Thank you very much for both responses. Also, thank you for the insightful
paper.
Here, I am going to describe a processing pipeline and I was wondering if
you could tell me if there is something wrong with this pipeline:
1) We read "rfMRI_REST{1,2}_{LR,RL}_Atlas_MSMAll_hp2000_clean.dtseries.nii"
with "ft_read_cifti.m" and
"${subject}.{L,R}.midthickness_MSMAll.32k_fs_LR.surf.gii" with "gifti.m" of
each subject.
2) We save four fields of the generated structure by "ft_read_cifti.m":
2-1) "dtseries" which contains the time-series of subcortical voxels
and cortical grayordinates.
2-2) "pos" which, I assume, contains the MNI coordinates of subcortical
voxels. [?]
2-3) "brainstructure" which labels each structure of brain with
different numbers.
2-4) "transform" which, I assume, has the matrix for transformation of
coordinates from MNI-mm space to MNI-matrix space (91,109,91). [?]
3) We save only the "vertices" field of the generated structure by
"gifti.m" which, I assume, contains the coordinates of cortical
grayordinates for left or right hemisphere in the MNI-mm space. [?]
4) Let's assume further that we want to apply a particular 3D mask in the
MNI-matrix space (91,109,91).
5) By using "brainstructure" and "vertices", we can complete the "pos" with
the correct coordinates of cortical grayordinates.
6) By using "transform", we can transform the coordinates of "pos" from the
MNI-mm space to the MNI-matrix space (91,109,91).
7) Now we have a complete set of time-series from "dtseries" with their
corresponding coordinates in the MNI-matrix space (91,109,91).
8) At this stage, we can apply our mask to this data.
Thank you in advance for your time and consideration.
Best regards,
Aslan
On Thu, Jul 19, 2018 at 1:15 AM Timothy Coalson <[email protected]> wrote:
> 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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