Unfortunately there is no good way to do that as after imaging data are 
averaged across subjects and smoothed in MNI space, it is very hard to know 
from which cortical areas that mask represents.  Have a look at this 
publication for more details:

http://www.pnas.org/content/early/2018/06/19/1801582115.short

Matt.

From: Aslan Satary Dizaji <[email protected]<mailto:[email protected]>>
Date: Wednesday, July 18, 2018 at 8:32 AM
To: Matt Glasser <[email protected]<mailto:[email protected]>>
Cc: "[email protected]<mailto:[email protected]>" 
<[email protected]<mailto:[email protected]>>, Mohammad 
Reza Khodaei <[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] The coordinates of surface time-series of Resting 
State fMRI FIX-Denoised (Compact)

Dear Matt,

Thank you very much for your response.

So if we have a mask in the MNI space which we want to apply to the rsfMRI 
data, what can we do without having the coordinates of surface time-series? I 
mean, how we can infer the map from mask to the rsfMRI data.

Best regards,

Aslan

On Wed, Jul 18, 2018 at 5:46 PM Glasser, Matthew 
<[email protected]<mailto:[email protected]>> wrote:
1.  rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii
2-3. 100307.L.midthickness_MSMAll.32k_fs_LR.surf.gii

Note that the surface coordinates or only valid for single individuals.  There 
is no “standard space” (like MNI space) that properly lines up the cortical 
areas, instead surface registration brings the data onto a standard 32k mesh 
where vertex 1000 has the same neuroanatomical location across subjects.  You 
probably don’t actually need the surface coordinates for your analysis unless 
you are doing something unusual.

Peace,

Matt.

From: Aslan Satary Dizaji <[email protected]<mailto:[email protected]>>
Date: Wednesday, July 18, 2018 at 12:57 AM
To: Matt Glasser <[email protected]<mailto:[email protected]>>
Cc: "[email protected]<mailto:[email protected]>" 
<[email protected]<mailto:[email protected]>>, Mohammad 
Reza Khodaei <[email protected]<mailto:[email protected]>>
Subject: Re: [HCP-Users] The coordinates of surface time-series of Resting 
State fMRI FIX-Denoised (Compact)

Dear Matt,

Thank you for your email.

In "Resting State fMRI FIX-Denoised (Compact)" of 100 unrelated subjects, 
inside folder "${StudyFolder}/${Subject}/MNINonLinear", there is only one 
folder, "Results", which inside it there are four folders "rfMRI_REST1_LR", 
"rfMRI_REST1_RL", "rfMRI_REST2_LR", "rfMRI_REST2_RL". And finally inside each 
one of these folders, there are two "*.dtseries.nii" files and two 
"*.dtscalar.nii" files. So basically, in "Resting State fMRI FIX-Denoised 
(Compact)" of 100 unrelated subjects, there is not any folder with the name of 
"fsaverage_LR32k". However, I checked the other data-sets of 100 unrelated 
subjects, and I found that "Structural Preprocessed" of 100 unrelated subjects 
has the  "fsaverage_LR32k" folder with the files that you mentioned. So my 
question is that, do we need to download this data-set too so to be able to get 
the coordinates of surface time-series?

Also, I have three other questions:

1) Which one of these "*.dtseries.nii" files do you recommend that we use:

rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii
rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii

2) For example, for subject 100307 and for left hemisphere, which one of these 
three "*.surf.gii" files do you recommend that we use:

100307.L.inflated.32k_fs_LR.surf.gii
100307.L.midthickness.32k_fs_LR.surf.gii
100307.L.very_inflated.32k_fs_LR.surf.gii

3) I assume that with "rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii", we 
should use one of the three above "*.surf.gii" files and with 
"rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii", we should use one of 
the three below "*.surf.gii" files:

100307.L.inflated_MSMAll.32k_fs_LR.surf.gii
100307.L.midthickness_MSMAll.32k_fs_LR.surf.gii
100307.L.very_inflated_MSMAll.32k_fs_LR.surf.gii

Am I right?

Many many thanks in advance for your time and consideration.

Best regards,

Aslan

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