Re: [HCP-Users] diffusion data merge pipeline

Look for the ${StudyFolder}/${Subject}/T1w/Diffusion/data.nii.gz file. Peace, Matt. From: > on behalf of Yeun Kim > Date: Monday, July 17, 2017 at 12:56 PM To:

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

Also you shouldn’t be using the HCP 7T fMRI data at this time. See the message about this on the list. Peace, Matt. From: > on behalf of Timothy Coalson > Date: Friday,

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

Most of the released HCP data are on a 32k mesh. You can find the Yeo parcellation on the 32k mesh here: https://balsa.wustl.edu/study/show/WG33 Peace, Matt. From: > on behalf of David Hartman

Re: [HCP-Users] HCP-style infant protocol: acquisition & parcellation questions

I would recommend that both images are 0.8mm isotropic, though there is no matrix size requirement (they just both need to cover the whole brain). Why do you want to use differing resolutions? You can download my percolation here: https://balsa.wustl.edu/file/show/3VLx Peace, Matt. From:

Re: [HCP-Users] Calculation of myelin maps

accurate due to bias correction. I will recalculate with the normal myelin maps. Can you please tell me why MyelinMaps are better for the stats than MyelinMaps_BC? And do I understand correctly that our acquisition protocol is okay? Thanks a lot! On 14 July 2017 at 02:52, Glasser, Matthew &

Re: [HCP-Users] Calculation of myelin maps

Are you using Myelin or MyelinMap_BC? For finding brain areas use Myelin_BC, for statistics on the myelin itself you will want to use MyelinMap. Peace, Matt. From: > on behalf of Lisa Kramarenko

Re: [HCP-Users] PreFreeSurfer: Cannot open volume None for reading!

for reading! Hi Matt, Please see attached. I also attached the log that is generated, in case this helps. Many thanks, Sara On 10 July 2017 at 22:12, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Can you post the code you are using the launch the pipeline? T

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

I am not part of such a consensus. I don’t know if there have been rigorous comparison of the two sequences or by what metrics it is being asserted that MGH outperforms CMRR. Perhaps you could ask your source for this recommendation why they say that? Peace, Matt. From:

Re: [HCP-Users] PreFreeSurfer: Cannot open volume None for reading!

Can you post the code you are using the launch the pipeline? Thanks, Matt. From: > on behalf of Sara Rafique > Date: Sunday, July 9, 2017 at 7:44 PM To:

Re: [HCP-Users] Potential issue with 7T retinotopy data

Hi Ahmad, I can confirm that there is an issue. Thank you for bringing it to our attention. A formal e-mail about this will be forthcoming. Matt. From: > on behalf of "Beyh, Ahmad"

Re: [HCP-Users] about brain region index on the surface

at is the index? Thanks 发自我的iPhone -- Original -- From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: 周四,7月 6,2017 11:54 下午 To: 罗 <963619...@qq.com<mailto:963619...@qq.com>>, hcp-users <hcp-users@humanconnectome.org<mai

Re: [HCP-Users] cifti-create-dense-scalar file not found

an Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ From: Glasser, Matthew <

Re: [HCP-Users] cifti-create-dense-scalar file not found

...@humanconnectome.org> <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Mandelli, Maria Luisa <marialuisa.mande...@ucsf.edu<mailto:marialuisa.mande...@ucsf.edu>> Sent: Wednesday, July 5, 2017 3:39:03 PM To: Glasser, Mat

Re: [HCP-Users] about brain region index on the surface

I would need more details about exactly what you did and what went wrong. Peace, Matt. From: > on behalf of 罗 <963619...@qq.com> Date: Thursday, July 6, 2017 at 8:10 AM To: hcp-users

Re: [HCP-Users] cifti-create-dense-scalar file not found

y Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> Sent: Wednesday, July 5, 2017 3:06:52 PM

Re: [HCP-Users] cifti-create-dense-scalar file not found

Is this running an HCP pipeline or something else? If it is a pipeline, which pipeline is it? That file is available in the HCP Pipelines repository: https://github.com/Washington-University/Pipelines/blob/master/global/templates/standard_mesh_atlases/L.atlasroi.32k_fs_LR.shape.gii

Re: [HCP-Users] about participant information

No they are not. This info should be in ConnectomeDB under the behavioral data. Peace, Matt. From: > on behalf of 罗 <963619...@qq.com> Date: Tuesday, July 4, 2017 at 9:07 AM To:

Re: [HCP-Users] Resting State processing

You can give MSMSulc and MSMAll a try if you wish using the latest version of the HCP pipelines and the MSM binary, which is here: https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v2/ Here is the recommended order of pipelines: 1. PreFreeSurfer 2. FreeSurfer 3. PostFreeSurfer (using MSMSulc)

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

I believe we use GPUs to speed this up. Peace, Matt. From: > on behalf of HMZ > Date: Thursday, June 29, 2017 at 11:23 PM To:

Re: [HCP-Users] How to choose high-pass filter cut-off period for the task data (block design)

We used a sigma of 200s for all tasks. In practice if you clean the data I doubt it matters whether you do anything more than a linear detrend. Peace, Matt. From: > on behalf of David Hofmann

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

sistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ _

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

D Assistant Professional Researcher University of California, San Francisco 675 Nelson Rising Lane, Suite 190 | San Francisco, CA 94158 Language Neurobiology Lab http://albalab.ucsf.edu/ Memory and Aging Center http://memory.ucsf.edu/ UCSF Dyslexia Center http://dyslexia.ucsf.edu/ __

Re: [HCP-Users] pipeline structural PostFreesurfer wmparc not found

Perhaps I missed it but I don’t actually see the error messages you are getting. Peace, Matt. From: > on behalf of "Timothy B. Brown" > Organization: Washington

Re: [HCP-Users] Libnetcdf.so.6 error during mris_make_surfaces

The package might be called netcdf in the package manager. Peace, Matt. From: > on behalf of Lisa Kramarenko > Date: Tuesday, June 27, 2017 at 1:46

Re: [HCP-Users] Custom visualisation help

I think you want wb_command -volume-label-import. Peace, Matt. From: > on behalf of Seán Froudist Walsh > Date: Tuesday, June 20, 2017 at 7:04 PM To:

Re: [HCP-Users] NEWMAT::SingularException

Is this an HCP Pipeline or some other pipeline? If it is an HCP Pipeline, which one is it and how did you call it? Peace, Matt. From: > on behalf of Marta Moreno

Re: [HCP-Users] values in myelin maps

gton University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173<tel:(314)%20747-6173> St. Louis, MO 63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl

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

I suppose it isn’t good enough given what we see in some subjects FD traces however… Matt. From: > on behalf of "Harms, Michael" > Date: Thursday, June 8, 2017 at 2:05

Re: [HCP-Users] [HCP-Info] [Contact Form]: Transforming Group MPM Parcellations to fsaverage

The parcellation file is available here: https://balsa.wustl.edu/file/show/3VLx Note that the preferred venue for asking questions about HCP data is the HCP-Users mailing list so that all list members have the benefit of the answer. Peace, Matt. From:

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

Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@h

Re: [HCP-Users] values in myelin maps

MRISreadAnnotationIntoArray: vertex index out of range: 146448 i=00190519, in_array_size=146066) it went without error and my myelin map looks good now. What do you think? Can I use it or should I change something else so that the complete pipeline finishes? Thanks! Lisa On 7 June 2017 at

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

What is most important is that they both cover the whole brain for gradient echo field maps. Matching geometry more exactly is nice but not necessary. Peace, Matt. From: > on behalf of Grant Sutcliffe

Re: [HCP-Users] values in myelin maps

s, as if you were running FS de-novo. cheers, -MH -- 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: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.

Re: [HCP-Users] values in myelin maps

-747-6173<tel:(314)%20747-6173> St. Louis, MO 63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kram

Re: [HCP-Users] About the .dlabel.nii file for the 180 parcellations in your study

Please see the FAQ #2: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ Peace, Matt. From: > on behalf of Manasij Venkatesh > Date: Wednesday, June 7,

Re: [HCP-Users] Similarity between thickness dscalar files and freesurfer 5.3 thickness files

They should be identical. Peace, Matt. From: > on behalf of Timothy Hendrickson > Date: Wednesday, June 7, 2017 at 9:51 AM To:

Re: [HCP-Users] smoothness of grayordinate data

For whatever reason this e-mail didn’t make it to me. Another thing to check is whether there is a difference between fslsmoothest and wb_command -volume-estimate-fwhm. It certainly may be that in 2D on the surface the data appears smoother than in 3D in the volume, as the surface is oriented

Re: [HCP-Users] Resample monkey surface

There is not currently a publicly available way of doing this, but we will discuss further of list. Peace, Matt. From: > on behalf of "lqcheng2...@gmail.com"

Re: [HCP-Users] Only positive coefficients in mean connectivity matrix from ICA-FIX rsfMRI data

That doesn’t surprise me at all. The AAL atlas has little to do with brain function and so the negatively correlated areas are probably mixed in with positively correlated ones. There is a positive bias in full correlations measured after ICA+FIX (or before for that matter) because ICA+FIX

Re: [HCP-Users] Convert NIfTI to CIFTI with wb_command

We don’t recommend trying to combine group average NIFTI data with CIFTI as there isn’t a good way to do it accurately. Better to map the data to individual subject surfaces and average on the surface. Peace, Matt. From:

Re: [HCP-Users] 答复: BOLD signal

em to get a time series corresponding to a ROI? Or, I can use ICA components ,each of which has a time series, as nodes of the network? In this case, how should I define ICA dimensionality, so I can think of each component as a node, not a network? Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发

Re: [HCP-Users] 答复: 回复： 回复：答复: 答复: 答复: GIFTI surface data

复: 答复: [HCP-Users] GIFTI surface data Hi, I have seen the technical report of MELODIC, there will be an automatic estimation of dimensionality, so the script should run properly, producting melodic_mix and melodic_IC. Why there are still many errors? Thanks. 发件人: Glasser, Matthew [mailto:glass...@

Re: [HCP-Users] about the explanation of some phrases

corrthickness is the thickness with curvature regressed out. It is appropriate for looking at differences between cortical areas in thickness. The regular thickness is appropriate for morphometrics. sulc is FreeSurfer’s sulc measure which is documented by them. MyelinMap_BC is the T1w/T2w

Re: [HCP-Users] values in myelin maps

a.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote: ok. so basically just go through recon-all output and manually correct whatever might have gone wrong? best, Lisa On 30 May 2017 at 16:13, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:

Re: [HCP-Users] values in myelin maps

fer-quality-control-guide/freesurfer-quality-control-step-1-fix-pial-surface/ ? And does it look like it affect both pial and white matter surfaces, so that both need to be fixed? Sorry for the naive questions and thanks again. On 30 May 2017 at 15:51, Glasser, Matthew <glass...@wust

Re: [HCP-Users] values in myelin maps

rrectly it can't be done post-hoc after acquisition and should have been done during scanning? Other patients from the same batch (acquired the same way) don't have this problem. What would be the way to fix the surfaces manually? Thanks a lot! On 30 May 2017 at 15:42, Glasser, Matthew &

Re: [HCP-Users] 回复： 回复：答复: 答复: 答复: GIFTI surface data

420(time point) after I converted it to GIFTI, how long does it take to run ICA? how do I set the -d flag? In my opinion, after ICA, the result will be something like A(smaller than 91282)*420, right? Thanks. -- 原始邮件 ---------- 发件人: "Glasser, Matthew"

Re: [HCP-Users] values in myelin maps

They are the ratio of the T1w/T2w images and are a relative measure of myelin content. See this publication for more details: http://www.jneurosci.org/content/31/32/11597.short Peace, Matt. From: > on

Re: [HCP-Users] Appropriate template for 7T movie volume data?

Generally I use an average T1w image or surfaces of the subjects whose group data I am looking at, or the individual¹s T1w or surface. Comparison across subjects and smoothing in the volume are not recommended with HCP data. Peace, Matt. On 5/28/17, 11:05 AM,

Re: [HCP-Users] rfMRI CIFTI

This is described in this publication: http://www.sciencedirect.com/science/article/pii/S1053811913005053 And implemented in this pipeline: https://github.com/Washington-University/Pipelines/tree/master/fMRISurface Peace, Matt. From:

Re: [HCP-Users] 答复: 答复: 答复: GIFTI surface data

An exception has been thrown ERROR: Could not open image /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseriesTrace: read_volumeROI. Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2

Re: [HCP-Users] rfMRI BOLD signal

That’s correct. We added this feature to allow easy viewing of functional connectivity without having to compute the whole matrix. You can still do that with wb_command -cifti-correlation Peace, Matt. From:

Re: [HCP-Users] load cifti file to MATLAB

Use these tools (option 2B): https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ Peace, Matt. From: > on behalf of wtj <1257735...@qq.com> Date: Saturday, May 27, 2017

Re: [HCP-Users] 答复: BOLD signal

t;> Subject: 答复: [HCP-Users] BOLD signal Hi, I open the file with SPM, but I see nothing. How can I map rfMRI BOLD signal grayordinates to each region of the functional parcellation? Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年5月26日 0:23 收件人: wtj <1257735...@qq.c

Re: [HCP-Users] 答复: 答复: GIFTI surface data

create directory /home/Tianjie/projects/WU-Minn_HCP_Lifespan_Pilot_Data_structure_preprocess/LS2001/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_Atlas.dtseries.ica What’s the problem? Thanks. 发件人: Glasser, Matthew [mailto:glass...@wustl.edu] 发送时间: 2017年5月25日 8:27 收件人

Re: [HCP-Users] BOLD signal

The database is back up and you can get the parcellation from here: https://balsa.wustl.edu/file/show/3VLx Peace, Matt. From: Matt Glasser > Date: Wednesday, May 24, 2017 at 10:49 AM To: wtj <1257735...@qq.com>,

Re: [HCP-Users] NaNs and grayordinates with constant timeseries

anted to share this finding just in case anyone else experiences this issue too. Best wishes, Leah From: Leah Moreno <mmorenoort...@icloud.com<mailto:mmorenoort...@icloud.com>> Date: Wednesday, May 17, 2017 at 5:56 PM To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@w

Re: [HCP-Users] create 2k space

ers@humanconnectome.org>> Subject: Re: [HCP-Users] create 2k space Oh interesting. Now I can't remember if I found that version and used it as a starting point. This was a couple of years ago. Regardless, either one should be able to make new templates to downscale or upscale as needed...

Re: [HCP-Users] create 2k space

.org>> Subject: Re: [HCP-Users] create 2k space You could take a look at this code and adapt as needed: https://github.com/alexlicohen/script-toolbox/blob/master/CreateNewTemplateSpace.sh -Alex On May 24, 2017, at 2:49 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.ed

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

nt it because we are considering using one run for analysis and other run for validation. Maybe we should generate level 1 processed data using your scripts if we really need it. Thanks!! Jiang Jian At 2017-05-24 23:50:20, "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...

Re: [HCP-Users] 答复: GIFTI surface data

1 1 d" invoked from within ".dialog1.cancel invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .dialog1.cancel" (command bou

Re: [HCP-Users] create 2k space

Probably also would need wb_command -surface-create-sphere to actually make the 2K space. Peace, Matt. From: > on behalf of Timothy Coalson > Date: Wednesday, May 24,

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

By level 1 do you mean subject wise? Peace, Matt. From: > on behalf of Jiang Jian > Date: Tuesday, May 23, 2017 at 9:11 PM To: "Harms, Michael"

Re: [HCP-Users] BOLD signal

The HCP has released a cortical areas atlas, but it is unfortunately unaccessible due to some IT problems. Hopefully it will be back up soon. Peace, Matt. From: > on behalf of wtj

Re: [HCP-Users] Overlaying atlas in Connectome Workbench

Is this a NIFTI file in each individual subject or a group average NIFTI file? There isn’t a great way for mapping from group average NIFTI to surface, as the group averaging process causes a lot of blurring across subjects all over the cortex and also group average surfaces have their own

Re: [HCP-Users] Incomplete diffuson datasets

Subject: Re: [HCP-Users] Incomplete diffuson datasets Sorry; tractography using the b1000 scans. On Tue, May 23, 2017 at 10:10 AM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: What is b1000 tractography and why would you want to do that? Peace, Matt.

Re: [HCP-Users] Incomplete diffuson datasets

sible to know which ones are missing. On Tue, May 23, 2017 at 10:03 AM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Why not use all of the diffusion data that is present? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-user

Re: [HCP-Users] Incomplete diffuson datasets

Why not use all of the diffusion data that is present? Peace, Matt. From: > on behalf of Ariana Cahn > Date: Tuesday, May 23, 2017 at 10:59 AM To:

Re: [HCP-Users] Question about DWI protocol

Yes as long as you have phase reversed b0s you can have the DWIs have unique directions. The HCP diffusion pipeline might need modification to accommodate that. Peace, Matt. From: > on behalf of HMZ

Re: [HCP-Users] rfMRI BOLD data

Use these files: ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii. Peace, Matt. From: > on behalf of "Harms, Michael"

Re: [HCP-Users] help

Thank you a lot. Best, Yafeng From: Glasser, Matthew [mailto:glass...@wustl.edu] Date: 2017年5月23日 0:33 To: Zhan Yafeng; HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> Subject: Re: [HCP-Users] help While it would definitely be beneficial to map your data onto the

Re: [HCP-Users] help

While it would definitely be beneficial to map your data onto the cortical surface, two aspects of your acquisition will make it difficult to use the HCP Pipelines in their current state: 1. Low resolution T2w scan (at 2.5mm) will make generation of myelin maps and using the T2w to help

[HCP-Users] Matt Glasser E-mail Bounces

Over the last couple of days my e-mail was not working due to some changes to the Wash U e-mail system. I have been told that these issues are now resolved, but if you sent an e-mail to this list and you wanted my help or sent me an e-mail off list to which I have not responded, please resend.

