[HCP-Users] Standard to Native Applywarp Error

Hello, I am trying to use the provided commands in the link below to transform a contrast from the social task to native space. https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-16.CanIgetthefMRIdatainasubject's'nativespace'? I used the pipeline in the second link to

[HCP-Users] nu_correct: crashed while running nu_evaluate

Dear all, I have been running the FreeSurferPipelineBatch script (v4 of the HCP pipeline) and I'm getting an error saying that nu_correct: crashed while running nu_evaluate. I didn't encounter this same issue with the previous version of the pipeline script. I've attached the recon-all.log

Re: [HCP-Users] A question about the HCP pipeline

You could interpolate it back to native space if you wanted with relatively little information loss if you use splines. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday, April 4, 2019 at 1:53 PM To: Aaron C

Re: [HCP-Users] nu_correct: crashed while running nu_evaluate

Are you using FreeSurfer 6.0? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Jayasekera, Dinal" mailto:dinal.jayasek...@wustl.edu>> Date: Thursday, April 4, 2019 at 11:25 AM To: "hcp-users@humanconnectome.org"

Re: [HCP-Users] MSM binaries versions

Use version 3.0.0 in GitHub. The one used in FSL is not supported by the HCP Pipelines as it does not have the HOCR options. All that is needed is the MSM binary. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Coalson mailto:tsc...@mst.edu>> Date: Thursday,

Re: [HCP-Users] A question about the HCP pipeline

No, since the subcortical data needed to be in MNI space, we chose to use MNI space surfaces for each subject so that we only needed to generate a single motion-corrected volume timeseries. Because the per-subject processing uses the individual surfaces and the same warpfield for surface and

Re: [HCP-Users] MSM binaries versions

The 1.0 and 3.0 versions on github are nearly identical, that was just a naming issue. The version in FSL may be based on version 2, and is missing a library needed for HOCR, so some options in v3 aren't available. You should be able to use the fsl versions of the executables other than msm (so,

Re: [HCP-Users] nu_correct: crashed while running nu_evaluate

In your log file it says you are using 5.3.0-HCP. Matt. From: "Jayasekera, Dinal" mailto:dinal.jayasek...@wustl.edu>> Date: Thursday, April 4, 2019 at 4:05 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org"

Re: [HCP-Users] MSM binaries versions

Thanks Matt! On Fri, Apr 5, 2019 at 12:39 AM +0100, "Glasser, Matthew" mailto:glass...@wustl.edu>> wrote: V2 is okay too. Matt. On 4/4/19, 6:18 PM, "Moataz Assem" wrote: >Thanks all for your replies. From what I understood from Emma's comments >it looks like v2 from this link

Re: [HCP-Users] Standard to Native Applywarp Error

Is this HCP data? What software are you using for tractography? If you want statistical maps in native volume space, it might be easiest to project them from the subject’s physical space surfaces in the T1w/fsaverage_LR32k or alternatively track the data to those surfaces. Matt. From:

Re: [HCP-Users] MSM binaries versions

Thanks all for your replies. From what I understood from Emma's comments it looks like v2 from this link (https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v2/) is very similar to the versions on github. Since I have already ran MSMSulc (PostFreeSurfer and fMRISurface HCPPipelines v3.27.0) using the v2

Re: [HCP-Users] MSM binaries versions

V2 is okay too. Matt. On 4/4/19, 6:18 PM, "Moataz Assem" wrote: >Thanks all for your replies. From what I understood from Emma's comments >it looks like v2 from this link >(https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v2/) is very similar to the >versions on github. > >Since I have already ran

Re: [HCP-Users] Standard to Native Applywarp Error

I would recommend using probtrackx2 and tracking directly to the surface and into the CIFTI space, rather than trying to go back to the volume. Matt. From: Haroon Popal mailto:tuk12...@temple.edu>> Date: Thursday, April 4, 2019 at 8:49 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc:

Re: [HCP-Users] Standard to Native Applywarp Error

Thanks for getting back to me. This is HCP data. Specifically, the social task. I am using FSL (probtrackx) for tractography. I used the cifti-separate command and the metric-resample command to extract the surface data. But I'm interested in doing a whole-brain tractography with subcortical

Re: [HCP-Users] MSM binaries versions

Also, see here https://github.com/ecr05/MSM_HOCR/issues/5 for some info from Emma. -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid

Re: [HCP-Users] nu_correct: crashed while running nu_evaluate

Yes I am Kind regards, Dinal Jayasekera PhD Candidate | InSITE Fellow Ammar Hawasli Lab Department of Biomedical Engineering | Washington University in St.

[HCP-Users] MSM binaries versions

Hi, What is the recommended version of the MSM binaries to use? The rep directory (https://github.com/ecr05/MSM_HOCR/releases) has v1.0.0 and v3.0.0 and I was previously using v2 from here: https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v2/ Also what is the difference between these binaries and the