Re: [HCP-Users] Troubleshooting error with gradunwarp

Thanks Mike. Matt. From: "Harms, Michael" Date: Thursday, June 27, 2019 at 3:02 PM To: "Jayasekera, Dinal" Cc: "Glasser, Matthew" Subject: Re: [HCP-Users] Troubleshooting error with gradunwarp Hi Dinal, This issue should be resolved with the commit that I just pushed to the master. Cheers,

Re: [HCP-Users] Troubleshooting error with gradunwarp

Hi, That sounds like this issue, which we haven’t patched quite yet: https://github.com/Washington-University/HCPpipelines/issues/119 Incidentally, you must be running off code in the current master branch, rather than the formally tagged “v4.0.0” release

[HCP-Users] Troubleshooting error with gradunwarp

Dear all, I'm trying to troubleshoot an error that I'm getting when running v4.0 PreFreeSurferPipelineBatch. I initially thought the error arose as a result of grandunwarp but I don't think that is the case anymore. This is the error I am receiving:

Re: [HCP-Users] MSMAll Failure Following hcp-fix_multi-run

Please upgrade to the latest version of the HCP Pipelines (the latest master has a few fixes relative to 4.0.0), the latest FSL 6.0.1, and the latest FIX. Matt. From: on behalf of Timothy Hendrickson Date: Sunday, June 23, 2019 at 4:32 PM To: "hcp-users@humanconnectome.org" Subject:

[HCP-Users] MSMAll Failure Following hcp-fix_multi-run

Hello, I am having issues running MSMAll following hcp-fix_multi-run for a study that I am doing processing for. The particular study that I am processing data for has 6 fMRI scans totalling 2950 timepoints per scanning session. I am certainly aware of the large amount of memory that

Re: [HCP-Users] matlab cifti io

Look at option B here: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ Matt. From: on behalf of Aaron R Date: Sunday, June 23, 2019 at 9:04 AM To: hcp-users Subject: [HCP-Users] matlab cifti io Dear HCP users, What's the current link for the matlab cifti i/o tools? The

[HCP-Users] matlab cifti io

Dear HCP users, What's the current link for the matlab cifti i/o tools? The link in the readme here (and everywhere else) is dead: https://github.com/Washington-University/cifti-matlab Thanks, Aaron ___ HCP-Users mailing list

Re: [HCP-Users] table for parcellation

(ii) Yes that is the right file. I would use the already concatenated one from MR+FIX, else you need to use the _vn files to concatenate yourself (demean, divide by _vn files, and merge). Matt. From: on behalf of Timothy Coalson Date: Friday, June 21, 2019 at 2:20 PM To: Marta Moreno Cc:

Re: [HCP-Users] NIFTI to CIFTI

I don't know what 3dDeconvolve does, but if you used it to try to do anything spatial (spatial sharpening, PSF, etc), then the files produced by wb_command -cifti-convert would be entirely inappropriate. The only meaningful operations that can be done on -cifti-convert "volume-ish" files are

Re: [HCP-Users] A question about scene file

As part of some other updates to the StructuralQC scenes themselves, I recently created a more sophisticated generation script that should use relative paths within the scene. Please try the just updated master branch of https://github.com/Washington-University/StructuralQC We have tested

Re: [HCP-Users] A question about scene file

Sorry, in my second paragraph I meant "breaking the usual convention of the scene file XML". Tim On Fri, Jun 21, 2019 at 2:28 PM Timothy Coalson wrote: > The paths inside a scene file's XML are supposed to be relative to the > location of the scene file. You are expected to usually have the

Re: [HCP-Users] A question about scene file

The paths inside a scene file's XML are supposed to be relative to the location of the scene file. You are expected to usually have the scene file in a directory nearby where the data it refers to is, to reduce how far it crosses your filesystem structure to generate the relative paths. You can

Re: [HCP-Users] table for parcellation

(i) You can use wb_command -cifti-label-export-table on the dlabel file to get the order of the parcels in a fixed format, though there are extra lines and numbers in the output text file. 360 parcels is a rather long table, you might consider a matrix figure instead, and only mention the

[HCP-Users] NIFTI to CIFTI

Hello All, I am relatively new to working with HCP tfMRI connectome data and am running into a bit of confusion about the following: I have statistical map outputs (in stats.nii.gz format) from, CIFTI data converted to NIFTI data that I put into AFNI 3dDeconvolve. I am interested in

[HCP-Users] A question about scene file

Dear HCP experts, The scene file (a structural processing QC scene) I generated in a Linux computer doesn't work in a Windows computer. It seems that the file paths were hard-coded in the scene file. Is there a way to make it more portable? Thank you.

[HCP-Users] table for parcellation

Dear experts, After running: 1. PreFreeSurfer 2. FreeSurfer 3. PostFreeSurfer 4. fMRIVolume 5. fMRISurface 6. ICA+FIX (MR+FIX) 7. MSMAll (Do MSM Surface Registration) 8. dedrift and resample pipeline 2 questions: (i) I used wb_command -cifti-parcellate and wb_command

Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

The more timepoints, the more components, so that aspect seems okay. As far as the new beta MR+FIX training file, I’ll send you a link off list. I would use that. Matt. From: Yizhou Ma Date: Thursday, June 20, 2019 at 4:36 PM To: "Glasser, Matthew" Cc: "hcp-users@humanconnectome.org" ,

Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

Dear Matt, I am writing to follow up with this issue. Per your suggestion 2), I looked at the number of signal components in my multi-run ICA-FIX of 20 healthy controls. Again, my data are HCP-style. Each subject has 4 resting state scans (TR=0.8s, length=6.5min each) and 3 task scans (TR=0.8s,

[HCP-Users] expanded data on drug usage

Dear HCP team, Is there additional data on drug usage for HCP investigators that's not already provided in the restricted dataset? In the following paper: https://www.ncbi.nlm.nih.gov/pubmed/26308883 the authors report on a subset of participants that "reported not using cannabis within the

Re: [HCP-Users] problems to download the example data to run HCP Pipelines and NHPPipelines

Hi Vanessa, I'm assuming there's either a firewall issue preventing the download or that the browser isn't allowing the plugin to launch. If you right click on Aspera in the system tray (start it up if it's not running), there should be a "Run Diagnostic" link that you can use to check for

Re: [HCP-Users] problems to download the example data to run HCP Pipelines and NHPPipelines

Yes. Here are the links, thank you. It looks like the links are the same for both human and NHP https://db.humanconnectome.org/app/action/ChooseDownloadResources?project=HCP_Resources=SampleData=HcpPipelinesExampleDataGDC.zip#

Re: [HCP-Users] problems to download the example data to run HCP Pipelines and NHPPipelines

This has got to be a link from the Github Pipelines, right Vanessa? Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387

Re: [HCP-Users] problems to download the example data to run HCP Pipelines and NHPPipelines

Could you clarify what exactly you tried to download? I don't know of any non-human data in connectomedb, either. Tim On Tue, Jun 18, 2019 at 9:17 AM DE CASTRO Vanessa wrote: > Good morning, I'm trying to download the example data to run the HCP > Pipelines, and also the ones related to the

[HCP-Users] problems to download the example data to run HCP Pipelines and NHPPipelines

Good morning, I'm trying to download the example data to run the HCP Pipelines, and also the ones related to the non-human primates, and there is no way; even with the last version of Aspera Connect. What can I do? Than you very much. Sincerely, -- Vanessa DeCastro, PhD Centre de Recherche

Re: [HCP-Users] film_gls error pinv() svd()

Not really. You could ask on the FSL list. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel:

Re: [HCP-Users] film_gls error pinv() svd()

