sdm-help-list > Mask has a wrong size
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Jul 24, 2020  06:07 AM | florian7
Mask has a wrong size
Dear Joaquim,

I would like to extract effect sizes from some pre-defined ROIs. However, the sdm always warned that my mask files have a wrong size. Which voxel and brain size should I use to create the masks?

I have also tried the "Create mask" function in SDM. The extraction worked well in this case, but the mask only has 1 voxel. Is it possible to create a circular mask with a required radius (e.g., 5mm)?

Thank you very much!
Florian
Aug 3, 2020  02:08 AM | Lydia Fortea - Instituto de Investigaciones Biom├ędicas August Pi i Sunyer (IDIBAPS)
RE: Mask has a wrong size
Dear Florian, 

It is not possible to specify the radio with the "Create mask" function of SDM, you should create the mask with another program and then use it in SDM.

Kind regards,
Lydia
Aug 3, 2020  06:08 AM | florian7
RE: Mask has a wrong size
Dear Lydia,

Thanks for your reply! I have used Pickatlas to create a circular ROI (img format) and converted it to nii.gz format using Mricron, but SDM warned that my mask file has a wrong size. How should I deal with this issue? Thank you very much!

Best regards,
Florian

Originally posted by Lydia Fortea:
Dear Florian, 

It is not possible to specify the radio with the "Create mask" function of SDM, you should create the mask with another program and then use it in SDM.

Kind regards,
Lydia
Aug 3, 2020  08:08 AM | Joaquim Radua
RE: Mask has a wrong size
Dear Florian

You may have to register the mask to the SDM template.
You can do it with the "-sdmreg" option of the "imgcalc" command.

With the best wishes,

Joaquim
Aug 4, 2020  01:08 AM | florian7
RE: Mask has a wrong size
Dear Joaquim,

thank you for your reply!

According to your suggestion, I moved the mask file ("mask_roi1.nii.gz") to the "masks" folder, and tried both: "imgcalc roi1 -sdmreg roi1r" and "imgcalc roi1 -sdmreg" in command line. Unfortunately, no new mask file was generated, and the size of the mask is still incorrect. I would appreciate it if you could tell me how to perform the mask register properly in this case.

Best,
Florian
Aug 5, 2020  09:08 AM | Joaquim Radua
RE: Mask has a wrong size
Deaf Florian,

If you want, send me the mask by email and I will have a look  ;-)

With the best wishes,

Joaquim