[HCP-Users] Fw:Welcome to the "HCP-Users" mailing list
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: 2016-05-25 20:54:22 To: xinyang_ie...@163.com Subject: Welcome to the "HCP-Users" mailing list Welcome to the HCP-Users@humanconnectome.org mailing list! PLEASE NOTE: You must reply to this email to verify your subscription. For security reasons, the list URL is no longer accessible to the public. To post to this list, send your email to: hcp-users@humanconnectome.org If you ever want to unsubscribe, visit the HCP list subscription page at: https://www.humanconnectome.org/contact/#subscribe You must know your password to change your options (including changing the password, itself) or to unsubscribe. It is: digest ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] How to find trial-level behavioral results
Hi, Greg. Thank you very much for your kind help. The "TAB.txt" provides the information for within scanner behavioral results, which are quite nice. But we also wish to acquire behavioral data for out of scanner tasks, that is the "NIT Toolbox Assessment" as mentioned in the manual (p.177). Do you have any idea for this part of data? Thanks. Best regards, Xinyang At 2017-07-12 23:11:17, "Burgess, Gregory" <gburg...@wustl.edu> wrote: >Hi Xinyang, > >The accuracy and RT for individual stimuli within a scan are in the >preprocessed directory for that scan (i.e., preproc resources). The files end >with “TAB.txt”, and are tab-delimited E-Prime outputs. If you need detail >about the variables contained in those TAB.txt outputs, you can review >Appendix 6 in the documentation (see >https://www.humanconnectome.org/study/hcp-young-adult/document/1200-subjects-data-release). > >--Greg > > >Greg Burgess, Ph.D. >Staff Scientist, Human Connectome Project >Washington University School of Medicine >Department of Psychiatry >Phone: 314-362-7864 >Email: gburg...@wustl.edu > >> On Jul 12, 2017, at 4:47 AM, Xinyang Liu <xinyang_ie...@163.com> wrote: >> >> Dear HCP fellows, >> >> May I ask for some help? >> We are very interested in the behavioral and individual difference >> measurement data, which are introduced in Chapter 5 of the Reference Manual. >> However, in the downloaded "behavioral data" file (in .csv version), I >> cannot find the result 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 regards, >> Xinyang Liu >> >> >> >> >> >> >> ___ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > > >The materials in this message are private and may contain Protected Healthcare >Information or other information of a sensitive nature. If you are not the >intended recipient, be advised that any unauthorized use, disclosure, copying >or the taking of any action in reliance on the contents of this information is >strictly prohibited. If you have received this email in error, please >immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] How to find trial-level behavioral results
Dear HCP fellows, May I ask for some help? We are very interested in the behavioral and individual difference measurement data, which are introduced in Chapter 5 of the Reference Manual. However, in the downloaded "behavioral data" file (in .csv version), I cannot find the result 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 regards, Xinyang Liu ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] failed running preprocessed dMRI data with FSL dtifit
Dear HCP fellows, Hi. Could I ask for some help? When I ran the HCP preprocessed diffusion data with the "dtifit" function in FSL, it always failed in the middle with a window came out saying "signal killed", which is strange. I then used another software called PANDA to check the detailed procedure, and found that the processing stopped at "extract B0", the log informations are as follows: *** The job starts now ! fslroi /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1 Killed fslroi /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1: Killed extracting b0 volume is done! Checking outputs The output file or directory /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz has not been generated! The output file or directory /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/OutputDone/extractB0_4.done was successfully 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
Dear Matthew, Oh, I just found out the reason, which is due to the very limited internal storage of my virtual machine. Now it runs very well after I enlarged it. :) Thanks a lot for your suggestion about the FSL list, which provides a new way to me when I have FSL running problems 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 <xinyang_ie...@163.com> Date: Monday, August 28, 2017 at 9:27 PM To: "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org> Subject: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit Dear HCP fellows, Hi. Could I ask for some help? When I ran the HCP preprocessed diffusion data with the "dtifit" function in FSL, it always failed in the middle with a window came out saying "signal killed", which is strange. I then used another software called PANDA to check the detailed procedure, and found that the processing stopped at "extract B0", the log informations are as follows: *** The job starts now ! fslroi /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1 Killed fslroi /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1: Killed extracting b0 volume is done! Checking outputs The output file or directory /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz has not been generated! The output file or directory /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/OutputDone/extractB0_4.done was successfully 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 ___ 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
Ok, thanks a lot for the information. We will surely use the command line after starting with the GUI as a new learner. ;) Best regards, Xinyang At 2017-08-29 11:07:50, "Glasser, Matthew" <glass...@wustl.edu> wrote: The reason I suggest the FSL list is that I don’t think 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: "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org> Subject: Re: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit Dear Matthew, Oh, I just found out the reason, which is due to the very limited internal storage of my virtual machine. Now it runs very well after I enlarged it. :) Thanks a lot for your suggestion about the FSL list, which provides a new way to me when I have FSL running problems 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 <xinyang_ie...@163.com> Date: Monday, August 28, 2017 at 9:27 PM To: "HCP-Users@humanconnectome.org" <HCP-Users@humanconnectome.org> Subject: [HCP-Users] failed running preprocessed dMRI data with FSL dtifit Dear HCP fellows, Hi. Could I ask for some help? When I ran the HCP preprocessed diffusion data with the "dtifit" function in FSL, it always failed in the middle with a window came out saying "signal killed", which is strange. I then used another software called PANDA to check the detailed procedure, and found that the processing stopped at "extract B0", the log informations are as follows: *** The job starts now ! fslroi /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1 Killed fslroi /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/test100206_4_DWI_01.nii.gz /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz 0 1: Killed extracting b0 volume is done! Checking outputs The output file or directory /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/data_b0.nii.gz has not been generated! The output file or directory /home/panda/ShareFolder/HCPDATA/output4_sub2/4/tmp/OutputDone/extractB0_4.done was successfully 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 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Structural space diffusion data
Dear HCP experts, When reading tutorials about the HCP preprocessing pipeline, I noticed that there is a registration processing of diffusion data to the 1.25 mm structural space. So does that mean all the diffusion data are already in the structural space now after preprocessing, together with the T1w_acpc_dc_restore_1.25.nii.gz native structural image? And if so, does that mean if we want to further do data registration to standard templates, we only need to transform between structural and standard space? Is my understanding correct? Any guidance would be very appreciated. 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
Dear Matthew,
Thank you very much for your helpful reply.
I've found the structural-to-standard transformation file you mentioned in the
databox. Now here are two new questions which I cannot make clear.
1. If the preprocessed diffusion data have already been transformed and stored
in the structural space, e.g. data.nii.gz, how to explain that these data can
be directly processed by DTIFIT, which are supposed only be done in the
diffusion space?
2. The resolution for diffusion data are 1.25mm, as well as the resampled
structural file T1w_acpc_dc_restore_1.25.nii.gz, which are also stored in the
diffusion data file. But the individual's structural image resolution in the
structural data files are actually 0.7mm. The resolutions are not match. So can
we directly use the acpc_dc2standard.nii.gz, or we need to do a second
registration?
Maybe my questions are too naïve, but look forward to your kind guidance.
Thanks a lot.
Best regards,
Xinyang
At 2017-11-21 11:37:42, "Glasser, Matthew" <glass...@wustl.edu> wrote:
That’s right and that transformation is already provided
${StudyFolder}/${Subject}/MNINonLinear/xfms/acpc_dc2standard.nii.gz.
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,
When reading tutorials about the HCP preprocessing pipeline, I noticed that
there is a registration processing of diffusion data to the 1.25 mm structural
space. So does that mean all the diffusion data are already in the structural
space now after preprocessing, together with the
T1w_acpc_dc_restore_1.25.nii.gz native structural image? And if so, does that
mean if we want to further do data registration to standard templates, we only
need to transform between structural and standard space? Is my understanding
correct?
Any guidance would be very appreciated. Thanks.
Best regards,
Xinyang Liu
___
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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
___
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Re: [HCP-Users] Structural space diffusion data
Dear Matt,
Great. Thanks a lot. My confusions are solved now. :)
Best regards,
Xinyang
At 2017-11-21 20:58:33, "Glasser, Matthew" <glass...@wustl.edu> wrote:
There is a rigid registration between diffusion and structural space and the
appropriate rotation is applied to the 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, November 21, 2017 at 2:58 AM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP 讨论组 <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Structural space diffusion data
Dear Matthew,
Thank you very much for your helpful reply.
I've found the structural-to-standard transformation file you mentioned in the
databox. Now here are two new questions which I cannot make clear.
1. If the preprocessed diffusion data have already been transformed and stored
in the structural space, e.g. data.nii.gz, how to explain that these data can
be directly processed by DTIFIT, which are supposed only be done in the
diffusion space?
