Re: [HCP-Users] misidentification of central sulcus in FreeSurfer and MSM

Hi Ely, That is helpful to know. We have not validated MSMAll for very small amounts of fMRI data, and recommend using as much fMRI data as is available for each subject. Matt. From: "Ely, Benjamin" mailto:benjamin@mssm.edu>> Date: Thursday, December 20, 2018 at 9:44 AM To: Matt Glasser

Re: [HCP-Users] Time series data

t can guide which component belongs to which network or how to name them? If somehow, I discover connectivity between Component_1 and Component_3 is significantly related to some behavior, how can I express it in neuroscience term? I believe my question is clear now. Thanks Rakib From: "G

Re: [HCP-Users] Time series data

What neuroscience questions are ICA timeseries unable to answer? Particularly that gyral/sulcal folding-based parcellation would be able to answer? If you want a neuroanatomical parcellation into cortical areas, this is available here: https://balsa.wustl.edu/file/show/3VLx Matt. From:

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

I think that just means there wasn’t much movement in that rotation direction. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Manasij Venkatesh mailto:mana...@umd.edu>> Date: Tuesday, December 18, 2018 at 12:06 PM To:

Re: [HCP-Users] Noise level estimate from the data

I agree with Mike, don’t use those values. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Harms, Michael" mailto:mha...@wustl.edu>> Date: Monday, December 17, 2018 at 3:35 PM To: Jeiran Choupan mailto:jeiran.chou...@loni.usc.edu>>,

Re: [HCP-Users] misidentification of central sulcus in FreeSurfer and MSM

Hi Ely, This happens occasionally but MSMAll should get it right based on the myelin and RSN information. It is not unlike any other part of cortex that is not well aligned after folding registration, just that usually this part of cortex is well aligned by folding registration. Matt. From:

Re: [HCP-Users] combining tabs from different scenes within a scene file

Hi Ely, Unfortunately this is not supported. I don’t know if it would be feasible to support or not either. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Ely, Benjamin" mailto:benjamin@mssm.edu>> Date: Friday, December 14, 2018 at 9:01 PM To:

Re: [HCP-Users] HCP_FIX

ns in these line is that if I don't have a training data file, it uses the hcp training data as default. but this is not our purpose - we wish to create our own training data file, based on the hand classification we did on our data. Shachar On Tue, 11 Dec 2018 at 21:58, Glasser, Matthew mailto:

Re: [HCP-Users] HCP_FIX

cp_fix solves the fact the the main FIX script expects several files that do are not available from the registration process in the hcp pipeline. Thanks for your patience, Shachar On Tue, Dec 11, 2018, 14:07 Glasser, Matthew mailto:glass...@wustl.edu>> wrote: You can still do training

Re: [HCP-Users] HCP_FIX

any further instructions as to the correct workflow for using the FIX pipelines. thank you On Mon, 10 Dec 2018 at 23:13, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Did you use the hcp_fix script or some other method of running FIX on HCP data. Matt. From: Shachar Gal mailt

Re: [HCP-Users] Extract Individual Maps from CIFTI File

wb_command -cifti-merge contains the functionality of fslmerge and fslroi. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Monday, December 10, 2018 at 4:54 PM To:

Re: [HCP-Users] HCP_FIX

Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>

Re: [HCP-Users] DTI retest

We haven’t looked at the test/retest for diffusion and that sounds too extreme, i.e. something that one could even visually spot. It is possible you have done something wrong in your processing? The only thing that we can imagine is whether positioning in the scanner for test/retest has been

Re: [HCP-Users] The order of task event blocks in task fMRI data

It is possible that these subjects required a subsequent section to complete the task using a backup task design. There should not be differences in the acquisition otherwise. As far as I know, you should be able to combine them in any analysis that does not assume temporal alignment across

Re: [HCP-Users] HCP parcellation template

A as the HCP pipelines? Thanks and best wishes, Zhi On Wed, 28 Nov 2018 at 19:45, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: I believe FSFAST is a surface-capable analysis stream, so reanalysis might not be necessary vs figuring out how to translate between FSFAST and HCP-S