Nope, Matt, no empty EVs and estimations worked fine for subcortex with the exact same design. Removing ‘--sa --ms=15 --epith=5’ did make it work. Any ideas what would this indicate? Moataz From: Glasser, Matthew [mailto:glass...@wustl.edu] Sent: 18 June 2019 02:54 To: Harms, Michael ; Moataz

[HCP-Users] HCP course virtual machine downloading error

Hello, I am Yucheng Liang, a current student at the University of Illinois at Urbana-Champaign. I am interested in downloading HCP course virtual machine, however, I have trouble doing so. I followed the tutorial on

Re: [HCP-Users] film_gls error pinv() svd()

Is there anything weird about your design like empty EVs? Matt. From: on behalf of "Harms, Michael" Date: Monday, June 17, 2019 at 12:55 PM To: Moataz Assem , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] film_gls error pinv() svd() Hmmm. Assuming the problem is reproducible,

Re: [HCP-Users] film_gls error pinv() svd()

Hmmm. Assuming the problem is reproducible, I think you’ll have to report this, to the FSL list. To provide additional information, it might be helpful to hack the TaskfMRILevel1.sh script to not use the ‘--sa --ms=15 --epith=5’ flags in the call to ‘film_gls’ (or, perhaps easier, just try

[HCP-Users] film_gls error pinv() svd()

Hi, I get the following fsl error related to the beta estimations (while running film_gls): Prewhitening and Computing PEs... Percentage done: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39, error: pinv(): svd failed pinv(): svd

Re: [HCP-Users] -volume-label-import

You cannot have multiple label keys with the same name in a single label map. There are two very separate things that label volumes can do in cifti create commands: one is to set the name of a particular subset of voxels to group them into a "structure" (which has a limited set of available

Re: [HCP-Users] Training data set for multi-run fix

I am happy to share the new training file on request as a beta. Once we’ve got a good look at the recently cleaned HCP-YA task fMRI data and haven’t found any issues, I think it would be okay to release generally. Matt. From: on behalf of "Harms, Michael" Date: Friday, June 14, 2019 at

Re: [HCP-Users] -volume-label-import

What are the input names? Matt. From: on behalf of "Sanchez, Juan (NYSPI)" Date: Friday, June 14, 2019 at 12:34 PM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] -volume-label-import Dear HCP community I am trying to create a labeled volume that will work with

Re: [HCP-Users] Myelin values from white matter

You would need to do things like that with the T1w/T2w ratio volume. I’ll note that the relationship between myelin and T1w/T2w is less well characterized in white matter. Matt. From: on behalf of Antonin Skoch Reply-To: Antonin Skoch Date: Wednesday, June 12, 2019 at 8:27 AM To:

Re: [HCP-Users] Training data set for multi-run fix

Hi, I’m not sure if the new training file is ready for public release yet, but just to clarify, to clean short fMRI runs, you really need to use multi-run FIX to get better separation of the signal/noise components. The new training file will help around the margins, but using MR-FIX is

[HCP-Users] -volume-label-import

Dear HCP community I am trying to create a labeled volume that will work with -cifti-create-dense-from-template The volume data has over 100 ROI's and the cifti create function only imports specified labels CORTEX_LEFT CORTEX_RIGHT CEREBELLUM ACCUMBENS_LEFT ACCUMBENS_RIGHT ALL_GREY_MATTER

[HCP-Users] Training data set for multi-run fix

Hello We are an HCP disease connectome site. At the HCP-Investigators meeting it was mentioned that a new training data set for multi-run fix would be available that could be used to clean short (~6 mins) fMRI runs. If the training data for FIX is already available, could anyone provide the

[HCP-Users] Corrupt Input Data

## In replies all text above this line is added to the ticket ## You are registered as a cc on this help desk request and are thus receiving email notifications on all updates to the request. Reply to this email to add a comment to the request. --

[HCP-Users] Myelin values from white matter

Dear experts, I was using s=my_subject_ID atlas=HCP_S1200_GroupAvg_v1/Gordon333.32k_fs_LR.dlabel.ni wb_command -cifti-parcellate $p/MNINonLinear/fsaverage_LR32k/${s}.MyelinMap_BC.32k_fs_LR.dscalar.nii $atlas COLUMN ${s}.MyelinMap_BC.pscalar.nii -method MEAN wb_command -cifti-convert

[HCP-Users] Welcome to HELP DESK

Welcome to National Institutes of Health. Please follow the link below to choose a password, and we will log you in right away. https://ndar.zendesk.com/verification/email/bDO5VTF4M2Y8EtMa86A6QQ20ArOlY10X This email is a service from HELP DESK .

Re: [HCP-Users] Corrupt Input Data

dcm2bids is not a part of the HCP Pipelines and this seems like a ABCD data corruption issue. Matt. From: on behalf of Eric Earl Date: Tuesday, June 11, 2019 at 5:59 PM To: NIMH Data Archive Help Desk Cc: Damien Fair , HCPhelp Subject: Re: [HCP-Users] Corrupt Input Data Sveta, Anders

Re: [HCP-Users] Corrupt Input Data

Sveta, Anders meant the ABCD baseline year 1 data. ~Eric [OHSU email via VMware Boxer] On Jun 11, 2019 7:52 AM, NIMH Data Archive Help Desk wrote: ## In replies all text above this line is added to the ticket ## You are registered as a cc on this help desk request and are thus receiving

Re: [HCP-Users] RE-POSTING: Duplicate subjects in Connectome in a Box?

Hi Christina, After discussion with the technician who produced the Connectome in a Box drives, we're thinking what you're seeing could be an issue specific to your copy of the drives. I'll contact you off-list to discuss. Regards, Mike From: hcp-users-boun...@humanconnectome.org On

Re: [HCP-Users] Cluster threshold by wb_command -metric-find-clusters

Got it. It works. Thank you so much. Best Zaixu On Sat, 8 Jun 2019 at 23:35, Glasser, Matthew wrote: > Looks like you can use wb_command -cifti-find-clusters with those 4 > files. Metric refers to a gifti file. > > > > Matt. > > > > *From: * on behalf of Zaixu Cui < >

Re: [HCP-Users] A question about the usage of Connectome Workbench

You can set number of rows, columns, and the space between slices. Then you can set the midpoint of the slices using the numbers next to the P, C, or A buttons. Matt. From: on behalf of Aaron C Date: Sunday, June 9, 2019 at 12:46 AM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users]

Re: [HCP-Users] Cluster threshold by wb_command -metric-find-clusters

Looks like you can use wb_command -cifti-find-clusters with those 4 files. Metric refers to a gifti file. Matt. From: on behalf of Zaixu Cui Date: Saturday, June 8, 2019 at 11:53 PM To: "HCP-Users@humanconnectome.org" Subject: [HCP-Users] Cluster threshold by wb_command

[HCP-Users] A question about the usage of Connectome Workbench

Dear HCP experts, I have a question about the usage of Connectome Workbench. In the "Volume" tab, when using "Montage", how could I control the range of slices? For example, if I view multiple parasagittal slices (by clicking the "P" button), how to vary X values? Thank you.

[HCP-Users] Last weeks to register for HCP Course 2019!