2. The resolution for diffusion data are 1.25mm, as well as the resampled
structural file T1w_acpc_dc_restore_1.25.nii.gz, which are also stored in the
diffusion data file. But the individual's structural image resolution in the
structural data files are actually 0.7mm. The resolutions are not match. So can
we directly use the acpc_dc2standard.nii.gz, or we need to do a second
registration?
Maybe my questions are too naïve, but look forward to your kind guidance.
Thanks a lot.
Best regards,
Xinyang
At 2017-11-21 11:37:42, "Glasser, Matthew" <glass...@wustl.edu> wrote:
That’s right and that transformation is already provided
${StudyFolder}/${Subject}/MNINonLinear/xfms/acpc_dc2standard.nii.gz.
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,
When reading tutorials about the HCP preprocessing pipeline, I noticed that
there is a registration processing of diffusion data to the 1.25 mm structural
space. So does that mean all the diffusion data are already in the structural
space now after preprocessing, together with the
T1w_acpc_dc_restore_1.25.nii.gz native structural image? And if so, does that
mean if we want to further do data registration to standard templates, we only
need to transform between structural and standard space? Is my understanding
correct?
Any guidance would be very appreciated. Thanks.
Best regards,
Xinyang Liu
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
___
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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] wb_command -metric-rois-from-extrema
Dear Tim, dear Glasser, Thank you very much for your answers. That's very clear to me now. :) By the way, I also have a question when counting the vertex number of surface ROIs (.func.gii) using the wb_command -metric-stats -reduce SUM. Among around 200 subjects, there are two subjects whose vertex number outcomes are two sum values (e.g. 63 97 in a column), which is strange. Do you know the possible reason for that? Thanks. Best regards, Xinyang At 2018-06-08 05:15:36, "Timothy Coalson" wrote: A picture is worth a thousand words, so here is a single subject 32k fs_LR surface, rendered to show edges between vertices, showing the variable spacing (you can check this on other surfaces by loading them in wb_view, and going to the Surface menu, clicking Properties, and setting "Drawin Type" to "Links (Edges)". In short, you shouldn't think of vertices like you do voxels, they don't use a fully regular grid. This is why wb_command spatial operations take nearly all distances in mm, not in neighbors. Tim On Thu, Jun 7, 2018 at 10:48 AM, Glasser, Matthew wrote: On a standard mesh anatomical surface the vertex spacing is non-uniform across the surface. If you used the spheres you could get a uniform number of vertices (though now the patches would cover different total areas). Probably the uniform in mm approach (on the midthickness with appropriate correction for shrinkage by vertex areas) is what you want. Peace, 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 on the fMRI surface, I found that with the same radium, the number of vertices inside the ROI can be different in different locations. For example, when r=5mm, the vertex number can range from around 30 to around 80. Maybe I do not understand very well about the parameter - geodesic distance limit from vertex, in mm. My understanding is that the distance is the radium around the extrema on the stretched surface, and the vertex numbers should be the same after the radium is set. Where do I misunderstand? Look forward to any kind guidance. Thanks a lot. Best regards, Xinyang ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] HCPID in TAB.txt
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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] connectivity matrices
Dear HCP experts, Hi. We are doing brain structural network study based on HCP diffusion data and FSL. We want to acquire 90*90 and 1024*1024 ROI connectivity matrices of the whole brain, which is based on probabilistic tracing with the FSL probtrackx2 --network mode. However, our running always got killed probably due to the limitation memory of the CPU. Could you please suggest a way for us to finish the running? For example, do we need split the matrix with some commands like -rseed in probtrackx2? Or is there any other approaches? Any guidance would be very appreciated. Thanks! 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
Dear Matt, Sorry I didn't get the point. Could you please explain more in detail? Your suggestion would be very important and helpful to us. Thank you very much. Best regards, Xinyang At 2018-02-01 19:30:12, "Glasser, Matthew" <glass...@wustl.edu> wrote: You can parallelize 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> Subject: Re: [HCP-Users] software to do deterministic tractography Dear Matt, Thanks a lot for your suggestion. Actually, probabilistic tractography with FSL was our first choice with HCP data. However, the executing time was too long when we tried to build a global network for single subject with FSL probtrackx2, and we don't know how to run in parallel without GPU. Therefore, we wanna try the deterministic way to shorten the time. Best, Xinyang At 2018-02-01 18:51:47, "Glasser, Matthew" <glass...@wustl.edu> wrote: In general we recommend probabilistic tractography with FSL, but other options include MRTriX. Peace, Matt. 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 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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] software to do deterministic tractography
Dear Matt, Thanks a lot for your suggestion. Actually, probabilistic tractography with FSL was our first choice with HCP data. However, the executing time was too long when we tried to build a global network for single subject with FSL probtrackx2, and we don't know how to run in parallel without GPU. Therefore, we wanna try the deterministic way to shorten the time. Best, Xinyang At 2018-02-01 18:51:47, "Glasser, Matthew" <glass...@wustl.edu> wrote: In general we recommend probabilistic tractography with FSL, but other options include MRTriX. Peace, Matt. 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 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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] software to do deterministic tractography
Dear Matt, That's really a great idea! I will try it then. Thanks a lot. By the way, for HCP data probabilistic tractography, are there suggested values for basic parameters like --nsamples, --nsteps, and --steplength ? For example, the dMRI resolution is 1.25mm, and the default --steplength is 0.5 mm. Does it matter if that is not a integral multiple relationship ? Best regards, Xinyang At 2018-02-01 19:47:59, "Glasser, Matthew" <glass...@wustl.edu> wrote: You can run with fewer --nsamples multiple runs of probtrackx2 on different computers each with a different --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] software to do deterministic tractography Dear Matt, Sorry I didn't get the point. Could you please explain more in detail? Your suggestion would be very important and helpful to us. Thank you very much. Best regards, Xinyang At 2018-02-01 19:30:12, "Glasser, Matthew" <glass...@wustl.edu> wrote: You can parallelize 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> Subject: Re: [HCP-Users] software to do deterministic tractography Dear Matt, Thanks a lot for your suggestion. Actually, probabilistic tractography with FSL was our first choice with HCP data. However, the executing time was too long when we tried to build a global network for single subject with FSL probtrackx2, and we don't know how to run in parallel without GPU. Therefore, we wanna try the deterministic way to shorten the time. Best, Xinyang At 2018-02-01 18:51:47, "Glasser, Matthew" <glass...@wustl.edu> wrote: In general we recommend probabilistic tractography with FSL, but other options include MRTriX. Peace, Matt. 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 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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] software to do deterministic tractography
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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] two maximum points using -metric-extrema
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 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] two maximum points using -metric-extrema
Dear Tim, dear Matt, Thank you very much for your helpful answers. Sorry that I may not described very clearly before. As Tim mentioned, we used the -metric-extrema to find the maximum point within a certain region (produce "maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs (produced "ROI.func.gii" file). Then there is a contradictory thing emerged. When we used "wb_command -metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few results showed two values, which might indicate two ROIs based on the two maximum points. We checked the maxima.func.gii files, and found there do existed two maximum points in such condition. However, when we looked at the created ROI images on Connectome Workbench, we only saw one target ROI drawn on the brain surface. This confused us a lot. We don't know whether there were one or two ROIs produced. Do you have any suggestions about that? Thanks. Best regards, Xinyang At 2018-08-25 04:16:48, "Timothy Coalson" wrote: The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or -1 based on if they are a local maximum or minimum. By default, if there are two equal values that are closer than the search range, then *neither* of them will be identified as an extrema. If they are further then the search range, then both may be extrema. The -consolidate-mode acts somewhat differently - if two equal values are touching, neither is treated as an initial extrema, but as long as there is at least one vertex separating them, they may both be treated as initial extrema. After the initial extrema are found, all extrema that are close to other extrema are "consolidated" together. The details 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 there are two maximum points with the same value, they were controlled in a limited distance and therefore, the final drawn ROI is a combined region of two drawings instead of two separate ones? Because the problem is that, when I count the total vertex number for each created ROI using -metric-stats, a few results showed two values for one ROI. I am wondering why this happen and how to deal with that. Best regards, Xinyang At 2018-08-24 19:14:56, "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 points using -metric-extrema 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 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] two maximum points using -metric-extrema
Hi, Matt. Thank you very much for your reply. The extreme point was searched in a certain surface area. Do you mean that even there are two maximum points with the same value, they were controlled in a limited distance and therefore, the final drawn ROI is a combined region of two drawings instead of two separate ones? Because the problem is that, when I count the total vertex number for each created ROI using -metric-stats, a few results showed two values for one ROI. I am wondering why this happen and how to deal with that. Best regards, Xinyang At 2018-08-24 19:14:56, "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 points using -metric-extrema 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 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] two maximum points using -metric-extrema
