Re: [HCP-Users] about the subject information

See explanation below, first posted in 2015 > On Apr 26, 2017, at 9:17 PM, 罗 <963619...@qq.com> wrote: > > Dear professors > I find that the subject with ID '142626' has no information in the newest > behavior data, but can be founded in the S500 behavior data, is it a mistake > or the subject

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

You should also consider the command -surface-geodesic-rois, which will act similar to a manual dilation of single vertex maps, but takes input as a text file, like -surface-closest-vertex generates: http://www.humanconnectome.org/software/workbench-command.php?function=-surface-geodesic-rois

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

That is a map of distances. You could threshold this at something, binarize it, and then dilate. Peace, Matt. From: Vadim Axel > Date: Wednesday, April 26, 2017 at 2:20 PM To: Matt Glasser > Cc:

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

Last question: why should it be different from the output of -surface-geodesic-distance? On Wed, Apr 26, 2017 at 10:15 PM, Glasser, Matthew wrote: > If you start from a single point and dilate the patches should be > approximately circular. > > Peace, > > Matt. > > From:

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

If you start from a single point and dilate the patches should be approximately circular. Peace, Matt. From: Vadim Axel > Date: Wednesday, April 26, 2017 at 2:13 PM To: Matt Glasser > Cc: "Elam,

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

Given your output of wb_command -surface-geodesic-distance is a metric GIFTI file you could use -metric-dilate. Peace, Matt. From: Vadim Axel > Date: Wednesday, April 26, 2017 at 1:40 PM To: Matt Glasser

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

Thank you, Matt. But can you please provide more details because I do not fully understand. There are -cifti-dilate, -metric-dilate and -label-dilate. Which one do I use? If this is the former, it seems that I still need to create the label manually. If you mean two former, it is not clear to me

Re: [HCP-Users] comparison across acquisitions

Thanks Michael and Matt. Were they all collected at the same site? If not, I'd expect this to make some difference. On Wed, Apr 26, 2017 at 2:00 PM, Glasser, Matthew wrote: > It is a variable in the .csv you download out of the database. Diffusion > isn’t affected by this,

Re: [HCP-Users] comparison across acquisitions

It is a variable in the .csv you download out of the database. Diffusion isn’t affected by this, just fMRI because diffusion was processed with the same recon version (old scans were reprocessed). Peace, Matt. From: Joelle Zimmermann

Re: [HCP-Users] comparison across acquisitions

The name of the variable that Matt is referring to is “fMRI_3T_ReconVrs”. Once you control for that, the main use of the “Acquisition” variable would be to see if there are any drifts in the results over time. If you find any, please let us know! cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] comparison across acquisitions

Thanks for your reply Matt. By version number, do you mean the "acquisition" - that is, the Q#? So you expect the fMRI to be more different across acquisitions than the diffusion? Do you recall at which acquisition the image reconstruction version change occurred? Joelle On Wed, Apr 26, 2017

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

You can identify a Surface vertex by number using the Identify Brain ordinate dialog (Window>Identify... or the button with the head icon at the top right). Click the bottom radio button, enter the vertex, then click apply and the vertex will show up as an ID sphere. Best, Jenn Jennifer

Re: [HCP-Users] comparison across acquisitions

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

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

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

[HCP-Users] comparison across acquisitions

Hi HCPers, I'm working with structural and functional connectomes from the S900 HCP. I'm wondering how the different acquisitions (ie Q1 Q2 etc) and releases would affect comparison across all SCs for example. Was data collected at different sites for example? - which may affect comparison across

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

Nice feature, thanks Jennifer. Though, not sure that it will help me because I have hundreds of patches that should be created automatically. As far as I understand, there is no functionality to create foci file automatically. BTW, unrelated, I wonder whether there is a way in the workbench to

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

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

[HCP-Users] [TaskfMRILevel2]feat_model error

Hello HCP experts, I get a fatal error during running Examples/Scripts/TaskfMRIAnalysisBatch.sh, the error info(also see attached file): terminate called after throwing an instance of 'NEWMAT::ProgramException'

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

Hi Vadim, You could also try creating foci at the coordinates of the electrodes in the wb_view GUI, which you could show as spheres like in the image you are trying to emulate. To create foci, click on "Foci" in the Mode section of the Toolbar and a set of Foci buttons will appear at the

Re: [HCP-Users] missing twin data

That is not going to change. The reason is explained on p. 80 of the release manual: **3 Subjects were not included in this listing due to their missing both ZygosityGT and ZygositySR (these 3 subjects self reported as twins but did not specify their zygosity, so ZygositySR is blank). Should

[HCP-Users] missing twin data

Dear HCP team Again thanks for your great work! In the S1200 release there are 3 subjects without information on twinstatus (Zygosity SR and GT; Subjects: 122418, 168240, 376247). Will that information be added at some point, or is it simply missing data? Thanks & best regards!! Chris Dr.

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

I find it helps to install something like gridengine which interfaces with fsl_sub. You can then queue up the jobs and they will all run automatically. You can choose how many to run at a time. I believe you don’t need to specify an openmp flag unless you want fewer than all of the cores.

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

Thanks for your quick answer! Just to make sure: it means I shouldn't specify -openmp 5 in the recon-all line and that the multi-threading happens automatically? So given that I have around 50 subjects who I need to run this on, would the best way to accelerate the performance be to just open