Reminder that it's the last few weeks to register for this year's HCP Course July 8 – 12, 2019 in beautiful, cool Portland, Oregon. We have room for you! Don't delay, our hotel booking deadline is one week from today, Saturday June 15. Check out the updated HCP Course schedule and faculty

[HCP-Users] Cluster threshold by wb_command -metric-find-clusters

Hi developers, I am trying to do cluster threshold by using command wb_command -metric-find-clusters. Thee manual is as follows: wb_command -metric-find-clusters - the surface to compute on - the input metric - threshold for data values - threshold for cluster

Re: [HCP-Users] Strange output when running ./FreeSurferPipelineBatch.sh

That is a normal, if a somewhat ominous informational message. Matt. From: on behalf of Kavinash Loganathan Date: Saturday, June 8, 2019 at 2:39 AM To: "HCP-Users@humanconnectome.org" Subject: [HCP-Users] Strange output when running ./FreeSurferPipelineBatch.sh Hi guys, I finished the

[HCP-Users] Strange output when running ./FreeSurferPipelineBatch.sh

Hi guys, I finished the PreFreesurfer run on the example file and just started Freesurfer pipeline when I got this output: This script must be SOURCED to correctly setup the environment prior to running any of the other HCP scripts contained here 100307 About to use fsl_sub to queue or run

Re: [HCP-Users] RE-POSTING: Duplicate subjects in Connectome in a Box?

Are you sure that there is duplication of actual *data* on the different drives? Just because a subject ID appears on multiple drives doesn’t mean that data under that subject ID is the same on the drives. Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] RE-POSTING: Duplicate subjects in Connectome in a Box?

1. I don’t know, but perhaps someone from NRG can answer. 2. Those are different smoothing levels. I do not recommend using more than s4 and personally don’t use anything but s2. You can see Coalson et al 2018 PNAS: https://www.pnas.org/content/115/27/E6356.short for the deleterious

[HCP-Users] RE-POSTING: Duplicate subjects in Connectome in a Box?

Hi HCP gurus: I'm reposting the following question(s) in hopes that one of you knows the answer. (1) On looking through the data, it appears that there is duplication between the drives delivered. Is that intentional? We received 12 drives, but four of them appear to be duplicates.

Re: [HCP-Users] wb_command -convert-matrix4-to-workbench-sparse

Tractography visualization is somewhat rough around the edges. What was the full probtrackx command you used? Do you have bingham parameter volumes for the fiber orientations (mean, stdev, theta, phi, psi, ka, kb), or only the fiber orientation sample volumes? Tim On Fri, Jun 7, 2019 at 7:48

Re: [HCP-Users] A minor question regarding HCP 7T movie data

Hi, It isn’t surprising that data will be missing in some subjects, due either to problems at the scanner, or problems during processing. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University

Re: [HCP-Users] A minor question regarding HCP 7T movie data

Thanks Keith! I am currently working with the Movie Task fMRI 2mm/32k FIX-Denoised (Compact) dataset, and I noticed the issues below: 1) Two subjects (126931 and 74) do not have MSMAll-registered time-series data. 2) Five subjects (181636, 473952, 536647, 552241, and 973770) have two runs

[HCP-Users] wb_command -convert-matrix4-to-workbench-sparse

Good morning, I would like to transform my data obtained with fsl's probtackx, to visualized them with wb_view. But the instructions to run the command is not clear for me. I've tried several choices but there is always something missing or nor recognized (I'm very naive with all this.. just

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

Yes the updates worked! I was actually about to comment on the github issue you posted about the similar issue with applywarp when you added the comment about flirt. -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A Institute for Neuroscience Texas

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

Try the very latest master, which should resolve this issue. (I was just working on this 30 min ago). Please let us know if it works. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine

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

We ran into the same problem with *flirt*. In FSL 6.0.1, *flirt *can't take a 4D file as a reference, but it could in fsl v5. Adding a line before 289 to extract the first volume of PhaseTwo_gdc, and modifying flirt accordingly fixes the problem: ${FSLDIR}/bin/fslroi ${WD}/PhaseTwo_gdc

Re: [HCP-Users] wb_command -cifti-gradient

"wb_command -gifti-help" is intended to help explain these file formats: https://www.humanconnectome.org/software/workbench-command/-gifti-help There are other -*-help options for other formats, and other aspects of wb_command, like how to read the command usage info:

