Re: [HCP-Users] Extracting Thalamus Brainordinates

2018-02-22 Thread Claude Bajada
Thanks Tim and Ely, This is helpful. Tim, I think I prefer your second suggestion (using the standard cifti MNINonLinear group definition). I need a one to one correspondence between every point in the thalamus across individuals and to a template thalamus. The reason (and perhaps I need to

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

2018-02-22 Thread Darko Komnenić
Hi Matt, yes, I am using bash. On Wed, Feb 21, 2018 at 9:56 PM, Glasser, Matthew wrote: > That is the shell command to source a script. Are you using bash as your > shell? > > Peace, > > Matt. > > From: on behalf of Darko Komnenić >

Re: [HCP-Users] Extracting Thalamus Brainordinates

2018-02-22 Thread Glasser, Matthew
They are in ${StudyFolder}/${Subject}/MNINonLinear/xfms Peace, Matt. From: > on behalf of Claude Bajada > Date: Thursday, February 22, 2018 at 2:50 AM To:

Re: [HCP-Users] Extracting Thalamus Brainordinates

2018-02-22 Thread Claude Bajada
Thanks On il-Ħamis, 22 ta Fra, 2018 12:41 , Glasser, Matthew wrote: They are in ${StudyFolder}/${Subject}/MNINonLinear/xfms Peace, Matt. From: > on behalf of Claude Bajada

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

2018-02-22 Thread Cook, Philip
Thanks everyone, this will be much faster to implement! On Feb 22, 2018, at 10:14 AM, Keith Jamison > wrote: This is not an official HCP answer, but I always delete the following after functional preprocessing:

[HCP-Users] NIH toolbox measures

2018-02-22 Thread Gilman, Jodi
Hi Jenn, I have a question about the scores from NIH toolbox on the domains of negative affect, psychological well-being, social relationships, and stress and self-efficacy. I see that the scores available for download are all unadjusted; I do not see a column for any adjusted scores on these

[HCP-Users] about interpreting EVs and .dtseries.nii files

2018-02-22 Thread Javier Zapata
Dear Professors, I am pretty new to task fMRI data and I would like to check how to use the files in the EVs folder to extract information from the .dtseries.nii file for the MOTOR dataset. As an example I chose subject 100307 with the LR phase and I was able to build this table from the files

Re: [HCP-Users] what is rfMRI_REST1_LR_Atlas.dtseries.nii

2018-02-22 Thread Harms, Michael
The files without any “registration suffix” came first temporally and were generated using “MSMSulc” registration. When the “MSMAll” registration was added later, we then added “MSMAll” as part of the file name. Cheers, -MH -- Michael Harms, Ph.D.

Re: [HCP-Users] about interpreting EVs and .dtseries.nii files

2018-02-22 Thread Glasser, Matthew
I would have a look at this file for the task design matrix: ${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${AnalysisName}.feat/design.mat Not sure if it is released or if you have to run the task analysis pipeline to generate it. Peace, Matt. From:

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

2018-02-22 Thread Glasser, Matthew
Yes we probably should do what Keith suggests by default. Peace, Matt. From: > on behalf of "Cook, Philip" > Date: Thursday, February 22,

Re: [HCP-Users] Extracting Thalamus Brainordinates

2018-02-22 Thread Timothy Coalson
Okay, but be aware that the volume registration isn't perfect even for subcortical structures. We go to some trouble to deal with the non-overlapping edges without mixing data across individually-identified subcortical structures when we put subcortical data into CIFTI. I don't know how bad the

Re: [HCP-Users] about interpreting EVs and .dtseries.nii files

2018-02-22 Thread Timothy Coalson
On the technical end, cifti dtseries are arranges such that a row is a timecourse - you will need to select columns rather than rows. wb_command -cifti-merge can do this. On the math side, I don't know the details needed to sync the EV files with the dtseries (whether the 0s from the EVs match

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

2018-02-22 Thread Glasser, Matthew
Is your FreeSurfer set up correctly? I just checked the current git master version of FreeSurferHighResWhite and there was no syntax issue or missing “ Peace, Matt. From: Darko Komnenić > Date: Thursday, February 22, 2018 at 4:49 AM To: Matt

[HCP-Users] About interpreting EVs and .dtseries.nii files

2018-02-22 Thread Sang-Yun Oh
Dear HCP-Users, I am pretty new to task fMRI data and I would like to check how to use the files in the EVs folder to extract information from the .dtseries.nii file for the MOTOR dataset. As an example, I chose subject 100307 with the LR phase and I was able to build this table from the files in

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

2018-02-22 Thread Keith Jamison
This is not an official HCP answer, but I always delete the following after functional preprocessing: $subj/rfMRI_REST1_LR/MotionMatrices/MAT*.nii.gz $subj/rfMRI_REST1_LR/OneStepResampling/prevols/ $subj/rfMRI_REST1_LR/OneStepResampling/postvols/ MotionMatrices/*.nii.gz alone accounts for nearly