Re: [HCP-Users] Cleaning up intermediate files from the minimal pre-processing pipelines

Yes that is particularly true when using the latest version of the pipelines. There are also files in T2w and T1w that could be deleted, but will not save as much space as Mike’s suggestion. Peace, Matt. From: "Harms, Michael" > Date: Wednesday,

Re: [HCP-Users] Extracting Thalamus Brainordinates

It may be better to use the individual subject's "native space" definitions. The files in the T1w folder are in what we refer to as native volume space (it is actually rigidly-aligned MNI space, but rigid alignment preserves shape, so it can be used as if it were distortion-corrected scanner

Re: [HCP-Users] Extracting Thalamus Brainordinates

Hi Claude, Are you using workbench viewer? If so, you should be able to identify particular thalamus or other subcortical MNI coordinates in the Volume tab (brainordinate subcortical coordinates = MNI coordinates). You can also split the thalamus structure out from subject¹s CIFTI file, if you

Re: [HCP-Users] gif surface to obj

It appears that .obj is a fairly simple text format ( https://en.wikipedia.org/wiki/Wavefront_.obj_file), so you could hack it together in shell, if nothing else. You can use wb_command -gifti-convert to convert to ASCII encoding, and that would allow you to get the coordinate and triangle

Re: [HCP-Users] An error in Post-FreeSurfer Pipeline

That is the shell command to source a script. Are you using bash as your shell? Peace, Matt. From: > on behalf of Darko Komnenić > Date: Wednesday, February 21,

Re: [HCP-Users] gif surface to obj

mris_convert from FreeSurfer may be able to. Or at least to convert a GIFTI file to another format that another converter can convert to obj. Peace, Matt. From: > on behalf of "Harwell, John"

Re: [HCP-Users] An error in Post-FreeSurfer Pipeline

Dear HCP experts, I wrote to this mailing list about a month ago with a problem that the FreeSurfer Pipeline would get interrupted after finishing recon-all, and starting FreeSurferHiResWhite script. The error log showed START: FreeSurferHighResWhite Unmatched ". and below set --

Re: [HCP-Users] gif surface to obj

Hello, No. Connectome Workbench is unable to convert GIFTI files to OBJ files. John Harwell On Feb 21, 2018, at 10:18 AM, Shadi, Kamal > wrote: Hi all, Does human connectome workbench have a tool to convert gii surfaces to obj?

Re: [HCP-Users] Cleaning up intermediate files from the minimal pre-processing pipelines

Hi, While the documentation is overall very good, I don’t know if I’d rely on that pdf for a detailed list of all the files that we recommend “keeping”. For that, you could download and unpack the packages for a subject with complete data (e.g., 100307), and see what you all get. As a

Re: [HCP-Users] scan order, session day, scan time variables

Hi Csaba, I believe that information is still only available per subject in the {Subject_ID}_3T.csv file in the Structural unprocessed and Structural preprocessed packages. Unpacked, the file should appear in the {Study_ID}/{Subject_ID}/unprocessed/3T and {Study_ID}/{Subject_ID}/T1w

[HCP-Users] gif surface to obj

Hi all, Does human connectome workbench have a tool to convert gii surfaces to obj? Thanks, Kamal ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] scan order, session day, scan time variables

Hi, I was wondering if it’s now possible to download scan order, session day, and scan time variables as part of the bulk csv downloads? A post from 2016 mentioned that it might become available in the S1200 release. hhttps://www.mail-archive.com/hcp-users@humanconnectome.org/msg02922.html