run the script, giving it the mask output from first_utils together with the corrected p-value output from randomise (the one including corrp in the name)
this script will open an FSLView window in which you must do the following
select "basestruct" in layer dialog (i.e. the list of images loaded), press "i" and turn "Image type" to "Mask/Label"
select the corrp image in the layer dialog (at the top of the list), press "i" and turn "Image type" to "Statistic"
via the menus select Tools -> 3D Viewer
turn Clipping on (tickbox)
press 'b' (make sure you've clicked inside the 3D rendered window)
adjust the clipped box such that the structure of interest is visible (and whatever brain sections you want - you can turn it all off by unclicking the Clipping box and double clicking on the MNI152_T1_2mm_brain in the layer dialog - to deselect it)
press 'b' again
select the top image (corrp) in the dialog of the 3D viewer
move transparency slider (underneath the layer dialog) to the left and back to the right (this will make the colours solid)
rotate to give a good view and save your image (via screen grab or with the camera button)

Note the first steps where you need to change some properties.

On Monday, September 14, 2015, Maria Serra <[log in to unmask]> wrote:

Hi Niels,

thanks for answering. This is the command line I'm using:

first3Dview mask_output_first_utils_mask.nii.gz corrp_fstat1_output_randomise.nii.gz

and then following the wiki steps. However, I do not have changed images properties, as I have not found such instructions. Which properties should I change?

Thank you again,

Maria

On Mon, Sep 14, 2015 at 5:01 PM, Niels Bergsland <[log in to unmask]');" target="_blank">[log in to unmask]> wrote:

Hi - what command are you using? (From the command line). Have you changed the properties of the images as described in the wiki?

On Monday, September 14, 2015, Maria Serra <[log in to unmask]');" target="_blank">[log in to unmask]> wrote:

Dear FSL users,

I am trying to display a result from randomise via the method described in the fsl wiki. However, only the "basestruct" (mask output) gets loaded, whereas the statistics are not shown in the rendering.

Anyone have some clue of what could be happening?

Thank you,

--

Maria Serra Blasco

--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
[log in to unmask]');" target="_blank">[log in to unmask]

--
Maria Serra Blasco
Institut d'Investigació Biomèdica de l'Hospital de la Santa Creu i Sant Pau, IIB-Sant Pau
Av. Sant Antoni Ma. Claret, 167
Tlf: +34 93 5537836
08025 Barcelona- Spain

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