Dear all, experts on Conn

I'm particularly interested in the post of scharpy from yesterday.

Indeed, I'm currently investigating resting state brain abnormalities in subjects with neurological disorders. For this, I'm using CONN which is a helpful toolbox using normalisation in MNI152.

In my lab, we also investigate brain abnormalities in baby, infants and I would also like to use CONN to normalise with indirect normalisation in other templates than the default template implemented in CONN.

I looked for how to use CONN and change the template for a baby template but couldn't find it.What is the procedure to use CONN (normalise step) with template of infant such as UNC template ? https://www.nitrc.org/projects/pediatric...

Thank you in advance for your help for solve this important issue,

Best

Jennifer

Hey Jennifer,

I was stuck at this exact point before 1 year or so. What I did is that I divided the preprocessing steps into 2 separate ways. In first step, I did the realignment and slice time correction in CONN. Then, I used SPM Coregister: Estimate and Reslice and then Old Normalize: Estimate and Write to normalize the scans to an infant template. You can find SPM Coregister: Estimate and Reslice and Old Normalize: Estimate and Write in SPM Batch. Then, after normalization with infant template, I performed the remaining preprocessing steps in CONN after importing the results of Old Normalize: Estimate and Write.

However it is just a one way. One more potential work around will be using infant TPMs instead of regular TPMs. In this case, you dont have to worry about the extra SPM Old Normalise step.

Hope it helps.

Best,
Sachin Patalasingh

Hey Sachin,

Thank you so much for your reply that would be really helpful to solve my issue.
I appreciate that you have described the procedure step by step.

I need more precision about your procedure to compute it in CONN and SPM in my images.

Did you coregister anatomical (T1 images) and functional images and then normalise functional images directly to infant template ? I'm starting to use for my preprocessing using the direct / indirect normalisation without the step of segmentation ?

Thank you for your help !

Best,

Jennifer

Dear Jennifer,

I would probably recommend creating first an infant TPM.nii file from your gray/white/CSF masks. To do that you will likely need to combine those three individual mask file into a single file and scale them accordingly (SPM TPM files should contain values between 0 and 1 describing the probability at each voxel of each tissue class, so they need to add up to one -you may need to add an 'other' tissue class for those areas that are neither of these three gm/wm/csf tissue classes-; see https://www.fil.ion.ucl.ac.uk/spm/doc/sp... for a description of the expected TPM.nii file contents).

After that you may then simply indicate in CONN gui when prompted (e.g. when running 'Preprocessing' from the Setup tab in CONN's gui) that you would like to use an alternative TPM, and then simply select there your newly created TPM.nii file (or alternatively see "help conn_batch" and look for tpm_template/tmp_ngaus fields to specify an alternative TPM when using batch scripts for preprocessing). 

Best
Alfonso
Originally posted by jennifer boisgontier: