Re: [HCP-Users] A question about the MSMSulc

<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] A question about the MSMSulc but regarding this repository, you mean MSM_HOCR/src/MSM ? because the files there are .cc, which is not what the pipeline codes look for.. On Mon, 25 M

Re: [HCP-Users] A question about the MSMSulc

It should point to where the compiled MSM binary is. Matt. From: Shachar Gal mailto:gal.shac...@gmail.com>> Date: Monday, March 25, 2019 at 3:17 AM To: "hcp-users@humanconnectome.org" mailto:hcp-users@humanconnectome.org>>, Matt Glasser

Re: [HCP-Users] Resting state networks

Right. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Claude Bajada mailto:c.baj...@fz-juelich.de>> Date: Monday, March 25, 2019 at 5:39 AM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc: "hcp-users@humanconnectome.org"

Re: [HCP-Users] Topup_AP dimension issue

peutics Department of Psychiatry Columbia University Medical Center 1051 Riverside Drive, Unit 21 New York, NY 10032 phone: (914) 218-7311 email: mm4...@cumc.columbia.edu<mailto:mm4...@cumc.columbia.edu> On Mar 24, 2019, at 10:58 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrot

Re: [HCP-Users] Topup_AP dimension issue

ment of Psychiatry Columbia University Medical Center 1051 Riverside Drive, Unit 21 New York, NY 10032 phone: (914) 218-7311 email: mm4...@cumc.columbia.edu<mailto:mm4...@cumc.columbia.edu> On Mar 24, 2019, at 10:47 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Not negati

Re: [HCP-Users] Topup_AP dimension issue

r response. Do you mean running this?: fslroi NTTMS_s037_181015_3T_SpinEchoFieldMap_AP_1.nii.gz test.nii.gz -16 96 -16 96 66 66 If that is the case the test file seams to be empty. Leah. On Mar 24, 2019, at 8:25 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Subtract 128 fr

Re: [HCP-Users] Topup_AP dimension issue

Subtract 128 from 96 and then take half of that as your start and 96 as your length. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno mailto:mmorenoort...@icloud.com>> Date: Sunday, March 24, 2019 at 6:40 PM To: HCP Users

Re: [HCP-Users] related parcellation

You can use wb_command -cifti-label-export-table or look inside the Workbench GUI. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno mailto:mmorenoort...@icloud.com>> Date: Sunday, March 24, 2019 at 11:59 AM To: HCP Users

Re: [HCP-Users] error using FreeSurferPipeline

What is present in here: /usr/local/freesurfer/subjects/fsaverage Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal mailto:gal.shac...@gmail.com>> Date: Saturday, March 23, 2019 at 1:54 PM To:

Re: [HCP-Users] Request for information

Our surface meshes are in the GIFTI file format. I believe you can use FreeSurfer’s mris_convert to convert them to other formats. What specific surface meshes are you interested in? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Prateek Sharma

Re: [HCP-Users] Issue about new FreeSurferPipeline

You can just delete the --printcom flag from the example script as it is not needed. This should be removed from the example script if it is no longer going to be supported in the main FreeSurfer pipeline. Matt. From: Qunjun Liang mailto:liangqun...@foxmail.com>> Date: Thursday, March 21,

Re: [HCP-Users] S1200 MSMSulc files

d this be accurate to obtain group-average MSMSulc curvature file? Vertex-wise arithmetic mean of xx.curvature.32k_fs_LR.dscalar.nii maps in Matlab On Thu, Mar 21, 2019 at 11:36 PM Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Are there not versions already? One simply merges and a

Re: [HCP-Users] S1200 MSMSulc files

there a procedure/command to generate those files from individual MSMSulc files? Thanks, Reza On Thu, Mar 21, 2019 at 11:09 PM Glasser, Matthew mailto:glass...@wustl.edu>> wrote: MSMSulc might not have a specific registration tag, did you check for such files? Matt. From

Re: [HCP-Users] S1200 MSMSulc files

MSMSulc might not have a specific registration tag, did you check for such files? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Reza Rajimehr mailto:rajim...@gmail.com>> Date: Thursday, March 21, 2019 at 4:42 PM To: hcp-users mailto:hcp-users@humanconnectome.org>>

Re: [HCP-Users] PostFreesurfer possible bug

As Mike says, you need to use --subjectDIR=/root/hcppilelines/piano_hcp/working_directory/102/T1w as in the example script. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal mailto:gal.shac...@gmail.com>> Date: Wednesday, March 20, 2019 at 3:31 PM To:

Re: [HCP-Users] Surface Contrast and Overlay Transparency

underlay, if selected as a curvature map, should be able to help w/ the contrast issue as well? Michael Riedel On Mar 19, 2019, at 2:09 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Right you would not use opacity but rather thresholding to accomplish what you want. It may be

Re: [HCP-Users] Issue about new FreeSurferPipeline

- Original -- From: "Glasser, Matthew"mailto:glass...@wustl.edu>>; Date: Thu, Mar 21, 2019 11:08 AM To: "Qunjun Liang"mailto:liangqun...@foxmail.com>>;"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"mailto:hcp

Re: [HCP-Users] Issue about new FreeSurferPipeline

How did you call the FreeSurfer pipeline? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Qunjun Liang mailto:liangqun...@foxmail.com>> Date: Wednesday, March 20, 2019 at 10:07 PM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] Surface Contrast and Overlay Transparency

1. I am not sure what you mean by surface contrast. 2. Use the thresholding in the overlay and settings toolbox. Post a picture in case I am not understanding correctly what you mean. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Michael Riedel

Re: [HCP-Users] multirun ICA question

manconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] multirun ICA question Thank you Matt. Just curious, will the tICA procedure in your new manuscript be included in this new pipeline? On Tue, Mar 12, 2019 at 2:28

Re: [HCP-Users] Problem with the freesurfer pipeline

Without prior messages appended it is hard to know what you are referring to; however, we will have a version that works with FreeSurfer 6.0 very soon. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Gina Henze mailto:gina.he...@psychologie.uni-regensburg.de>> Date:

Re: [HCP-Users] structural preprocessing on Philips data?

And you’ll need to be specific about any error messages. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Harms, Michael" mailto:mha...@wustl.edu>> Date: Wednesday, March 13, 2019 at 9:48 AM To: Lucy Evans mailto:lucy.ev...@manchester.ac.uk>>,

Re: [HCP-Users] multirun ICA question

will have 3302 timepoints in total. On Tue, Mar 12, 2019 at 2:24 PM Glasser, Matthew mailto:glass...@wustl.edu>> wrote: What you concatenate is entirely up to the user, so you can set it up to concatenate all the subject’s fMRI data if you like. An official HCP Pipelines release in imminent

Re: [HCP-Users] multirun ICA question

What you concatenate is entirely up to the user, so you can set it up to concatenate all the subject’s fMRI data if you like. An official HCP Pipelines release in imminent, but we have a couple of last things we want to get in there. We will be requiring FSL 6.0.1 going forward for all HCP

Re: [HCP-Users] rs-fMRI with-in subject comparison

the titles of each of the 360 parcels? 2. I want to classify the parcel to networks (DMN, visual...)? is there a script in HCP that do it? From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Sunday, March 03, 2019 5:12 PM To: Tal

Re: [HCP-Users] MSMAll, missing _vn file

This issue will be resolved in the upcoming MR+FIX release. There is no simple workaround. Matt. Sent from my Verizon, Samsung Galaxy smartphone Original message From: Marta Moreno Date: 3/4/19 10:30 AM (GMT-06:00) To: HCP Users Subject: [HCP-Users] MSMAll, missing _vn

Re: [HCP-Users] rs-fMRI with-in subject comparison

.nlm.nih.gov/pubmed/29925602 What is your recommendation to define subcortical volume? My analysis is “within subject” paradigm (comparing the scans in different days). ____________ From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Thursday,

Re: [HCP-Users] extract myelin content of individual subjects in Gordon parcels

I think it looks okay. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Antonin Skoch mailto:a...@ikem.cz>> Reply-To: Antonin Skoch mailto:a...@ikem.cz>> Date: Saturday, March 2, 2019 at 4:40 AM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] generating z-stat file

