help
help > RE: Normalisation using a study template
Mar 31, 2016 08:03 PM | Alfonso Nieto-Castanon - Boston University
RE: Normalisation using a study template
Hi Will,
I am not familiar with the ADNI study template, but assuming this defines a tissue-probability map (e.g. alternative TPM.nii file to be used by SPM's unified segmentation/normalization procedure) then yes, it is possible to do this using CONN's preprocessing stream. While the option to use alternative TPM files is currently only available through batch commands (not through the GUI yet, sorry), the command for your preprocessing pipeline should be simple enough, something along the lines of:
conn_batch(...
'Setup.preprocessing.steps',{'functional_slicetime','functional_realign','functional_coregister','structural_segment&normalize'},...
'Setup.preprocessing.coregtomean', true,...
'Setup.preprocessing.applytofunctional', true,...
'Setup.preprocessing.tpm_template', template_tpmfile,...
'Setup.preprocessing.tpm_ngauss', template_ngauss);
where the last two variables (template_*) define the location of your template TPM file and the number of gaussians per tissue-class to be used by SPM's unified segmentation/normalization procedure.
Hope this helps
Alfonso
EDIT: fixed the command-line syntax in the original post
Originally posted by Will Khan:
I am not familiar with the ADNI study template, but assuming this defines a tissue-probability map (e.g. alternative TPM.nii file to be used by SPM's unified segmentation/normalization procedure) then yes, it is possible to do this using CONN's preprocessing stream. While the option to use alternative TPM files is currently only available through batch commands (not through the GUI yet, sorry), the command for your preprocessing pipeline should be simple enough, something along the lines of:
conn_batch(...
'Setup.preprocessing.steps',{'functional_slicetime','functional_realign','functional_coregister','structural_segment&normalize'},...
'Setup.preprocessing.coregtomean', true,...
'Setup.preprocessing.applytofunctional', true,...
'Setup.preprocessing.tpm_template', template_tpmfile,...
'Setup.preprocessing.tpm_ngauss', template_ngauss);
where the last two variables (template_*) define the location of your template TPM file and the number of gaussians per tissue-class to be used by SPM's unified segmentation/normalization procedure.
Hope this helps
Alfonso
EDIT: fixed the command-line syntax in the original post
Originally posted by Will Khan:
Hi Alfonso,
I am looking to perform an ICA analysis on the freely available ADNI dataset. As I am attempting to replicate work that was published recently, I need to perform a unified segmentation and normalisation using the ADNI study template. Is there a way to achieve this via the preprocessing stream in the CONN toolbox?
I have attached a flow diagram of the proposed preprocessing steps if this helps
Thanks very much,
Will
I am looking to perform an ICA analysis on the freely available ADNI dataset. As I am attempting to replicate work that was published recently, I need to perform a unified segmentation and normalisation using the ADNI study template. Is there a way to achieve this via the preprocessing stream in the CONN toolbox?
I have attached a flow diagram of the proposed preprocessing steps if this helps
Thanks very much,
Will
Threaded View
| Title | Author | Date |
|---|---|---|
| Will Khan | Mar 18, 2016 | |
| Alfonso Nieto-Castanon | Mar 31, 2016 | |