Re: [HCP-Users] Some questions about using the HCP structural preprocessing pipeline

1. You can edit the launcher scripts to point to the files however you want to name them. 2. Yes if they are both at least 1mm isotropic resolution. 3. You can turn on gradient distortion correction if you want and have the appropriate coefficients file from your scanner. Matt. From: mailto

[HCP-Users] Some questions about using the HCP structural preprocessing pipeline

Dear HCP experts, I have some questions about using the HCP structural preprocessing pipeline. 1. To apply this pipeline on non-HCP data, do I have to rename the filenames of my data similar to the HCP unprocessed data as follows? T1w _MPR1/ {Subject_ID}_3T_AFI.nii.gz {Subject_ID}_3T_BIAS_32CH.

Re: [HCP-Users] Workbench tools installation in Ubuntu 18.04

Thank you very much! I will give that a try. Best, Erik On Fri, Feb 1, 2019 at 8:23 PM Takuya Hayashi wrote: > We've recently encountered similar problem in our Ubuntu 18.04 and solved > this by the followings: > > Download Zlib 1.2.9 from here: > > https://sourceforge.net/projects/libpng/files

Re: [HCP-Users] Workbench tools installation in Ubuntu 18.04

We've recently encountered similar problem in our Ubuntu 18.04 and solved this by the followings: Download Zlib 1.2.9 from here: https://sourceforge.net/projects/libpng/files/zlib/1.2.9/zlib-1.2.9.tar.gz/download tar -xvf ~/Downloads/zlib-1.2.9.tar.gz cd zlib-1.2.9 ./configure; make; make install

Re: [HCP-Users] Workbench tools installation in Ubuntu 18.04

Thanks Takuya. Matt. From: Takuya Hayashi mailto:takuya.haya...@riken.jp>> Date: Friday, February 1, 2019 at 8:23 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: erik lee mailto:erik.lee...@gmail.com>>, "hcp-users@humanconnectome.org" mailto:hcp-users@h

Re: [HCP-Users] Workbench tools installation in Ubuntu 18.04

The person to address this is on vacation and will be back next week. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of erik lee mailto:erik.lee...@gmail.com>> Date: Friday, February 1, 2019 at 6:20 PM To: "hcp-users@humanconnectome.org

Re: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

Do you have an SBRef image? Can you use that instead of the MB images for the purposes of this comparison (better grey-white contrast)? We expect gradient echo signal dropout which cannot be fixed by any known processing approach. This is different from EPI distortion which we can fix. That

[HCP-Users] Workbench tools installation in Ubuntu 18.04

Hi, I am trying to install the Connectome Workbench software on my linux machine (Ubuntu 18.04). When I try to run wb_view or wb_command, I get the following error: /usr/local/workbench/bin_linux64/../exe_linux64/wb_view: /usr/local/workbench/bin_linux64/../libs_linux64/libz.so.1: version `ZLIB_1

Re: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

How does the data look if you overlay the white and pial surface contours in MNI space using Connectome Workbench. If there are slice-based intensity fluctuations in physical space, those can turn into curvy lines after non-linear registration to MNI space. I don’t see anything obviously wrong

Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm MNI Surface and Volume space

I suggested he use the mapping from FreeSurfer space not HCP space implemented in PostFreeSurfer for wmparc.mgz. Matt. From: "Harms, Michael" mailto:mha...@wustl.edu>> Date: Friday, February 1, 2019 at 11:18 AM To: "Srivastava, Benjamin (NYSPI)" mailto:benjamin.srivast...@nyspi.columbia.edu>>,

Re: [HCP-Users] Distortion of fMRI image in MNI space after preprocessing

Can you put an arrow on what is bothering you? I’m not sure what you are referring to. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Friday, February 1, 2019 at 3:29 PM To: "hcp-users@humanconnectome.org

Re: [HCP-Users] Transforming Freesurfer .mgz segmented files into HCP_2mm MNI Surface and Volume space

So, I’m assuming you ran it using the outputs from PreFreeSurfer as its inputs? Otherwise, the mapping that Matt suggested you use from PostFreeSurfer won’t be appropriate! ☺ Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of

Re: [HCP-Users] Regress confounds out of CIFTIs

Hi - yes IIRC it's only the demeaning that is important - the scaling of the regressors makes no difference to the output from the deconfounding. Normalising SD is a "sane" step in such processing in general, and sometimes is of value (depending on what outputs one is interested in wrt the inter