Inplane Axial display instead of Coronal

[maalbe]

Dear mrVista experts,
I am writing because I am trying to do retinotopy using mrVista and I’ve been having some problems with the inplane.
We did not collect an inplane, so I did the average of a functional scan and used this as an inplane using the code you provided in #179:

ni = niftiRead('myEPI.nii');
data = mean(niftiGet(ni, 'data'), 4);
ni = niftiSet(ni, 'data', data);
dims = niftiGet(ni, 'dim');
ni = niftiSet(ni, 'dim', [dims(1:3) 1]);
ni.fname = 'myInplane.nii';
niftiWrite(ni);I

But when displaying the inplane both in mrVista and rxAlign the orientation is axial, and I would like to have the coronal.

Is there a way to change this display? Is there any other way to get the inplane when you only have the functionals and the t1?

I would really appreciate some help,
Thank you so much in advance:)

[JWinawer]

The INPLANE view is for viewing the slices as they were acquired. The code does not reslice in the inplane view. You could transfer to the volume 3-view if you would like to see different planes. Jon

On Sun, Mar 1, 2020 at 13:17 maalbe ***@***.***> wrote: Dear mrVista experts, I am writing because I am trying to do retinotopy using mrVista and I’ve been having some problems with the inplane. We did not collect an inplane, so I did the average of a functional scan and used this as an inplane using the code you provided in #179 <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_vistalab_vistasoft_issues_179&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=W4u2U_DhoNoJOD0UdsYQiqH56Bg3zFfOtNa0RCuuEIs&m=P-KI4bH72lEvgdCOyZP1I8uMYCNN_-qrX3uv4nZpHxY&s=uQ6bzIwEd437TtSHJnGXszSlr7kmyO40tvoqOBmqsxs&e=> : ni = niftiRead('myEPI.nii'); data = mean(niftiGet(ni, 'data'), 4); ni = niftiSet(ni, 'data', data); dims = niftiGet(ni, 'dim'); ni = niftiSet(ni, 'dim', [dims(1:3) 1]); ni.fname = 'myInplane.nii'; niftiWrite(ni);I But when displaying the inplane both in mrVista and rxAlign the orientation is axial, and I would like to have the coronal. [image: mrvista] <https://urldefense.proofpoint.com/v2/url?u=https-3A__user-2Dimages.githubusercontent.com_57325406_75629578-2D66e1cf80-2D5be3-2D11ea-2D8694-2D68b5667a6033.png&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=W4u2U_DhoNoJOD0UdsYQiqH56Bg3zFfOtNa0RCuuEIs&m=P-KI4bH72lEvgdCOyZP1I8uMYCNN_-qrX3uv4nZpHxY&s=ONeRT70ciThHxCdi4BQ0usBjJS16rEsbwxwB-hvAuEQ&e=> Is there a way to change this display? Is there any other way to get the inplane when you only have the functionals and the t1? I would really appreciate some help, Thank you so much in advance:) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_vistalab_vistasoft_issues_332-3Femail-5Fsource-3Dnotifications-26email-5Ftoken-3DAAQFPXVKXU2SZTAAMKQP5MLRFKRELA5CNFSM4K7HCIYKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4IRQJSHQ&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=W4u2U_DhoNoJOD0UdsYQiqH56Bg3zFfOtNa0RCuuEIs&m=P-KI4bH72lEvgdCOyZP1I8uMYCNN_-qrX3uv4nZpHxY&s=G3s8BpA-3wXFwUmoORJhq0Etb7KfJcCmQTIkC9x3SAU&e=>, or unsubscribe <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AAQFPXVHAZQ7ZBHT7FXYEW3RFKRELANCNFSM4K7HCIYA&d=DwMFaQ&c=slrrB7dE8n7gBJbeO0g-IQ&r=W4u2U_DhoNoJOD0UdsYQiqH56Bg3zFfOtNa0RCuuEIs&m=P-KI4bH72lEvgdCOyZP1I8uMYCNN_-qrX3uv4nZpHxY&s=ugcrcUrr6oO-7dw_qZ1UEnQR85SDvlEZB8m5Sez46_M&e=> .

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