help > RE: Lesion Masks
Dec 5, 2018  04:12 PM | Giuliana Giorjiani
RE: Lesion Masks
Dear all,

How could I modify the TPM.nii file? Should I add a new 3D image to the TPM.nii file with the lesion masks of all my subjects?


Originally posted by Alfonso Nieto-Castanon:
Hi Cole,

The procedure in SPM12 to include lesion masks is to modify the file TPM.nii (tissue probability maps) by adding a new tissue class indicating the spatial distribution of the lesions. You may either modify SPM's TPM.nii file directly (located in spm12/tpm/TPM.nii), or define your own TPM.nii file and let CONN know that you would like to use that alternative tpm file instead (e.g. if using batch scripts in CONN you would do this using the fields batch.Setup.preprocessing.tpm_template and batch.Setup.preprocessing.tpm_ngauss)  

Hope this helps
Originally posted by Cole Sugden:
Some of my participants have very large lesions due to arterial stroke and the segmentation process has incorrectly classified the lesion as grey and white matter rather than CSF. To try to adjust for this and to help with normalisation, I would like to use  Cost Function masking to individually fix the issue.  

My question is, at which point in preprocessing can I enter the lesion mask image? It does not seem to be an option in SPM12 and I prefer to use CONN. Is there a way I would be able to manually enter them somewhere?



Threaded View

Cole Sugden May 26, 2016
Marcela Takahashi Mar 21, 2019
Alfonso Nieto-Castanon May 28, 2016
Gianluca Saetta Feb 16, 2019
RE: Lesion Masks
Giuliana Giorjiani Dec 5, 2018
Matthew Heard Jan 21, 2019
Wouter De Baene Apr 25, 2019