Hi, Matt. I saw the second ROI on WB as you said then. Thank you so much！ Then another left question is, when I use $FSL/surf2surf to change the .func.gii file (with two ROIs included) to .asc format, I only saw the coordinates information of one ROI (vertices with 1 values). The .func.gii showed vertex number of two ROIs, i.e. 127, 48. But when checking the transformed .asc file, I only found the ROI coordinates of the first ROI (127 vertices), not the second. Does it mean the two produced ROIs are saved separately in .func.gii, but the "surf2surf "command can only transform one of them to .asc? Best regards, Xinyang At 2018-08-27 01:12:54, "Glasser, Matthew" 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 Hi, Matt. Sure. I attached two pictures and two produced GIFTI files here. In data processing, I first used -metric-extrema to find the maximum point within a certain fMRI region. The "maximum_IPS.JPG" attached was among the condition that two maximum points were found (please see the two yellow points in the first attached picture). The corresponding GIFTI file is "L.maxima.func.gii". Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to draw ROIs, the result only showed one created ROI based on one maximum point, as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" file is also attached. I also used the -metric-stats to calculate the vertex number of the created ROI, but the result provided two values: 127, 48. So I am quite confusing about what happened here. Best regards, 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 maximum points using -metric-extrema Dear Tim, dear Matt, Thank you very much for your helpful answers. Sorry that I may not described very clearly before. As Tim mentioned, we used the -metric-extrema to find the maximum point within a certain region (produce "maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs (produced "ROI.func.gii" file). Then there is a contradictory thing emerged. When we used "wb_command -metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few results showed two values, which might indicate two ROIs based on the two maximum points. We checked the maxima.func.gii files, and found there do existed two maximum points in such condition. However, when we looked at the created ROI images on Connectome Workbench, we only saw one target ROI drawn on the brain surface. This confused us a lot. We don't know whether there were one or two ROIs produced. Do you have any suggestions about that? Thanks. Best regards, Xinyang At 2018-08-25 04:16:48, "Timothy Coalson" wrote: The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or -1 based on if they are a local maximum or minimum. By default, if there are two equal values that are closer than the search range, then *neither* of them will be identified as an extrema. If they are further then the search range, then both may be extrema. The -consolidate-mode acts somewhat differently - if two equal values are touching, neither is treated as an initial extrema, but as long as there is at least one vertex separating them, they may both be treated as initial extrema. After the initial extrema are found, all extrema that are close to other extrema are "consolidated" together. The details 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 there are two maximum points with the same value, they were controlled in a limited distance and therefore, the final drawn ROI is a combined region of two drawings instead of two separate ones? Because the problem is that, when I count the total vertex number for each created ROI using -metric-stats, a few results showed two values for one ROI. I am wondering why this happen and how to deal with that. Best regards, Xinyang At 2018-08-24 19:14:56, "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
Re: [HCP-Users] two maximum points using -metric-extrema
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] two maximum points using -metric-extrema Hi, Matt. I saw the second ROI on WB as you said then. Thank you so much！ Then another left question is, when I use $FSL/surf2surf to change the .func.gii file (with two ROIs included) to .asc format, I only saw the coordinates information of one ROI (vertices with 1 values). The .func.gii showed vertex number of two ROIs, i.e. 127, 48. But when checking the transformed .asc file, I only found the ROI coordinates of the first ROI (127 vertices), not the second. Does it mean the two produced ROIs are saved separately in .func.gii, but the "surf2surf "command can only transform one of them to .asc? Best regards, Xinyang At 2018-08-27 01:12:54, "Glasser, Matthew" 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 Hi, Matt. Sure. I attached two pictures and two produced GIFTI files here. In data processing, I first used -metric-extrema to find the maximum point within a certain fMRI region. The "maximum_IPS.JPG" attached was among the condition that two maximum points were found (please see the two yellow points in the first attached picture). The corresponding GIFTI file is "L.maxima.func.gii". Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to draw ROIs, the result only showed one created ROI based on one maximum point, as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" file is also attached. I also used the -metric-stats to calculate the vertex number of the created ROI, but the result provided two values: 127, 48. So I am quite confusing about what happened here. Best regards, 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 maximum points using -metric-extrema Dear Tim, dear Matt, Thank you very much for your helpful answers. Sorry that I may not described very clearly before. As Tim mentioned, we used the -metric-extrema to find the maximum point within a certain region (produce "maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs (produced "ROI.func.gii" file). Then there is a contradictory thing emerged. When we used "wb_command -metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few results showed two values, which might indicate two ROIs based on the two maximum points. We checked the maxima.func.gii files, and found there do existed two maximum points in such condition. However, when we looked at the created ROI images on Connectome Workbench, we only saw one target ROI drawn on the brain surface. This confused us a lot. We don't know whether there were one or two ROIs produced. Do you have any suggestions about that? Thanks. Best regards, Xinyang At 2018-08-25 04:16:48, "Timothy Coalson" wrote: The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or -1 based on if they are a local maximum or minimum. By default, if there are two equal values that are closer than the search range, then *neither* of them will be identified as an extrema. If they are further then the search range, then both may be extrema. The -consolidate-mode acts somewhat differently - if two equal values are touching, neither is treated as an initial extrema, but as long as there is at least one vertex separating them, they may both be treated as initial extrema. After the initial extrema are found, all extrema that are close to other extrema are "consolidated" together. The details 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 there are two maximum points with the same value, they were controlled in a limited distance and therefore, the final drawn ROI is a combined region of two drawings instead of two separate ones? Because the problem is that, when I count the total vertex number for each created ROI using -metric-stats, a few results showed two values for one ROI. I am wondering w
Re: [HCP-Users] two maximum points using -metric-extrema
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 displayed in separate maps of Connectome Workbench instead of simultaneously shown on one brain surface, does it mean the two ROIs are saved separately with two sets of global grayordinate coordinates? Thanks. Best regards, Xinyang At 2018-08-27 11:16:42, "Glasser, Matthew" 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] two maximum points using -metric-extrema Hi, Matt. I saw the second ROI on WB as you said then. Thank you so much！ Then another left question is, when I use $FSL/surf2surf to change the .func.gii file (with two ROIs included) to .asc format, I only saw the coordinates information of one ROI (vertices with 1 values). The .func.gii showed vertex number of two ROIs, i.e. 127, 48. But when checking the transformed .asc file, I only found the ROI coordinates of the first ROI (127 vertices), not the second. Does it mean the two produced ROIs are saved separately in .func.gii, but the "surf2surf "command can only transform one of them to .asc? Best regards, Xinyang At 2018-08-27 01:12:54, "Glasser, Matthew" 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 Hi, Matt. Sure. I attached two pictures and two produced GIFTI files here. In data processing, I first used -metric-extrema to find the maximum point within a certain fMRI region. The "maximum_IPS.JPG" attached was among the condition that two maximum points were found (please see the two yellow points in the first attached picture). The corresponding GIFTI file is "L.maxima.func.gii". Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to draw ROIs, the result only showed one created ROI based on one maximum point, as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" file is also attached. I also used the -metric-stats to calculate the vertex number of the created ROI, but the result provided two values: 127, 48. So I am quite confusing about what happened here. Best regards, 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 maximum points using -metric-extrema Dear Tim, dear Matt, Thank you very much for your helpful answers. Sorry that I may not described very clearly before. As Tim mentioned, we used the -metric-extrema to find the maximum point within a certain region (produce "maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs (produced "ROI.func.gii" file). Then there is a contradictory thing emerged. When we used "wb_command -metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few results showed two values, which might indicate two ROIs based on the two maximum points. We checked the maxima.func.gii files, and found there do existed two maximum points in such condition. However, when we looked at the created ROI images on Connectome Workbench, we only saw one target ROI drawn on the brain surface. This confused us a lot. We don't know whether there were one or two ROIs produced. Do you have any suggestions about that? Thanks. Best regards, Xinyang At 2018-08-25 04:16:48, "Timothy Coalson" wrote: The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or -1 based on if they are a local maximum or minimum. By default, if there are two equal values that are closer than the search range, then *neither* of them will be identified as an extrema. If they are further then the search range, then both may be extrema. The -consolidate-mode acts somewhat differently - if two equal values are touching, neither is treated as an initial extrema, but as long as there is at least one vertex separating them, they may both be treated as initial extrema. After the initial extrema are found, all extrema that are close to other extrema are "consolidated" together. The details 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 there are two maximum poin
