Hi,

I have a question regarding visualizing the results of a VBM meta-analysis (after running the \"Threshold\" command). MRICron is not launching (I have it downloaded and the correct path set), therefore I\'d like to manually load the ICBM template and results overlaid, but I was wondering which files I should load to overlay atop the template (for instance, to create images like the ones in Figure 3 and 4 in "Neuroanatomical Maps of Psychosis Onset: Voxel-wise Meta-Analysis of Antipsychotic-Naive VBM Studies"). I\'m assuming the correct files to overlay are the \"mask_MyMean_z_p_0.00500_1.000_10_peak1.nii.gz\" (for peak1, peak2, etc.), but SDM produces a number of output files and I wanted to confirm. I was also wondering what the differences between these output files were and whether any others would be useful for visualization:
mask_MyMean_z_p_0.00500_1.000_10_peak1.nii.gz
mask_MyMean_z_p_0.00500_1.000_10_blob1.nii.gz
MyMean_z_p_0.00500_1.000_10.nii.gz
MyMean_z_p_0.00500_1.000_10_p.nii.gz
MyMean_z_p.nii.gz
MyMean_z_QH_p.nii.gz

Thanks in advance for your help!
Kind regards,
Colleen

Dear Colleen,

Regarding which maps to visualize in MRICron, what SDM does is load the SDM template (located in the 'share' folder of the SDM package) and then add two overlays: the one for the activations map (MyMean_z_p_0.00500_1.000_10_p.nii.gz in your case) and the other for the deactivations map (in your case it should be named MyMean_z_p_0.00500_1.000_10_p_neg.nii.gz)

Regarding of the bug of MRICron not being launched, could you please let us know which OS you're using and which version of SDM?

Kind regards,

Anton

Originally posted by Colleen Rollins:

Dear Anton,

Many thanks for your quick reply. I'm using MacOS High Sierra v10.13.2 and SDM v5.141.
Are the overlays concatenations of the peak files? (Ie. would MyMean_z_p_0.00500_1.000_10_p.nii.gz be equivalent to each of the mask_MyMean_z_p_0.00500_1.000_10_peak1.nii.gz files being loaded?) I'm just trying to clarify what the other nifty files show. Also, I just wanted to confirm that MyMean_z_p_0.00500_1.000_10_p.nii.gz (and neg) are already thresholded, or is any more correction/thresholding required?

Thanks again,
Colleen

Dear Collen,

Another user reported a problem with the MRICron launch while using Sierra. We are working on it, preparing an updated version fixing the issue.

The masks for peaks are just masks with the voxel of the peak valued at 1 and the rest valued at 0. The masks for the blobs are masks with 1 for the cluster, 0 elsewhere. Therefore, concatenating peak masks or blob masks would only give you the map of peak locations for the former or the shape of all the clusters for the later. But all 1 and 0 images.
Yes, the file MyMean_z_p_0.00500_1.000_10_p.nii.gz is already thresholded,being 0.005 the threshold valued used, 1.000 the peak height threshold and 10 the extent threshold.

Best regards,

Anton

Originally posted by Colleen Rollins:

Dear Collen,

We just uploaded to the web an updated version of SdmGui for OSX. This should fix the issue at the time of launching viewers (MRICron and FSLView). However, please take into account that MRICron for OSX doesn't let us directly load overlays, so you'll have to add them manually in order to obtain the same image you would obtain in Linux or Windows. FSLView works the same in any host OS.

Could you please let us know if you had the chance to try it, and to confirm it solves the problem?

Thanks,

Anton
Originally posted by Anton Albajes-Eizagirre:

Dear Anton,

Yes, problem solved! MRICron now opens the SDM template brain automatically when I threshold my results.
Thanks very much for the update.

Colleen

Hello, 
I have exactly the same problem with MacOS Catalina (10.15.2) with SDM 6.21. 

Layla