About T1 images

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Ashkan Jafari

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Sep 30, 2021, 8:19:17 AM9/30/21
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Hello Everybody!
I am working on a HCP 100 unrelated data. I have a problem in finding T1 images because when I import my T1 files into DPARSF toolbox, It shows an error.
Here I attach my the data directory pictures and I would appreciate if anyone tell me which one of these three files in T1 folder is the main T1 file.

Thanks for your attention,
-Ashkan JafariCapture.PNGCapture1.PNG
Capture4.PNG
Capture3.PNG
Capture2.PNG

Glasser, Matt

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Sep 30, 2021, 8:59:01 AM9/30/21
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I’m not sure if anyone here uses the DPARSF toolbox.  There is a T1w image in subject’s physical space ${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore.nii.gz and in MNI space ${StudyFolder}/${Subject}/MNINonLinear/T1w_restore.nii.gz.

 

Matt.

-Ashkan Jafari

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Elam, Jennifer

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Sep 30, 2021, 10:28:56 AM9/30/21
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Hi Ashkan,
It looks like you are looking at files in the Resting_State_fMRI_1_Preprocessed package that don't contain the T1w images. You need to download the Structural Preprocessing package to get the T1w images that Matt references. 

Best,
Jenn
From: Glasser, Matt <glas...@wustl.edu>
Sent: Thursday, September 30, 2021 7:58 AM
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Subject: Re: [hcp-users] About T1 images
 

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Ashkan Jafari

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Oct 2, 2021, 5:40:36 AM10/2/21
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Thanks for your reply!
I have this directory which is attached here. there is a T1w folder and it contains 3 files. Do you mean none of them are the right T1w image? I am really confused.
Capture3.PNG

Coalson, Timothy Scott (S&T-Student)

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Oct 4, 2021, 4:25:27 PM10/4/21
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None of thse are T1w images, they are (processed) spin echo fieldmaps and "single band reference" for a BOLD run.  The "T1w" folder really just means rigidly-aligned space.

The actual T1w images you are looking for are not in the fMRI package you downloaded, they are in the structural package.  You need to download something else for this subject from ConnectomeDB.

Tim

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Subject: Re: [hcp-users] About T1 images
 
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Elam, Jennifer

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Oct 4, 2021, 4:33:37 PM10/4/21
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I guess I somehow didn't reply all earlier. In case others on the list can benefit....
From: Elam, Jennifer <el...@wustl.edu>
Sent: Monday, October 4, 2021 11:17 AM
To: Ashkan Jafari <ashkan.j...@gmail.com>

Subject: Re: [hcp-users] About T1 images
 
Yes, none of them in the folder you show are the T1w image, those are distortion correction files for the first Resting state run. The Resting state data doesn't include the structural data. The T1w images are available in the when you download the Structural_Preprocessed package from ConnectomeDB.

As Matt says, there is a T1w image in subject’s physical space ${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore.nii.gz and in MNI space ${StudyFolder}/${Subject}/MNINonLinear/T1w_restore.nii.gz. 
From: Ashkan Jafari <ashkan.j...@gmail.com>
Sent: Saturday, October 2, 2021 4:40 AM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: Elam, Jennifer <el...@wustl.edu>
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