What code are you using to make the beta map? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Yu Han mailto:yu@uvm.edu>> Date: Saturday, March 2, 2019 at 1:36 PM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] ICA FIX output missing

o:tsc...@mst.edu>> Date: Tuesday, February 26, 2019 at 4:38 PM To: Leonardo Tozzi mailto:lto...@stanford.edu>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, "Glasser, Matthew" mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mail

Re: [HCP-Users] rs-fMRI with-in subject comparison

1. You would need to post the full path and filename. 2. This will be handled by multi-run sICA+FIX in the future. We will recommend all data be cleaned with sICA+FIX. Really you want to be dividing by the unstructured noise standard deviation, rather than the overall standard deviation. 3.

Re: [HCP-Users] ICA FIX output missing

Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" mailto:mha...@wustl.edu>> Date: Tuesday, February 26, 2019 at 7:37 AM To: "Glasser, Matthew" mailto:glass...@wustl.edu>>, Leonardo Tozz

Re: [HCP-Users] structural QC and medial wall

cp-users@humanconnectome.org>> Subject: RE: [HCP-Users] structural QC and medial wall Hi Matt, Figures attached. Looks like for issue (1), fig3 shows that the cortical ribbon is included in the native FS ROI… while for issue (2), fig 4 shows that the ventricle error is not include

Re: [HCP-Users] ICA FIX output missing

You’ll want to be using wb_command 1.3.2. I am not aware of any modifications that are necessary to use the TaskfMRIAnalysis scripts on MR+FIX data and have analyzed hundreds of subjects after MR+FIX. As for this issue, is wb_command set properly here:

Re: [HCP-Users] structural QC and medial wall

What does the FreeSurfer ROI look like? ${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.${Hemisphere}.roi.native.shape.gii? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Moataz Assem mailto:moataz.as...@mrc-cbu.cam.ac.uk>> Date: Monday, February 25, 2019

Re: [HCP-Users] Surface area size of fsLR space

gest..." Today's Topics: 1. Confusion about Destrieux labels (Reza Rajimehr) 2. Re: Confusion about Destrieux labels (Timothy Coalson) 3. Surface area size of fsLR space (Huang Taicheng) 4. Re: Surface area size of fsLR space (Glasser, Matthew) 5. Re: Surface area size of fsLR space (Tim

Re: [HCP-Users] Surface area size of fsLR space

Some more details on why you want to do this would be helpful to provide the most useful response. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Huang Taicheng mailto:hitech9...@gmail.com>> Date: Friday, February 22, 2019 at 8:29 PM To:

Re: [HCP-Users] unwarping 164k surface to subject-specific ACPC-aligned headcoordinate space

That’s right. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of CHAUMON Maximilien mailto:maximilien.chau...@icm-institute.org>> Date: Friday, February 22, 2019 at 5:03 AM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc:

Re: [HCP-Users] what is behind the spin-echo based bias field correction

Please see the Supplementary Methods Section 1.9 of this paper: https://www.nature.com/articles/nature18933 Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Viessmann, Olivia M." mailto:oviessm...@mgh.harvard.edu>> Date: Tuesday, February 19, 2019 at 11:04 AM To:

Re: [HCP-Users] Some questions about data quality check

1. FreeSurfer does not fully segment the hippocampus on the surface. 2. I probably wouldn’t look at this in this way. In general, one wants the brain to be roughly aligned well without major obvious deformations. If you want an example of too much distortion, try ANTs. 3. The parcellation

Re: [HCP-Users] Individualized HCP parcel to MNI coord

If we leave out the “MNI coordinates” part of this question and think in terms of the volume space coordinates of the individual being studied, it is perfectly valid to bring results from the group surface back to an individual’s physical volume space. Is a single coordinate what you need or

Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?

Yes. Sent from my Verizon, Samsung Galaxy smartphone Original message From: Yael Shavit Date: 2/12/19 8:18 AM (GMT-06:00) To: "Glasser, Matthew" Cc: hcp-users , NEUROSCIENCE tim Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI sp

Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?

to:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>> Subject: Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space? Thanks. Another question -are individual mesh surfaces comparable across subjects? בתאריך יום ד׳, 30 בינו׳ 2019, 1:34, מאת Glasse

Re: [HCP-Users] FreeSurfer6 subcortical segmentation

them into the subject MNI Surface Space. J ________ From: Glasser, Matthew mailto:glass...@wustl.edu>> Sent: Wednesday, February 6, 2019 6:29:21 PM To: Sanchez, Juan (NYSPI); hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] FreeSurfer6 subcortical se

Re: [HCP-Users] Problem with the freesurfer pipeline

___ >From: hcp-users-boun...@humanconnectome.org > on behalf of Glasser, Matthew > >Sent: Wednesday, January 30, 2019 6:37:42 PM >To: Gina Henze; hcp-users@humanconnectome.org >Subject: Re: [HCP-Users] Problem with the freesurfer pipeline > >External Email

Re: [HCP-Users] Sharing HCP-derived brain networks and graph-theoric measures

Do you not think it would be valuable to visualize these parcel results on cortical surfaces? CIFTI would be good for that, and can easily be read into matlab as a matrix. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date:

Re: [HCP-Users] Some questions about using HCP structural preprocessing pipeline

1. This depends on the acquisition parameters. You can find this in the DICOM header in the named fields. 2. How do the T2w data look in the T1w folder? That matters most. 3. You need to update Connectome Workbench. 4. Doesn’t matter. 5. I hope so. Matt. From:

Re: [HCP-Users] Sharing HCP-derived brain networks and graph-theoric measures

How is the data organized in those CSV files? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Caio Seguin mailto:caioseg...@gmail.com>> Date: Wednesday, February 6, 2019 at 7:33 PM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] FreeSurfer6 subcortical segmentation

I don’t see these being generated in our current test FreeSurfer 6.0 runs. How are they generated? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" mailto:juan.sanc...@nyspi.columbia.edu>> Date: Wednesday, February 6, 2019 at 12:56 PM To:

Re: [HCP-Users] Bandpass filtering ICA-FIX resting data

It’s better to remove structured noise with ICA-based techniques, and we really essentially are only detrending HCP data. For unstructured noise, this will not affect regression-based analyses much, but will affect correlation analyses. I’d recommend parcellating your data to reduce

Re: [HCP-Users] HCP-Aging/Development protocol

I think there might have been a bug in it that is getting fixed. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Roeland Hancock mailto:rhanc...@gmail.com>> Date: Tuesday, February 5, 2019 at 4:36 PM To:

Re: [HCP-Users] A question about the MSMSulc

Please use the MSM binary available here: https://github.com/ecr05/MSM_HOCR The MSM binary distributed with FSL is not compatible with the HCP pipelines and is based on older code. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C mailto:aaroncr...@outlook.com>>

Re: [HCP-Users] Some questions about using the HCP structural preprocessing pipeline

1. You can edit the launcher scripts to point to the files however you want to name them. 2. Yes if they are both at least 1mm isotropic resolution. 3. You can turn on gradient distortion correction if you want and have the appropriate coefficients file from your scanner. Matt. From:

Re: [HCP-Users] Workbench tools installation in Ubuntu 18.04

o avoid permission issue. Takuya 2019年2月2日(土) 10:06 Glasser, Matthew mailto:glass...@wustl.edu>>: The person to address this is on vacation and will be back next week. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of erik lee mailto:erik.lee...@gmail.com&

Re: [HCP-Users] Workbench tools installation in Ubuntu 18.04

The person to address this is on vacation and will be back next week. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of erik lee mailto:erik.lee...@gmail.com>> Date: Friday, February 1, 2019 at 6:20 PM To:

Re: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Friday, February 1, 2019 at 1:55 PM To: Leonardo Tozzi mailto:

Re: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

low Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Friday, February 1, 2019 at 1:41 PM To: Leonardo Tozzi mailto:lto...@stanford.edu>>, "h

Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm MNI Surface and Volume space

stava, Benjamin (NYSPI)" mailto:benjamin.srivast...@nyspi.columbia.edu>> Date: Wednesday, January 30, 2019 at 4:40 PM To: "Harms, Michael" mailto:mha...@wustl.edu>>, "Glasser, Matthew" mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.o

Re: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

Can you put an arrow on what is bothering you? I’m not sure what you are referring to. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Friday, February 1, 2019 at 3:29 PM To:

Re: [HCP-Users] Problem with the freesurfer pipeline

There is a fix for this very soon to be available. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Gina Henze mailto:gina.he...@psychologie.uni-regensburg.de>> Date: Wednesday, January 30, 2019 at 8:21 AM To:

Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?

For the cortex you can do as Tim suggests and map either to the native mesh and then resample on the surface to the standard mesh or directly to the standard mesh. It is important that you use the meshes that are in the subject’s real physical space, as that is where the diffusion data is.

Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm MNI Surface and Volume space

As far as the volume space, have a look at the PostFreeSurfer pipeline for how wmparc.mgz gets mapped. The hippocampus is not fully represented on FreeSurfer cortical surfaces. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Srivastava, Benjamin (NYSPI)"

Re: [HCP-Users] Missing shared library for wb_command

nSITE Fellow<https://www.insitefellows.org/> Ammar Hawasli Lab<https://hawaslilab.weebly.com/> Department of Biomedical Engineering<https://bme.wustl.edu/Pages/default.aspx> | Washington University in St. Louis<https://wustl.edu/> From:

Re: [HCP-Users] Missing shared library for wb_command

ult.aspx> | Washington University in St. Louis<https://wustl.edu/> From: Glasser, Matthew Sent: Monday, January 28, 2019 5:41:12 PM To: Jayasekera, Dinal; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] Missing shared library for

Re: [HCP-Users] Missing shared library for wb_command

Dinal Jayasekera<https://dinaljay.weebly.com/> PhD Candidate | InSITE Fellow<https://www.insitefellows.org/> Ammar Hawasli Lab<https://hawaslilab.weebly.com/> Department of Biomedical Engineering<https://bme.wustl.edu/Pages/default.aspx> | Washington University in St. Louis

Re: [HCP-Users] Missing shared library for wb_command

Did this suddenly start happening? You have been running workbench successfully for a while. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Jayasekera, Dinal" mailto:dinal.jayasek...@wustl.edu>> Date: Monday, January 28, 2019 at 5:37 PM To:

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

What are you planning to do with the data? It’s not clear to me whether cutting the data is a good idea or not. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Daniel KRISTANTO <18481...@life.hkbu.edu.hk> Date: Sunday, January 27,

Re: [HCP-Users] about the correspondences of vertices across individuals

We used MSMAll areal-feature-based cortical alignment. Here are several articles on the topic: https://www.nature.com/neuro/journal/v19/n9/abs/nn.4361.html https://www.sciencedirect.com/science/article/pii/S1053811917308649 http://www.pnas.org/content/early/2018/06/19/1801582115.short Matt.

Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?

Of the cortex only or subcortical also? Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Monday, January 28, 2019 at 1:55 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>>, Timothy Coalson mailto:tsc...@mst.edu>> Subject: Re:

Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?

I guess you are going to have to be a lot more specific as to what kind of analysis you are trying to do. I guess that is the only way we will be able to give you good advice. Matt. From: Yael Shavit mailto:yael.sh...@gmail.com>> Date: Sunday, January 27, 2019 at 2:39 AM To: hcp-users

Re: [HCP-Users] Regress confounds out of CIFTIs

We do this in matlab. It is not necessary to loop, just use proper matrix math. For example: newdtseries = dtseries - (demean(regressor) * (pinv(demean(regressor)) * dtseries'))’; Where demean(regressor) removes the mean of each regressor. Matt. From:

Re: [HCP-Users] NaN introduced in cifti

Does your FOV cover the whole brain? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" mailto:juan.sanc...@nyspi.columbia.edu>> Date: Thursday, January 24, 2019 at 1:29 PM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] Sharing HCP derivatives

Hi Ariel, Do you have a publication for this data? There certainly is precedent for this, as you can see with the HCP’s 7T retinotopy data: https://balsa.wustl.edu/study/show/9Zkk Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson

Re: [HCP-Users] How can the diffusion HCP data be registered to the MNI space?

