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Hi, Can you provide a screenshot of your 3D rendering in FIRST? Keep in mind that it will need to be relatively small in size in order to go through on the mailing list. Also, what is the output of the following command? fslstats corrp_fstat1_output_randomise -R On Tue, Sep 15, 2015 at 10:33 AM, Maria Serra <[log in to unmask]> wrote: > Dear Niels, > > Thank you for your help. > > I already changed the image properties specified in the wiki. I thought you > were referring to some change in images theirselfs (so as converting the > stat file to 3D or something like that). > > Any idea of what could be happening? > > On Sep 14, 2015 5:46 PM, "Niels Bergsland" <[log in to unmask]> wrote: >> >> Hi - these are the instructions I was referring to from the wiki: >> >> 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]> >>> 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]> >>>> 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] >>> >>> >>> >>> >>> -- >>> 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 >>> >>> P Abans d'imprimir aquest correu electrònic pensa bé si és necessari >>> fer-ho. >>> >>> >> >> >> -- >> Niels Bergsland >> Integration Director >> Buffalo Neuroimaging Analysis Center >> 100 High St. Buffalo NY 14203 >> [log in to unmask] -- Niels Bergsland Integration Director Buffalo Neuroimaging Analysis Center 100 High St. Buffalo NY 14203 [log in to unmask]