Re: [HCP-Users] Concatenate sessions from Emotion task

Alright, thanks a bunch :) greetings David 2018-02-28 18:05 GMT+01:00 Harms, Michael : > > > Just compute the length of the run implied by the number of frames (# > frames * TR), and check if any events in the .txt files from the first run > have an onset later than that! > >

[HCP-Users] FreeSurfer processing in Structural preprocessing

Hi all, I am trying to adopt the HCP pipeline to preprocess our data. As the first step I am trying the execution of the pipeline with the example data that is given in the tutorial. The first part which is the PreFreeSurfer processing was completed successfully. But I am having a problem with

[HCP-Users] Neighbors of a vertex

Hello experts, I would like to get a list of neighbors of each vertex in a 32k surface file. How can I do this with workbench? If not with workbench, is there another way to get this info? Thank you. Best, Shankar ___ HCP-Users mailing list

Re: [HCP-Users] Neighbors of a vertex

On Wed, 28 Feb 2018, Shankar Tumati wrote: > Hello experts, > I would like to get a list of neighbors of each vertex in a 32k surface file. > How can I do this with workbench? If not with workbench, is there another way > to get this info? quick one: we rely on neighborhood information in

Re: [HCP-Users] wbsparse

wb_command -convert-matrix4-to-matrix2 will convert wbsparse to a dense connectome file. I’m not sure you can actually do what you are asking, because all that is stored are counts of streamlines that use a particular fiber orientation in a voxel. Peace, Matt. From: "Shadi, Kamal"

Re: [HCP-Users] wbsparse

Is there anyway I can do the surface-to-surface tractography myself given the data provided in https://balsa.wustl.edu/study/show/W336. I can see there is a fiberTEMP.nii file there but I do not know if I can run probtrackx using it. Regards, Kamal From: Timothy Coalson

Re: [HCP-Users] wbsparse

Did you get that from BALSA? Peace, Matt. From: > on behalf of "Shadi, Kamal" > Date: Wednesday, February 28, 2018 at 4:25 PM To:

Re: [HCP-Users] Neighbors of a vertex

Workbench does this internally, but it doesn't currently have a command to output it (the number of neighbors varies per vertex, so it could be hard to make efficient use of in something like matlab). The .surf.gii file has this information in it, in the triangles array, so if you load it, you

Re: [HCP-Users] wbsparse

Also beware, since one of the dimensions is white matter voxels, the dconn from -convert-matrix4-to-matrix2 will be larger than a standard 91k dconn (78GB based on the information you posted, versus ~30GB for a 91k dconn). Surface-to-surface tractography would normally be done with a different

Re: [HCP-Users] Pittsburgh Sleep Quality Index Component Scores

Hi Greg and co, What’s the status on the planned release of PSQI component scores? Also, are there plans to release the MMSE (aka Mini) component scores? Thank you! -Ely ___ HCP-Users mailing list HCP-Users@humanconnectome.org

Re: [HCP-Users] wbsparse

Yes, It’s in https://balsa.wustl.edu/study/show/W336. From: "Glasser, Matthew" > Date: Wednesday, February 28, 2018 at 5:28 PM To: "Shadi, Kamal" >,

Re: [HCP-Users] wbsparse

The fiberTemp.nii file doesn't contain the specific data that probtrackx needs, so no. It contains orientation distribution parameters suitable for visualization, while probtrackx expects many precomputed direction samples - the visualization distribution is an approximation based on those. Tim

Re: [HCP-Users] Concatenate sessions from Emotion task

Sure, that’s close. (I get 158.787, 200.93, and 243.073). Make sure you use the actual number of frames in the first run (to properly determine the correct offset in the case that the first emotion run was aborted a little early). i.e., don’t assume that the first emotion run will *always*

[HCP-Users] rerunning FreeSurferPipelineBatch script

Dear HCP experts, if the PreFreeSurferPipelineBatch script finished successfully, and then the FreeSurfer one finished with errors, but made some new output files before stopping, is it OK to just simply rerun FreeSurferPipeline script on the same participants? Or should I first delete all the new

Re: [HCP-Users] path to bbregister .dat file for REST call

Hi Olivia, You can use a script similar to this to iterate over all the experiments and preprocessing resources and pull down these files for all subjects: #!/bin/bash # # ITERATE OVER 3T EXPERIMENTS # for CSVROW in $(curl -s -k --cookie JSESSIONID=$JSESSIONID

Re: [HCP-Users] Concatenate sessions from Emotion task

Ok, there were some rounding inaccuracies, get the same onsets as you now! Thanks for the hint, I will make sure to check the number of frames for each file. Thanks again, David 2018-02-28 15:05 GMT+01:00 Harms, Michael : > > > Sure, that’s close. (I get 158.787, 200.93,

Re: [HCP-Users] Concatenate sessions from Emotion task

Hi Michael, there is an SPM function that handles the concatenation by adding session regressors and adjusting the high-pass filter. I'm still pondering if I want to include a regressor that accounts for the transition between sessions, but not sure how it would look like. Any ideas on that? Ok,

Re: [HCP-Users] rerunning FreeSurferPipelineBatch script

Thanks a lot! On Wed, Feb 28, 2018 at 3:51 PM, Glasser, Matthew wrote: > I think it will be okay to just rerun the FreeSurferPipeline if you delete > the FreeSurfer folder > > ${StudyFolder}/${Subject}/T1w/${Subject} > > Peace, > > Matt. > > From:

Re: [HCP-Users] Concatenate sessions from Emotion task

Also, there may (very rarely) be cases where the first emotion run was aborted (or recon stopped/crashed), while the EPRIME script itself continued to completion. I’m not sure if we edited those condition .txt files to ensure that there were no events listed beyond the actual available number

Re: [HCP-Users] rerunning FreeSurferPipelineBatch script

I think it will be okay to just rerun the FreeSurferPipeline if you delete the FreeSurfer folder ${StudyFolder}/${Subject}/T1w/${Subject} Peace, Matt. From: > on behalf of Darko Komnenić

Re: [HCP-Users] Concatenate sessions from Emotion task

Hey again, how can I check for this? 2018-02-28 15:52 GMT+01:00 Harms, Michael : > > > Also, there may (very rarely) be cases where the first emotion run was > aborted (or recon stopped/crashed), while the EPRIME script itself > continued to completion. I’m not sure if we

Re: [HCP-Users] Concatenate sessions from Emotion task

Just compute the length of the run implied by the number of frames (# frames * TR), and check if any events in the .txt files from the first run have an onset later than that! -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience