Hi,
Glad to hear, that this script is making you happy. So, apparently you
figured out how to use it. Just a tip, I think best images are achieved
when using the options '-thick -s 2' together with all other necessary
ones. Let me know, if you come across problem (it is a script growing
with my demands, so it is not perfectly working in general I guess...)
Have fun,
wolf
On 12/21/2012 02:30 PM, bettyann wrote:
> Best. Christmas. Present. Ever.
> Thank you!
>
>
>> Hi BettyAnn,
>>
>> I wrote me a little tool to create some overlay png files in a simple
>> way, wrapping around the frustrating slicer part. So maybe this could
>> help you (hope it does not cause further problems and frustration though).
>>
>> See the help information to see, how it works. In your case, the -neg
>> option might be the desire one. Let me know, if you have further
>> questions or come accross bugs...
>>
>> good luck,
>> wolf
>>
>>
>> On 12/20/2012 10:09 AM, Mark Jenkinson wrote:
>>> Dear BettyAnn,
>>>
>>> Sorry to hear about your long-term frustration.
>>> The easiest way to achieve your goal is to use the Renderstats GUI which will output the desired overlay command. For instance, I just ran one to do the sort of thing you are saying and it produced the command:
>>>
>>> /usr/local/fsl/bin/overlay 1 0 /Users/mark/testdir/example_func 0.000000 8836.757812 /Users/mark/testdir/zstat1 2.5 15.546515 /Users/mark/testdir/zstat1 -2.5 -10 /Users/mark/testdir/outputimage
>>>
>>> This command was displayed in the terminal window, so you can then use this for subsequent scripting calls or just avoid the GUI thereafter.
>>>
>>> I suspect that your command were probably failing just due to the order of the negative thresholds (which are confusing).
>>>
>>> Once you have this image file output from overlay, slicer works straightforwardly (no need to specify any colourmap options at all).
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>>
>>>
>>> On 19 Dec 2012, at 20:56, bettyann <[log in to unmask]> wrote:
>>>
>>>> Okay, no really. After years of trying (and I'm not kidding), I still cannot create an overlay/slicer .png displaying both positive voxels in red-yellow scale and negative voxels in blue-white scale.
>>>>
>>>> Searching the archives, I see replies that imply, 'Oh, this is simple,' or 'Just do [blah].' Sigh.
>>>>
>>>> I've tried a few things but below is the least frantic rendition:
>>>>
>>>> rng1=`fslstats zstat1 -l 0.0001 -R`
>>>> rng2=`fslstats zstat1 -u -0.0001 -R`
>>>> echo $rng1 # 0.000111 10.265674
>>>> echo $rng2 # -5.066993 -0.000104
>>>>
>>>> oVol=zstat1_render_posNeg
>>>> cmd="overlay 1 0 ../example_func -a zstat1 $rng1 zstat1 $rng2 $oVol"
>>>> echo $cmd
>>>> # overlay 1 0 ../example_func -a zstat1 0.000111 10.265674 zstat1 -5.066993 -0.000104 zstat1_render_posNeg
>>>> eval $cmd
>>>>
>>>> fslstats zstat1_render_posNeg -R
>>>> 11.559369 45.564034
>>>>
>>>> I get it that the 'composite' volume does not have negative values. I am assuming that some range of voxel values in the composite volume represents the positive values in the original volume and another range represents the negative values. But how
>>>> do I tell slicer to use Red-Yellow for some range (that I don't know) and Blue-White for some other range (that I also do not know)?
>>>>
>>>> These commands do not do it:
>>>> slicer zstat1_render_posNeg -S 2 750 zstat1_render_posNeg.png
>>>> slicer zstat1_render_posNeg -l [anyLUT] -S 2 750 zstat1_render_posNeg.png
>>>>
>>>> Do I need to construct my own color table -- half red; half blue -- to match the two ranges in the output from overlay?
>>>>
>>>> If it matters, I am running FSL v4.1.8.
>>>>
>>>> I would be very, very grateful if someone could help me.
>>>>
>>>> Hang doggedly,
>>>> - BettyAnn
>>>>
|