Re: [HCP-Users] About the .dlabel.nii file for the 180 parcellations in your study

First, "invalid file identifier" is likely a secondary error, see if there is another error before it. Check the permissions on the file, as that could cause opening to fail. As Matt hinted at, we recommend a different set of scripts for reading cifti into matlab, in order to not change the data

Re: [HCP-Users] values in myelin maps

Right she would want to comment out stuff that had already been done. Matt. From: "Harms, Michael" > Date: Wednesday, June 7, 2017 at 12:50 PM To: Matt Glasser >, Lisa Kramarenko

Re: [HCP-Users] values in myelin maps

I haven’t thought this all through, but I think that one of the main things you’d need to hack is to be able to make use of an already existing FS output. Currently, I believe that re-running the pipeline will simply overwrite any existing FS files, as if you were running FS de-novo. cheers,

Re: [HCP-Users] values in myelin maps

Hi Lisa, I was going to suggest that you hack the pipeline yourself if you are comfortable with that. You might try starting at line 167 of the FreeSurfer pipeline to incorporate the brainmask edits (the WM edits might not be needed then). As for the control points, I don’t know enough about

Re: [HCP-Users] values in myelin maps

so that means if something went wrong with the skull strip and surfaces during the FreeSurfer Pipeline there is no other alternative than to exclude these subjects? On 7 June 2017 at 18:04, Harms, Michael wrote: > > Unfortunately, the HCP Pipelines do not currently support

Re: [HCP-Users] values in myelin maps

Unfortunately, the HCP Pipelines do not currently support rerunning FreeSurfer after editing. It is on our list of “things to do” to add that functionality. cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of

Re: [HCP-Users] values in myelin maps

Dear Matthew, I have now manually edited brainmask.gmz ans wm.gmz to remove dura that was still mistaken for a surface. Now I am not sure from which step to re-run these participants. 1. Do I understand it correctly that after replacing brainmask.gmz and wm.gmz in the /mri I need to start the

Re: [HCP-Users] About the .dlabel.nii file for the 180 parcellations in your study

Please see the FAQ #2: https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ Peace, Matt. From: > on behalf of Manasij Venkatesh > Date: Wednesday, June 7,

Re: [HCP-Users] Similarity between thickness dscalar files and freesurfer 5.3 thickness files

Okay, I thought as much. Thanks for clarifying Matt! Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) On Wed, Jun 7, 2017 at 10:37 AM, Glasser, Matthew

Re: [HCP-Users] Similarity between thickness dscalar files and freesurfer 5.3 thickness files

They should be identical. Peace, Matt. From: > on behalf of Timothy Hendrickson > Date: Wednesday, June 7, 2017 at 9:51 AM To:

[HCP-Users] About the .dlabel.nii file for the 180 parcellations in your study

Hi, I've been having some issues importing a *.dlabel.nii file to matlab using ft_read_cifti. The error I obtain is "Invalid file identifier. Use fopen to generate a valid file identifier" but the *.dtseries.nii imports just fine. Has this bug been fixed? After looking at some old posts, I