help > modality
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Nov 1, 2017  01:11 PM | Andrew Taylor - MUSC
Hello! I am trying to use the NiiStat function directly (I put it in a script): 

   NiiStat('..\DEMO.xlsx', 5, 7,5000, 0.10, 3, 0, file.nii, 0, 0, 0, 0)

It seems the third argument, "7", should denote that my modality is DTI. However, when I try to run NiiStat, it prints out a number of things, and among them is

   Analyzing roi=0, modality=1, permute=5000, design=DEMO

So my modality seems to be set to "lesion". My output folders also begin with "lesion_". Why is my modality input not being used? And does this matter? I'm wondering if I can still use stats from outputs which were called in this way. I'm worried, however, that maybe information is lost in conversion from .nii to .mat if NiiStat assumes that my file should have values from 0..1, for instance.
Jun 21, 2018  11:06 AM | Chris Rorden
RE: modality
OK, I have no insight into your data, but I am going to guess you did two things:
 1. You analyzed NIfTI images that do not report their modality (rather than mat files created by nii_preprocess or nii_nii2mat that store the modality)
 2. You did not explicity name your stat file.

In this case, prior versions would use the label 'lesion_' for output data. I just changed this so it now defaults to 'nii_' - the results will be the same, but the file name no longer makes any guess regarding modality.