[HCP-Users] Fw:Welcome to the "HCP-Users" mailing list

2016-05-25 Thread Xinyang Liu
Dear Sir/Madam, Hello! I apply for joining the "HCP-Users" mailing list. I would be very appreciative if I could have the honor to be added. Thank you very much! :) Best regards, Xinyang Liu Forwarding messages From: hcp-users-requ...@humanconnectome.org Date: 201

Re: [HCP-Users] How to find trial-level behavioral results

2017-07-12 Thread Xinyang Liu
es. For example, in one emotion task, the >> reaction time was recorded as "Emotion_Task_Median_RT" in one column. Do you >> know how to get the trial-level behavioral results? Thank you very much. >> >> Best regards, &g

[HCP-Users] How to find trial-level behavioral results

2017-07-12 Thread Xinyang Liu
for single stimulus. The behavioral results for each subject are all median values. For example, in one emotion task, the reaction time was recorded as "Emotion_Task_Median_RT" in one column. Do you know how to get the trial-level behavioral results? Thank you very much. Best

[HCP-Users] failed running preprocessed dMRI data with FSL dtifit

2017-08-28 Thread Xinyang Liu
generated! Could you suggest possible reasons of how this happened? Thanks a lot! Best regards, Xinyang Liu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit

2017-08-28 Thread Xinyang Liu
in the future. Best regards, Xinyang At 2017-08-29 10:29:57, "Glasser, Matthew" <glass...@wustl.edu> wrote: If this is with FSL’s GUI, you might need to ask about it on the FSL list. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of Xinyang Liu <xi

Re: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit

2017-08-28 Thread Xinyang Liu
those of us who answer questions on this list know much about the FSL GUIs. We generally are more knowledgable about the FSL command line. Peace, Matt. From: Xinyang Liu <xinyang_ie...@163.com> Date: Monday, August 28, 2017 at 10:04 PM To: Matt Glasser <glass...@wustl.edu> Cc: &q

[HCP-Users] Structural space diffusion data

2017-11-20 Thread Xinyang Liu
. Thanks. Best regards, Xinyang Liu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Structural space diffusion data

2017-11-21 Thread Xinyang Liu
Peace, Matt. From: <hcp-users-boun...@humanconnectome.org> on behalf of Xinyang Liu <xinyang_ie...@163.com> Date: Monday, November 20, 2017 at 9:33 PM To: HCP 讨论组 <hcp-users@humanconnectome.org> Subject: [HCP-Users] Structural space diffusion data Dear HCP experts, Wh

Re: [HCP-Users] Structural space diffusion data

2017-11-21 Thread Xinyang Liu
bvecs so dtifit or bedpostx are still valid to apply. Resolution is separate from registration. For example you can overlay images in the same mm space but different resolutions in Connectome Workbench. Peace, Matt. From: Xinyang Liu <xinyang_ie...@163.com> Date: Tuesday, Novemb

Re: [HCP-Users] wb_command -metric-rois-from-extrema

2018-06-08 Thread Xinyang Liu
ce, Matt. From: on behalf of Xinyang Liu Date: Thursday, June 7, 2018 at 8:33 AM To: HCP 讨论组 Subject: [HCP-Users] wb_command -metric-rois-from-extrema Dear HCP experts, Hi. I have some confusions when using the workbench command -metric-rois-from-extrema. When using it to draw ROIs

[HCP-Users] HCPID in TAB.txt

2018-06-21 Thread Xinyang Liu
Dear HCP experts, In the behavioral TAB.txt of each participant's tfMRI folder, there is a column named HCPID. In this column, each participant's ID number is followed by a "_fnca" or "_fncb". Could you please tell what these fnca and fncb mean? Thank you very much. Best regards, Xinyang

[HCP-Users] connectivity matrices

2018-01-08 Thread Xinyang Liu
! Best regards, Xinyang Liu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] software to do deterministic tractography

2018-02-01 Thread Xinyang Liu
elize with fewer samples and using different random numbers and then combine after the fact. Peace, Matt. From: Xinyang Liu <xinyang_ie...@163.com> Date: Thursday, February 1, 2018 at 5:20 AM To: Matt Glasser <glass...@wustl.edu> Cc: HCP 讨论组 <hcp-users@humanconnectome.org>

Re: [HCP-Users] software to do deterministic tractography

2018-02-01 Thread Xinyang Liu
tt. From: <hcp-users-boun...@humanconnectome.org> on behalf of Xinyang Liu <xinyang_ie...@163.com> Date: Thursday, February 1, 2018 at 3:14 AM To: HCP 讨论组 <hcp-users@humanconnectome.org> Subject: [HCP-Users] software to do deterministic tractography Dear HCP experts, Could you

Re: [HCP-Users] software to do deterministic tractography

2018-02-01 Thread Xinyang Liu
ifferent --rseed and then combine them afterwards for a full dataset. Peace, Matt. From: Xinyang Liu <xinyang_ie...@163.com> Date: Thursday, February 1, 2018 at 5:44 AM To: Matt Glasser <glass...@wustl.edu> Cc: HCP 讨论组 <hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] softwar

[HCP-Users] software to do deterministic tractography

2018-02-01 Thread Xinyang Liu
Dear HCP experts, Could you please recommend us some software for the deterministic tractography analysis of HCP data? We are at the beginning to do that and wondering what to choose for the high-quality data. Any suggestions would be very appreciated. Thanks. Best regards, Xinyang Liu

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

2018-08-24 Thread Xinyang Liu
Dear HCP experts, Hi. When using workbench command "-metric-extrema" to draw ROI around the maximum point of the fMRI surface region, what would happen if there are two maximum points? Will the software keep both of them or only keep one? Thanks a lot. Best regards, Xinyang

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

2018-08-25 Thread Xinyang Liu
are somewhat complicated, and it was implemented by request of others, it is not something that we use. Tim On Fri, Aug 24, 2018 at 7:11 AM, Xinyang Liu wrote: Hi, Matt. Thank you very much for your reply. The extreme point was searched in a certain surface area. Do you mean that even

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

2018-08-24 Thread Xinyang Liu
, "Glasser, Matthew" wrote: I believe there is a configurable setting that sets the minimum distance between extrema. It is a local min/max that is found. Matt. From: on behalf of Xinyang Liu Date: Friday, August 24, 2018 at 4:21 AM To: HCP 讨论组 Subject: [HCP-Users] two maximum po

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

2018-08-26 Thread Xinyang Liu
nsform one of them to .asc? Best regards, Xinyang At 2018-08-27 01:12:54, "Glasser, Matthew" wrote: The other should be in the next map of the ROI file. Matt. From: Xinyang Liu Date: Sunday, August 26, 2018 at 2:41 AM To: Matt Glasser Cc: Timothy Coalson , HCP 讨论组 Subject:

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

2018-08-26 Thread Xinyang Liu
Ok, I will do that. Thanks. :) Best, Xinyang At 2018-08-27 11:16:42, "Glasser, Matthew" wrote: Would have to ask that on the FSL list. Matt. From: Xinyang Liu Date: Sunday, August 26, 2018 at 10:14 PM To: Matt Glasser Cc: Timothy Coalson , HCP 讨论组 Subject: Re: [HCP-Users] t

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

2018-08-28 Thread Xinyang Liu
are saved separately with two sets of global grayordinate coordinates? Thanks. Best regards, Xinyang At 2018-08-27 11:16:42, "Glasser, Matthew" wrote: Would have to ask that on the FSL list. Matt. From: Xinyang Liu Date: Sunday, August 26, 2018 at 10:14 PM To: Matt Glasser C

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

2018-08-29 Thread Xinyang Liu
d in a different way (and with different, more elaborate metadata). Tim On Tue, Aug 28, 2018 at 10:55 PM, Xinyang Liu wrote: Dear experts, Could I ask an additional question following my previous emails about the CIFTI data display? If two surface ROIs of one .func.gii file are displa

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

2018-08-26 Thread Xinyang Liu
rds, Xinyang At 2018-08-26 13:03:42, "Glasser, Matthew" wrote: How about posting some screen captures so we know what is happening? Matt. From: Xinyang Liu Date: Saturday, August 25, 2018 at 11:51 PM To: Timothy Coalson Cc: Matt Glasser , HCP 讨论组 Subject: Re: [HCP-Users] two maxi

