCP-Users] HCP Pipeline BIDS app - fMRI processing with reversed phase-encode file in "fmap" directory?

2018-04-06 Thread Harms, Michael
Hi, We didn’t create the HCP Pipeline BIDS app, and have no experience using it. Users should be aware that the current BIDS App “hides” various choices that one would normally have to make when running the HCP Pipelines, and I’m not sure what particular choices it has implemented. In that

Re: [HCP-Users] -surface-distortion -local-affine-method

2018-04-04 Thread Harms, Michael
That feature isn’t yet in the released wb_command. Try using the latest “released” version of the Pipelines from GitHub, rather than the master branch. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University

Re: [HCP-Users] Please inform me the actual value of echo timing used in HCP lifespan pilot 1a

2018-04-03 Thread Harms, Michael
That page appears to be down for the moment. We’ll get it fixed. The Echo Spacing for the dMRI from the Lifespan1a pilot was 0.69 ms. (Although, FWIW, if you already processed your data using 0.78 ms, it doesn’t matter in this particular case. You’ll still get a completely correct

Re: [HCP-Users] Convert activation cifti data to volume nifti

2018-03-27 Thread Harms, Michael
, 2018 at 12:08 PM To: "Harms, Michael" <mha...@wustl.edu> Cc: hcp-users <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Convert activation cifti data to volume nifti Thank you for the clarification. Here is a tree structure of one subject folder "tfMRI_EMOTION

Re: [HCP-Users] Convert activation cifti data to volume nifti

2018-03-27 Thread Harms, Michael
: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Yassine Benhajali <yanama...@gmail.com> Date: Tuesday, March 27, 2018 at 11:05 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: NEUROSCIENCE tim <tsc...@mst.edu>, hcp-users <hcp-use

Re: [HCP-Users] Fwd: analysing the 7T rsfMRI

2018-03-26 Thread Harms, Michael
Hi, “AP” (short for anterior-to-posterior) and “PA” (short for posterior-to-anterior) refer to the phase encoding direction. In general, as Jenn said, we recommend using both the AP and PA data, so that your results aren’t “biased” toward a particular phase-encoding direction. Is there a

Re: [HCP-Users] Simple GLM for cordial thickness and myelin maps in workbench?

2018-03-17 Thread Harms, Michael
Hi, Not in wb_command at the current time. You could of course load the data into Matlab and run a regression there, if all you care about is the effect size of the relationship. What PALM nicely gives you is the ability to control for multiple comparisons in a statistically rigorous manner

Re: [HCP-Users] Melodic ICA idle

2018-03-13 Thread Harms, Michael
I think the issue, as I read it, is that Will’s data is only NIFTI currently, so he doesn’t have any subject CIFTI that he could use for the stage 1 of dual reg. Our suggestion of course to remedy that would be that you process your data into CIFTI, using the HCP Pipelines. ☺ Cheers, -MH --

Re: [HCP-Users] Concatenating resting state runs

2018-03-07 Thread Harms, Michael
Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: Timothy Coalson <tsc...@mst.edu> Date: Wednesday, March 7, 2018 at 5:19 PM To: "Harms, Michael" <mha...@wust

Re: [HCP-Users] Concatenating resting state runs

2018-03-07 Thread Harms, Michael
mann <davidhofma...@gmail.com> Cc: "Harms, Michael" <mha...@wustl.edu>, hcp-users <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Concatenating resting state runs The basic idea for variance normalization is to equalize the variance of the noise. It is very hel

Re: [HCP-Users] Concatenating resting state runs

2018-03-07 Thread Harms, Michael
...@wustl.edu> Date: Wednesday, March 7, 2018 at 11:24 AM To: "Harms, Michael" <mha...@wustl.edu>, David Hofmann <davidhofma...@gmail.com> Cc: hcp-users <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Concatenating resting state runs Hi Mike, Not

Re: [HCP-Users] Concatenating resting state runs

2018-03-07 Thread Harms, Michael
Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of "Harms, Michael" <mha...@wustl.edu> Date: Wednesda

Re: [HCP-Users] Concatenating resting state runs

2018-03-07 Thread Harms, Michael
Matt, Don’t we compute an estimate of the unstructured noise variance as part of RestingStateState, and then place that into one of the packages? -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School