If this is about tractography, the advice will be different however. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday, January 17, 2019 at 12:57 PM To: Yael Shavit mailto:yael.sh...@gmail.com>> Cc: hcp-users

Re: [HCP-Users] CIFTI to Matlab

That could also be due to it not finding the file or not finding wb_command. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Harms, Michael" mailto:mha...@wustl.edu>> Date: Thursday, January 17, 2019 at 4:05 PM To: Anita Sinha mailto:amsi...@wisc.edu>>,

Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis

PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Wednesday, January 9, 2019 at 9:02 AM To: "Glasser, Matthew" mailto:glass..

Re: [HCP-Users] Information of HCP Data

hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Glasser, Matthew mailto:glass...@wustl.edu>> Sent: Wednesday, January 9, 2019 9:41:50 AM To: Daniel KRISTANTO; hcp-users@humanconnecto

Re: [HCP-Users] Display of the metric map in Workbench

Sure this is the purpose of the CIFTI file format. You can use wb_command -cifti-create-dense-scalar. That will take care of the hemisphere setting, but that also can be set with wb_command -set-structure. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Zaixu Cui

Re: [HCP-Users] Inquiry of how to process HCP structural data

.nii and load it into FreeSurfer? Or which file(s) have already been through FreeSurfer’s gyral and sulcal parcellation? Best, Andy From: Timothy Coalson mailto:tsc...@mst.edu>> Sent: Friday, January 11, 2019 3:16 To: Glasser, Matthew Cc: ndyeun

Re: [HCP-Users] Inquiry of how to process HCP structural data

1. These would not be with the HCP's parcellation, but rather with FreeSurfer’s gyral and sulcal parcellation. The values are of the subject’s physical brain space, not after registration to MNI space. 2. You could load the label file in Connectome Workbench and turn off the other

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

wb_command -show-scene. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C mailto:aaroncr...@outlook.com>> Date: Wednesday, January 9, 2019 at 10:01 AM To: "hcp-users@humanconnectome.org" mailto:hcp-users@humanconnectome.org>>

Re: [HCP-Users] Information of HCP Data

If you want to learn more about the tasks, there is a paper about them: https://www.sciencedirect.com/science/article/pii/S1053811913005272 What specifically are you wanting to do with the task data? Unless you are actually interested in statistical significance information, effect sizes are

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

test between those two enhanced metric surface groups. Can I use wb_command to do that? Or other method? Best Guoyuan -原始邮件- 发件人:"Glasser, Matthew" mailto:glass...@wustl.edu>> 发送时间:2018-11-28 06:38:30 (星期三) 收件人: "杨国元" mailto:yangguoy...@pku.edu.cn>> 抄

Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis

ord.edu> | (650) 5615738 From: "Harms, Michael" mailto:mha...@wustl.edu>> Date: Tuesday, January 8, 2019 at 1:58 PM To: Leonardo Tozzi mailto:lto...@stanford.edu>>, "Glasser, Matthew" mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] Identifying noise co

Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis

I would recommend running the multi-run FIX pipeline for that on all the fMRI data together. That works on the volume data and then also cleans the CIFTI data at the same time. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi

Re: [HCP-Users] stable version with freesurfer 6

We are still working on the FS 6.0 stuff. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sanchez, Juan (NYSPI)" mailto:juan.sanc...@nyspi.columbia.edu>> Date: Thursday, January 3, 2019 at 8:45 AM To:

Re: [HCP-Users] generating a CIFTI file wit a different resolution

What measures and what resolution? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Sina Mansour L." mailto:sina.mansour.lakou...@gmail.com>> Date: Thursday, January 3, 2019 at 11:49 PM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] Warping volume atlas and X, Y, Z of single point with standard2acpc_dc.nii.gz

