Re: [HCP-Users] using Amazon S3 on NITRC-CE

hi Tim, I tied to mount data using terminal, and I entered command: sudo s3fs hcp-openaccess /s3mnt, and still, I got nothing under s3mnt folder. And then I tried to use command: sudo mount hcp-openaccess /s3mnt I think I input the bucket's name correctly,and I have entered the new

Re: [HCP-Users] ROIs and Betas from Cifti Data

Unfortunately there isn't a particularly easy way to do this. There is -cifti-label-export-table, from which you'd need to strip out the color information (every other line). The label table of a dlabel file is also shown in -file-information. These will work as long as all of the labels have no

Re: [HCP-Users] ROIs and Betas from Cifti Data

Hi, Tim, Thank you very much for your help! -cifti-parcellate and -cifti-convert -to-text works. What is the easiest way to output label names (i.e. PUTAMEN_RIGHT) into txt file using this approach? Best regards, Serguei Astafiev From: Timothy Coalson [mailto:tsc...@mst.edu] Sent: Tuesday, May

Re: [HCP-Users] ROIs and Betas from Cifti Data

There is a bug in that command in the current release (1.2.3). Try the "dev_latest" version matching your operating system here: http://brainvis.wustl.edu/workbench/ You might also consider using -cifti-parcellate to get the average values within all subcortical structures at the same time. If

Re: [HCP-Users] Gradient nonlinearity correction on Prisma

The Prisma coefficient file contains more harmonics than the original gradient_unwarp.py could handle. Although, I thought that we had fixed that in the version that we are hosting on github… (Tim Brown?) -- Michael Harms, Ph.D. --- Conte C

[HCP-Users] Gradient nonlinearity correction on Prisma

Hi, I was trying to do gradient nonlinearity correction as part of the structural pre-processing pipeline, which failed. Calling gradient_unwarp.py independently produces the same error: gradient_unwarp.py T1w.nii.gz trilinear.nii.gz siemens -g coeff.grad -n gradient_unwarp.py fails to read

Re: [HCP-Users] Download aparc+aseg.nii.gz, aseg.stats, lh/rh.aparc.stats of S1200 new subjects

Hi Jingwei, You’ll want to use a mechanism similar to that discussed in this thread: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg04448.html You can use the XNAT REST protocol to iterate over sessions and resources. The files you’re wanting are structural preprocessing file o

Re: [HCP-Users] using Amazon S3 on NITRC-CE

>From what I recall, the mounting tools for S3 don't properly notify the web interface when they fail. Try mounting it in the terminal like "sudo mount /s3mnt" and see what error you get. You may have entered the authentication incorrectly, or requested a new authentication token, but then entere

[HCP-Users] ROIs and Betas from Cifti Data

Hello, I am trying to create ROI from FS parcellation and extract z-values from it. Steps 1 and 2 works. Step 3 gives me error message (core dumped): wb_command -cifti-create-dense-from-template 100307_zstat1.dtseries.nii 14035rois_subcort_ACCUMBENS_RIGHT_f.dscalar.nii -cifti 14035rois_subcort_A

[HCP-Users] using Amazon S3 on NITRC-CE

Dear HCP teams, I am now trying to use Amazon S3 on NITRC-CE, and I stucked with mounting data from hcp-openaccess bucket to my instance. After I filled in blanks, the system told me I had mount it successfully. But when I check the folder though terminal, it shows nothing below. I