Re: [HCP-Users] Issue about new FreeSurferPipeline

You can just delete the --printcom flag from the example script as it is not needed. This should be removed from the example script if it is no longer going to be supported in the main FreeSurfer pipeline. Matt. From: Qunjun Liang mailto:liangqun...@foxmail.com>> Date: Thursday, March 21,

Re: [HCP-Users] S1200 MSMSulc files

Yes that is what was done. Matt. From: Reza Rajimehr mailto:rajim...@gmail.com>> Date: Thursday, March 21, 2019 at 6:48 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] S1200 MSMSulc files Would this be accurate to

Re: [HCP-Users] S1200 MSMSulc files

Would this be accurate to obtain group-average MSMSulc curvature file? Vertex-wise arithmetic mean of xx.curvature.32k_fs_LR.dscalar.nii maps in Matlab On Thu, Mar 21, 2019 at 11:36 PM Glasser, Matthew wrote: > Are there not versions already? One simply merges and averages the files. > >

Re: [HCP-Users] S1200 MSMSulc files

Are there not versions already? One simply merges and averages the files. Matt. From: Reza Rajimehr mailto:rajim...@gmail.com>> Date: Thursday, March 21, 2019 at 6:34 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: hcp-users mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users]

Re: [HCP-Users] S1200 MSMSulc files

Thanks Matt! In the fsaverage_LR32k folder of one subject, we have two versions of files. E.g.: 100206.curvature.32k_fs_LR.dscalar.nii 100206.curvature_MSMAll.32k_fs_LR.dscalar.nii So the first file is MSMSulc? How about the group-average MSMSulc files? Is there a procedure/command to generate

Re: [HCP-Users] S1200 MSMSulc files

MSMSulc might not have a specific registration tag, did you check for such files? Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Reza Rajimehr mailto:rajim...@gmail.com>> Date: Thursday, March 21, 2019 at 4:42 PM To: hcp-users mailto:hcp-users@humanconnectome.org>>

Re: [HCP-Users] PostFreesurfer possible bug

As Mike says, you need to use --subjectDIR=/root/hcppilelines/piano_hcp/working_directory/102/T1w as in the example script. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal mailto:gal.shac...@gmail.com>> Date: Wednesday, March 20, 2019 at 3:31 PM To:

[HCP-Users] S1200 MSMSulc files

For a control analysis, we would like to have access to the following files: 32k MSMSulc files for curvature, thickness, and myelin (individual subjects and group average) The current S1200 release only has the MSMAll files. How can we have access to the MSMSulc files? Thanks, Reza

Re: [HCP-Users] Surface Contrast and Overlay Transparency

Thank you Matt. Adding an underlay did indeed fix the transparency issue. I assume changing the thresholds of the underlay, if selected as a curvature map, should be able to help w/ the contrast issue as well? Michael Riedel On Mar 19, 2019, at 2:09 PM, Glasser, Matthew

Re: [HCP-Users] PostFreesurfer possible bug

i am using version 4. this is my call - /root/hcppilelines/HCPpipelines-master/FreeSurfer/FreeSurferPipeline.sh --subject=102 --subjectDIR=/root/hcppilelines/piano_hcp/working_directory/102 --t1=/root/hcppilelines/piano_hcp/working_directory/102/T1w/T1w_acpc_dc_restore.nii.gz

Re: [HCP-Users] Surface Contrast and Overlay Transparency

I’m still not entirely clear what you want the contrast to do. Matt. From: Michael Riedel mailto:mirie...@fiu.edu>> Date: Thursday, March 21, 2019 at 5:13 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org"

Re: [HCP-Users] Issue about new FreeSurferPipeline

What is the command line that it produced. Matt. From: Qunjun Liang mailto:liangqun...@foxmail.com>> Date: Thursday, March 21, 2019 at 2:34 AM To: Matt Glasser mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] Issue about new FreeSurferPipeline Hi, Matt. Thank you for the prompt reply. I