Re: [HCP-Users] Concatenate sessions from Emotion task

2018-02-28 Thread Harms, Michael
; Date: Wednesday, February 28, 2018 at 11:03 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: "Glasser, Matthew" <glass...@wustl.edu>, hcp-users <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Concatenate sessions from Emotion task Hey again, how can I

Re: [HCP-Users] Concatenate sessions from Emotion task

2018-02-28 Thread Harms, Michael
Hofmann <davidhofma...@gmail.com> Date: Wednesday, February 28, 2018 at 8:45 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: "Glasser, Matthew" <glass...@wustl.edu>, hcp-users <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Concatenate sessions fro

Re: [HCP-Users] Concatenate sessions from Emotion task

2018-02-28 Thread Harms, Michael
-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: David Hofmann <davidhofma...@gmail.com> Date: Wednesday, February 28, 2018 at 7:50 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: "Glasser, Matthew" <glass..

Re: [HCP-Users] Concatenate sessions from Emotion task

2018-02-27 Thread Harms, Michael
Well, you know the TR, and the number of frames in the first run, so just add the product of those two to the times in the 2nd run (unless you are manually deleting additional frames at the start of either run). Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] Concatenate sessions from Emotion task

2018-02-27 Thread Harms, Michael
What tools are you planning on using for the GLM fitting? Concatenating the runs will lead to some inaccuracies in the auto-correlation modeling at the point of concatenation, although I don’t know if anyone has ever investigated whether it matters much empirically. Cheers, -MH -- Michael

Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii

2018-02-23 Thread Harms, Michael
.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: redhatw <redh...@gmail.com> Date: Friday, February 23, 2018 at 9:37 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: "Glasser, Matthew"

Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii

2018-02-23 Thread Harms, Michael
Email: mha...@wustl.edu From: redhatw <redh...@gmail.com> Date: Friday, February 23, 2018 at 8:03 AM To: "Glasser, Matthew" <glass...@wustl.edu> Cc: "Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users

Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii

2018-02-22 Thread Harms, Michael
The files without any “registration suffix” came first temporally and were generated using “MSMSulc” registration. When the “MSMAll” registration was added later, we then added “MSMAll” as part of the file name. Cheers, -MH -- Michael Harms, Ph.D.

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

2018-02-21 Thread Harms, Michael
Hi, While the documentation is overall very good, I don’t know if I’d rely on that pdf for a detailed list of all the files that we recommend “keeping”. For that, you could download and unpack the packages for a subject with complete data (e.g., 100307), and see what you all get. As a

Re: [HCP-Users] setting up hcp protocols in Prisma

2018-01-18 Thread Harms, Michael
An importable protocol for Siemens is available here: http://protocols.humanconnectome.org/CCF/ -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of

Re: [HCP-Users] about the unrestricted data

2018-01-18 Thread Harms, Michael
nned in each scanner. Thank you so much for your help. Best Luo -- Original ---------- From: Harms, Michael <mha...@wustl.edu> Date: 周四,1月 18,2018 0:14 下午 To: 罗 <963619...@qq.com>, hcp-users <hcp-users@humanconnectome.org> Subject: Re: [HCP

Re: [HCP-Users] about the unrestricted data

2018-01-17 Thread Harms, Michael
Hi, It’s an indication of the “quarter” (Q) of the project that the data was acquired. Cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of

Re: [HCP-Users] ubuntu

2017-12-20 Thread Harms, Michael
We suggest using the latest version of the HCP Pipelines with the latest version of Workbench. Cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine

Re: [HCP-Users] A question about the unprocessed structural data

2017-12-07 Thread Harms, Michael
What subject are you looking at that has a “T1w_MPR1_reorient_sformMod.nii.gz” file? I’m not seeing that file in our “unprocessed” packages for any of a handful of HCP-Young Adult subjects that I just checked… The other files are as Matt explained, and are also explained in the release

Re: [HCP-Users] HCP protocol for Skyra VE11C

2017-11-28 Thread Harms, Michael
: mha...@wustl.edu From: <hcp-users-boun...@humanconnectome.org> on behalf of "Harms, Michael" <mha...@wustl.edu> Date: Tuesday, November 28, 2017 at 8:49 AM To: Live Eikenes <live.eike...@ntnu.no>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.o

