sdm-help-list > ROI mask not found
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Jul 28, 2021  01:07 PM | Simon Dover
ROI mask not found
Hi all, 

I'm trying to use an ROI mask for my meta-analysis. In the preprocessing step, I am using the command pp gray_matter,1,20,metaROI,20 
Name of ROI mask (in shared directory): "mask_metaROI.nii.gz" It is in a gzip compressed format. 

I get the following error; execution log pasted below: 

Home dir /Users/Mol/.libsdm/sdm.conf
wParser warning: argument 'Voxel size' missing or incorrect, it will be set to '2'.

WARNING: Copy: source file '/private/var/folders/x1/sthv5r315w96zgl_46_pxcmm0000gn/T/AppTranslocation/C4E2076A-A632-4BB4-8546-6D958D94C20D/d/SdmPsiGui.app/Contents/MacOS/../Resources/bin/osx/../..//share/mask_metaROI_2mm.nii.gz' not found.
The program will close as this problem could cause fatal errors.

I have tried renaming the file to mask_metaROI_2mm.nii.gz , but I get a similar error message: 

Home dir /Users/Mol/.libsdm/sdm.conf
wParser warning: argument 'Voxel size' missing or incorrect, it will be set to '2'.

WARNING: Copy: source file '/private/var/folders/x1/sthv5r315w96zgl_46_pxcmm0000gn/T/AppTranslocation/C4E2076A-A632-4BB4-8546-6D958D94C20D/d/SdmPsiGui.app/Contents/MacOS/../Resources/bin/osx/../..//share/mask_metaROI_2mm_2mm.nii.gz' not found.
The program will close as this problem could cause fatal errors.

Any guidance? 

(One submission on the forum said they solved this issue by renaming the mask "mask_ROI_2mm.nii", i.e. specifying the voxel size in then mask and also that the mask file was zipped, by the .gz extension was not present in the file name. However, I can't try that as renaming the file automatically changes the file type, i.e. changing the file extension to .nii converts it to a NIFTI file, and this also results in the same errors as above.)

Any help would be hugely appreciated. Thank you!
Aug 3, 2021  08:08 AM | Anton Albajes-Eizagirre - FIDMAG - Germanes Hospitalaries
RE: ROI mask not found
Hi Simon,

A wild guess: can you duplicate the mask file, one named mask_metaROI.nii.gz and the other mask_metaROI_2mm.nii.gz?

Also, keep in mind that if you didn't get a indexes file for that mask, you won't be able to run the fwe correction. Custom indexes file are usually generated by us (the sdm team). Did you contact any of the members of the team in order to generate the indexes file?

Hope this helps,

best,

Anton
Aug 4, 2021  05:08 PM | Simon Dover
RE: ROI mask not found
Hi,