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You need to define mapparameters first.

Then use:
peak_nii(imagename,mapparameters)



Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Wed, Dec 4, 2013 at 10:56 AM, M.Momenian <[log in to unmask]> wrote:

> Dear Donald
>
> Thanks for your kind reply. Your comments really helped me. I've got
> another problem related to peak_nii toolbox. I downloaded it and put it in
> the toolbox directory of my spm folder. I added the path in MATLAB as well.
> Peak_nii toolbox appears in the SPM 8 toolbox menu, but when I click it,
> the following message just pops out: Error using peak_nii (line 75)
> Not enough input arguments.
>
> Error in spm (line 965)
>     evalin('base',xTB(i).prog);
>
> Error while evaluating uicontrol Callback
>
> Where do you think I might have gone wrong? Thanks again for everything
>
> Best wishes
> Mohammad
>
>
>   On Wednesday, December 4, 2013 1:40 AM, "MCLAREN, Donald" <
> [log in to unmask]> wrote:
>
> On Tue, Dec 3, 2013 at 2:55 PM, M.Momenian <[log in to unmask]> wrote:
>
> Dear Donald
>
> Thanks for the kind answer. I loaded the T-maps as the input file in
> imcalc. The result is an .img file with three colours in it when I display
> it: white, gray, and black. Which of these colours is the overlap area?
>
>
> >> I'd assume white. The overlap will have a value of 3, voxels with a
> value of 1 are unique to the first contrast, while voxels values of 2 are
> are unique to the second contrast.
>
>
> I'd like to report where the clusters overlap across the two groups. How
> should I load this image and report the overlap coordinates?
>
>
> >> You can either use FIVE (functional image visualization environment) or
> the peak_nii toolbox to get the coordinates of the areas of overlap.
>
>
>
>  I highly appreciate your comments
>
> best wishes
> Mohammad
>
>
>   On Tuesday, December 3, 2013 7:47 PM, "MCLAREN, Donald" <
> [log in to unmask]> wrote:
>  An alternative approach:
>
> Save the thresholded maps. Then use the following equation in imcalc:
> (i1>0)+2*(i2>0)
>
> This will show you where significant clusters are located for the 2 groups
> and where the clusters overlap.
>
> On Mon, Dec 2, 2013 at 2:31 PM, Colin Hawco <[log in to unmask]> wrote:
>
> Hah, SPM does so  many strange things!
>
> I don't have a script for this, but I can give you the code to use. You
> need to generate t-maps separately for each contrast. Then, lets call the
> first contrast FileA, and the second FileB.
>
> %masks file B with A, and output t-value from fileB, butonly for voxels
> overlapping with significant voxels in FileA. Note that an extent threshold
> is not applied.
> fileA = 'spmT_0001.img' %for example
> fileB = 'spmT_0002.img' %for example again
>
> v=spm_vol(fileA)
> data = spm_read_vols(v);
>
> v2= spm_vol(fileB)
> data2 = spm_read_vols(v2);
>  t_thresh = 3.5 %% significant t-stat threshold, change as needed
> data2(data<=t_thresh) = 0;
>
>  v2.fname = 'spmt_conjunction.img' %renames the output file
>  spm_write_vol(v2, data2)
> %% done
>
>
> Now, here is a trick I think should work. If you load the SPM.mat file and
> rename the name of the T-map, it will then load this image into SPM results
> and you can get the activation tables, etc.
>
> SPM.xCon(1).Vspm.fname =  'spmt_conjunction.img'
>
> i am not 100% sure if that will work. Alternately  if instead of changing
> v2.fname you leave it the same, SPM should load the conjunction map if you
> select the contrast from fileB.
>
> Let me know if you need a bit more help.
> Colin
>
>
> On 2 December 2013 13:55, M.Momenian <[log in to unmask]> wrote:
>
> Dear Colin
>
> Thanks a lot for your kind reply. I ran the inclusive masking two times in
> the following order: once I inclusively masked A with B, and once B with A.
> The results were again different. They should be. You said inclusive
> masking is fit for "detecting things which are significant in both groups".
> I guess inclusive masking is putting all significant voxels from two
> contrasts together, rather than coming up with the ovarlap between the two
> contrasts. I am interested in the overlap in the two groups. I wonder if I
> can have your script written to detect the overlap as well. It would be so
> kind of you.
>
> Best wishes
> Mohammad
>
>
>   On Monday, December 2, 2013 9:58 PM, Colin Hawco <[log in to unmask]>
> wrote:
>  Hello Mohammed,
>
> I have never run a conjunction analysis in SPM, so I cannot directly
> address your issue. However, for what it is worth, I would prefer to use an
> inclusive masking approach, in which the results of one t-map are used to
> mask another, provided a masked conjunction of the results. I have used
> a similar approach in some of my work, but I wrote a script to find overlap
> rather than using SPM. This is a very valid form of conjunction analysis
> for detecting things which are significant in both groups.
>
> I also believe it is a very statistically robust approach to use inclusive
> masking, assuming the two analysis you are using are properly
> corrected for multiple comparisons.
>
> The reason your results are different between conjunction and masking is
> due to the nature of the "conjunction" analysis, which is a statistical
> approach. It attempts to find voxels where Beta A and Beta B are both not
> zero. However, it can potentially detect a conjunction in which the voxels
> from Beta B, while non-zero, do not survive statistical significance in an
> analysis of only Beta B. This may happen when Beta B is small and Beta A is
> very large. At least according to my admittedly limited understanding.
>
> So, my 2 cents, you can't go wrong using inclusive masking, a "masked
> conjunction". You know for sure that all voxels are significant in
> both contrasts.
>
>  Colin.
>
>
> On 2 December 2013 11:49, M.Momenian <[log in to unmask]> wrote:
>
> Dear SPMers
>
> I just sent an email yesterday, but there was no answer. I know my
> question was simple. but I couldn't find a clear answer to the question. I
> read in SPM8 manual that if I want to see the effects which are common across
> the two groups in my study, I can either use inclusive masking or
> conjunction analysis. I did both of them, but the results are different. I
> also searched the list, but it did not soothe my confusion. I decided to
> write again and ask how I should solve this problem of mine. I want to see
> the brain activations which are common across my two groups in Task A.
> Then, I want to see these common areas in Task B across the two groups.
> Which method is more reliable? I highly appreciate your comments dear all.
>
> Reading you soon
> Mohammad
>
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