Re: [HCP-Users] Troubleshooting error with gradunwarp

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

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

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

Re: [HCP-Users] matlab cifti io

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

Re: [HCP-Users] table for parcellation

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

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

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

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

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

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

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

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

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

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

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

Re: [HCP-Users] Corrupt Input Data

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

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

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

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

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

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

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

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

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

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

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

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

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

Re: [HCP-Users] pdconn analysis problems

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

Re: [HCP-Users] pdconn analysis problems

cKCRVdqX0=jwPQkvc49uGNzjH-ER9ry1R9fgOMJ093SIy8J5g11Nk=> -- Joseph M. Orr, Ph.D. Assistant Professor Department of Psychological and Brain Sciences Texas A Institute for Neuroscience Texas A University College Station, TX On Sat, Jun 1, 2019 at 1:31 PM Glasser, Matthew mailto:glass...@wustl

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

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

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

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

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

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

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

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

Re: [HCP-Users] pdconn analysis problems

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

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

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

Re: [HCP-Users] *WU-SPAM* [suspect] assessing MSMAll quality

users@humanconnectome.org" , "Glasser, Matthew" Subject: Re: *WU-SPAM* [suspect][HCP-Users] assessing MSMAll quality Thanks Matt. and are acceptable ranges for values of those files less than 2 also? Moataz On Mon, May 27, 2019 at 5:47 AM +0100, "Glasser, Matthew" mailto:glass..

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

That file does exist in the structural package then. Matt. From: Jaime Caballero Date: Monday, May 27, 2019 at 3:20 PM To: "Glasser, Matthew" Cc: "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical) Sorry for the

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

I thought you said you were using a locally collected sample you ran the HCP Pipelines on? Matt. From: Jaime Caballero Date: Monday, May 27, 2019 at 3:10 PM To: "Glasser, Matthew" Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical) Ok, thank you! I will tr

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

-template you mention. Matt. From: Jaime Caballero Date: Monday, May 27, 2019 at 12:56 PM To: "Glasser, Matthew" Cc: "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical) The objective is to extract functional connectiv

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

What do you plan to do with the file? Matt. From: Jaime Caballero Date: Monday, May 27, 2019 at 12:08 PM To: "Glasser, Matthew" Cc: "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical) A .dscalar.nii output, I thi

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

Are you wanting a .dlabel.nii output or a .dscalar.nii output? Matt. From: on behalf of Jaime Caballero Date: Monday, May 27, 2019 at 10:37 AM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] Convert nifti-ROIs to cifti format (subcortical) Dear experts In my center we are studying

Re: [HCP-Users] DeDriftAndResamplePipelineBatch.sh

Yes. Matt. From: on behalf of Marta Moreno Date: Monday, May 27, 2019 at 11:15 AM To: HCP Users Subject: [HCP-Users] DeDriftAndResamplePipelineBatch.sh Dear Experts, If I run MR ICAFIX regressing motion parameters as part of the cleaning, do I need to set

Re: [HCP-Users] *WU-SPAM* [suspect] assessing MSMAll quality

Hi Moataz, I check the StrainJ (isotropic areal distortion) and StrainR (shape distortion) and the overall alignment. Beyond that, there isn’t currently a quantitative way to do this. Matt. From: on behalf of Moataz Assem Date: Sunday, May 26, 2019 at 10:03 AM To:

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

There could be a bug here related to new FSL 6.0+ fslmaths behavior. Please try modifying: https://github.com/Washington-University/HCPpipelines/blob/master/global/scripts/TopupPreprocessingAll.sh line 189 to: ${FSLDIR}/bin/fslmaths ${WD}/PhaseOne_mask_gdc -mas ${WD}/PhaseTwo_mask_gdc -ero

Re: [HCP-Users] A question about the HCP brain registration

No, but you could make one pretty easily. Scenes are text files and if your data are structured in a regular format, you could make a template scene and sed replace stuff in and out of the scene. The PostFix does this for propagating a template scene for checking sICA components. Matt.