.nii.gz On Thu, Jan 3, 2019 at 10:47 AM Glasser, Matthew mailto:glass...@wustl.edu>> wrote: 1) FSL does not respect Workbench’s header info, so the labels get removed. You might need to use wb_command -volume-resample or copy over the header info. Yes, use wb_command -volume-warpfield-resamp

Re: [HCP-Users] Warping volume atlas and X, Y, Z of single point with standard2acpc_dc.nii.gz

1) FSL does not respect Workbench’s header info, so the labels get removed. You might need to use wb_command -volume-resample or copy over the header info. 2) FSL has a utility to do this I believe (std2imgcoord), but it will be slow (we used to use this for warping surfaces before we had the

Re: [HCP-Users] Troubleshooting fMRIVolume pipelines results

Hi Dinal, The main stderr and stdout would be where I would start. I don’t think fMRIVolume has any weird secondary log files like FIX. If you post the errors, perhaps we can sort this out. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Jayasekera, Dinal"

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

There are 6 dof rigid registration images and nonlinear. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C mailto:aaroncr...@outlook.com>> Date: Friday, December 28, 2018 at 1:29 AM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] export workbench scenes as vector graphics

Hi Ely, Not at this time. You can export at whatever resolution you want, however, so you could think of the scene as the vector graphics file and export at the desired resolution for a given purpose. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Ely, Benjamin"

Re: [HCP-Users] MSMAll

MSMAll is aligned to fs_LR. I believe there are instructions on the HCP FAQ to get to fsaverage space, though you could also just downsample in fs_LR space by creating a less dense spheres with wb_command -surface-create-sphere, following the instructions in the usage and then using wb_command

Re: [HCP-Users] 7T movie data

It is in fs_LR just like the MSMSulc data without any registration specifier. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Haohao Bai <744652...@qq.com> Date: Tuesday, December 25, 2018 at 6:21 AM To: hcp-users

Re: [HCP-Users] Postfix

iginal Message- >From: Glasser, Matthew [mailto:glass...@wustl.edu] >Sent: 23 December 2018 18:17 >To: Moataz Assem ; >hcp-users@humanconnectome.org >Subject: Re: [HCP-Users] Postfix > >How are you running PostFix's matlab code? Compiled? Interpreted? Octave? > >Ma

Re: [HCP-Users] Postfix

appening. > >Moataz > >-Original Message- >From: hcp-users-boun...@humanconnectome.org >[mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Moataz Assem >Sent: 23 December 2018 16:21 >To: Glasser, Matthew ; D0O0D ; >hcp-users@humanconnectome.org >Subj

Re: [HCP-Users] Postfix

An earlier error message in PostFix. It seems there is no indication that the matlab code ran… Matt. On 12/23/18, 10:21 AM, "Moataz Assem" wrote: >Nope. hcp_fix ran without errors > >Moataz > >-Original Message- >From: Glasser, Matthew [mailto:glass...@w

Re: [HCP-Users] Postfix

00.ica/filtered_func_data.ica/melodic_oIC_vol.dscalar.nii >-name-file >/imaging/ma07/TaskBattery/mri_data/S01/MNINonLinear/Results/rfMRI_r1_AP/rf >MRI_r1_AP_hp2000.ica/ComponentList.txt > >ERROR: name list file doesn't exist > >Moataz > >-Original Message- >From

Re: [HCP-Users] Postfix

Is this a file that should have been created at some step during one of >the hcp_fix steps? > >Thanks > >Moataz > >-Original Message- >From: hcp-users-boun...@humanconnectome.org >[mailto:hcp-users-boun...@humanconnectome.org] On Behalf Of Glasser, >Matthew >Sent

Re: [HCP-Users] Myelin Mapping Metrics

Do you mean GIFTI surface files? Matt. On 12/20/18, 11:33 AM, "hcp-users-boun...@humanconnectome.org on behalf of Anna Chen" wrote: >Dear experts, > >I've processed my data through the HCP structural pipeline >(prefreesurfer, freesurfer, and postfreesurfer), and was wondering if >there is a

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