Re: [HCP-Users] wb_command -cifti-gradient

A 32k fs_LR surface file with suffix of dscalar.nii, and a thickness.32k_fs_LR.dscalar.nii can be an example. | | 秦键 | | 邮箱：qinjian...@126.com | 签名由 网易邮箱大师 定制 On 06/05/2019 10:36, Glasser, Matthew wrote: What file did you try to run this on? Matt. From: on behalf of 秦键 Date:

Re: [HCP-Users] wb_command -cifti-gradient

You can use the midthickness surfaces .surf.gii in the same folder. Matt. From: 秦键 Date: Tuesday, June 4, 2019 at 10:02 PM To: "Glasser, Matthew" Cc: "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] wb_command -cifti-gradient A 32k fs_LR surface file with suffix of dscalar.nii, and a

Re: [HCP-Users] wb_command -cifti-gradient

What file did you try to run this on? Matt. From: on behalf of 秦键 Date: Tuesday, June 4, 2019 at 9:32 PM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] wb_command -cifti-gradient Dear professors, When I used the wb_command -cifti-gradient for fs_LR 32k cifti file, I was asked to

[HCP-Users] wb_command -cifti-gradient

Dear professors, When I used the wb_command -cifti-gradient for fs_LR 32k cifti file, I was asked to input the left and right surface files, where can I find the left and right surface files and what are the format of them? Can I have an example of the use of the wb_command -cifti-gradient?

Re: [HCP-Users] pdconn analysis problems

Got it, thanks! -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A Institute for Neuroscience Texas A University College Station, TX On Mon, Jun 3, 2019 at 8:14 PM Timothy Coalson wrote: > If you just want to look at them first, you can load them

Re: [HCP-Users] pdconn analysis problems

Also, if you literally want spatial gradient magnitude, you can run -cifti-gradient on the correct dimension of the pdconn (or dpconn) file. Tim On Mon, Jun 3, 2019 at 8:14 PM Timothy Coalson wrote: > If you just want to look at them first, you can load them into wb_view. > Depending on

Re: [HCP-Users] pdconn analysis problems

If you just want to look at them first, you can load them into wb_view. Depending on whether it is pdconn or dpconn (via a transpose), you will either get a dense map when you click a parcel, or a parcellated map when you click a vertex/voxel. Tim On Mon, Jun 3, 2019 at 8:04 PM Joseph Orr

Re: [HCP-Users] pdconn analysis problems

You don't need matlab for that, -cifti-change-mapping will let you reset a dimension to scalars. Depending on the input file, you may also need a -cifti-transpose to get a dscalar. Tim On Mon, Jun 3, 2019 at 7:58 PM Glasser, Matthew wrote: > Are you wanting to view the files? You could

Re: [HCP-Users] pdconn analysis problems

Each row or column (the shorter dimension) will be a dense map for connectivity to a parcel. Matt. From: Joseph Orr Date: Monday, June 3, 2019 at 8:03 PM To: "Glasser, Matthew" Cc: HCP Users Subject: Re: [HCP-Users] pdconn analysis problems I wanted to contrast the connectivity of the

Re: [HCP-Users] pdconn analysis problems

I wanted to contrast the connectivity of the different parcels in order to look for evidence of gradients in networks. I'll try it in matlab. -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A Institute for Neuroscience Texas A University College

Re: [HCP-Users] pdconn analysis problems

Are you wanting to view the files? You could probably translate the file into a .dscalar.nii using matlab. Matt. From: on behalf of Joseph Orr Date: Monday, June 3, 2019 at 7:55 PM To: HCP Users Subject: Re: [HCP-Users] pdconn analysis problems Thanks Tim, running cifti-transpose and

Re: [HCP-Users] pdconn analysis problems

Thanks Tim, running cifti-transpose and separating on COLUMN solved both issues. Is there a way to separate the different parcels that make up a pdconn so that I can compare the connectivity maps between parcels? Thanks, Joe -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological

Re: [HCP-Users] A minor question regarding HCP 7T movie data

Hi Reza, Your interpretation of the timing is correct. The validation segment in each movie scan was shifted by 40-200ms for the "v2" version. This was done in order to make that final 83 second clip begin precisely at the start of the next TR for all 4 movie sessions. Given HRF variability,

Re: [HCP-Users] MMP parcellation for 7T

In particular, if you are only tracking the parcels x parcels matrix, using the 59k surfaces should make effectively no difference. They mostly exist to try to capture the higher resolution fMRI data. Even if you were capturing per-vertex tractography counts, the uncertainty in the probabilistic

Re: [HCP-Users] MMP parcellation for 7T

With the 3T data. Matt. From: "Shadi, Kamal" Date: Sunday, June 2, 2019 at 8:00 PM To: "Glasser, Matthew" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] MMP parcellation for 7T I see. In that case, where should I find the 32k meshes for 7T? I only see 59k meshes in the 7T

Re: [HCP-Users] MMP parcellation for 7T

If you haven’t run the analysis yet, I would encourage you to just use the 32k meshes. No one has shown the 59k meshes to have a clear benefit and they take up a lot more space. Matt. From: "Shadi, Kamal" Date: Sunday, June 2, 2019 at 7:35 PM To: "Glasser, Matthew" ,

Re: [HCP-Users] MMP parcellation for 7T

I take it you are using the experimental 59k surfaces, rather than the 32k surfaces for general use? Matt. From: "Shadi, Kamal" Date: Sunday, June 2, 2019 at 6:40 PM To: "Glasser, Matthew" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] MMP parcellation for 7T Is there a

Re: [HCP-Users] MMP parcellation for 7T

There isn’t a separate 7T file yet. We do plan to investigate the parcellation with 7T fMRI data. Matt. From: on behalf of "Shadi, Kamal" Date: Sunday, June 2, 2019 at 11:32 AM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] MMP parcellation for 7T Dear HCP Experts, Is there a

[HCP-Users] MMP parcellation for 7T

Dear HCP experts, Is there a dlabel.nii file containing 180 MMP ROIs per hemisphere for 7T data release? I can find the file for 3T release in BALSA (Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii) but I could not find the similar file for 7T? Regards, Kamal

[HCP-Users] MMP parcellation for 7T

Dear HCP Experts, Is there a dlabel.nii file containing 180 MMP ROIs per hemisphere for 7T data release? I can find the file for 3T release in BALSA (Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii) but I could not find the similar file for 7T? Thanks in advance,

Re: [HCP-Users] pdconn analysis problems

It sounds like there might be both Workbench and PALM bugs here. Perhaps you could upload the data somewhere (off list if needed), so Tim and Anderson could take a look? Matt. From: on behalf of Joseph Orr Date: Saturday, June 1, 2019 at 1:00 PM To: HCP Users Subject: [HCP-Users] pdconn

[HCP-Users] pdconn analysis problems

I have a pdconn input (cortical ptseries by subcortical dtseries) that I'd like to analyze with PALM, but I'm having some trouble. I only found one old post related to this, but the only suggestion was to use -transpose data flag in palm. When palm tries to read in the pdconn, I get an error

[HCP-Users] A minor question regarding HCP 7T movie data

Hi, The HCP S1200 Reference Manual says that there are two versions of 4 movie files. Some subjects have been scanned with one version, and the remaining subjects have been scanned with another version. Version 2 includes these changes: 7T_MOVIE1_CC1_v2 remains unchanged. 7T_ MOVIE2_HO1_v2

Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)

Thank you so much! I understand it better now. best regards Jaime El mié., 29 may. 2019 a las 21:43, Timothy Coalson () escribió: > Yes, it is a similar problem to working in "image space", basically the > FSL tools work in a space resulting from taking the voxel indices and > multiplying them