Re: [HCP-Users] NaNs and grayordinates with constant timeseries

Do you have those issues if you just run the HCP minimal preprocessing pipelines and ICA+FIX cleanup? I am guessing the issue lies with the extensive temporal preprocessing that you are doing and not with the wb_command -cifti-average-roi-correlation command or the CIFTI grayordinates

Re: [HCP-Users] Infinite values in Group average data

Right. Peace, Matt. From: > on behalf of Sang-Yun Oh > Date: Tuesday, May 16, 2017 at 11:25 AM To: Timothy Coalson > Cc:

Re: [HCP-Users] Parcellation of subcortical areas

There are a variety of subcortical parcellations out there including these: https://surfer.nmr.mgh.harvard.edu/fswiki/StriatumParcellation_Choi2012 http://www.freesurfer.net/fswiki/CerebellumParcellation_Buckner2011 These were made with a very different approach than the HCP’s multi-modal

Re: [HCP-Users] Regression of Physiological Noise -- updates?

Some physiological noise is regressed out through the ICA+FIX cleanup (where it is part of the noise components). What is not regressed out is the global physiological noise, e.g. related to respiration. We are indeed working on a method for doing this in a data-driven (as opposed to using

Re: [HCP-Users] Replicating "Resting-state fMRI in the Human Connectome Project"

ting "Resting-state fMRI in the Human Connectome Project" Hi Matt, Does that mean matrix G is subjects ICA+FIX is concatenated? Thank you, Sang On Fri, May 12, 2017, 5:56 PM Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: ICA+FIX precedes FSLNets and

Re: [HCP-Users] Replicating "Resting-state fMRI in the Human Connectome Project"

...@wustl.edu> From: Sang-Yun Oh <san...@gmail.com<mailto:san...@gmail.com>> Date: Friday, May 12, 2017 at 4:44 PM To: Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>

Re: [HCP-Users] Replicating "Resting-state fMRI in the Human Connectome Project"

Steve Smith would have generated that matrix. I would have been after running ICA+FIX, which would remove linear trends, 24 movement regressors and ICA noise component timeseries. The matrix would have been made with FSLNets. Peace, Matt. From:

Re: [HCP-Users] Fwd: Fwd: Error in fMRI Volume Processing Pipeline

. I am not sure as to where find the necessary DICOM fields ((0019,1028) for BandwidthPerPixelPhaseEncode and (0051,100b) for # of phase encoding samples). Where should I look for them? Thanks again! On 3 May 2017 at 21:08, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu

Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation

ation_${sub}_average.dscalar.nii The resulting files appear as expected (similar to the smoothed-ROI-to-smoothed-cifti results but with more variation/less smooth appearance). Please let me know if you see any errors. Thanks again! -Ely From: Glasser, Matthew

Re: [HCP-Users] unsmoothed ROI to smoothed cifti correlation

Hi Ely, We don’t have a function like this yet, but have been discussing making one. I think matlab is your best bet at this time. Peace, Matt. From: > on behalf of "Ely, Benjamin"

Re: [HCP-Users] Question concerning SNR info

Yes we hope to do this in the future. tfMRI runs are shorter than rfMRI runs, however, so some new code needed to be written to combine across runs for denoising and then split the data back out. Peace, Matt. From:

Re: [HCP-Users] variation across connectomes

Undoubtably. Perhaps the megatrawl would be of interest: https://db.humanconnectome.org/megatrawl/ Peace, Matt. From: Joelle Zimmermann <joelle.t.zimmerm...@gmail.com> Sent: Saturday, April 29, 2017 9:15:31 AM To: Glasser, Matthew Cc: hcp

Re: [HCP-Users] [SPAM] Re: [SPAM] Re: [SPAM] Re: [SPAM] Re: [TaskfMRILevel2]feat_modelerror

--- Original ------ From: "Glasser, Matthew";<glass...@wustl.edu<mailto:glass...@wustl.edu>>; Date: Sat, Apr 29, 2017 12:47 PM To: "--"<744652...@qq.com<mailto:744652...@qq.com>>; "hcp-users"<hcp-users@humanconnectom

Re: [HCP-Users] [SPAM] Re: [SPAM] Re: [SPAM] Re: [TaskfMRILevel2]feat_modelerror

Re: [HCP-Users] [TaskfMRILevel2]feat_model error The data and the Pipeline scripts are all included in the 2015 HCP Course, and the subject ID is 100307. Besides, I have already running three structural pipelines and two functional pipelines. Best, Bai Haohao -- Original

Re: [HCP-Users] variation across connectomes

What is it that you are trying to do? Control for uninteresting sources of variance? Peace, Matt. From: > on behalf of Joelle Zimmermann >

Re: [HCP-Users] comparison across acquisitions

w subjects have: r177 r227 for the fMRI recon. Does this mean both were done? Which of the two was used for these subjects for the S900 release? Thanks, Joelle On Wed, Apr 26, 2017 at 2:05 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Yes. Peace,

Re: [HCP-Users] Fwd: Using multiple cores while running Structural Pipelines

ral >>Pipelines >> >> Alright, thanks! And just for clarification for dummies: if not >>installing something like grid_engine, will running all 50 subjects in >>one Terminal window or 10 subjects in each of five different windows be >>more efficient? Or doesn't it ma

Re: [HCP-Users] [SPAM] Re: [SPAM] Re: [TaskfMRILevel2]feat_model error

bject ID is 100307. Besides, I have already running three structural pipelines and two functional pipelines. Best, Bai Haohao -- Original ------ From: "Glasser, Matthew";<glass...@wustl.edu<mailto:glass...@wustl.edu>>; Date: Thu, Apr 27, 2017 0

Re: [HCP-Users] [SPAM] Re: [TaskfMRILevel2]feat_model error

generate_level1_fsf.sh to generate the files. Followed Day4_Practical7_Task_fMRI tutorial, I install level2.fsf file. After that, bash TaskfMRIAnalysisBatch.sh --runlocal Best, Bai Haohao -- Original ------ From: "Glasser, Matthew";<glass...@wustl.ed

Re: [HCP-Users] automatic drawing of circles on a surface

a" <do...@wustl.edu<mailto:do...@wustl.edu>> Subject: Re: [HCP-Users] automatic drawing of circles on a surface Last question: why should it be different from the output of -surface-geodesic-distance? On Wed, Apr 26, 2017 at 10:15 PM, Glasser, Matthew <glass...@wustl.ed

Re: [HCP-Users] automatic drawing of circles on a surface

is not clear to me what dilate function tries to achieve... Thanks again. On Wed, Apr 26, 2017 at 9:53 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Given your output of wb_command -surface-geodesic-distance is a metric GIFTI file you could use -metric-

Re: [HCP-Users] automatic drawing of circles on a surface

one do I use? If this is the former, it seems that I still need to create the label manually. If you mean two former, it is not clear to me how I "start with values at the vertices". On Wed, Apr 26, 2017 at 8:50 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>

Re: [HCP-Users] comparison across acquisitions

acquisition the image reconstruction version change occurred? Joelle On Wed, Apr 26, 2017 at 1:51 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: The main thing to consider was a an image reconstruction version change that occurred relatively early in the p

Re: [HCP-Users] comparison across acquisitions

The main thing to consider was a an image reconstruction version change that occurred relatively early in the project. Diffusion data were retroreconned (and so all data have the same version), but fMRI raw data had not been saved and could not be retroreconned. We advise using a covariate of

Re: [HCP-Users] automatic drawing of circles on a surface

You should be able to start with values at the vertices and then use a dilate command to make the circles. Peace, Matt. From: > on behalf of Vadim Axel >

Re: [HCP-Users] [TaskfMRILevel2]feat_model error

How did you call the task analysis pipeline? Peace, Matt. From: > on behalf of -- <744652...@qq.com> Date: Wednesday, April 26, 2017 at 10:35 AM To:

Re: [HCP-Users] Using multiple cores while running Structural Pipelines

n one window? I considered looking into GNU parallel, but not sure it would make sense. What would your advice for such a number of subjects be? Thanks so much for your help. V 2017-04-25 16:55 GMT+02:00 Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>: PreFreeSurfer uses most

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