Re: [HCP-Users] drawing borders

Thanks; drawing borders will be easier and more accurate with smaller sphere sizes _ gaurav patel gauravpa...@gmail.com pateldsclab.net > On Oct 10, 2018, at 6:45 PM, Timothy Coalson wrote: > > To clarify the phrasing: the existing release doesn't have a way to

Re: [HCP-Users] hcp_fix_multi_fix errors

It might fix the problem. Matt. On 10/10/18, 4:42 PM, "Shankar Tumati" wrote: >Hi Matt, > >No, its 3.14. >Is the latest (3.15, I believe) needed for the script? > >Best, >Shankar > >From: Glasser, Matthew [glass...@wustl.edu] >Sent: Wednesday, October

Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

Is it having problems reading files (in the D state?). Matt. From: ARMAN PRAFUL KULKARNI mailto:apkulkar...@wisc.edu>> Date: Wednesday, October 10, 2018 at 3:55 PM To: Matt Glasser mailto:glass...@wustl.edu>>, Timothy Coalson mailto:tsc...@mst.edu>> Cc:

Re: [HCP-Users] drawing borders

To clarify the phrasing: the existing release doesn't have a way to change the size of these symbols. We will consider making the size controllable in the next release, but that may be a while off. Tim On Wed, Oct 10, 2018 at 12:15 PM, Harwell, John wrote: > When drawing a border, I am able

Re: [HCP-Users] hcp_fix_multi_fix errors

Hi Matt, No, its 3.14. Is the latest (3.15, I believe) needed for the script? Best, Shankar From: Glasser, Matthew [glass...@wustl.edu] Sent: Wednesday, October 10, 2018 4:28 PM To: Shankar Tumati; hcp-users@humanconnectome.org Subject: Re: [HCP-Users]

Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

Hi Matt, Currently, this process is using 0.7% of the CPU--it doesn't appear to be the issue. In terms of where the pipeline is currently at, from the output script (PostFreeSurferPipeline.sh.o) it has been stuck on the following for the past hour or greater: parsed 'var * -1' as

Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

What is using the CPU? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of ARMAN PRAFUL KULKARNI mailto:apkulkar...@wisc.edu>> Date: Wednesday, October 10, 2018 at 3:27 PM To: Timothy Coalson mailto:tsc...@mst.edu>> Cc:

Re: [HCP-Users] hcp_fix_multi_fix errors

Is this with the latest melodic? Matt. On 10/10/18, 2:54 PM, "hcp-users-boun...@humanconnectome.org on behalf of Shankar Tumati" wrote: >Hi > >We get these seemingly random errors when implementing the >hcp_fix_multi_run code on the task data with some subjects. We need help >to figure it out.

Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

Hi Tim, I have the updated version of workbench now, and have tried running the pipeline again. PostFreeSurferPipelineBatch.sh has now been running for over 5 hours. To my knowledge, prior to this update, it only took around 45 minutes when successful. Is this normal for this version of the

[HCP-Users] hcp_fix_multi_fix errors

Hi We get these seemingly random errors when implementing the hcp_fix_multi_run code on the task data with some subjects. We need help to figure it out. Below is the output for two of the subjects. It the same error in all cases but with different column numbers. Thanks, Shankar -

Re: [HCP-Users] Visualizing Greyordinate Masks

The surfaces are fine, we generally recommend very_inflated for viewing data. To expand on what Matt said, the data in the map you are displaying in that image appears to have an unusual distribution, with most values near the minimum value, and a few spots with higher values (or perhaps the

Re: [HCP-Users] Visualizing Greyordinate Masks

Try changing the color windowing. Matt. From: Cathy Chen mailto:c...@alumni.princeton.edu>> Date: Wednesday, October 10, 2018 at 7:55 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org" mailto:hcp-users@humanconnectome.org>>

[HCP-Users] Postdoctoral positions available

[https://tr.cloudmagic.com/h/v6/emailtag/tag/2.0/1539197810/b66430ca7e69eb44a2365b99bb8d8527/2/37dc7c4101057d665b3af19baa29b2ed/91e47bcc09b97ecb510bd665381a6240/9efab2399c7c560b34de477b9aa0a465/newton.gif] [Apologies for cross-posting] The Brain Dynamics Lab (http://bdl.stanford.edu) at Stanford

Re: [HCP-Users] drawing borders

Borders are not annotations and that is why borders are not in the annotations guide. Borders are always attached to a surface whereas annotations may or may not be attached to a surface. Visualizing borders is covered in the Workbench 1.0 - 1.3.2 Tutorial

Re: [HCP-Users] drawing borders

When drawing a border, I am able to reproduce the border sizes displayed in your image. I would describe the border symbols as a little bigger, but not huge. We understand this is not optimal for you, but there is nothing we can do to immediately change the border drawing symbol size. > On

Re: [HCP-Users] drawing borders

This is an interesting topic. Despite the 3% being a good idea the border depends more on the structure being traced than on the brain itself (arguably those two are also related). I haven’t managed to find border tracing on the tutorial of annotations. Am I looking on the wrong place? Also are

Re: [HCP-Users] drawing borders

this is the tutorial 1.0 brain (Q1-Q6_R440.R.veryinflated.32k_fs_LR.surf.gii). 2mm was actually much smaller than the current 3% standard for the adult brain. Are you able to reproduce the issue with the same surface? gaurav patel gauravpa...@gmail.com

Re: [HCP-Users] drawing borders

There is nothing in the user interface to adjust the size of the spheres while drawing a border. In a previous version of Workbench, the size was 2mm. However, 2mm was far too large when drawing borders on very small brains (babies, mice, etc) so the size was changed to 3% of the longest

Re: [HCP-Users] Visualizing Greyordinate Masks

Hi Matt, I loaded the file as an overlay with the various .surf.gii files in the folder "100206_3T_Structural_preproc\100206\MNINonLinear\fsaverage_LR32k". When I step through the 15 images corresponding to the 15 parcellation dimensions, I see very sparse visualizations. For example, this is the