Re: [HCP-Users] average dconn from individual dconns

To be more specific: In the HCP we use a technique called MIGP to make group fMRI data and generate dense connectomes from that. Concatenated dense timeseries get very large when you have a lot of subjects and timepoints. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf

Re: [HCP-Users] HCP parcellation template

I believe FSFAST is a surface-capable analysis stream, so reanalysis might not be necessary vs figuring out how to translate between FSFAST and HCP-Style CIFTI stuff. I am sure that is possible but have not used FSFAST myself. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on

Re: [HCP-Users] Question about HCP pipeline structural data

Hi Guoyuan, Surfaces were made in native subject’s physical space (in ${StudyFolder}/${Subject}/T1w) after correcting for distortions. They can be transformed into MNI space after the fact using the same registration as was run on the volume files. If you wanted to make group average surface

Re: [HCP-Users] libnetcdf.so.6

You will need to find the error in the recon-all log. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of 南 修司郎 mailto:shujiromin...@me.com>> Date: Monday, November 26, 2018 at 10:29 PM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] Number of Scanners used in S1200 release

For 3T all subjects were scanned on a single custom connectome scanner. For 7T all subjects were scanned on one scanner. Matt. On 11/23/18, 5:49 AM, "hcp-users-boun...@humanconnectome.org on behalf of Nicola Toschi" wrote: >Dear List, > >a basic piece of info which I would like to put in

Re: [HCP-Users] Question about 24 parameter head motion regression

I wouldn’t do that. If you want to denoise the task fMRI data I would use the multi-run sICA+FIX (actually with turning off the movement regressors). Movement regressors are not very effective at reducing motion affects in the images and also remove some of your neural signal. Spatial ICA is

Re: [HCP-Users] HCP_FIX

ail: mha...@wustl.edu<mailto:mha...@wustl.edu> From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Thursday, November 22, 2018 at 8:29 AM To: Shachar Gal mailto:gal.shac...@gmail.com>> Cc: "hcp-

Re: [HCP-Users] HCP_FIX

e "fix cleaned" volume to surface, so when does that happen? considering that you mentioned you're currently editing these scripts, I think we would just use the original FSL FIX, and later project the fix cleaned volume to surface using your 'fMRISurface' pipeline. thanks, Shachar On

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

Subject: Re: [HCP-Users] Number of cortical vertices in cifti and gifti files Thanks Matt! Yes, having symmetric medial wall and having registered left and right hemispheres would be helpful and important. On Tue, Nov 20, 2018 at 5:54 AM Glasser, Matthew mailto:glass...@wustl.edu>> wrote: We

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

te: Friday, November 16, 2018 at 1:50 PM To: "Harms, Michael" mailto:mha...@wustl.edu>> Cc: "Glasser, Matthew" mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org&

Re: [HCP-Users] HCP_FIX

The hcp_fix script is for enabling a few enhancements specific to HCP-Style processing. These scripts are currently being edited and tested and we will have new versions announced soon. PostFix generates the Workbench scenes for hand classification of components. Matt. From:

Re: [HCP-Users] Perl issues with Freesurfer5.3

rc etc and recompiled from source code but do you think this would fix 6.0 for the pipelinesIs it known what change from 5.3 to 6.0 caused the issues? On Mon, Nov 19, 2018 at 6:26 AM Glasser, Matthew mailto:glass...@wustl.edu>> wrote: This is still being actively worked on. Unfortunat

Re: [HCP-Users] Perl issues with Freesurfer5.3

This is still being actively worked on. Unfortunately FS6.0 doesn’t work well for highres T1w and T2w (we will be using FreeSurfer’s own functionalities for this in the future once they are working). Once we have something ready and vetted, we will announce it and make it available to

Re: [HCP-Users] Number of cortical vertices in cifti and gifti files

That is correct, the medial wall is kept out. Usually when I want to do that I split the CIFTI file into hemispheric GIFTI files, but perhaps there is a good way to load in a specific mapping based on something we can output from wb_command. Matt. From:

Re: [HCP-Users] Problem with gradunwarp

HD<http://www.sshdonline.org/> # Check out the new book<http://www.routledge.com/9781138960039>: Dick, A.S., & Müller, U. (2018). Advancing Developmental Science: Philosophy, Theory, and Method. Taylor & Francis. From: "Glasser, Matthew" mailto:glass...@wustl.edu

Re: [HCP-Users] Problem with gradunwarp

Is this the latest version of gradunwarp? What python are you using? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Anthony Dick mailto:ad...@fiu.edu>> Date: Thursday, November 15, 2018 at 8:49 AM To:

Re: [HCP-Users] help with cifti command and 7T data - parcellating 64k per hemisphere?

I would use the 32k/91282 7T data instead of the 59k/170494 7T data unless you are explicitly testing the high resolution relative to the lower resolution. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of CARRISA COCUZZA mailto:cv...@scarletmail.rutgers.edu>> Date:

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

the script hardcodes a path to a 0.7mm mask. Tim On Fri, Nov 9, 2018 at 7:13 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Yes you probably need to have bash instead of a non-bash shell. Perhaps fixing that will solve the problem. As far as the resolution of the T1w and T2

Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation

| Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: Timothy Coalson mailto:tsc...@mst.edu>> Date: Friday, November 9, 2018 at 5:02 PM To: Leonardo Tozzi mailto:lto...@stanford.edu>> Cc: "Glas

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

ington University in St. Louis ________ From: Dierker, Donna Sent: Saturday, November 3, 2018 7:39:51 AM To: Jayasekera, Dinal Cc: Glasser, Matthew; Harms, Michael; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Debugging Ica

Re: [HCP-Users] White matter and CSF masks after minimal HCP processing

Those are generated by the RestingStateStats pipeline, but were mainly for an exploratory analysis that didn’t work. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Friday, November 9, 2018 at 12:47 PM To:

Re: [HCP-Users] Different resolution in T1w and T2w image

That should be okay. It will be about as good as a 1mm isotropic T2w image. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Darko Komnenić mailto:komnen...@gmail.com>> Date: Friday, November 9, 2018 at 11:16 AM To:

Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation

.edu> | (650) 5615738 From: Timothy Coalson mailto:tsc...@mst.edu>> Date: Friday, November 9, 2018 at 4:11 PM To: Leonardo Tozzi mailto:lto...@stanford.edu>> Cc: "Glasser, Matthew" mailto:glass...@wustl.edu>>, Stamatios Sotiropoulos mailto:stamatios.sotiropou...@ndcn.ox.a

Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation

lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: Timothy Coalson mailto:tsc...@mst.edu>> Date: Friday, November 9, 2018 at 4:11 PM To: Leonardo Tozzi mailto:lto...@stanford.edu>> Cc: "Glasser, Matthew" mailto:glass...@wustl.edu>>, Stamatios S

Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation

ces (need to convert them to ASCII using surf2surf) and subcortical volumes you can merge them into text files and use those as seeds. This will get you a dense connectome which you can then parcellate using any parcellation scheme you would like. Best wishes Stam On 30 Oct 2018, at 23:3

Re: [HCP-Users] MSMall Question

There is no specific cost function weighting being used (i.e. each feature has the same weight). Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Curtis, Mark T" mailto:mac...@pitt.edu>> Date: Monday, November 5, 2018 at 4:52 PM To:

Re: [HCP-Users] Questions about sulc, curvature, and thickness files

, and thickness files Thanks Matt! And: What the midthickness dscalar.nii files are? What does BC in MyelinMap_BC stand for? Reza On Mon, Nov 5, 2018 at 11:51 PM Glasser, Matthew mailto:glass...@wustl.edu>> wrote: 1. They are the same 2. Mean curvature same as FreeSurfer 3. Thickn

Re: [HCP-Users] Questions about sulc, curvature, and thickness files

1. They are the same 2. Mean curvature same as FreeSurfer 3. Thickness is same as FreeSurfer, CorrThickness has the curvature regressed out. Peace, Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Reza Rajimehr mailto:rajim...@gmail.com>> Date: Monday,

[HCP-Users] FW: Job announcement

Hi Everyone, We are looking for two computational neuroimaging scientists to join our Primate Connectome Project in Kobe, Japan. We hope to fill the positions soon and look forward to hearing from you. Please see the attached abridged job descriptions. Full job descriptions and details on how

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

CA+FIX as well and upgrade to FSL 6.0 and let you know how things change. Kind regards, Dinal Jayasekera PhD Candidate | InSITE Fellow Ammar Hawasli Lab Department of Biomedical Engineering | Washington University in St. Louis From: Glasser, Matthew Sent: Th

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

Hi Dinal, Also make sure you have the absolutely latest version of sICA+FIX, as there were recent changes and upgrade to FSL 6.0. Finally, we are testing some updates to hcp_multi_run_fix that you will need to be using for your project, and we can let you know when that is available. For

Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation

s case, what would be the argument for “ - the structure to output” ? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Glasser, Matthew&quo

Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation

I would separate the CIFTI file into GIFTI and NIFTI components with wb_command -cifti-separate and follow the instructions for surface tracking on FSL’s website. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>> Date:

Re: [HCP-Users] Question about dense functional connectome

basically interested in the functional connectivity matrix just for these 913 voxels (i.e. a 913 * 913 matrix). Is it possible to use wb_command to select part of *.dconn.nii corresponding to the voxels of interest? Best, Reza On Thu, Oct 25, 2018 at 3:49 AM Glasser, Matthew mailto:glass...@wustl.e

Re: [HCP-Users] Question about dense functional connectome

Use swap space. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Wednesday, October 24, 2018 at 4:57 PM To: Reza Rajimehr mailto:rajim...@gmail.com>> Cc: "hcp-users@humanconnectome.org"

Re: [HCP-Users] Fiber tracking starting from PTM volumetric labels

I would do something like that with the MSMAll CIFTI data. Matt. On 10/23/18, 6:49 PM, "hcp-users-boun...@humanconnectome.org on behalf of Nicola Toschi" wrote: >Hello List, > >I would like to ask the experts an opinion about an analysis we are >thinking of running. > >Would there be any

Re: [HCP-Users] dlabel file with FSL HistThal Atlas

It would need to be via wb_command -cifti-label-import and following the instructions in the usage there. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Hendrickson mailto:hendr...@umn.edu>> Date: Tuesday, October 23, 2018 at 5:43 PM To:

Re: [HCP-Users] Questions on libnetcdf.so.6 and HCP custom version of FreeSurfer (5.3.0-HCP)

Soon we should have a version compatible with FS 6.0+ Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Georgios Michalareas mailto:g...@ae.mpg.de>> Date: Tuesday, October 16, 2018 at 4:49 AM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] stable pipeline version

p-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] stable pipeline version Thank you Matt. Will there be an announcement re: the FreeSurfer? Best Juan ________ From: Glasser, Matth

Re: [HCP-Users] Inquiry regarding the applicability of HCP pipeline on conventional MRI dataset

This isn’t currently available, but there is work in progress to make available a legacy mode of the minimal preprocessing pipelines. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Zhi Li mailto:lizhi.ps...@gmail.com>> Date: Friday, October 12, 2018 at 2:05 PM To:

Re: [HCP-Users] hcp_fix_multi_fix errors

It might fix the problem. Matt. On 10/10/18, 4:42 PM, "Shankar Tumati" wrote: >Hi Matt, > >No, its 3.14. >Is the latest (3.15, I believe) needed for the script? > >Best, >Shankar >____________ >From: Glasser, Matthew [glass...@wu

Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

lortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) ---- Sincerely, Arman From: Glasser, Matthew mailto:glass...@wustl.edu>>

Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

What is using the CPU? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of ARMAN PRAFUL KULKARNI mailto:apkulkar...@wisc.edu>> Date: Wednesday, October 10, 2018 at 3:27 PM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc:

Re: [HCP-Users] hcp_fix_multi_fix errors

Is this with the latest melodic? Matt. On 10/10/18, 2:54 PM, "hcp-users-boun...@humanconnectome.org on behalf of Shankar Tumati" wrote: >Hi > >We get these seemingly random errors when implementing the >hcp_fix_multi_run code on the task data with some subjects. We need help >to figure it out.

Re: [HCP-Users] Visualizing Greyordinate Masks

to have 1s and 0s rather than the regression coeffecients), or if there is something else I need to change or add. Best, Cathy Am Mi., 10. Okt. 2018 um 04:14 Uhr schrieb Glasser, Matthew mailto:glass...@wustl.edu>>: Steve and I think you have the right file, but are not understanding what is confusi

Re: [HCP-Users] Visualizing Greyordinate Masks

Steve and I think you have the right file, but are not understanding what is confusing about viewing that file in Connectome Workbench, assuming you have loaded the appropriate surfaces and volumes. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Cathy Chen

Re: [HCP-Users] MSMAll for MultiRunICAFIX

Watch this space for an update on MSMAll with MultiRunFIX. The pipelines in the current master aren¹t all working together and we are working on fixing that. Matt. On 10/9/18, 9:58 AM, "hcp-users-boun...@humanconnectome.org on behalf of Sang-Young Kim" wrote: >Dear Experts: > >I have a

Re: [HCP-Users] stable pipeline version

If you can wait a week or two we will have some useful updates out. Also there is the impending switch to FreeSurfer 6.0 that would be good to have. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" mailto:juan.sanc...@nyspi.columbia.edu>> Date:

Re: [HCP-Users] archiving the results from HCP pipellines

I would save the list of files we release with the HCP Pipelines. If you search the list, you will see some other specific posts about saving space. I would be sure you don’t delete anything in an .spec file either. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of

Re: [HCP-Users] using the 360 area parcellation

Perhaps if you ran the dlabel file through a simple wb_command -cifti-math “x” .dscalar.nii -var x .dlabel.nii command and then loaded that in together with the dlabel you would get both pieces of info. The information window is in need of improvement and we can add this in the future. Note

Re: [HCP-Users] Question about MSMAll pipeline output

Is this with single run or multi-run FIX? Did you get any errors? Matt. On 10/5/18, 6:16 PM, "hcp-users-boun...@humanconnectome.org on behalf of Sang-Young Kim" wrote: >Dear Experts: > >We¹re acquiring HCP-style data, and running HCP pipelines. We are >following the order of pipelines as Matt

Re: [HCP-Users] MSMAll

There are a couple of things that we need to sort out to make MSMAll work with the new multi-run FIX code. We will be working on that next week. Matt. On 10/5/18, 3:05 PM, "hcp-users-boun...@humanconnectome.org on behalf of Shankar Tumati" wrote: >Hello, > >After running the

Re: [HCP-Users] Do we need to perform extra preprocessing on FIX-Denoised data-set?

The files you would optimally be using are: ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii — for general cross-subject analysis of the greymatter.

Re: [HCP-Users] Converting greyordinates to

That’s right, you would want to use the MSMAll aligned CIFTI task fMRI data. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Cathy Chen mailto:c...@alumni.princeton.edu>> Date: Wednesday, October 3, 2018 at 1:06 AM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc:

Re: [HCP-Users] Converting greyordinates to

Can you give some specific examples including file names? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Cathy Chen mailto:c...@alumni.princeton.edu>> Date: Monday, October 1, 2018 at 3:15 PM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] A question about white matter atlas for HCP diffusion data

I think you can use the default TBSS pipeline but you can confirm on the FSL list. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C mailto:aaroncr...@outlook.com>> Date: Tuesday, October 2, 2018 at 8:26 AM To:

Re: [HCP-Users] Resample *.dtseries.nii to native surface space

#16 in that FAQ is not at all relevant to this situation. If you have FreeSurfer label files, convert them to GIFTI with mris_convert and then use wb_command -label-resample to get them onto the 32k mesh. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson

Re: [HCP-Users] Question about Multi-Modal Surface Mapping

quality of individual spatial map of ICA component is bad. The alignment should have large error, right? Are there any methods to handle this kind of data? Any comments would be greatly appreciated. Best, Sang-Young On Sep 29, 2018, at 2:48 PM, Glasser, Matthew mailto:glass...@wustl.edu>>

