There are four rfMRI runs per subject. LR vs RL refers to the phase encoding
direction and 1 and 2 refers to the session each run was acquired in. You
should use balanced amounts of RL and LR data ideally, as the phase encoding
direction does create some asymmetry in the data. You want to use the
MSMAll_hp2000_clean dtseries file, as this file has its cortical areas aligned
across subjects. If you wish to concatenate across runs, you should remove the
mean image. You could also variance normalize the data with by multiplying by
the bias field and dividing by the variance normalization map though these maps
would need to be resampled into MSMAll alignment as the currently distributed
files are in MSMSulc alignment. This can be done using:
#Create spheres for resampling from MSMSulc to MSMAll on the 32k mesh
wb_command -surface-project-unproject
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.L.sphere.32k_fs_LR.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.L.sphere.MSMSulc.native.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.L.sphere.MSMAll.native.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.L.sphere.MSMSulc_MSMAll.32k_fs_LR.surf.gii
wb_command -surface-project-unproject
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.R.sphere.32k_fs_LR.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.R.sphere.MSMSulc.native.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.R.sphere.MSMAll.native.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.R.sphere.MSMSulc_MSMAll.32k_fs_LR.surf.gii
#Resample Variance Normalization Map
wb_command -cifti-resample
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_hp2000_clean_vn.dscalar.nii
COLUMN
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_hp2000_clean_vn.dscalar.nii
COLUMN ADAP_BARY_AREA ENCLOSING_VOXEL
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean_vn.dscalar.nii
-surface-postdilate 30 -nearest -left-spheres
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.L.sphere.MSMSulc_MSMAll.32k_fs_LR.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.L.sphere.32k_fs_LR.surf.gii
-left-area-surfs
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.L.midthickness.32k_fs_LR.surf.gii
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.L.midthickness_MSMAll.32k_fs_LR.surf.gii
-right-spheres
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.R.sphere.MSMSulc_MSMAll.32k_fs_LR.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.R.sphere.32k_fs_LR.surf.gii
-right-area-surfs
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.R.midthickness.32k_fs_LR.surf.gii
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.R.midthickness_MSMAll.32k_fs_LR.surf.gii
#Resample Bias Field Map
wb_command -cifti-resample
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_hp2000_clean_bias.dscalar.nii
COLUMN
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_hp2000_clean_bias.dscalar.nii
COLUMN ADAP_BARY_AREA ENCLOSING_VOXEL
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean_bias.dscalar.nii
-surface-postdilate 30 -nearest -left-spheres
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.L.sphere.MSMSulc_MSMAll.32k_fs_LR.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.L.sphere.32k_fs_LR.surf.gii
-left-area-surfs
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.L.midthickness.32k_fs_LR.surf.gii
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.L.midthickness_MSMAll.32k_fs_LR.surf.gii
-right-spheres
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.R.sphere.MSMSulc_MSMAll.32k_fs_LR.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.R.sphere.32k_fs_LR.surf.gii
-right-area-surfs
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.R.midthickness.32k_fs_LR.surf.gii
${StudyFolder}/${Subject}/T1w/fsaverage_LR32k/${Subject}.R.midthickness_MSMAll.32k_fs_LR.surf.gii
#Remove spheres from above
rm
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.L.sphere.MSMSulc_MSMAll.32k_fs_LR.surf.gii
rm
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.R.sphere.MSMSulc_MSMAll.32k_fs_LR.surf.gii
#Create mean image for demeaning
wb_command -cifti-reduce
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii
MEAN
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean_mean.dscalar.nii
#Demean and variance normalize timeseries (and revert bias field correction)
wb_command -cifti-math “((TCS - Mean) * Bias) / VN”
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean_nobias_vn.dtseries.nii
-var TCS
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean.dtseries.nii
-var Mean
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean_mean.dscalar.nii
-var Bias
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean_bias.dscalar.nii
-var VN
${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas_MSMAll_hp2000_clean_vn.dscalar.nii
Peace,
Matt.
From:
<[email protected]<mailto:[email protected]>>
on behalf of Qasim Bukhari
<[email protected]<mailto:[email protected]>>
Date: Sunday, April 9, 2017 at 11:54 AM
To: "[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] problems in understanding the FIX denoised data downloaded
from HCP1200
Dear all,
I am very new to using the HCP dataset. I have downloaded some parts of the FIX
denoised data from HCP1200. However I am not abnle to understand what the data
downloaded really means. There are the following folders
rfMRI_REST1_LR rfMRI_REST1_RLrfMRI_REST2_LR rfMRI_REST2_RL
Inside each of these folders; there are following corresponding files.
Atlas_hp_preclean.dtseries.nii
rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii
rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii
rfMRI_REST1_LR_Atlas_hp2000_clean_bias.dscalar.nii
rfMRI_REST1_LR_Atlas_hp2000_clean_vn.dscalar.nii
Can someone please guide me to which of these files belong to what ?
And what does those 4 folders meant ? I assume that REST1 and REST2 are the two
sessions, but I m not sure what does RL and LR means.
Please guide me to the literature or file that explain what each of these files
mean. I would be extremely grateful.
Another issue is; I was only able to download partial dataset; then for some
reason my computer restarted and now I am only getting the connection error in
Aspera every time I try to reconnect. I even tried downloading an entirely new
version of this dataset, but still got the connection error problem. Any help
would be extremely appreciated
best regards,
Qasim
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