Steve and I think you have the right file, but are not understanding what is
confusing about viewing that file in Connectome Workbench, assuming you have
loaded the appropriate surfaces and volumes.
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Cathy Chen
Watch this space for an update on MSMAll with MultiRunFIX. The pipelines
in the current master aren¹t all working together and we are working on
fixing that.
Matt.
On 10/9/18, 9:58 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Sang-Young Kim" wrote:
>Dear Experts:
>
>I have a
If you can wait a week or two we will have some useful updates out. Also there
is the impending switch to FreeSurfer 6.0 that would be good to have.
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of "Sanchez, Juan (NYSPI)"
mailto:juan.sanc...@nyspi.columbia.edu>>
Date:
Hi Jodi,
If you look at the "Current Project" selector at the top of the page, there
should be another selector next to the project that says "Open Access". If you
see that and select one of the restricted access views, you should get a
download link for the restricted data.
Regards,
Mike
You need to update workbench to the latest release, that option is a recent
addition to the command that is failing.
Tim
On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI
wrote:
> Hi,
>
> I have been running the HCP Pipeline (v 3.27.0) on one subject's
> unprocessed data from the HCP-1200
Hi,
I have been running the HCP Pipeline (v 3.27.0) on one subject's unprocessed
data from the HCP-1200 dataset. Below is what I have in the SetUpHCPPipeline.sh
file. I have been able to run PreFreeSurferPipelineBatch.sh and
FreeSurferPipelineBatch.sh with no issues. However, when running
Hi Jodi,
Let me have the database people look into this.
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
Hello,
I applied for (and was granted) access to the restricted HCP database; however,
when I log onto https://db.humanconnectome.org/data/projects/HCP_1200
I no longer see an option to download the restricted data. Please help!
Best,
Jodi
Jodi Gilman, Ph.D.
Associate Professor, Harvard
here’s a screen shot of the draw borders output vs. a finished border (symbol
diameter set to 2mm). I tried to change the ID sphere size property, and that
did not change. On a machine with 1.23 still installed, the draw borders
output is the same size as the 2mm diameter finalized borders.
I had an issue with baby brains where the sphere had too small a diameter.
This caused an issue where ID nodes were displaying with a sphere larger than
the surface.
This is probably not your issue -- sorry.
From: Gaurav Patel on behalf of Gaurav Patel
In the borders menu? Changing that changes the size of the final border, but
not the border as I draw it
_
gaurav patel
gauravpa...@gmail.com
pateldsclab.net
> On Oct 9, 2018, at 12:42 PM, Dierker, Donna wrote:
>
> Check the diameter of your sphere, Gaurav.
>
>
>
Check the diameter of your sphere, Gaurav.
From: hcp-users-boun...@humanconnectome.org
on behalf of Gaurav Patel
Sent: Tuesday, October 9, 2018 11:37 AM
To: hcp-users@humanconnectome.org Users
Subject: [HCP-Users] drawing borders
Hi—when I am drawing borders
Hi—when I am drawing borders in wb_view 1.31, the diameters of the red spheres
is huge, making is difficult to see what I am drawing. This was not the case
in 1.23. Is there a way to change that setting? Finishing the border reduces
the size of the spheres to the setting in the borders menu,
Thanks so much Michael!
This link is also very helpful
https://github.com/Washington-University/HCPpipelines/blob/master/PreFreeSurfer/PreFreeSurferPipeline.sh
Best,
Xiangzhen
On Tue, Oct 9, 2018 at 4:44 PM Harms, Michael wrote:
>
>
> Hi,
>
> See http://www.ncbi.nlm.nih.gov/pubmed/23668970
>
>
Dear Experts:
I have a question for MSMAll alignment for MultiRunICAFIX cleaned data.
Once I run the MultiRunICAFIX pipeline, I get the output like
"${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii".
But I want to align the data (e.g.,
${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii)
Hi,
See http://www.ncbi.nlm.nih.gov/pubmed/23668970
specifically Figure 9.
“dc” is the readout distortion correction.
“restore” is the bias field correction (for the receive bias field)
The gradient distortion correction is not included as part of the filename, so
the file could just as well
We have been using the 3.4 version of the pipelines to process data acquired
locally. Our lab wants to switch over to the latest versions as we upgrade
our magnet. Is there a stable release of the pipelines? I was going to clone
the 3.27 version from github and proceed from there. However,
Dear HCP experts,
I'm working with subject-specific parcellations (for instance, "
HCP_S1200_PTNmaps_d15_25_50_100\3T_HCP1200_MSMAll_d15_ts2_Z\100206.dtseries.nii"
) and would like to visualize the greyordinates corresponding to each of
the 15 (or 25, 50, or 100) spatial maps.
I've been using
Hi,
I am using the HCP data. Here I came across a question about the file
*T1w_acpc_dc_restore_brain.nii.gz*
I am curious what have been done between T1w.nii.gz and this file. From the
document, I guess that
*acpc* indicate linear registriation (flirt) with dof=6;
*dc* might indicate distortion
Thanks!
On Mon, Oct 8, 2018 at 9:46 PM Glasser, Matthew wrote:
> I would save the list of files we release with the HCP Pipelines. If you
> search the list, you will see some other specific posts about saving
> space. I would be sure you don’t delete anything in an .spec file either.
>
>
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