Re: [HCP-Users] HCP protocol for Skyra VE11C

2017-11-28 Thread Harms, Michael
Hi, We have a VE11C protocol, but built on a Prisma, that various sites have used a starting point available here: http://protocols.humanconnectome.org/CCF/ You can try importing it, and see what sort of adaptations it makes, due to the lower strength gradients of the Skyra. (The main

Re: [HCP-Users] FreeSurfer brain volume question

2017-11-22 Thread Harms, Michael
Hi, In FS, “Intracranial volume”, renamed to “EstimatedTotalIntraCranialVol” (aka “eTIV”) in more recent FS versions, is solely based on the determinant of a talairach transform that is internal to FS. That particular transform does not necessarily need to be accurate for FS to generate

Re: [HCP-Users] How does the HCP calculate the Cohen d effect in S1200 GroupAvg results?

2017-11-22 Thread Harms, Michael
Hi, It’s a standard Cohen’s d calculation -- mean of the individual subject (lev2) copes, divided by the std of the individual subject copes In terms of FSL code, if $mergedcope is the 4D file containing all the individual subject cope estimates, the code is just: fslmaths $mergedcope

Re: [HCP-Users] access to files with realilgnment parameter in language task

2017-11-14 Thread Harms, Michael
Sure, you can download individual files using REST calls – see previous posts in the list for example syntax. Or, you could access the files via Amazon S3 and identify the subjects that way. The Movement_RelativeRMS_mean.txt file that accompanies each fMRI run is the mean of the relative

Re: [HCP-Users] mcflirt_acc in ABCD

2017-11-08 Thread Harms, Michael
Hi, No. I believe the switch to using FSL’s ‘mcflirt’ as the “default” motion correction was around release 3.15. I’d suggest you switch to using the latest release in the 3.x line, which is 3.22. For additional context, since the original post referenced the ABCD study, I assume that the

Re: [HCP-Users] Inaccurate b0 Image from DTIFIT

2017-10-31 Thread Harms, Michael
Hi, I don’t think the following is necessarily your problem, but know that the simple tensor model is not appropriate at high b-values. You should either 1) use the “—kurt” or “—kurtdir" flags which will add a “mean kurtosis” or “parallel/perpendicular kurtosis” parameters that can account

Re: [HCP-Users] Test-retest data on AWS?

2017-10-30 Thread Harms, Michael
Yes, there was a ‘melodic’ failure for the rfMRI_REST1_RL run that we were never able to resolve. Thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine

Re: [HCP-Users] about the hcp data

2017-10-24 Thread Harms, Michael
f of 罗 <963619...@qq.com> Date: Tuesday, October 24, 2017 at 9:23 AM To: "Harms, Michael" <mha...@wustl.edu> Cc: hcp-users <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] about the hcp data I'm sorry. I question is that whether all the 1113 subjects with MRI are av

Re: [HCP-Users] about the hcp data

2017-10-24 Thread Harms, Michael
Hi, Can you rephrase your question? Are you asking if the S1200 data release is available for purchase as part of the “Connectome in a Box” program? If so, the answer is yes: https://store.humanconnectome.org/data/ cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] netmats prediction of fluid intelligence

2017-10-10 Thread Harms, Michael
Germane to this discussion is that using the same methodology, but a different sample of subjects, the same Yale group has recently reported that the correlation of predicted gF (from netmats) and observed gF was r=0.22. https://www.ncbi.nlm.nih.gov/pubmed/28968754 cheers, -MH -- Michael

Re: [HCP-Users] dtifit, bedpostx, voxel-wise correction of dMRI gradients

2017-10-09 Thread Harms, Michael
Also, if you fitting a simple tensor model via ‘dtifit’, you may want to consider limiting yourself to just the b=1000 shell (+ b=0’s), because the simple tensor model breaks down for high b-values. There should be a post in the archive about this. Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] netmats prediction of fluid intelligence

2017-10-05 Thread Harms, Michael
In the context of the long resting state runs that we have available, I would argue that throwing in additional possible confounds is the appropriate thing to do. Are you suggesting that sex, age, age^2, sex*age, sex*age^2, brain size, head size, and average motion shouldn’t all be included?

Re: [HCP-Users] Mean and variance normalization

2017-10-05 Thread Harms, Michael
Email: mha...@wustl.edu From: hercp <he...@uw.edu> Date: Thursday, October 5, 2017 at 3:39 PM To: "Harms, Michael" <mha...@wustl.edu> Subject: Re: [HCP-Users] Mean and variance normalization Hi Michael, Thanks for the input. Are you aware of any utility t

Re: [HCP-Users] Mean and variance normalization

2017-10-05 Thread Harms, Michael
Re (2) (expanding on Matt’s response): Demeaning and variance normalizing a parcellated timeseries (or equivalently the time series for a single ROI), and then concatenating those, is not the same as demeaning and variance normalizing the dense time series, concatenating those, and then

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

2017-09-29 Thread Harms, Michael
And it is all handled automatically for the dMRI data in the HCP Pipeline. Cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box

Re: [HCP-Users] HCP Longitudinal Pipeline

2017-09-20 Thread Harms, Michael
Hi Tim, We plan on creating at least a structural pipeline that will support the use of FreeSurfer’s longitudinal processing. Unfortunately, there is no beta version, and I don’t want to speculate at this time on a timeline. Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] clustering of subcortical structures - flipping and smoothing

2017-09-01 Thread Harms, Michael
@Matt: The minimally preprocessed subcortical data in the CIFTI was smoothed with a 2 mm FWHM “parcel-constrained” kernel, right? (i.e, the smoothing does not cross boundaries of subcortical structures). In that case, if they were to then further smooth the subcortical data, but smooth

Re: [HCP-Users] intracranial volume < brain volume!

2017-08-31 Thread Harms, Michael
IntraCranial volume is based entirely on the determinant of the talairch transform. We don’t check the accuracy of that transform because it doesn’t even need to be accurate for FreeSurfer to generate correct surfaces and segmentations. So, frankly, I wouldn’t use the IntraCranial volume

Re: [HCP-Users] motion parameters

2017-08-29 Thread Harms, Michael
Hi, We don’t have a single average head motion for each subject stored as a variable in ConnectomeDB. You can find the average frame-to-frame motion for each fMRI run (rfMRI or tfMR) in the Movement_RelativeRMS_mean.txt file for that run. Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] dMRI: Error while running "eddy_postproc.sh"

2017-08-25 Thread Harms, Michael
See the --combine-data-flag in DiffPreprocPipeline.sh The default value of 1 is intended for acquisitions in which you have acquired the full vector table with both polarities, which isn’t how you acquired your data. In your case, you’ll need to use a value of ‘2’ for that flag. Cheers, -MH

Re: [HCP-Users] residuals fmri

2017-08-23 Thread Harms, Michael
There is no “modeling” of the rfMRI data, and thus no residuals (unlike the task data). Cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of

Re: [HCP-Users] Offline vs. online gradient nonlinearity correction

2017-08-04 Thread Harms, Michael
FYI: We are switching over to using ‘dcm2niix’, which is Chris Rorden’s newer, actively maintained conversion tool. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine

Re: [HCP-Users] Follow-up to: Obtaining the MNI coordinates of cluster peaks in the melodic_IC.dscalar.nii ICA maps

2017-08-03 Thread Harms, Michael
Creating an “average-surface” is fine, and we in fact to that and provide it as part of our “group-average” data (available for download from ConnectomDB). But, those average surfaces are just a “back-drop” for overlaying/visualizing the metric/cifti data, and aren’t intended to be used as a

Re: [HCP-Users] CIFTI and MATLAB

2017-07-31 Thread Harms, Michael
Yes, unless you want to deal with the NaNs. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel:

Re: [HCP-Users] signal to noise ratio

2017-07-19 Thread Harms, Michael
Sure, we have data, but I'm not sure how useful it would be to you without getting into various details. e.g., What type of preprocessing are you intending? Does it include any denoising? How are you going to define your spatial mask? Etc... How exactly were you thinking of quantifying

Re: [HCP-Users] Statistical comparison of whole brain (surface "voxels" + subcortical / cerebellar voxels) connectivity between two explicitly defined voxels

2017-07-18 Thread Harms, Michael
Hi, A couple extensions to Tim’s recipe. PALM has a “transposedata” option, so you can always transpose at the PALM stage if you prefer to not explicitly create a transposed CIFTI file. PALM can indeed accept CIFTI files “as is”, *if* you want to do permutation on the max statistic across

Re: [HCP-Users] mapping HCP data into 7 functional networks (using Thomas Yeo parcellation)

2017-07-17 Thread Harms, Michael
Hi, There are actually 4 different maps in that file. If you load it into Workbench, the name associated with each map tells you what each map is. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental

Re: [HCP-Users] diffusion data merge pipeline

2017-07-17 Thread Harms, Michael
Hi, Is there a particular reason that you can’t provide all the dMRI scans at once, and let the pipeline handle the merging for you? If you process each dMRI run separately, then the individual runs will not be in optimal alignment. (You would be relying on the registration of each run to the

Re: [HCP-Users] Questions about reconstruction speed of Multi-band EPI sequence in LSCMRR

2017-07-17 Thread Harms, Michael
one 300 GB system hard disk, 3. one 300 GB hard disk for database, 4. one 300 GB hard disk for image data and 5. one CD-R/DVD-R drive for image storage, Any relevant information and idea would help a lot. Thank you very much! Looking forward to your reply. -- Meizhen Han PhD Candida

Re: [HCP-Users] CMRR vs MGH multiband/SMS sequences

2017-07-14 Thread Harms, Michael
What banding artifact are you referring to? Could you post a picture to a sharing site? thx -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of

Re: [HCP-Users] CMRR vs MGH multiband/SMS sequences

2017-07-12 Thread Harms, Michael
Essa Yacoub from CMRR sent me the following for distribution to the HCP-User list on this issue: "A lot of investigators have done comparisons between the sequences. Most of this data is not public, although there are some sites that have published things - e.g.

Re: [HCP-Users] Diffusion Preprocessing Error/Bug

2017-07-06 Thread Harms, Michael
Which version of FSL are you using? I believe that the eddy_unwarped_images.eddy_rotated_bvecs file will be created by the version of ‘eddy’ that comes with the newest FSL (5.0.10), but if you are using FSL 5.0.9, you needed to install the “eddy patch” to get that functionality. cheers, -MH

Re: [HCP-Users] Convert a .dscalar.nii to multiple nifti files?

2017-07-05 Thread Harms, Michael
multiple nifti files contains only cerebellar data, which is not surface information. Would there be any way of converting that to multiple nifti files? Thank you very much, Xavier. ____ From: Harms, Michael [mha...@wustl.edu<mailto:mha...@wustl.edu>] Sent:

Re: [HCP-Users] Maximal number of unrelated subjects that have complete 3T resting state and task data

2017-06-30 Thread Harms, Michael
Hi, No plans to provide such a subject group in the interface, but it is easy enough to compute such a group using the variables that we have provided in the database. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the

Re: [HCP-Users] Questions about reconstruction speed of Multi-band EPI sequence in LSCMRR

2017-06-30 Thread Harms, Michael
We have a more recent (and importable) protocol available here that I would suggest you use as a starting point: http://protocols.humanconnectome.org/CCF/ Your Prisma should already come with GPUs. Are you using the 64 channel coil? That will be a slower recon than the 32 ch coil, but I

Re: [HCP-Users] mapping of ROIs to networks - "posted question"

2017-06-30 Thread Harms, Michael
We’ve run InfoMap on them, but I haven’t had a chance to review them. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South

Re: [HCP-Users] Structural Protocol

2017-06-23 Thread Harms, Michael
ural Protocol Thanks Michael. Do you think my study would be eligible for registration with the HCP? If so, how would I go about setting this up? Best wishes, Rachel On 22 June 2017 at 18:46, Harms, Michael <mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote: Hi, Check out the vario

Re: [HCP-Users] Structural Protocol

2017-06-22 Thread Harms, Michael
hed sighted controls is actually more difficult than recruiting patients. Best wishes, Rachel On 21 June 2017 at 14:33, Harms, Michael <mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote: Hi, You can find an importable protocol here: http://protocols.humanconnectome.org/CCF/ The pr