[HCP-Users] Inquiry about data

Dear Prof. I am from Central South University. Thank you very much for providing the Connectome Coordination Facility platform and collecting so much data as public data. This provides brain researchers with great convenience and a large amount of data, which is a very important and meaningful

Re: [HCP-Users] Inquiry about data

Hi, You need to complete the process for “Restricted Access” in ConnectomeDB, and then you’ll have access to the more granular age information. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington

Re: [HCP-Users] Group-averaging of task fMRI data

Ah yes, that was probably indeed the case upon further reflection. Thanks for the correction. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660

Re: [HCP-Users] Group-averaging of task fMRI data

Hi Mike, My recollection was that the unnamed .dscalar.nii files were zstats, not beta maps. I added the beta maps later when it became clear that using statistical significance maps was inappropriate for parcellation. Matt. From: on behalf of Reza Rajimehr Date: Thursday, May 30, 2019 at

Re: [HCP-Users] Downloading movement regressors from HYA release

Thank you very much! Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd lto...@stanford.edu | (650) 5615738 From: "Hodge, Michael" Date: Thursday, May 30, 2019 at 7:24 AM To: "Harms, Michael" , Leonardo Tozzi ,

Re: [HCP-Users] Group-averaging of task fMRI data

Thanks Michael for your detailed and helpful answers. Best, Reza On Thu, May 30, 2019 at 6:10 PM Harms, Michael wrote: > > > Hi Reza, > > > > 1) We’ve already generated Cohen’s d-style effect size maps for all > contrasts, using all subjects, as part of the “Group Average Dataset” > available

Re: [HCP-Users] Group-averaging of task fMRI data

Hi Reza, 1) We’ve already generated Cohen’s d-style effect size maps for all contrasts, using all subjects, as part of the “Group Average Dataset” available at https://db.humanconnectome.org/data/projects/HCP_1200. If you need it computed for a specific subset of subjects, then yes, you can

Re: [HCP-Users] Item data for NIH Emotion battery

Hi Leonardo, Do you mean the NIH Toolbox Emotion domain? I can send you the TB data as a spreadsheet off list. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue

Re: [HCP-Users] PRISM DWI Parameter Request

Hi, All those details, including an importable VE11C protocol are available at http://protocols.humanconnectome.org/ Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine

[HCP-Users] PRISM DWI Parameter Request

Hello, I am emailing you as recommended by the HCP_S1200 User manual to request the diffusion parameters and gradient table that we would want to use the HCP diffusion sequence on a 3T PRISMA. Could you kindly tell me what changes in TE, resolution, and b-values would be needed for the PRISMA.

Re: [HCP-Users] Downloading movement regressors from HYA release

Hi Leonardo, There was a problem with the resource catalogs for those 5 subjects. I believe the files should now be accessible via the URL you were using. Let me know if that’s not the case. Regards, Mike From: Harms, Michael Sent: Wednesday, May 29, 2019 1:51 PM To: Leonardo Tozzi ;

[HCP-Users] Group-averaging of task fMRI data

Hi, For a group of subjects (e.g. 100 subjects in HCP S1200), we want to generate a group-average Cohen’s d map for a particular contrast in the working memory task. For this, we take level2 “cope1.dtseries.nii” file in cope20.feat folder of all those subjects, merge them using -cifti-merge, then

Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical)

Yes, it is a similar problem to working in "image space", basically the FSL tools work in a space resulting from taking the voxel indices and multiplying them by the voxel dimensions, so a particular corner voxel always has coordinates of (0, 0, 0)mm. Because of the transition from origin-less

Re: [HCP-Users] Downloading movement regressors from HYA release

Which specific files (i.e., which runs) is curl not finding for those remaining subjects? Mike Hodge will likely need to investigate further, because I’m able to find the expected files on our local file systems for 101006 at least. It may be something specific to how REST works, with

  1   2   3   4   5   6   7   8   9   10   >