Re: [HCP-Users] volumetric segmentation of subcortical structures

${StudyFolder}/${Subject}/MNINonLinear/wmparc.nii.gz in the structural packages. Matt. From: on behalf of "Mazzetti, C. (Cecilia)" Date: Thursday, May 16, 2019 at 3:51 AM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] volumetric segmentation of subcortical structures Dear all, I

Re: [HCP-Users] Quick questions

To: "Glasser, Matthew" Cc: Erez Simony , michael tolochinsky Subject: Quick questions Dear Matthew, We are looking at the HCP resting-state data (grayordinate) coming from the 7T and 3T magnets, and have quick questions: 1) We would like to work on results of 3T and 7T data of the same 18

Re: [HCP-Users] error about subcortical processing in HCP fMRI-surface pipeline

14, 2019 at 3:40 AM To: "Glasser, Matthew" Cc: "simon.w...@ur.de" Subject: error about subcortical processing in HCP fMRI-surface pipeline Dear Dr. Glasser, we are experiencing the very same error posted here https://www.mail-archive.com/hcp-users@humanconnectome.org/

Re: [HCP-Users] Local Gyrification Index

We didn’t generate any non-default FreeSurfer outputs. Matt. From: Reza Rajimehr Date: Saturday, May 11, 2019 at 12:46 PM To: "Glasser, Matthew" Subject: Re: [HCP-Users] Local Gyrification Index Thanks Matt! LGI should be a map (a value for each vertex). It is not generated

Re: [HCP-Users] Local Gyrification Index

I believe the all the default FreeSurfer stats made it into the database in one way or another. Have you looked? Matt. From: on behalf of Reza Rajimehr Date: Saturday, May 11, 2019 at 12:36 PM To: hcp-users Subject: [HCP-Users] Local Gyrification Index Hi, Does HCP database have

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

is not determined solely by the distortions, but rather their magnitude with respect to known good data, the quality of the alignment itself, and the test-retest reproducibility of the alignment. Matt. From: Maria Sison Date: Friday, May 10, 2019 at 3:15 PM To: "Glasser, Matthew" , "

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

This issue of what kind of data and how much is something we plan to investigate in detail for MSMAll (and the cortical areal classifier). Matt. From: "Harms, Michael" Date: Thursday, May 9, 2019 at 4:41 PM To: "Glasser, Matthew" , Maria Sison , Steve Smith Cc: HCP 讨论

Re: [HCP-Users] MSMAll vs. MSMSulc reliability in our data

Not running sICA+FIX might well be a part of the problem. The TR is quite long as Steve says, which will limit the accuracy of sICA+FIX cleanup some also. Also, surface area and thickness might prefer MSMSulc due to correlations with folding patterns. Myelin, task, and resting state fMRI

Re: [HCP-Users] temporal ICA code

We haven’t released the code for a temporal ICA pipeline yet because we don’t have an automated pipeline. We do hope to get the HCP-YA data cleaned with temporal ICA and released and make an automated pipeline. For a group spatial ICA, one needs to use MIGP. For group temporal ICA, the

Re: [HCP-Users] Gambling task: clarification of Reward vs Loss being mostly random noise

Those are the observations. Perhaps Greg might have some thoughts on the explanations. Matt. From: on behalf of Filip Grill Date: Wednesday, May 8, 2019 at 8:31 AM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] Gambling task: clarification of Reward vs Loss being mostly random

Re: [HCP-Users] Probabilistic tractography for dense connectome

nates in this connectivity matrix? Thank you! Aaron From: Stamatios Sotiropoulos mailto:stamatios.sotiropou...@nottingham.ac.uk>> Sent: Friday, April 26, 2019 10:58 AM To: Aaron C Cc: Glasser, Matthew; hcp-users@humanconnectome.org<mailto:hcp-u

Re: [HCP-Users] Reporting dense analysis results

If you want to make a cluster table, I think percent overlaps with areas is a very reasonable way to do it. I would recommend you follow Tim’s suggestion with vertex areas as well. I would strongly recommend sharing your data as well (if it is CIFTI/GIFTI/NIFTI, the balsa.wustl.edu database

Re: [HCP-Users] Probabilistic tractography for dense connectome

Not as far as I am aware, but Stam might know. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C mailto:aaroncr...@outlook.com>> Date: Thursday, April 25, 2019 at 9:15 AM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] "activation" tables for reporting pscalar results

I do not report MNI coordinates for any studies because I don’t think they add a lot of value for the reasons described in Tim’s PNAS paper. Studies that provide actual results on the surface are much more useful, and I have extensively used such studies to make incisive neuroanatomical

Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects?

Also ReApplyFixMultiRunPipeline.sh is not affected at all by this bug. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Matt Glasser mailto:glass...@wustl.edu>> Date: Tuesday, April 23, 2019 at 7:47 PM To: Timothy Coalson mailto:tsc...@mst.edu>>, "Harms, Michael"

Re: [HCP-Users] hp2000 filter not applied to hp2000_clean.nii.gz volume data for some (one?) subjects?

This is a bug affecting the use of ReApplyFix to re-clean data using a hand classification instead of the original FIX classification (and does not affect the use of ReApplyFix in MSMAll). It has been present since the release of ReApplyFix and will affect the volume data of all HCP-YA

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

>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Multi-run ICA-FIX with excessive movement Thank you Matt. This is really helpful. Any idea when the new classifier you mentioned in 1. will be available? On Mon, Apr 22, 2019 at 8:50 PM Glasser, Matthew mailto:glass...@wustl.e

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

Matt. Do you have some suggestions for the metrics to use to determine scan quality after ICA FIX? Thanks, Cherry On Mon, Apr 22, 2019 at 8:15 PM Glasser, Matthew mailto:glass...@wustl.edu>> wrote: I would decide after cleaning with MR ICA+FIX if you actually have to exclude the s

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

I would decide after cleaning with MR ICA+FIX if you actually have to exclude the scans and run with them all. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Yizhou Ma mailto:maxxx...@umn.edu>> Date: Monday, April 22, 2019 at 3:47 PM To:

Re: [HCP-Users] DeDriftAndResamplePipeline error

fix, please update to the latest master. Tim On Mon, Apr 15, 2019 at 8:27 PM Timothy Coalson mailto:tsc...@mst.edu>> wrote: They weren't instructions, I pushed an edit, and it was a different script. Tim On Mon, Apr 15, 2019 at 8:08 PM Glasser, Matthew mailto:glass...@wustl.edu>>

Re: [HCP-Users] Assigning the results of -cifti-correlation to appropriate resting state networks

I think you guys already have the corresponding label file. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Wednesday, April 17, 2019 at 1:10 PM To: "Jayasekera, Dinal" mailto:dinal.jayasek...@wustl.edu>> Cc:

Re: [HCP-Users] question about making RSFC matrices available

Hi Tim, I guess we have treated such derivative results similarly and put them behind the HCP data use terms. One easy solution would be to upload the results to the BALSA database and add the HCP data use terms. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of

Re: [HCP-Users] DeDriftAndResamplePipeline error

am attaching log files. Does the folder containing fix1.067 need to include all the ICAFIX files? Thanks a lot! Leah. On Apr 15, 2019, at 12:19 AM, Marta Moreno mailto:mmorenoort...@icloud.com>> wrote: It seams to be working now. Thanks a lot! Leah. On Apr 15, 2019, at 12:04 AM, Glass

Re: [HCP-Users] Motion files missing for the HCP data

This is an excellent question for the HCP users list where folks who know the REST interface better than me can help. Matt. From: "Li, Jin" mailto:li.9...@buckeyemail.osu.edu>> Date: Monday, April 15, 2019 at 2:53 PM To: Matt Glasser mailto:glass...@wustl.edu>> Subject: Motion files missing

Re: [HCP-Users] DeDriftAndResamplePipeline error

quot;1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab, Mode=2 octave #MatlabMode="0" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab, Mode=2 octave But the script does not run and it is aborted with the following message: DeDriftAndResamplePipeline.sh - ABORTING: unrecognized opti

Re: [HCP-Users] DeDriftAndResamplePipeline error

In this case you do run it with the individual fMRI names and that doesn’t look like the version 4.0.0 example script... Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno mailto:mmorenoort...@icloud.com>> Date: Sunday, April 14, 2019 at 10:06 PM To: HCP

Re: [HCP-Users] Subject list for the HCP Q2 release

We might be able to dig that up, but perhaps if you contacted the authors they might simply have the list they used in an old script? Also, it is worth keeping in mind that subjects who were released were occasionally later excluded for one reason or another. Thus, it may not be possible to

Re: [HCP-Users] MSMAllPipeline error

- File: /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/global/templates/MSMAll/rfMRI_REST_Atlas_MSMAll_2_d41_WRN_DeDrift_hp2000_clean_PCA.ica_d40_ROW_vn/Weights.txt EXISTS Leah. On Apr 13, 2019, at 4:45 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: https://githu

Re: [HCP-Users] MSMAllPipeline error

RI_MR Sat Apr 13 16:29:46 EDT 2019 - SingleSubjectConcat.sh - MATH: ((TCS - Mean)) parsed '((TCS - Mean))' as '(TCS-Mean)' Leah. On Apr 13, 2019, at 4:10 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: You could try setting line 353 to NO: https://github.com/Washington-Un

Re: [HCP-Users] MSMAllPipeline error

Unit 21 New York, NY 10032 phone: (914) 218-7311 email: mm4...@cumc.columbia.edu<mailto:mm4...@cumc.columbia.edu> On Apr 13, 2019, at 3:39 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: If you ran MR+FIX, your data are already concatenated for MSMAll, so just provide t

Re: [HCP-Users] MSMAllPipeline error

TTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_1/RS_fMRI_1_Atlas_hp0_clean_vn_tempcompute.dscalar.nii', file does not exist, or folder permissions prevent seeing it Leah. On Apr 13, 2019, at 3:22 PM, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: You can just put your MR+FIX c

Re: [HCP-Users] MSMAllPipeline error

ica/.fix','/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Results/RS_fMRI_MR/RS_fMRI_MR_Atlas_hp0_clean_vn_tempcompute.dscalar.nii','/Applications/workbench/bin_macosx64//wb_command'); Sat Apr 13 15:09:44 EDT 2019 - SingleSubjectConcat.sh - MATH: ((TCS - Mean)) / max(VN,0.001) Le

Re: [HCP-Users] MSMAllPipeline error

x 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu> On 4/13/19, 11:28 AM, "hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org> on b

Re: [HCP-Users] MSMAllPipeline error

I wouldn¹t use hp=pd2 unless you know what you are doing, as that option has not been fully tested. I run with hp=0. Matt. On 4/13/19, 10:41 AM, "hcp-users-boun...@humanconnectome.org on behalf of Marta Moreno" wrote: >Dear Experts, > >I am running the following script MSMAllPipelineBatch.sh

Re: [HCP-Users] beta bias correction

This wasn’t done on any of the released HCP data. When we released temporal ICA cleaned fMRI data I plan to include this. The version of the HCP pipelines that has this correction was coded up after the HCP data were processed, so it is not in the 3T HCP data. I believe the 7T data do have

Re: [HCP-Users] Surface Parcelations Area

wb_command -cifti-weighted-stats with the areas as binary ROIs and the appropriate surfaces in the case of individuals or group average vertex areas in the case of the group will give the surface areas. I don’t know that you can do it directly from a dlabel, but can convert a dlabel to binary

Re: [HCP-Users] connectome for monkeys // fiber trajectories

The main current limitation with the probabilistic trajectory feature (which tracks exactly which fiber is chosen by the tractography algorithm out of the 1-3 modeled fibers in each voxel) is that it only works with single threaded probtrackx2, and not with the GPU accelerated version. Matt.

Re: [HCP-Users] An error about subcorticalprocessinginHCPfMRI-surface pipeline

It is hard to keep track of these threads when they don’t contain the prior info below. I did find that you are not using FSL 6.0.1, so I would retry with that. Matt. From: Qunjun Liang mailto:liangqun...@foxmail.com>> Date: Wednesday, April 10, 2019 at 9:24 PM To: Matt Glasser

Re: [HCP-Users] Query: Error: Spin echo fieldmap has different dimensions than scout image, this requires a manual fix

If you run fslhd on the SBRef and SE fieldmap images, are they different? Ideally these are matched exactly on the scanner. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Bourguignon, Nicolas" mailto:nicolas.bourguig...@uconn.edu>> Date: Wednesday, April 10, 2019

Re: [HCP-Users] An error about subcortical processinginHCPfMRI-surface pipeline

aset preprocessing by HCP pipeline and confirmed that the y dimension of 108 in FunTask_AP.nii.gz is a wrong number. For now, I still have no idea about what caused this error. Could you give me a cue? Sincerely, Qunjun -- Original ------ From: "Glasser, Matthew&

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

ou mean that these brain extracted T1w and T2w images "T1w_acpc_dc_restore_brain.nii.gz" and "T2w_acpc_dc_restore_brain.nii.gz" were actually not used in the FreeSurfer pipeline? Thank you. Aaron From: Glasser, Matthew mailto:glass...@wustl.edu>>

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

The brain masked file should not be used for surface estimation. How are you calling the FreeSurfer pipeline? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Aaron C mailto:aaroncr...@outlook.com>> Date: Monday, April 8, 2019 at 9:41 PM To:

Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing taking suspiciously long while

k 13 hours, but it completed the execution, and the final atlas.dtseries output looks good.. so it just takes a REALLY long time, and it takes a crazy amount of CPU [image.png] let me know if anything else happens when you run it I your environment? Shachar On Mon, 1 Apr 2019 at 00:19, Glasser, Matt

Re: [HCP-Users] MR ICA+FIX error

I would use mode=1 Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno mailto:mmorenoort...@icloud.com>> Date: Saturday, April 6, 2019 at 2:46 PM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc: HCP Users mailto:hcp-users@humanconnectome.org>> Subject: Re:

Re: [HCP-Users] An error about subcortical processing inHCPfMRI-surface pipeline

unjun -- Original ------ From: "Glasser, Matthew"mailto:glass...@wustl.edu>>; Date: Sat, Apr 6, 2019 11:32 AM To: "Qunjun Liang"mailto:liangqun...@foxmail.com>>; Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnec

Re: [HCP-Users] An error about subcortical processing in HCPfMRI-surface pipeline

le is placed in the attachment. Sincerely, Qunjun -- Original ------ From: "Glasser, Matthew"mailto:glass...@wustl.edu>>; Date: Sat, Apr 6, 2019 10:39 AM To: "Qunjun Liang"mailto:liangqun...@foxmail.com>>;"hcp-users@humanco

Re: [HCP-Users] An error about subcortical processing in HCP fMRI-surface pipeline

Please post how you called PreFreeSurfer, PostFreeSurfer, fMRIVolume, and fMRISurface. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Qunjun Liang mailto:liangqun...@foxmail.com>> Date: Friday, April 5, 2019 at 9:37 PM To:

Re: [HCP-Users] nu_correct: crashed while running nu_evaluate

u/Pages/default.aspx> | Washington University in St. Louis<https://wustl.edu/> From: Glasser, Matthew Sent: Friday, April 5, 2019 5:19:49 PM To: Jayasekera, Dinal; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users]

Re: [HCP-Users] nu_correct: crashed while running nu_evaluate

tps://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: Glasser, Matthew Sent: Thursday, Apri

Re: [HCP-Users] Volumetric subcortical group-averaged data: what is the exact MNI template you used?

Xavier. On Fri, Apr 5, 2019 at 5:48 PM Glasser, Matthew mailto:glass...@wustl.edu>> wrote: FSL’s MNI152. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis mailto:xavie...@mit.edu>> Date: Friday, April 5, 2019 at 4:46 PM To: "hcp

Re: [HCP-Users] Volumetric subcortical group-averaged data: what is the exact MNI template you used?

FSL’s MNI152. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis mailto:xavie...@mit.edu>> Date: Friday, April 5, 2019 at 4:46 PM To: "hcp-users@humanconnectome.org" mailto:hcp-users@humanconnectome.org>> Subject:

Re: [HCP-Users] Standard to Native Applywarp Error

/freesurfer/subjects/fsaverage/mri.2mm/subcort.mask.mgz On Thu, Apr 4, 2019 at 9:32 PM Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Is this HCP data? What software are you using for tractography? If you want statistical maps in native volume space, it might be easiest to project

Re: [HCP-Users] Standard to Native Applywarp Error

Is this HCP data? What software are you using for tractography? If you want statistical maps in native volume space, it might be easiest to project them from the subject’s physical space surfaces in the T1w/fsaverage_LR32k or alternatively track the data to those surfaces. Matt. From:

Re: [HCP-Users] MSM binaries versions

>it? > >and just for future reference, by the msm binary, do you mean to just >download e.g. msm_centos from github? In that case its only compiled for >v1.0.0 and not v3.0.0, am I right? > >Thanks > >Moataz > >From: Harms, Micha

Re: [HCP-Users] nu_correct: crashed while running nu_evaluate

r 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: Glasser, Matthew Sent: Thursday, April 4, 2019 3:01:18

Re: [HCP-Users] MSM binaries versions

Use version 3.0.0 in GitHub. The one used in FSL is not supported by the HCP Pipelines as it does not have the HOCR options. All that is needed is the MSM binary. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday,

Re: [HCP-Users] nu_correct: crashed while running nu_evaluate

Are you using FreeSurfer 6.0? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Jayasekera, Dinal" mailto:dinal.jayasek...@wustl.edu>> Date: Thursday, April 4, 2019 at 11:25 AM To: "hcp-users@humanconnectome.org"

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

You could interpolate it back to native space if you wanted with relatively little information loss if you use splines. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday, April 4, 2019 at 1:53 PM To: Aaron C

Re: [HCP-Users] FSL 6 compatibility

Please use FSL 6.0.1. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Jayasekera, Dinal" mailto:dinal.jayasek...@wustl.edu>> Date: Tuesday, April 2, 2019 at 6:10 PM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] ICA+FIX error

Did you update to the latest version of FIX from FSL’s website? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno mailto:mmorenoort...@icloud.com>> Date: Sunday, March 31, 2019 at 6:44 PM To: HCP Users mailto:hcp-users@humanconnectome.org>> Subject:

Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing taking suspiciously long while

sub-cortical processing taking suspiciously long while yes, it happened for each of my subjects. these are the input files for the command - temp_subject_smooth.dtseries.nii, temp_template.dlabel.nii where should i upload them to? On Sun, 31 Mar 2019 at 18:56, Glasser, Matthew mailto:glass.

Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing taking suspiciously long while

other than temp_subject_smooth.dtseries.nii, temp_template.dlabel.nii and the registered volume? thanks, Shachar On Sun, 31 Mar 2019 at 18:37, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Perhaps you should upload the various input files to the specific wb_command command somewhere s

Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing taking suspiciously long while

ly, the fmri pipelines.. Cheers Shachar On Sun, Mar 31, 2019, 18:13 Glasser, Matthew mailto:glass...@wustl.edu> wrote: How many volumes and did you look at the data being input yet? This code didn’t change so we don’t expect any difference. Matt. From: Shachar Gal mailto:gal.shac...@gmail.com

Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing taking suspiciously long while

How did you call fMRISurface and what kind of data is this in terms of spatial and temporal resolution? Do the input and template data line up and look reasonable? Matt From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal mailto:gal.shac...@gmail.com>> Date: Sunday,

Re: [HCP-Users] HCP-Users] Extracting mean relative motion from XNAT

I think you can use this file: ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/Movement_RelativeRMS.txt Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Martina Jonette Lund mailto:m.j.l...@medisin.uio.no>> Date: Friday, March 29, 2019 at 9:39 AM To:

Re: [HCP-Users] Question on fsl 6.0.1

We expect these to work together however. These announcements were made on the various lists over the past couple of weeks. Matt. On 3/29/19, 1:10 PM, "hcp-users-boun...@humanconnectome.org on behalf of Harms, Michael" wrote: > >The MR-FIX releases as part of HCPpipelines v4.0.0 should work

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