Re: [HCP-Users] Structural Protocol

2017-06-21 Thread Harms, Michael
Hi, You can find an importable protocol here: http://protocols.humanconnectome.org/CCF/ The protocols that we are using for the HCP-Aging/Development projects are highly similar, but include a few additions (e.g., switch to navigator-corrected anatomicals; addition of PCASL scan). Those will

Re: [HCP-Users] rejected datasets

2017-06-16 Thread Harms, Michael
Hi, We will not be releasing any additional data that hasn’t already been released. (Such subjects have been reported to our IRB as excluded from the Young Adult HCP, and are not eligible for release). Information on existing released subjects with identified quality control issues can be

Re: [HCP-Users] Question about unprocessed fMRI data

2017-06-08 Thread Harms, Michael
This is via Essa: It is the same as what is done in the Siemens product - these are Siemens code/algorithms. But yes - they do B0 corrections, including in post-processing. -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of

Re: [HCP-Users] Matching field map resolutions to images

2017-06-08 Thread Harms, Michael
In theory, the resolutions and matrix size don’t need to match. But I thought that, as a practical matter, the Pipelines don’t work if they don’t match. At least that was the case at some point in the past... -- Michael Harms, Ph.D. ---

Re: [HCP-Users] values in myelin maps

2017-06-08 Thread Harms, Michael
tional if it doesn’t already exist. Peace, Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Thursday, June 8, 2017 at 4:21 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Harms,

Re: [HCP-Users] values in myelin maps

2017-06-07 Thread Harms, Michael
ce tuning happens in between –white and –smooth2 whereas the pial surface tuning happens between -pial and -surfvolume on this table: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3 Peace, Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...

Re: [HCP-Users] values in myelin maps

2017-06-07 Thread Harms, Michael
Unfortunately, the HCP Pipelines do not currently support rerunning FreeSurfer after editing. It is on our list of “things to do” to add that functionality. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of

Re: [HCP-Users] slice-to-volume registration in DWI - venetian blind artifact

2017-06-05 Thread Harms, Michael
Jesper’s plan is to release an updated version of ‘eddy’ that includes the slice-to-volume registration after OHBM. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School

Re: [HCP-Users] (no subject)

2017-05-25 Thread Harms, Michael
Hi Ariana, If you were referring to asymmetry in the ventricles, I passed an image on to our radiologist, and he confirmed that the ventricular asymmetry is within normal variability. If there was something else that you were referring to, please let us know off the list. thanks, -MH --

Re: [HCP-Users] cifti file

2017-05-25 Thread Harms, Michael
They were acquired with opposite phase encoding (PE) directions, and thus will have differing areas of susceptibility dropout. We recommend using them together, as a *pair* of scans, so as to avoid potential biases from using just one of the two PE directions. cheers, -MH -- Michael Harms,

Re: [HCP-Users] run-level (level 1) functional MRI data

2017-05-23 Thread Harms, Michael
{fMRIName}_{LR,RL}__{L,R}.native.func.gii? Thanks, Jiang Jian At 2017-05-23 22:31:34, "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote: Hi, Do you want the “Level 1” results processed through the task model (GLM)? Or, do you just want the “minimally p

Re: [HCP-Users] run-level (level 1) functional MRI data

2017-05-23 Thread Harms, Michael
Hi, Do you want the “Level 1” results processed through the task model (GLM)? Or, do you just want the “minimally preprocessed” data that entered into the task analysis scripts? These are available in:

Re: [HCP-Users] Question about DWI protocol

2017-05-23 Thread Harms, Michael
Yes, in DiffPreprocPipeline_PostEddy.sh you’ll need to use “--combine-data-flag=2” Also, I want to caution you about collecting only half of the total dMRI data that we collected in the UMN Lifespan piloting. There is a reason that we collected a full 20 min of dMRI when using 1.5 mm

Re: [HCP-Users] Subject keys

2017-05-23 Thread Harms, Michael
Yes, you can use the subject IDs in a public document, PROVIDED that NOTHING that comes from the RESTRICTED data is associated with that subject ID in your public document. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the

Re: [HCP-Users] cifti MATLAB

2017-05-23 Thread Harms, Michael
Hi, Are you using the latest gifti library available via the link mentioned here? https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB? cheers, -MH -- Michael Harms, Ph.D. ---

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