Re: [HCP-Users] two maximum points using -metric-extrema
Hi, Tim. Thank you very much for your detailed and helpful explanation. I finally understand how the two maps are stored in the .func.gii file. The problem I met is that the FSL surf2surf command can only convert the format of one ROI map even though there are two. I haven't got their reply yet. Maybe I should ask again. Best regards, Xinyang At 2018-08-29 12:36:17, "Timothy Coalson" wrote: .func.gii files are simply arrays of values, where one dimension is the number of vertices in the surface, and the other is the number of maps in the file. Every vertex of the relevant surface gets a value. The special case of "ROIs" is just that the values are all either 0 or 1. So, while in the second ROI map, different vertices have values of 1 than the first ROI map, both maps span all vertices. Surface coordinates are stored in .surf.gii files - neither .func.gii nor cifti files contain vertex coordinates. Cifti does not support using a different set of brainordinates in different maps of the file - every map in a single cifti file uses the same set of brainordinates. Internally cifti files are just another rectangular matrix, but used 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 displayed in separate maps of Connectome Workbench instead of simultaneously shown on one brain surface, does it mean the two ROIs are saved separately with two sets of global grayordinate coordinates? Thanks. Best regards, Xinyang At 2018-08-27 11:16:42, "Glasser, Matthew" 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] two maximum points using -metric-extrema Hi, Matt. I saw the second ROI on WB as you said then. Thank you so much！ Then another left question is, when I use $FSL/surf2surf to change the .func.gii file (with two ROIs included) to .asc format, I only saw the coordinates information of one ROI (vertices with 1 values). The .func.gii showed vertex number of two ROIs, i.e. 127, 48. But when checking the transformed .asc file, I only found the ROI coordinates of the first ROI (127 vertices), not the second. Does it mean the two produced ROIs are saved separately in .func.gii, but the "surf2surf "command can only transform one of them to .asc? Best regards, Xinyang At 2018-08-27 01:12:54, "Glasser, Matthew" 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 Hi, Matt. Sure. I attached two pictures and two produced GIFTI files here. In data processing, I first used -metric-extrema to find the maximum point within a certain fMRI region. The "maximum_IPS.JPG" attached was among the condition that two maximum points were found (please see the two yellow points in the first attached picture). The corresponding GIFTI file is "L.maxima.func.gii". Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to draw ROIs, the result only showed one created ROI based on one maximum point, as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" file is also attached. I also used the -metric-stats to calculate the vertex number of the created ROI, but the result provided two values: 127, 48. So I am quite confusing about what happened here. Best regards, 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 maximum points using -metric-extrema Dear Tim, dear Matt, Thank you very much for your helpful answers. Sorry that I may not described very clearly before. As Tim mentioned, we used the -metric-extrema to find the maximum point within a certain region (produce "maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs (produced "ROI.func.gii" file). Then there is a contradictory thing emerged. When we used "wb_command -metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few results showed two values, which might indicate two ROIs based on the two maximum points. We checked the maxima.func.gii files, and found there do existed two maximum points in such condition. However, when we looked at the created ROI images on Connecto
Re: [HCP-Users] two maximum points using -metric-extrema
Hi, Matt. Sure. I attached two pictures and two produced GIFTI files here. In data processing, I first used -metric-extrema to find the maximum point within a certain fMRI region. The "maximum_IPS.JPG" attached was among the condition that two maximum points were found (please see the two yellow points in the first attached picture). The corresponding GIFTI file is "L.maxima.func.gii". Then I continued using the "L.maxima.func.gii" and -metric-rois-from-extrema to draw ROIs, the result only showed one created ROI based on one maximum point, as the second picture (IPS_ROI.JPG) attached. The "TARGET_ROI_IPS_L.func.gii" file is also attached. I also used the -metric-stats to calculate the vertex number of the created ROI, but the result provided two values: 127, 48. So I am quite confusing about what happened here. Best regards, 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 maximum points using -metric-extrema Dear Tim, dear Matt, Thank you very much for your helpful answers. Sorry that I may not described very clearly before. As Tim mentioned, we used the -metric-extrema to find the maximum point within a certain region (produce "maxima.func.gii" file) and then use the -metric-rois-from-extrema to draw ROIs (produced "ROI.func.gii" file). Then there is a contradictory thing emerged. When we used "wb_command -metric-stats ROI.func.gii -reduce -SUM "to count the ROI vertex number, a few results showed two values, which might indicate two ROIs based on the two maximum points. We checked the maxima.func.gii files, and found there do existed two maximum points in such condition. However, when we looked at the created ROI images on Connectome Workbench, we only saw one target ROI drawn on the brain surface. This confused us a lot. We don't know whether there were one or two ROIs produced. Do you have any suggestions about that? Thanks. Best regards, Xinyang At 2018-08-25 04:16:48, "Timothy Coalson" wrote: The -metric-extrema command doesn't draw ROIs, it sets single vertices to 1 or -1 based on if they are a local maximum or minimum. By default, if there are two equal values that are closer than the search range, then *neither* of them will be identified as an extrema. If they are further then the search range, then both may be extrema. The -consolidate-mode acts somewhat differently - if two equal values are touching, neither is treated as an initial extrema, but as long as there is at least one vertex separating them, they may both be treated as initial extrema. After the initial extrema are found, all extrema that are close to other extrema are "consolidated" together. The details 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 there are two maximum points with the same value, they were controlled in a limited distance and therefore, the final drawn ROI is a combined region of two drawings instead of two separate ones? Because the problem is that, when I count the total vertex number for each created ROI using -metric-stats, a few results showed two values for one ROI. I am wondering why this happen and how to deal with that. Best regards, Xinyang At 2018-08-24 19:14:56, "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 points using -metric-extrema 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 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sende
[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 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 TB Pattern Comparison Process Speed 7+ v 1.1". Could you please tell whether these two groups of measurements are the same for this task? 2. Also in this task, we found that the trial number varies a lot across participants, not like in other tasks where the trial numbers are consistently the same within one task. Could we ask why? Any of your kind guidance would be very appreciated. Thank you very much. Best regards, Xinyang ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] questions about the out-scanner NIH Processing speed task
Hi Jennifer, Ok, I see. Thank you so much for your detailed and very helpful reply! :) Best regards, Xinyang At 2018-07-07 02:23:01, "Elam, Jennifer" wrote: Hi Xinyang, From the NIH Toolbox website: Some PROMIS domains (processing speed is a PROMIS measurement) have multiple versions of instruments (i.e. v1.0, v1.1, v2.0). Generally, it is recommended that you use the most recent version available which can be identified as the instrument with the highest version number. In most cases, an instrument that has a decimal increase (v1.0 to v1.1) retains the same item-level parameters as well as instrument reliability and validity. From the Processing Speed Test description in the NIH Toolbox Scoring and Interpretation Manual 9-27-12 (versions that were used for HCP Young Adult): Scoring Process: The participant’s raw score is the number of items answered correctly in a 90-second period, with a range of 0-130. This score is then converted to the Toolbox normative scale scores. With that information, I would say that the difference between v1.0 and 1.1 is probably not consequential and the reason that you see a range of numbers of trials for the subjects is that they completed a different number of items within the 90 second measurement period. If you want more information, you will have to contact the NIH Toolbox support team at h...@nihtoolbox.org or perhaps their support is now fully switched over to h...@healthmeasures.net. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 e...@wustl.edu www.humanconnectome.org From:hcp-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 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 TB Pattern Comparison Process Speed 7+ v 1.1". Could you please tell whether these two groups of measurements are the same for this task? 2. Also in this task, we found that the trial number varies a lot across participants, not like in other tasks where the trial numbers are consistently the same within one task. Could we ask why? Any of your kind guidance would be very appreciated. Thank you very much. Best regards, Xinyang ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking
Dear Tim,
Hi. Lots of thanks to your very detailed answer! :)
Yes, I agree with you that it would be better to do tractography in the subject
native volume space. And it is good to know that the MMP1.0 can be also used in
"T1w"-space surfaces. However, there is one existed problem that I cannot
figure out. The tfMRI outputs (e.g. tstat1.dtseries.nii) of the
"$Subject_3T_tfMRI_$TASK_analysis_s2.zip" are in the CIFTI grayordinates
standard space, with the directory of "MNINonlinear". There is no T1w folder
for the native cortical surface in the tfMRI s2 file.
To do tractography in native volume space, I suppose the surface ROIs should
also go back to the native surface. But with the only standardly registered
tfMRI grayordinate output, how should I change back?
Best regards,
Xinyang
At 2018-04-05 04:54:04, "Timothy Coalson" <tsc...@mst.edu> wrote:
Inline replies to some comments.
Tim
On Wed, Apr 4, 2018 at 7:38 AM, Xinyang Liu <xinyang_ie...@163.com> wrote:
Dear Matthew,
Thank you very much for your detailed explanation!
1. The current situation of our study is that, we used the HCP MMP1.0 atlas to
sample the tfMRI data in order to localize specific functional areas. Since the
HCP MMP1.0 is in the MNI space,
No, it isn't, because version 1.0 is a surface-only parcellation.
Surface-based labels or scalar data are not in any volume space, it is only the
geometry files (*.surf.gii) that have any coordinates in them at all. It is
also correct to use the MMP1.0 with "T1w"-space surfaces (MSMAll is
recommended).
we used
"$SUBJECT/MNINonLinear/fsaverage_LR32k/$SUBJECT.L.midthickness._MSMAll.32k_fs_LR.surf.gii"
to do the multiplication. Then I suppose the surface ROI to be acquired in the
MNI standard space, and therefore need to use the --xfm and --invxfm in
probtrackx2. Is my understanding correct?
As I understand it, tracking in subject native (T1w) volume space is strongly
recommended, because the nonlinear MNI warp could change the paths that
tractography takes to be something unrealistic. The T1w space is an
undistorted, rigid aligned version of the scanner space of the anatomical
images (and the T1w space diffusion data has had its vectors rotated to match
this rigid alignment), and thus the white matter is the same shape as it is in
the subject's head.
2. In this way, do the HCP data contain files that can be used in --xfm,
--invxfm and --seedref in surface prob-tracking?
3. In the FSL "surf2surf" format conversion from .func.gii to ASCII type
(.asc), is it correct to use
"$Subject/MNINonLinear/fsaverage_LR32k/${Subject}.R.white.32k_fs_LR.surf.gii"
as the input (-i) and the acquired "ROI.func.gii" as --value?
I haven't used this, I would say try it and see what happens. Maybe someone
else can tell you what they did.
Look forward to your kind guidance. Thanks a lot!
Best regards,
Xinyang
At 2018-04-04 18:44:25, "Glasser, Matthew" <glass...@wustl.edu> wrote:
1. Files in ${StudyFolder}/${Subject}/T1w are in subject’s physical space and
files in ${StudyFolder}/${Subject}/MNINonLinear are in MNI standard space.
Surfaces without MSMAll are registered with MSMSulc and surfaces with MSMAll
are registered with MSMAll. In general MSMAll will have better alignment of
cortical areas across subjects.
2. There 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 you do.
Peace,
Matt.
From: Xinyang Liu <xinyang_ie...@163.com>
Date: Wednesday, April 4, 2018 at 2:36 AM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP 讨论组 <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking
Dear Matthew,
Thank you very much for your kind reply!
Could I continue asking two more new questions?
1. In the preprocessed structural data, both the
/${Subject}/T1w/fsaverage_LR32k and /${Subject}/MNINonLinear/fsaverage_LR32k
contain white surface files with the same names, such as
"${Subject}.L.white.32k_fs_LR.surf.gii" and
"${Subject}.L.white.MSMAll.32k_fs_LR.surf.gii". Is there any difference
between these files of the same name but under different routes?
2. I am kind of confusing about the space transformation in surface ROI fibre
tracking. In the volume-based analysis, there is native diffusion space and
standard space, and tractograhpy is done in native diffusion space. For surface
data, I suppose the files like "${Subject}.L.white.32k_fs_LR.surf.gii" have
already been registered to a 32k standard mesh. Then should the surface ROI
fibre tracking go back to native sp
Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking
Dear Tim, Hi. Thanks a lot to your very detailed explanation, I am more clear now about the underpinning relationships. :) Just to make sure one more thing, when you mentioned "if ignoring the subcortical part, then everything will work with T1w surfaces", does this "everything" also include the GIFTI files (.func.gii) which were converted from the tfMRI CIFTI (.dtseries.nii) files, apart from the original CIFTI files themselves? Thanks! Best regards, Xinyang 在 2018-04-06 12:36:26，"Timothy Coalson" <tsc...@mst.edu> 写道： On Thu, Apr 5, 2018 at 11:18 PM, Xinyang Liu <xinyang_ie...@163.com> wrote: Dear Tim, Hi. Lots of thanks to your very detailed answer! :) Yes, I agree with you that it would be better to do tractography in the subject native volume space. And it is good to know that the MMP1.0 can be also used in "T1w"-space surfaces. However, there is one existed problem that I cannot figure out. The tfMRI outputs (e.g. tstat1.dtseries.nii) of the "$Subject_3T_tfMRI_$TASK_analysis_s2.zip" are in the CIFTI grayordinates standard space, with the directory of "MNINonlinear". CIFTI files contain both surface data and voxel-based data. We generally only release cifti files that use MNI space for the subcortical voxels. This is why they are in MNINonLinear, not because of the surface data. There is no T1w folder for the native cortical surface in the tfMRI s2 file. The surface files (.surf.gii) are in the structural packages, not in fMRI packages. The fMRI CIFTI files will only have versions in the MNINonLinear directory, but as explained, the surface data values are not tied to any volume space, only the subcortical values are. You can use T1w surfaces with the fMRI CIFTI files, despite them being in MNINonLinear, as long as you understand that the subcortical voxels will not line up properly with respect to the surfaces. If you only care about the cortical data, you can ignore the subcortical stuff entirely, and everything will work with surfaces in the T1w folder. To do tractography in native volume space, I suppose the surface ROIs should also go back to the native surface. But with the only standardly registered tfMRI grayordinate output, how should I change back? No, you don't need to do anything about native mesh, just use the MSMAll 32k_fs_LR surface data with the T1w folder MSMAll 32k_fs_LR anatomical surfaces, and things will work. I think you have encountered an unfortunate terminology choice on our part - the "native mesh" does not refer to anything related to the "native volume space", they are orthogonal concepts. "Native mesh" just means the subject-specific, haphazard mesh that comes out of freesurfer (approximately 140k vertices per hemisphere, as I recall). This doesn't prevent the application of volume registration to their coordinates - indeed, there are "native mesh" surfaces in the MNINonLinear folder, where this is exactly what we did. However, you don't need to use them, or the native mesh surfaces in T1w space either. Best regards, Xinyang At 2018-04-05 04:54:04, "Timothy Coalson" <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 sample the tfMRI data in order to localize specific functional areas. Since the HCP MMP1.0 is in the MNI space, No, it isn't, because version 1.0 is a surface-only parcellation. Surface-based labels or scalar data are not in any volume space, it is only the geometry files (*.surf.gii) that have any coordinates in them at all. It is also correct to use the MMP1.0 with "T1w"-space surfaces (MSMAll is recommended). we used "$SUBJECT/MNINonLinear/fsaverage_LR32k/$SUBJECT.L.midthickness._MSMAll.32k_fs_LR.surf.gii" to do the multiplication. Then I suppose the surface ROI to be acquired in the MNI standard space, and therefore need to use the --xfm and --invxfm in probtrackx2. Is my understanding correct? As I understand it, tracking in subject native (T1w) volume space is strongly recommended, because the nonlinear MNI warp could change the paths that tractography takes to be something unrealistic. The T1w space is an undistorted, rigid aligned version of the scanner space of the anatomical images (and the T1w space diffusion data has had its vectors rotated to match this rigid alignment), and thus the white matter is the same shape as it is in the subject's head. 2. In this way, do the HCP data contain files that can be used in --xfm, --invxfm and --seedref in surface prob-tracking? 3. In the FSL "surf2surf" format conversion from .func.gii to ASCII type (.asc), is
Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking
Dear Matthew,
Thank you very much for your detailed explanation!
1. The current situation of our study is that, we used the HCP MMP1.0 atlas to
sample the tfMRI data in order to localize specific functional areas. Since the
HCP MMP1.0 is in the MNI space, we used
"$SUBJECT/MNINonLinear/fsaverage_LR32k/$SUBJECT.L.midthickness._MSMAll.32k_fs_LR.surf.gii"
to do the multiplication. Then I suppose the surface ROI to be acquired in the
MNI standard space, and therefore need to use the --xfm and --invxfm in
probtrackx2. Is my understanding correct?
2. In this way, do the HCP data contain files that can be used in --xfm,
--invxfm and --seedref in surface prob-tracking?
3. In the FSL "surf2surf" format conversion from .func.gii to ASCII type
(.asc), is it correct to use
"$Subject/MNINonLinear/fsaverage_LR32k/${Subject}.R.white.32k_fs_LR.surf.gii"
as the input (-i) and the acquired "ROI.func.gii" as --value?
Look forward to your kind guidance. Thanks a lot!
Best regards,
Xinyang
At 2018-04-04 18:44:25, "Glasser, Matthew" <glass...@wustl.edu> wrote:
1. Files in ${StudyFolder}/${Subject}/T1w are in subject’s physical space and
files in ${StudyFolder}/${Subject}/MNINonLinear are in MNI standard space.
Surfaces without MSMAll are registered with MSMSulc and surfaces with MSMAll
are registered with MSMAll. In general MSMAll will have better alignment of
cortical areas across subjects.
2. There 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 you do.
Peace,
Matt.
From: Xinyang Liu <xinyang_ie...@163.com>
Date: Wednesday, April 4, 2018 at 2:36 AM
To: Matt Glasser <glass...@wustl.edu>
Cc: HCP 讨论组 <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking
Dear Matthew,
Thank you very much for your kind reply!
Could I continue asking two more new questions?
1. In the preprocessed structural data, both the
/${Subject}/T1w/fsaverage_LR32k and /${Subject}/MNINonLinear/fsaverage_LR32k
contain white surface files with the same names, such as
"${Subject}.L.white.32k_fs_LR.surf.gii" and
"${Subject}.L.white.MSMAll.32k_fs_LR.surf.gii". Is there any difference
between these files of the same name but under different routes?
2. I am kind of confusing about the space transformation in surface ROI fibre
tracking. In the volume-based analysis, there is native diffusion space and
standard space, and tractograhpy is done in native diffusion space. For surface
data, I suppose the files like "${Subject}.L.white.32k_fs_LR.surf.gii" have
already been registered to a 32k standard mesh. Then should the surface ROI
fibre tracking go back to native space and how if needed?
Best regards,
Xinyang
At 2018-04-04 00:49:09, "Glasser, Matthew" <glass...@wustl.edu> wrote:
1. Yes, though they can come from a certain (configurable) radius around the
vertex, rather than all from the point location with --sampvox.
2. I think probtrackx2 looks for greater than zero, but you could of course
binarize them.
3. I believe you can display the surface counts in GIFTI format with --fopd,
you might ask more on the FSL list as I haven’t done much tractorgraphy in a
while.
Peace,
Matt.
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,
Hi. As a new learner of the HCP tfMRI surface data, I have some questions when
using them as ROIs to do probabilistic tractography. I would be very thankful
to receive any of your kind guidance. My questions are as below.
1. I know that in FSL probtrackx2 voxel-based fibre tracking, 5000 streamlines
(default) come out from each voxel. How about the case in the surface vertices
of the HCP grayordinate space? Is it similar with the voxel-based tracking,
like 5000 streamlines coming out from each vertex?
2.The tfMRI surface ROIs usually contain information of signal intensities,
would this influence the diffusion tracking results if using them as masks?
3. How to display the surface ROIs (.func.gii or .asc) and output tracking
paths (.nii.gz in FSL results) in the same figure?
Look forward to your feedbacks. Thank you very much！
Best regards,
Xinyang Liu
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Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking
Dear Tim, Great to know. Thank you so much for your kind patience and help! :) Best regards, Xinyang At 2018-04-09 02:52:06, "Timothy Coalson" <tsc...@mst.edu> wrote: Yes, vertex-based data is not tied to any volume space, whether it is stored in cifti or gifti. Tim 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 subcortical part, then everything will work with T1w surfaces", does this "everything" 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 at 11:18 PM, Xinyang Liu <xinyang_ie...@163.com> wrote: Dear Tim, Hi. Lots of thanks to your very detailed answer! :) Yes, I agree with you that it would be better to do tractography in the subject native volume space. And it is good to know that the MMP1.0 can be also used in "T1w"-space surfaces. However, there is one existed problem that I cannot figure out. The tfMRI outputs (e.g. tstat1.dtseries.nii) of the "$Subject_3T_tfMRI_$TASK_analysis_s2.zip" are in the CIFTI grayordinates standard space, with the directory of "MNINonlinear". CIFTI files contain both surface data and voxel-based data. We generally only release cifti files that use MNI space for the subcortical voxels. This is why they are in MNINonLinear, not because of the surface data. There is no T1w folder for the native cortical surface in the tfMRI s2 file. The surface files (.surf.gii) are in the structural packages, not in fMRI packages. The fMRI CIFTI files will only have versions in the MNINonLinear directory, but as explained, the surface data values are not tied to any volume space, only the subcortical values are. You can use T1w surfaces with the fMRI CIFTI files, despite them being in MNINonLinear, as long as you understand that the subcortical voxels will not line up properly with respect to the surfaces. If you only care about the cortical data, you can ignore the subcortical stuff entirely, and everything will work with surfaces in the T1w folder. To do tractography in native volume space, I suppose the surface ROIs should also go back to the native surface. But with the only standardly registered tfMRI grayordinate output, how should I change back? No, you don't need to do anything about native mesh, just use the MSMAll 32k_fs_LR surface data with the T1w folder MSMAll 32k_fs_LR anatomical surfaces, and things will work. I think you have encountered an unfortunate terminology choice on our part - the "native mesh" does not refer to anything related to the "native volume space", they are orthogonal concepts. "Native mesh" just means the subject-specific, haphazard mesh that comes out of freesurfer (approximately 140k vertices per hemisphere, as I recall). This doesn't prevent the application of volume registration to their coordinates - indeed, there are "native mesh" surfaces in the MNINonLinear folder, where this is exactly what we did. However, you don't need to use them, or the native mesh surfaces in T1w space either. Best regards, Xinyang At 2018-04-05 04:54:04, "Timothy Coalson" <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 sample the tfMRI data in order to localize specific functional areas. Since the HCP MMP1.0 is in the MNI space, No, it isn't, because version 1.0 is a surface-only parcellation. Surface-based labels or scalar data are not in any volume space, it is only the geometry files (*.surf.gii) that have any coordinates in them at all. It is also correct to use the MMP1.0 with "T1w"-space surfaces (MSMAll is recommended). we used "$SUBJECT/MNINonLinear/fsaverage_LR32k/$SUBJECT.L.midthickness._MSMAll.32k_fs_LR.surf.gii" to do the multiplication. Then I suppose the surface ROI to be acquired in the MNI standard space, and therefore need to use the --xfm and --invxfm in probtrackx2. Is my understanding correct? As I understand it, tracking in subject native (T1w) volume space is strongly recommended, because the nonlinear MNI warp could change the paths that tractography takes to be something unrealistic. The T1w space is an undistorted, rigid aligned version of the scanner space of the anatomical images (and the T1w spa
Re: [HCP-Users] using surfaces as termination masks
Dear Matt, dear Tim, Lots of thanks! I have a better understanding now owing to your detailed explanation. :) By the way, is there any command in the workbench to count the vertex number on single surface ROI? Best regards, Xinyang At 2018-04-17 08:11:23, "Glasser, Matthew" <glass...@wustl.edu> wrote: It is better to have the termination surface outside the counting surface (e.g. count on white, terminate on pial). I do not remember if they can be the same surface or not, so you would need to ask this on the FSL list. Peace, Matt. From: Timothy Coalson <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 Sun, Apr 15, 2018 at 9:42 AM, Xinyang Liu <xinyang_ie...@163.com> wrote: Dear Matt, dear Tim, Very grateful for both of your kind replies. :) Here are some further questions based on your feedbacks. 1. For the ROI of neocortex (atlasroi.shape.gii), does it mean this shape file includes pial, midthickness and white surfaces? I previously thought the .shape.gii file provides cortical shape information, like curvature. But then I found the value of each atlasroi vertex is 1. Is it just an atlas map? Why was it chosen to set the value of L/R white.asc in surf2surf for brain surfaces? How do we usually give the --values in surf2surf? .shape.gii is a file extension, it does not tell you what is in the file. It is actually the same file format as .func.gii, and we are not entirely consistent about when we choose to use each one. "atlasroi.shape.gii" is just a binary roi, as "atlasroi" is intended to imply - it has values of 1 on vertices that get used in our standard cifti space, and 0 on vertices that don't get used. There are no coordinates or topology in it, no white, no pial, no midthickness - it is not a .surf.gii file, and we don't use the "combined data and coordinates" type files that other software does (unfortunately, probtrackx requires such "combined" files, adding to your confusion). In workbench, surfaces are always loaded from a different file than the data to display on them. 2. For the CIFTI and GIFTI matrices, I didn't intend to get the value of each element, but preferred to know what kind of data is stored, which might be shown by the name of each column, or data can be recognized as coordinates. I am wondering how to check this. They can store any type of measure. You can get the names of the maps, if they have been named at all, by using "wb_command -file-information -only-map-names ". Cifti files only store data values, and do not additionally contain surface coordinates or topology. You have to load surfaces separately from the cifti file. 3. I could not understand well that the cortex ROI would allow connections to pass through the medial wall. Because when looking at the surface outlines of "L/R.white.32k_fs_LR.surf.gii", it seems that the left and white surfaces are closed regions (please see the figure attached). Then how do connections pass through the middle surfaces? The atlasroi.shape.gii has values of 0 on the vertices that cut through the corpus callosum - if you generate the files correctly, the tractography software will see these values of 0 and know not to terminate a streamline that hits the surface where the value is 0, and continue until it hits a vertex with a value of 1. You will need to specify the files for both hemispheres to the tractography command, I assume. 4. If we acquire seed ROIs from the midthickness surface, does it mean that the termination surface masks can only come from the pial surface then? Because the white surface is in the inner layer and therefore would stop the streamlines coming from the mid-surface to go inside the brain. Is my understanding correct? I don't understand this question. I don't know if it is even possible to specify multiple stopping surfaces for one hemisphere in probtrackx. If it were, and you used the white surface as one of them, then it should stop all streamlines before they reach midthickness or pial (unless you did something wrong). I think the general guidance is to use the white matter surface, as fiber directions become less reliable in gray matter. Look forward to your further guidance. Many thanks! Best regards, Xinyang At 2018-04-14 05:42:36, "Timothy Coalson" <tsc...@mst.edu> wrote: Inline comment. Tim On Thu, Apr 12, 2018 at 11:01 PM, Xinyang Liu <xinyang_ie...@163.com> wrote: 2. How to look at the CIFTI and GIFTI files as matrices? I haven't found a proper way to look at the information inside as rows and columns. Gifti files, and dense cifti files, have too many e
Re: [HCP-Users] surface with and without MSMAll
Ok, I've made clear about the reason. The T1w image opened from the workbench
tutorial data has also been registered to the MNI space. Therefore, the MNI
surface matches well with this T1w_restore.nii.gz image in MNI space, and the
T1w surface matches well with the T1_acpc_dc_restore.nii.gz 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.white.32k_fs_LR.surf.gii" was provided from the MNI folder in the
workbench tutorial data, and the MSMAll file came from T1w folder. There is
only tiny difference from the MSMAll registration.
Therefore, the difference actually lies in the surfaces from the MNI and T1w
folder. It turns out that the surfaces with the same name from these two
folders differ a lot in their shapes (please see the new screenshot attached),
which I didn't expect to be so obvious. We can see that the MNI surfaces have
better alignment with individual brain structure, not T1w. Why does that
happen? In this way, should we change to choose the surface in MNI folder
instead of T1w to produce surface ROI in fibre tracking?
Look forward to your reply. Thanks.
Best regards,
Xinyang
At 2018-04-18 14:59:10, "Xinyang Liu" <xinyang_ie...@163.com> wrote:
Dear HCP experts,
Hi. In previous discussions about using surface ROIs in fibre tracking,
surfaces in ${StudyFolder}/${Subject}/T1w/fsaverage_LR32k with MSMAll was
recommended.
However, I just found that the surface files with and without MSMAll
registration differ a lot within individuals. I put a screenshot attached,
which includes "100307.L.white_MSMAll.32k_fs_LR.surf.gii" and
"100307.L.white.32k_fs_LR.surf.gii". From the white surface outlines, we can
see that the surface without MSMAll registration
(100307.L.white.32k_fs_LR.surf.gii) has better alignment with the brain GM/WM
structure.
Could you please tell me the reason why we should use MSMAll surface in
individual fibre tracking? Thank you very much.
Best regards,
Xinyang
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[HCP-Users] the wmparc file
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 matter, for example CSF? 2. Is there any way to separate the grey and white matter voxels, as well as subcortical part with cortical part? We would like to acquire global white matter voxels. 3. If used as a termination mask in fibre tracking, will this voxel mask have the same effect as the surface mask (e.g. the pial surface)? Look forward to your kind guidance. Thanks. Best regards, Xinyang ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] questions about using HCP surface ROIs in prob-tracking
Dear Matthew,
Thank you very much for your kind reply!
Could I continue asking two more new questions?
1. In the preprocessed structural data, both the
/${Subject}/T1w/fsaverage_LR32k and /${Subject}/MNINonLinear/fsaverage_LR32k
contain white surface files with the same names, such as
"${Subject}.L.white.32k_fs_LR.surf.gii" and
"${Subject}.L.white.MSMAll.32k_fs_LR.surf.gii". Is there any difference
between these files of the same name but under different routes?
2. I am kind of confusing about the space transformation in surface ROI fibre
tracking. In the volume-based analysis, there is native diffusion space and
standard space, and tractograhpy is done in native diffusion space. For surface
data, I suppose the files like "${Subject}.L.white.32k_fs_LR.surf.gii" have
already been registered to a 32k standard mesh. Then should the surface ROI
fibre tracking go back to native space and how if needed?
Best regards,
Xinyang
At 2018-04-04 00:49:09, "Glasser, Matthew" <glass...@wustl.edu> wrote:
1. Yes, though they can come from a certain (configurable) radius around the
vertex, rather than all from the point location with --sampvox.
2. I think probtrackx2 looks for greater than zero, but you could of course
binarize them.
3. I believe you can display the surface counts in GIFTI format with --fopd,
you might ask more on the FSL list as I haven’t done much tractorgraphy in a
while.
Peace,
Matt.
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,
Hi. As a new learner of the HCP tfMRI surface data, I have some questions when
using them as ROIs to do probabilistic tractography. I would be very thankful
to receive any of your kind guidance. My questions are as below.
1. I know that in FSL probtrackx2 voxel-based fibre tracking, 5000 streamlines
(default) come out from each voxel. How about the case in the surface vertices
of the HCP grayordinate space? Is it similar with the voxel-based tracking,
like 5000 streamlines coming out from each vertex?
2.The tfMRI surface ROIs usually contain information of signal intensities,
would this influence the diffusion tracking results if using them as masks?
3. How to display the surface ROIs (.func.gii or .asc) and output tracking
paths (.nii.gz in FSL results) in the same figure?
Look forward to your feedbacks. Thank you very much！
Best regards,
Xinyang Liu
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[HCP-Users] problems about fibre tracking between surface ROIs
Dear HCP experts, Hi. We just started to learn tractography between functional ROIs and met some problems. Our purpose is to do fibre-tracing between face-related functional ROIs. We got the surface ROIs (.func.gii) with HCP fMRI data and Glasser MMP atlas. However, in our initial try of fibre tracing, there was no streamline coming out from the seed ROI. Our seed and target ROIs were separately the FFA and OFA surface regions in the right hemisphere. Our command was: probtrackx2 -x /.../100307_thickness_analysis_ROI_FFA/R.2stat.func.gii --seedref=/.../100307/T1w/Diffusion/B0_brain.nii.gz -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --meshspace=caret --forcedir --opd -s /.../100307/T1w/Diffusion.bedpostX/merged -m /.../100307/T1w/Diffusion.bedpostX/nodif_brain_mask --dir=/.../face_network_tracking/output/output1 --waypoints=/.../100307_thickness_analysis_ROI_OFA_R/R.2stat.func.gii -o FFAtoOFA The output waytotal is 0 and the fdt_path image is empty. My questions are as follows: 1. Why there was no streamline coming out from the seed surface ROI? 2. Is it better that we change the surface ROI to volume ROI? If so, how to acquire the cortical functional volume 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 mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Repeated measurement in HCP outscanner behavioral data
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 experimental trials apart from the practice part. However, the excel recording shows that some participants finished 60 trials. We would like to know what was the situation and does it mean the first round of measurement invalid? Thanks a lot. Best regards, Xinyang ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Repeated measurement in HCP outscanner behavioral data
Dear Jennifer, Thanks a lot for your reply. So in this case, either set is ok to use, right? :) Please find the subID list of the DCCS task attached. Apart from that, there is also a subject (No.341935) with 2 trials and a subject (No.638049) with 27 trials. Best regards, Xinyang At 2018-06-29 19:09:53, "Elam, Jennifer" wrote: Can you share a list of subjects where you see 60 trials for the DCCS task? Likely these subjects are HCP Retest subjects who went through the entire protocol twice (about 6 months or so between acquisitions, depending on the subject) and therefore have two sets of responses/imaging datasets. Best, Jenn Jennifer Elam, Ph.D. Scientific Outreach, Human Connectome Project Washington University School of Medicine Department of Neuroscience, Box 8108 660 South Euclid Avenue St. Louis, MO 63110 314-362-9387 e...@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 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 experimental trials apart from the practice part. However, the excel recording shows that some participants finished 60 trials. We would like to know what was the situation and does it mean the first round of measurement invalid? Thanks a lot. Best regards, Xinyang ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users 103818 105923 111312 114823 115320 122317 125525 130518 135528 137128 139839 143325 144226 146129 149337 149741 151526 169343 172231 172332 175439 177746 179548 185442 187547 192439 194140 195041 200109 200614 204521 250427 287248 341834 433839 562345 599671 601127 627549 660951 662551 783462 859671 861456 877168 917255
[HCP-Users] rfMRI connecitivity
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 correlations. We have several questions to ask: 1. The HCP user manual suggests to use dtseries.nii data in the FIX folder. However, there are two rfMRI dtseries.nii files there, one with MSMALL, and one without it. Which one is more recommended to use? 2. We are quite lost in using the wb_commands. By checking previous emails, it seems that we could use "-cifti-parcellate" to compute the ROI-wise averaged time series. But before that, it seems that we also need to create some .dlabel files. So, (1) which command should we use to extract dtseries covered by those .func.gii ROIs? (2) To compute the averaged time series, should we merge all ROIs together in one cortical surface or compute one by one? Because the .func.gii surface ROIs are saved as separate files. (3) We would like to compute rfMRI connectivity for single individuals, not group average. Is -cifti-cross-correlation the correct choice? Look forward to your kind guidance. Thank you very much. Best regards, Xinyang ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] rfMRI connectivity
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}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii
2.1 wb_command -cifti-parcellate after wb_command -metric-merge wb_command
-metric-label-import and wb_command -cifti-create-dense-label
2.2 See above
2.3 wb_command -cifti-correlation on the individual subject dense timeseries
above (ideally after demeaning, potentially variance normalizing, 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 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 correlations.
We have several questions to ask:
1. The HCP user manual suggests to use dtseries.nii data in the FIX folder.
However, there are two rfMRI dtseries.nii files there, one with MSMALL, and one
without it. Which one is more recommended to use?
2. We are quite lost in using the wb_commands. By checking previous emails, it
seems that we could use "-cifti-parcellate" to compute the ROI-wise averaged
time series. But before that, it seems that we also need to create some .dlabel
files. So,
(1) which command should we use to extract dtseries covered by those
.func.gii ROIs?
(2) To compute the averaged time series, should we merge all ROIs together
in one cortical surface or compute one by one? Because the .func.gii surface
ROIs are saved as separate files.
(3) We would like to compute rfMRI connectivity for single individuals, not
group average. Is -cifti-cross-correlation the correct choice?
Look forward to your kind guidance. Thank you very much.
Best regards,
Xinyang
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Re: [HCP-Users] rfMRI connectivity
Dear Tim,
Thank you so much for this detailed explanation. I will combine both of your
suggestions and have a try then. :)
Best regards,
Xinyang
At 2018-09-22 04:43:55, "Timothy Coalson" wrote:
-cifti-cross-correlation is for when you want to correlate between two
different files. If you want roi-to-roi correlations, it is not the best way
to get them.
The easy way to get roi-to-roi correlations is to use -cifti-parcellate and
then -cifti-correlation. However, you first need to convert your ROIs into a
cifti dlabel file. To do that, first use -cifti-create-dense-from-template to
convert your ROI files to cifti dscalar, using some standard 91282 grayordinate
file as the template, then concatenate them. You then need to use
-cifti-reduce, computing both the INDEXMAX and the MAX reductions, and then use
-cifti-math to multiply the INDEXMAX file by whether the MAX file is nonzero at
that location (something like 'index * (max > 0)'). The point of this is to
make a single map where each ROI has a different nonzero integer value, and
where there is no ROI, it is zero. This file can then be used in
-cifti-label-import to make the dlabel 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}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii
2.1 wb_command -cifti-parcellate after wb_command -metric-merge wb_command
-metric-label-import and wb_command -cifti-create-dense-label
2.2 See above
2.3 wb_command -cifti-correlation on the individual subject dense timeseries
above (ideally after demeaning, potentially variance normalizing, 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 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 correlations.
We have several questions to ask:
1. The HCP user manual suggests to use dtseries.nii data in the FIX folder.
However, there are two rfMRI dtseries.nii files there, one with MSMALL, and one
without it. Which one is more recommended to use?
2. We are quite lost in using the wb_commands. By checking previous emails, it
seems that we could use "-cifti-parcellate" to compute the ROI-wise averaged
time series. But before that, it seems that we also need to create some .dlabel
files. So,
(1) which command should we use to extract dtseries covered by those
.func.gii ROIs?
(2) To compute the averaged time series, should we merge all ROIs together
in one cortical surface or compute one by one? Because the .func.gii surface
ROIs are saved as separate files.
(3) We would like to compute rfMRI connectivity for single individuals, not
group average. Is -cifti-cross-correlation the correct choice?
Look forward to your kind guidance. Thank you very much.
Best regards,
Xinyang
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[HCP-Users] preprocessing of released behavioral data
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 ask:
1. Is there any preprocessing work which has been done for the median RT
values? For example, how were the missing trials and extreme values considered?
Does the computation only include correct trials?
2. Apart from the median RT values, could we find mean values of RT somewhere?
Always appreciated for your kind helps.
Best regards,
Xinyang
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[HCP-Users] A few questions about HCP behavioral data
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 between NIH-task data and Penn- and Working Memory data we would like to know more about the NIH IRT-scores. We hope you can help us out. In the "NIH Toolbox Scoring and Interpretation Guide" it is mentioned that IRT-scores were calculated before the consecutive scores, such as Age-adjusted or Unadjusted. Was that also true for the HCP data? What was the database to estimate the IRT model for the HCP data? Was the model estimated based on the HCP data only or was it somehow combined with the norming sample of the NIH Toolbox? What type of IRT model was run? A simple Rasch model or did you add other free parameters, such as guessing probability (2PL)? Thank you very much for your help. Kind regards, Xinyang ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Inconsistency in the Working Memory tfMRI behavioral scores
Dear Greg, Thank you very much for your kind reply. Yes, it indeed makes sense to account for "NLR", which we didn't considered before. I rechecked the raw data and then have another doubt. Let's take participant No.100206 for example. In the integrated behavioral data table, the "WM_Task_2bk_Face_Acc" score is 81.25, which indicates that there are some NLR trials for him/her. However, in the raw trial-level data (20 trials in total, attached), there is no "NonResp" trials, and the Stim.RT were all recorded within the limitation of 2.5s. The Stim.ACC has 3 errors, therefore the accuracy is 17/20=0.85. I've no idea where I made a mistake for this difference. Could you please help figure it out? Thanks a lot. Best regards, Xinyang At 2019-03-13 01:39:29, "Burgess, Gregory" wrote: Hello Xinyang, Most likely, you haven’t accounted for “NLR”, which stands for “no logged responses”. If the response period timed out without an overt response, we can’t be sure whether the participant would have made a correct response or an error response. Since NLRs are neither correct or error trials, they’re omitted from the accuracy calculations like missing data might be handled. For example, if a condition had 4 NLRs, 13 correct responses and 3 error responses, they could have an accuracy rate of 81.25% = [ 100 x 13 / (20 - 4) ]. Hope this helps! --Greg 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 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 behavioral data file downloaded from the HCP website (named "unrestricted"). We attached an example in this email, showing that the average values of "LR" and "RL" raw scores are not equal to the analyzed values, although they have a trend to match each other. There are 20 trials (LR an RL) together in each task. However, the analyzed scores like "68.75" or "81.25" does not seem to be computed based on 20 trials as a total number. Was there any deletion of trials during processing? If so, what is the reason to do this? Another thing we found is that, for some participants, like No.104012 (not shown in the example file), they have raw behavioral data in the data boxes, but the results were not provided in the analyzed behavioral data file. What is the reason for that? We would be very appreciated to receive any feedbacks. Thank you very much! Best regards, Xinyang ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users subID task_name trial_numbertrial.RTtrial.ACC 100206 WM_2-Back_Face_RL 1 741 1 100206 WM_2-Back_Face_RL 2 12021 100206 WM_2-Back_Face_RL 3 772 1 100206 WM_2-Back_Face_RL 4 840 1 100206 WM_2-Back_Face_RL 5 881 0 100206 WM_2-Back_Face_RL 6 10190 100206 WM_2-Back_Face_RL 7 806 1 100206 WM_2-Back_Face_RL 8 736 1 100206 WM_2-Back_Face_RL 9 910 1 100206 WM_2-Back_Face_RL 10 10051 100206 WM_2-Back_Face_LR 1 535 1 100206 WM_2-Back_Face_LR 2 537 1 100206 WM_2-Back_Face_LR 3 759 1 100206 WM_2-Back_Face_LR 4 759 1 100206 WM_2-Back_Face_LR 5 693 1 100206 WM_2-Back_Face_LR 6 889 1 100206 WM_2-Back_Face_LR 7 687 1 100206 WM_2-Back_Face_LR 8 763 1 100206 WM_2-Back_Face_LR 9 743 1 100206 WM_2-Back_Face_LR 10 989 0
[HCP-Users] Inconsistency in the Working Memroy tfMRI behavioral scores
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 behavioral data file downloaded from the HCP website (named "unrestricted"). We attached an example in this email, showing that the average values of "LR" and "RL" raw scores are not equal to the analyzed values, although they have a trend to match each other. There are 20 trials (LR an RL) together in each task. However, the analyzed scores like "68.75" or "81.25" does not seem to be computed based on 20 trials as a total number. Was there any deletion of trials during processing? If so, what is the reason to do this? Another thing we found is that, for some participants, like No.104012 (not shown in the example file), they have raw behavioral data in the data boxes, but the results were not provided in the analyzed behavioral data file. What is the reason for that? We would be very appreciated to receive any feedbacks. Thank you very much! Best regards, Xinyang ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users Example of accuracy inconsistency.xlsx Description: MS-Excel 2007 spreadsheet
[HCP-Users] HCP lifespan data
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 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
