sdm-help-list > [solved issue] useful tip for working with t-maps as meta-analysis input in sdm 6.21
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Aug 6, 2020  09:08 AM | Matthias Schurz - Dept. of Experimental Psychology, University of Oxford
[solved issue] useful tip for working with t-maps as meta-analysis input in sdm 6.21
Dear sdm users,

Just to post a tip I got from Anton and Joaquim, when we were discussing how to fix my analysis in sdm 6.21:

If you want to use t-maps as input in sdm 6.21, and your analysis does not work for some reason...
You can check if what happens if you convert your t-maps to coordinate text files, and then run a meta-analysis that only consists of text files. For conversion, you can use the sdm imgcalc function. In a ubuntu shell, the command would be something like (assuming that you are in the directory .../SdmPsiGui-linux64-v6.21/ and you can see the file Imgcalc.sh with an "ls" command)
./imgcalc.sh 1stAnalysis_sdm/YourImageName.nii.gz -blobs blob_output
This creates a .htm file called blob_output, which you can easily convert to a plain text file.
(If you want to use a different tool,I think you can also use fsl's cluster command).

Good luck for your analyses!
Matthias
Aug 6, 2020  06:08 PM | Matthias Schurz - Dept. of Experimental Psychology, University of Oxford
RE: [solved issue] useful tip for working with t-maps as meta-analysis input in sdm 6.21
Here is an addition to my previous post:

In case of doubt, you can also use the -altas argument of imgcalc, which sometimes works better than -blobs. 
In that case, try the -sdmreg argument to get your image in the right form.
So the commands would be something like:

(1)
./imgcalc.sh YourImageName.nii.gz -sdmreg YourImageNameRegistered

(2)
./imgcalc.sh YourImageNameRegistered.nii.gz -atlas atlas_output

Best,
Matthias

PS: In my previous post, the command:
./imgcalc.sh 1stAnalysis_sdm/YourImageName.nii.gz -blobs blob_output 
can be simplified to:
./imgcalc.sh YourImageName.nii.gz -blobs blob_output
(I just used a file from a subfolder in my original call)