Re: [HCP-Users] SE Fieldmap - apply_topup HCP replacement

Yes that is the reason we didn’t use apply_topup. I’m not sure why we used more iterations. Perhaps Jesper changed the config at some point or knows why. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Kastman, Erik" mailto:kast...@fas.harvard.edu>> Date: Monday,

Re: [HCP-Users] Resample *.dtseries.nii to native surface space

That would tremendously upsample the fMRI data to a very irregular mesh and is not generally recommended. The individual subject 32k surfaces in the ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/ folder are in the subject’s native volume space and have the same shape as the subject’s native

Re: [HCP-Users] Question about Multi-Modal Surface Mapping

You want to run MSMAll on sICA+FIX cleaned data for sure. As far as your question about the MSMAll pipeline inputs, I would need to see what you have. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Sang-Young Kim mailto:sykim...@gmail.com>> Date: Friday, September

Re: [HCP-Users] Gambling tfMRI

I wouldn’t trust the results of the Reward vs Loss task, as they are mostly random noise with some structured artifact. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Zhuochen Wang mailto:zhuoc...@usc.edu>> Date: Thursday, September 27, 2018 at 5:00 PM To: "Burgess,

Re: [HCP-Users] Bandpass filtering of the RS fix-extended dataset?

Low-pass filtering is not a selective data cleanup method and the spatially specific structured noise has already been removed by sICA+FIX. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of David Hofmann mailto:davidhofma...@gmail.com>> Date: Saturday, September 22,

Re: [HCP-Users] beta extraction from ROI using cifti data - ERROR: roi cifti does not match input cifti along columns

I am guessing that somehow the medial wall ROIs did not get used in the PALM analysis. Perhaps Anderson can help us understand how that could have happened. It would probably help to give the command lines you used with PALM. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on

Re: [HCP-Users] RestingStateStats.m

Hi Mike, The available version of RestingStateStats is not meant to do any data cleanup. The WM and CSF stuff was investigational and the failure of it to work very well led to the temporal ICA paper available here: https://www.sciencedirect.com/science/article/pii/S1053811918303963 My

Re: [HCP-Users] MATLAB libraries in Resting State Stats script

normalise is the custom function, not rms. Matt. On 9/19/18, 4:10 PM, "Matthew Brett" wrote: >Hi, > >On Wed, Sep 19, 2018 at 7:52 PM, Glasser, Matthew >wrote: >> It is a custom function that I already pointed to. > >Am I right in thinking that the rms func

Re: [HCP-Users] MATLAB libraries in Resting State Stats script

Not sure, I think over all of the HCP and related pipelines the signal toolbox will have to remain a dependency. Matt. On 9/19/18, 4:16 PM, "Matthew Brett" wrote: >Hi, > >On Wed, Sep 19, 2018 at 8:13 PM, Glasser, Matthew >wrote: >> normalise is the custom func

Re: [HCP-Users] MATLAB libraries in Resting State Stats script

'normalise'. Tim On Wed, Sep 19, 2018 at 11:15 AM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: I believe rms is a matlab provided function. The custom functions are in here: https://github.com/Washington-University/HCPpipelines/tree/master/global/matlab Matt. From: mailto:hcp-

Re: [HCP-Users] FIX denoised 3T task data release?

We do plan to release denoised 3T task data, but I don¹t have a time-table on that. We didn¹t specifically make a 59k version of the parcellation, but that is easy to create with wb_command -cifti-resample and the appropriate spheres + vertex area maps. Matt. On 9/19/18, 2:08 PM,

Re: [HCP-Users] SNR in WU-Minn HCP 1200 Subjects protocol

That number is something that may be useful when on the scanner fiddling with the protocols, but is otherwise irrelevant. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Jinxia Yao mailto:yao...@purdue.edu>> Date: Tuesday, September 18, 2018 at 6:41 PM To:

Re: [HCP-Users] An error when running AtlasRegistionToMNI152_FLIRTandFNIRT.sh

You didn’t set all of the required options: --ref= --refbrain= --refmask= --ref2mm= --ref2mmmask= Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "outlook_c843878f00767...@outlook.com"

Re: [HCP-Users] MATLAB libraries in Resting State Stats script

I believe rms is a matlab provided function. The custom functions are in here: https://github.com/Washington-University/HCPpipelines/tree/master/global/matlab Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Andrew Poppe mailto:poppe...@gmail.com>> Date: Wednesday,

Re: [HCP-Users] Can't use boto to download HCP subjects from AWS server anymore

Are you using the temp server instead of the reactivated real server? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Rutger Fick mailto:fick.rut...@gmail.com>> Date: Wednesday, September 19, 2018 at 6:54 AM To:

Re: [HCP-Users] Need to truncate dummy scans for 7T data?

- we have automated scripts to do this - but I would just like >to know whether its advisable and if so if you have any specific >recommendations as to how many volumes to remove. > >Thanks >Nina > > >On Fri, 7 Sep 2018, Glasser, Matthew wrote: > >> I think

Re: [HCP-Users] Need to truncate dummy scans for 7T data?

I think you should be okay if you use the sICA+FIX cleaned data. Matt. On 9/7/18, 11:22 PM, "hcp-users-boun...@humanconnectome.org on behalf of Nina de Lacy" wrote: >Hi there: > >Was still hoping to get input on this question. > >Thanks >Nina > > > >-- Forwarded message --

Re: [HCP-Users] Bias Field setting in Resting State Stats script

manconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Bias Field setting in Resting State Stats script We used "SEBASED" for the bias correction setting in the fmri volume step. Andrew On Tue, Sep 4, 20

Re: [HCP-Users] FSL FIX no memory with hcp_fix_multi_run

/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) On Tue, Aug 21, 2018 at 6:47 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Sorry that is actually a FSL bug that I have

Re: [HCP-Users] wb_command failed to convert text to number

Getting extremely large numbers like that suggests something may have gone wrong with your processing also. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday, September 6, 2018 at 7:04 AM To: Eric Earl

Re: [HCP-Users] completely processed HCP data

Have a look at the PTN release. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Bo Xu mailto:box...@gmail.com>> Date: Wednesday, September 5, 2018 at 12:50 PM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] Bias Field setting in Resting State Stats script

What setting did you use in fMRIVolume? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Andrew Poppe mailto:poppe...@gmail.com>> Date: Wednesday, September 5, 2018 at 4:35 AM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] TOPUP Settings

Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Keith Jamison mailto:kjami...@umn.edu>> Date: Thursday, August 30, 2018 at 8:51 AM To: "Glasser, Matthew" mailto:glass...@wustl.edu

Re: [HCP-Users] TOPUP Settings

Hi Mike, As far as I know the only sure way is with trial and error, but perhaps the latest dcm2niix has eliminated that. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Stevens, Michael" mailto:michael.stev...@hhchealth.org>> Date: Wednesday, August 29, 2018 at

Re: [HCP-Users] two maximum points using -metric-extrema

he two ROIs are saved separately with two sets of global grayordinate coordinates? Thanks. Best regards, Xinyang At 2018-08-27 11:16:42, "Glasser, Matthew" mailto:glass...@wustl.edu>> wrote: Would have to ask that on the FSL list. Matt. From: Xinyang Liu mailto:xinyang_ie

Re: [HCP-Users] Resting State Stats Following hcp_fix_multi_run and MSMAll

Hi Tim, I’m sorry but the publicly available version of RestingStateStats is not yet compatible with multi-run FIX. Getting this script updated is on the to-do list. If you want to e-mail me off list about why you need RestingStateStats now, we can work something out. Matt. From:

Re: [HCP-Users] two maximum points using -metric-extrema

separately in .func.gii, but the "surf2surf "command can only transform one of them to .asc? Best regards, Xinyang At 2018-08-27 01:12:54, "Glasser, Matthew" mailto:glass...@wustl.edu>> wrote: The other should be in the next map of the ROI file. Matt. From: Xinyang Liu mail

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