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]> 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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