Some questions

[lyesbachatene]

Hi, i got some problems trying to do some prf analyses:
1- since dicom import is not working anymore, what do you mean by 'inplane anatomical' ? I only have a T1 image and fumctional images.
2- my corAnal give me systematically some errors (reshape) because of the number of voxels, do you think i did something wrong in the preprocessing?
3- to generate the time series (raw/original/tseries) do i have to use the loadtseries function or it will be done automatically with the corAnal ?
4- The last problem is the trilinear interpolation which i guess it does not work because of the above issues

Cordially

[JWinawer]

Some answers below.

On Wed, Aug 10, 2016 at 4:03 PM, lyesbachatene notifications@github.com
wrote:

Hi, i got some problems trying to do some prf analyses:
1- since dicom import is not working anymore, what do you mean by 'inplane
anatomical' ? I only have a T1 image and fumctional images.

Vistasoft assumes you have acquired an an anatomical image aligned to your
functional images. This anatomical image is called the 'inplane'. Because
the tissue contrast in the inplane is better than a functional image, and
because the inplane typically has higher resolution than a functional
image, it is easier to align the inplane to the volume anatomy than to
align the functional data to the volume anatomy. If you did not collect an
inplane, you can save the average of a functional scan prior to
initializing a session, and use this as the inplane. Something like this,
but I haven't checked the code:

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);

2- my corAnal give me systematically some errors (reshape) because of the
number of voxels, do you think i did something wrong in the preprocessing?

Normally the corAnal does not return an error so it sounds like something
is wrong either in the preprocessing or in the parameters specified for the
scan. For example, the number of volumes need to be an integer multiple of
the number of cycles.

3- to generate the time series (raw/original/tseries) do i have to use the
loadtseries function or it will be done automatically with the corAnal ?

The original time series is supplied by you as a nifti. You do not need to
create a separate time series. There are tutorials that show you how to
initialize a session. This tutorial shows you how to arrange your files in
order to initialize a session:
https://github.com/vistalab/vistasoft/blob/master/tutorials/bold/session/t_initVistaSession.m

4- The last problem is the trilinear interpolation which i guess it does
not work because of the above issues

Can't tell without more information. The test function, test_xformInplaneToVolume.m,
shows how to transform data from the inplane view to the gray view using
trilinear interpolation.

Generally, it might help to go through some of the test functions in the
folder mrTest/bold/core/test*.m to get familiar with basic operations in
vistasoft. We hope to add more tutorials over time.

Cordially

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Jonathan Winawer
Assistant Professor of Psychology and Neural Science

New York University
6 Washington Place
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jonathan.winawer@nyu.edu
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[JWinawer]

Hi Lyes. I am closing this issue. Please feel free to reopen it if you have further questions.

-Jon