As an additional note, if you do use the non-MSMAll data, you should not
use an MSMAll surface with it.  The data and surface file should go through
the same registration and resampling.  The files without MSMAll in their
names are registered/resampled using MSMSulc.

Tim


On Wed, Jul 18, 2018 at 8:16 AM, Glasser, Matthew <[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]>
> Date: Wednesday, July 18, 2018 at 12:57 AM
> To: Matt Glasser <[email protected]>
> Cc: "[email protected]" <[email protected]>,
> Mohammad Reza Khodaei <[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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