[HCP-Users] questions about the out-scanner NIH Processing speed task

2018-07-06 Thread Xinyang Liu
Dear HCP experts, Hi. We are currently looking at the out-scanner behavioral data. There are two questions about the NIH Processing speed task: 1. In the Processing speed raw data, there are two similar task names. One is "NIH TB Pattern Comparison Processing Speed Age 7+", the other is "NIH

Re: [HCP-Users] questions about the out-scanner NIH Processing speed task

2018-07-06 Thread Xinyang Liu
users-boun...@humanconnectome.org on behalf of Xinyang Liu Sent: Friday, July 6, 2018 5:52 AM To: HCP 讨论组 Subject: [HCP-Users] questions about the out-scanner NIH Processing speed task Dear HCP experts, Hi. We are currently looking at the out-scanner behavioral data. There are two questions about the NIH

Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking

2018-04-05 Thread Xinyang Liu
<tsc...@mst.edu> wrote: Inline replies to some comments. Tim On Wed, Apr 4, 2018 at 7:38 AM, Xinyang Liu <xinyang_ie...@163.com> wrote: Dear Matthew, Thank you very much for your detailed explanation! 1. The current situation of our study is that, we used the HCP MMP1.0 atlas to

Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking

2018-04-08 Thread Xinyang Liu
verything" also include the GIFTI files (.func.gii) which were converted from the tfMRI CIFTI (.dtseries.nii) files, apart from the original CIFTI files themselves? Thanks! Best regards, Xinyang 在 2018-04-06 12:36:26,"Timothy Coalson" <tsc...@mst.edu> 写道: On Thu, Apr 5, 2018

Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking

2018-04-04 Thread Xinyang Liu
ere is no native diffusion space, as this is unnecessary. Tracking occurs subject’s physical space and you can use the surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k with MSMAll if you don’t use --xfm and --invxfm or those in ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k if

Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking

2018-04-09 Thread Xinyang Liu
On Sun, Apr 8, 2018 at 5:27 AM, Xinyang Liu <xinyang_ie...@163.com> wrote: Dear Tim, Hi. Thanks a lot to your very detailed explanation, I am more clear now about the underpinning relationships. :) Just to make sure one more thing, when you mentioned "if ignoring the subcor

Re: [HCP-Users] using surfaces as termination masks

2018-04-17 Thread Xinyang Liu
<tsc...@mst.edu> Date: Monday, April 16, 2018 at 4:10 PM To: Xinyang Liu <xinyang_ie...@163.com> Cc: HCP 讨论组 <hcp-users@humanconnectome.org>, Matt Glasser <glass...@wustl.edu> Subject: Re: [HCP-Users] using surfaces as termination masks Inline replies. Tim On S

Re: [HCP-Users] surface with and without MSMAll

2018-04-18 Thread Xinyang Liu
image. Problem solved. Sorry to disturb with such a hurried asking. Wish everyone a good day. :) Best regards, Xinyang 在 2018-04-18 16:00:36,"Xinyang Liu" <xinyang_ie...@163.com> 写道: Dear experts, Hi. Sorry that I made a mistake in my last email. The "100307.L.whi

[HCP-Users] the wmparc file

2018-04-25 Thread Xinyang Liu
Dear HCP experts, Hi. In the subject's structural folder, there is a file called "wmparc", which seems to be the combination of the white matter and grey matter according to fslview. My questions are: 1. Is there any other brain structures included in this data apart from grey and white

Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking

2018-04-04 Thread Xinyang Liu
From: <hcp-users-boun...@humanconnectome.org> on behalf of Xinyang Liu <xinyang_ie...@163.com> Date: Tuesday, April 3, 2018 at 1:52 AM To: HCP 讨论组 <hcp-users@humanconnectome.org> Subject: [HCP-Users] questions about using HCP surface ROIs in prob-tracking Dear HCP experts,

[HCP-Users] problems about fibre tracking between surface ROIs

2018-03-22 Thread Xinyang Liu
ROI with HCP data? 3. The FSL says that it now accepts surface data, does it mean we don't need to do transfer between surface and diffusion space and then set parameters like --xmf, --meshspace and --seedref? Any guidance would be very appreciated. Best regards, Xinyang Liu

[HCP-Users] Repeated measurement in HCP outscanner behavioral data

2018-06-29 Thread Xinyang Liu
Dear HCP experts, Hi. We are looking at the HCP battery of behavioral measures. We found that in the recordings of individual performances, there are some participants who repeated the task for a second time. For example, in the Executive Function DCCS task (on manual page 183), there are 30

Re: [HCP-Users] Repeated measurement in HCP outscanner behavioral data

2018-06-29 Thread Xinyang Liu
@wustl.edu www.humanconnectome.org From:hcp-users-boun...@humanconnectome.org on behalf of Xinyang Liu Sent: Friday, June 29, 2018 3:50:06 AM To: HCP 讨论组 Subject: [HCP-Users] Repeated measurement in HCP outscanner behavioral data Dear HCP experts, Hi. We are looking at the HCP battery of behavioral me

[HCP-Users] rfMRI connecitivity

2018-09-21 Thread Xinyang Liu
Dear HCP experts, Hi. We are trying to compute resting state fMRI connectivity between several ROIs for single individuals. The surface ROIs (.func.gii) were acquired from task fMRI data. The plan is to compute the averaged rfMRI timeseries within each ROI, and then compute their

Re: [HCP-Users] rfMRI connectivity

2018-09-21 Thread Xinyang Liu
ormalizing, and concatenating across the runs in each subject—see wb_shortcuts). Matt. From: on behalf of Xinyang Liu Date: Friday, September 21, 2018 at 4:00 AM To: HCP 讨论组 Subject: [HCP-Users] rfMRI connecitivity Dear HCP experts, Hi. We are trying to compute resting state fMRI co

Re: [HCP-Users] rfMRI connectivity

2018-09-22 Thread Xinyang Liu
l file. Tim On Fri, Sep 21, 2018 at 7:22 AM, Xinyang Liu wrote: Dear Matt, Thank you very much for your prompt reply. I will have a try according to your suggestions. Best regards, Xinyang At 2018-09-21 19:37:13, "Glasser, Matthew" wrote: 1. ${StudyFolder}/${Subject}/MNINonLi

[HCP-Users] preprocessing of released behavioral data

2018-09-22 Thread Xinyang Liu
Dear experts, Hi again. :) We have some questions about the behavioral data of S1200 subjects. We would like to use the reaction time of some tfMRI tasks. We found that in the released behavioral data file("unrestricted_xxx.csv"), only median_RT was recorded for each task. We would like to

[HCP-Users] A few questions about HCP behavioral data

2019-02-21 Thread Xinyang Liu
Dear HCP experts, We're currently analyzing some of the behavioral data from your dataset and have three short questions about the IRT-modelling and theta-score derivation that is also mentioned in the "NIH Toolbox Scoring and Interpretation Guide". To be able to build comparable scores

Re: [HCP-Users] Inconsistency in the Working Memory tfMRI behavioral scores

2019-03-17 Thread Xinyang Liu
_ Greg Burgess, Ph.D. Senior Scientist, Human Connectome Project Washington University School of Medicine Department of Psychiatry Phone: 314-362-7864 Email: gburg...@wustl.edu On Mar 12, 2019, at 7:44 AM, Xinyang Liu wrote: Dear HCP experts, Hi. We are currently analyzing the behavioral

[HCP-Users] Inconsistency in the Working Memroy tfMRI behavioral scores

2019-03-12 Thread Xinyang Liu
Dear HCP experts, Hi. We are currently analyzing the behavioral accuracy scores from the Working Memory(WM) tfMRI task. However, we found an inconsistency between computed accuracy scores from the WM trial-level raw data and the "WM_Task_2bk_*_Acc" analyzed data columns in the integrated

[HCP-Users] HCP lifespan data

2019-05-06 Thread Xinyang Liu
Dear HCP experts, Hi. We are very interested in your lifespan dataset. Currently, there are only pilot data of 27 participants released. Do you have a timeline about when you may release data of more participants? Thanks a lot. :) Best regards, Xinyang