Re: [HCP-Users] White matter and CSF masks after minimal HCP processing

[Glasser, Matthew]

Those are generated by the RestingStateStats pipeline, but were mainly for an 
exploratory analysis that didn’t work.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Friday, November 9, 2018 at 12:47 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] White matter and CSF masks after minimal HCP processing

To Whom it may concern,

In this thread: 
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06276.html


I found a reference to eroded white matter masks for HCP subjects that should 
be stored in


MNINonLinear/ROIs/CSFReg.2.nii

MNINonLinear/ROIs/WMReg.2.nii



but after running the HCP pipeline on my own data, these outputs don’t seem to 
be there. Were these files created ad hoc for this release and would you have a 
recommended way of obtaining comparable masks? To give you a context, I would 
like to extract white matter and CSF signals to use aCompCor and add confound 
regressors to my task GLMs.

I was also wondering, in the absence of these masks would it make sense to use 
atlas-based masks in MNI space and extract the signals from the MNI warped 
images, like for example 
/Volumes/LT_storage/Trevor_study/EMOTION_PREPROC/100307/MNINonLinear/Results/tfMRI_EMOTION_LR
 . Would this be acceptable, for example in the case in which I were to 
download only the task data from your release (so I wouldn’t have the original 
T1s)? If not, is there another approach you would recommend?

Thank you very much,


Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


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[HCP-Users] White matter and CSF masks after minimal HCP processing

[Leonardo Tozzi]

To Whom it may concern,

In this thread: 
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06276.html


I found a reference to eroded white matter masks for HCP subjects that should 
be stored in


MNINonLinear/ROIs/CSFReg.2.nii

MNINonLinear/ROIs/WMReg.2.nii



but after running the HCP pipeline on my own data, these outputs don’t seem to 
be there. Were these files created ad hoc for this release and would you have a 
recommended way of obtaining comparable masks? To give you a context, I would 
like to extract white matter and CSF signals to use aCompCor and add confound 
regressors to my task GLMs.

I was also wondering, in the absence of these masks would it make sense to use 
atlas-based masks in MNI space and extract the signals from the MNI warped 
images, like for example 
/Volumes/LT_storage/Trevor_study/EMOTION_PREPROC/100307/MNINonLinear/Results/tfMRI_EMOTION_LR
 . Would this be acceptable, for example in the case in which I were to 
download only the task data from your release (so I wouldn’t have the original 
T1s)? If not, is there another approach you would recommend?

Thank you very much,


Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu | (650) 5615738


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