[HCP-Users] Recon-all errors when calculating Talaraich coordinates

Dear all, I've been running the FreeSurferPipelineBatch code with some of the data that we have and the program exits out of this when calculating the Talairach coordinates using the recon-all script from the FreeSurfer directory. I've attached the log file I get when I run the script. I also

[HCP-Users] Recon-all errors when calculating Talaraich coordinates

. in Biomedical Engineering | Minor in Biophysics and Electrical Engineering The George Washington University From: Glasser, Matthew Sent: Friday, July 20, 2018 5:26:40 PM To: Jayasekera, Dinal Cc: NEUROSCIENCE tim; Hawasli, Ammar; Brown, Tim Subject: Re: Environmental variable settings

[HCP-Users] Recon-all errors when calculating Talaraich coordinates

Dear all, I've been running the FreeSurferPipelineBatch code with some of the data that we have and the program exits out of this when calculating the Talairach coordinates using the recon-all script from the FreeSurfer directory. I've attached the recon-all log file and MNI log file I get

[HCP-Users] Required Ubuntu libraries for HCP minimal preprocessing

Dear all, I am using an Ubuntu 16.04 LTS system to run the preprocessing pipelines. Since I am not aware of the preprocessing pipelines being completely run on a 16.04 system, is there a list of required Linux software libraries (apart from FSL, FreeSurfer, Workbench and gradunwarp) to

[HCP-Users] Debugging IcaFIxProcessingBatch.sh

Dear HCP community, I am currently running the IcaFixProcessingBatch script on the data processing using the minimal functional pipelines. However, for each of my resting state conditions, I get the following error: /home/Desktop/Applications/fix1.066/fix: 252:

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

From: Glasser, Matthew Sent: Thursday, November 1, 2018 6:56:26 PM To: Harms, Michael; Jayasekera, Dinal; hcp-users@humanconnectome.org Cc: NEUROSCIENCE tim Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh Hi Dinal, Also make sure you have the absolutely latest version of sICA+FIX

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

, 2018 8:33:58 PM To: Jayasekera, Dinal; Harms, Michael; hcp-users@humanconnectome.org Cc: NEUROSCIENCE tim Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh That doesn’t discount Mike’s advice on needing to sort out R packages. Matt. From: "Jayasekera, Dinal" mailto:din

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

inal Jayasekera PhD Candidate | InSITE Fellow Ammar Hawasli Lab Department of Biomedical Engineering | Washington University in St. Louis From: Glasser, Matthew Sent: Thursday, November 1, 2018 8:33:58 PM To: Jayasekera, Dinal; Harms, Michael; hcp-users@humanconnectome.org

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

I forgot to attach the matlab dump file. Kind regards, Dinal Jayasekera PhD Candidate | InSITE Fellow Ammar Hawasli Lab Department of Biomedical Engineering | Washington University in St. Louis From: Jayasekera, Dinal Sent: Thursday, November 8, 2018 1:36:15 PM

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

From: Timothy Coalson Sent: Thursday, November 8, 2018 6:03:10 PM To: Jayasekera, Dinal Cc: Dierker, Donna; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh FSL 6 requires openblas, and specifically a build of openblas that contains lapack

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

Candidate | InSITE Fellow Ammar Hawasli Lab Department of Biomedical Engineering | Washington University in St. Louis From: Timothy Coalson Sent: Monday, November 12, 2018 4:04:33 PM To: Jayasekera, Dinal Cc: Glasser, Matthew; Dierker, Donna; hcp-users@humanconnectome.org

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

_fix? Kind regards, Dinal Jayasekera PhD Candidate | InSITE Fellow Ammar Hawasli Lab Department of Biomedical Engineering | Washington University in St. Louis From: Glasser, Matthew Sent: Friday, November 9, 2018 7:36:59 PM To: NEUROSCIENCE tim Cc: Jayasekera, D

Re: [HCP-Users] PostFreeSurfer debugging

? From: Timothy Coalson Sent: Friday, September 28, 2018 1:57:25 PM To: Jayasekera, Dinal Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] PostFreeSurfer debugging It looks like the step that uses it in the PostFreeSurfer pipeline is generating a spherical rotation

Re: [HCP-Users] PostFreeSurfer debugging

Tim, That was actually the only file that was generated. I also see all the expected files which is great. From: Timothy Coalson Sent: Friday, September 28, 2018 4:34:06 PM To: Jayasekera, Dinal Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users

[HCP-Users] PostFreeSurfer debugging

Dear all, I've completely run the PreFreeSurfer and FreeSurfer batch scripts on our patietn data and am currently running the PostFreeSurfer script. However, when running the script on the patients I got the following message: WARNING: input sphere is either unusually irregular or not

Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh

ering | Washington University in St. Louis From: Timothy Coalson Sent: Tuesday, November 13, 2018 4:50:07 PM To: Jayasekera, Dinal Cc: Glasser, Matthew; Dierker, Donna; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh Yes,

[HCP-Users] Troubleshooting fMRIVolume pipelines results

Dear all, I noticed that for some of the resting state conditions of certain patients who were processed using the fMRIVolume pipeline, the pipeline didn't produce all the desired outputs that were observed with the other resting state conditions for the same patient. Which log files would I

[HCP-Users] FSL 6 compatibility

Dear all, Is version 4 of the HCP Pipelines functional with fsl version 6.0? Kind regards, Dinal Jayasekera PhD Candidate | InSITE Fellow Ammar Hawasli Lab Department of Biomedical

[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] nu_correct: crashed while running nu_evaluate

hington University in St. Louis<https://wustl.edu/> From: Glasser, Matthew Sent: Friday, April 5, 2019 5:19:49 PM To: Jayasekera, Dinal; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] nu_correct: crashed while running nu_evaluate What OS are you

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

Engineering<https://bme.wustl.edu/Pages/default.aspx> | Washington University in St. Louis<https://wustl.edu/> From: Glasser, Matthew Sent: Thursday, April 4, 2019 6:05:48 PM To: Jayasekera, Dinal; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] nu_

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

hington University in St. Louis<https://wustl.edu/> From: Glasser, Matthew Sent: Thursday, April 4, 2019 3:01:18 PM To: Jayasekera, Dinal; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] nu_correct: crashed while running nu_evaluate Are you usin

[HCP-Users] Exporting dynconn layer for statistical analysis

Dear all, I have processed some patient data through the dedrift pipeline and I've been been using wb_view to look at the ${fMRIConcatName}_Atlas_MSMAll_hp0_clean.dtseries.nii file along with using the .dynconn layer to do point and click functional connectivity. Is it possible to export

Re: [HCP-Users] Missing shared library for wb_command

li Lab<https://hawaslilab.weebly.com/> Department of Biomedical Engineering<https://bme.wustl.edu/Pages/default.aspx> | Washington University in St. Louis<https://wustl.edu/> From: Glasser, Matthew Sent: Monday, January 28, 2019 5:41:12 PM To

Re: [HCP-Users] Missing shared library for wb_command

ilab.weebly.com/> Department of Biomedical Engineering<https://bme.wustl.edu/Pages/default.aspx> | Washington University in St. Louis<https://wustl.edu/> From: Glasser, Matthew Sent: Monday, January 28, 2019 5:39:08 PM To: Jayasekera, Dinal; hcp-users@humanco

Re: [HCP-Users] Missing shared library for wb_command

t.aspx> | Washington University in St. Louis<https://wustl.edu/> From: Glasser, Matthew Sent: Monday, January 28, 2019 6:10:23 PM To: Jayasekera, Dinal; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Missing shared library for wb_command You could try the

[HCP-Users] Missing shared library for wb_command

Dear all, I've been trying to run wb_command but I continue to keep getting this error: ./wb_command: error while loading shared libraries: libOSMesa.so.6: cannot open shared object file: No such file or directory I've looked online but can't seem to find much advice about what supporting

[HCP-Users] Troubleshooting error with gradunwarp

Dear all, I'm trying to troubleshoot an error that I'm getting when running v4.0 PreFreeSurferPipelineBatch. I initially thought the error arose as a result of grandunwarp but I don't think that is the case anymore. This is the error I am receiving:

[HCP-Users] Assigning the results of -cifti-correlation to appropriate resting state networks

Dear all, I have run a wb_command, specifically -cifti-parcellate, -cifti-reorder and -cifti-correlation, on some functional connectivity data to extract and plot an adjacency matrix on MATLAB. The matrix that is generated is a 360x360 (360 parcels x 360 parcels) matrix and I'm trying to