Re: [HCP-Users] An error about subcortical processinginHCPfMRI-surface pipeline

Okay, I got it. The fslhd message was packed and added to the attachment. But I couldn't see any problem with the header... Sincerely, Qunjun -- Original -- From: "Glasser, Matthew"; Date: Sat, Apr 6, 2019 12:13 PM To: "Qunjun Liang"; Cc:

Re: [HCP-Users] An error about subcortical processing inHCPfMRI-surface pipeline

The files in the error message. Matt. From: Qunjun Liang mailto:liangqun...@foxmail.com>> Date: Friday, April 5, 2019 at 11:10 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org" mailto:hcp-users@humanconnectome.org>>

Re: [HCP-Users] An error about subcortical processing inHCPfMRI-surface pipeline

Hi Matt, Yes, we don't have an SBRef image. Because at the beginning of this experiment, the sequence was set referring to the UK Biobank Project. BTW, the scanner is Siemens 3T trio. Sorry I don't know clearly about what files you mean... But I searched the MNINonLinear/ directory and

Re: [HCP-Users] An error about subcortical processing in HCPfMRI-surface pipeline

Do you not have an SBRef image? I wonder if that feature is not working. You could paste in fslhd from those two files. Matt. From: Qunjun Liang mailto:liangqun...@foxmail.com>> Date: Friday, April 5, 2019 at 10:23 PM To: Matt Glasser mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] An

Re: [HCP-Users] An error about subcortical processing in HCP fMRI-surface pipeline

Please post how you called PreFreeSurfer, PostFreeSurfer, fMRIVolume, and fMRISurface. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Qunjun Liang mailto:liangqun...@foxmail.com>> Date: Friday, April 5, 2019 at 9:37 PM To:

[HCP-Users] An error about subcortical processing in HCP fMRI-surface pipeline

Dear HCP experts, An error was occurred when I used fMRI surface generation pipeline: #-- While running: wb_command -cifti-create-dense-timeseries /{PATH to subject}/MNINonLinear/Results/{task name}/{task name}_temp_subject.dtseries.nii -volume /{PATH to

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

Maybe look on the FreeSurfer list for a solution to this? MNI tools is something that FreeSurfer is including and perhaps it is very sensitive to the OS version you use. Could see if going back to Ubuntu 16.04 gets rid of the error. Matt. From: "Jayasekera, Dinal"

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

Ubuntu 14.04 Kind regards, Dinal Jayasekera PhD Candidate | InSITE Fellow Ammar Hawasli Lab Department of Biomedical Engineering | Washington University in

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

What OS are you on? Matt. From: "Jayasekera, Dinal" mailto:dinal.jayasek...@wustl.edu>> Date: Friday, April 5, 2019 at 5:18 PM To: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org" mailto:hcp-users@humanconnectome.org>> Subject:

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

Interestingly I had set the path to Freesurfer v6, but the script was calling on Freesurfer 5.3.0-HCP. After deleting the Freesurfer 5.3.0-HCP folder, the attached log file showed that the script was using the updated version of Freesurfer. However, as you can see, the log file still reported

Re: [HCP-Users] Volumetric subcortical group-averaged data: what is the exact MNI template you used?

The files themselves are in the pipelines repository, if that helps: https://github.com/Washington-University/HCPpipelines/tree/master/global/templates It is visually obvious that they are not left/right symmetric, assuming that is what you were asking. Tim On Fri, Apr 5, 2019 at 4:54 PM

Re: [HCP-Users] Volumetric subcortical group-averaged data: what is the exact MNI template you used?

I don’t know, you can ask on the FSL list. Matt. From: Xavier Guell Paradis mailto:xavierguellpara...@gmail.com>> Date: Friday, April 5, 2019 at 4:49 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: Xavier Guell Paradis mailto:xavie...@mit.edu>>,

Re: [HCP-Users] Volumetric subcortical group-averaged data: what is the exact MNI template you used?

FSL’s MNI152. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Xavier Guell Paradis mailto:xavie...@mit.edu>> Date: Friday, April 5, 2019 at 4:46 PM To: "hcp-users@humanconnectome.org" mailto:hcp-users@humanconnectome.org>> Subject:

[HCP-Users] Volumetric subcortical group-averaged data: what is the exact MNI template you used?

Dear HCP experts, I am interested in analyzing your group-averaged subcortical volumetric data. My understanding is that your volumetric data is registered to MNI space. I was wondering if you could let me know what specific MNI template you used. I am especially interested in knowing whether

Re: [HCP-Users] Glasser Parcellation MNI Coordinates

You could use the group average MNI surfaces from connectomedb for visualization. If you need a single coordinate per parcel, you can use wb_command -surface-coordinates-to-metric on the surfaces, combine those metric files into a cifti file with -cifti-create-dense-from-template, and use

[HCP-Users] Glasser Parcellation MNI Coordinates

To Whom It May Concern, I am using Glasser parcellation for some fMRI analysis and wanted to know where I could access the MNI coordinates for the parcellation scheme, so I can generate glass brain figures to visualize the regions and their corresponding networks. If you could point me to

[HCP-Users] Postdoc or Research Associate/Scientist at Northwestern in Chicago

*Apologies for cross-posting* Northwestern University’s Mesulam Center for Cognitive Neurology and Alzheimer’s Disease Imaging Core is seeking a research associate or postdoctoral fellow. Prior experience with Alzheimer's disease is *not a requirement*. The primary responsibility of this