Dear SPM Experts,
I am interested in using the New Segment tool in combination with DARTEL for my EPI data. I would like to clarify some things before I begin and make sure I have a decent understanding of what each of these modules is actually doing and with what data I should be supplying. I am fairly new to SPM, so I apologize if this has been covered in detail somewhere that I have missed, or that some of the questions might be trivial.
New Segment
This step is to be done in place of the original segment module available for preprocessing, following realignment/slice-timing/coregistration. Instead of 3 tissue probability maps, 6 are used.
Data:Channel:Volumes= structural image/t1 resulting from the co-registration to the mean epi image in the previous step.
Native Tissue= My first question: It is not clear what tissue class(es) I need. Should I select Native + DARTEL Imported for each? It seems the Native produces the c1* images and the DARTEL Imported produces rc1* images, but I am still not clear on when I would need each of these types.
This module then produces rigidly aligned tissue class images, i.e. rc1*.nii through rc6*.nii, (and potentially c1*-c6*) with each containing information in the headers about the transformation parameters required to get from the original T1 image to the new aligned tissue image.
Run DARTEL (create Template)
This next module then takes each of the 6 rc* tissue class images, but NOT the c1* images, and estimates the deformations required to align them all together.
Images= is it the case that I need to enter rc1*.nii, rc2*.nii, etc., separately under a new "Images"? I am currently attempting this with a single subject, but when I am running multiple it is my understanding that I would enter all subject's rc1*.nii file under the first "Images", and all subject's rc2*.nii file under the second. etc.? Is it necessary to include all 6 tissue types here for use with epi data, or are grey and white matter sufficient?
The outputs of this step are 6 templates, with the 6th being the most accurate, and u_rc1-6*.nii files, but it is not clear to me what these last files are. Do these flow fields contain information about the deformations made to create each of the templates, or something else? The manual mentions that each of the u_rc1* outputs contains multiple volumes per file, and it is not clear to me what is contained within.
DARTEL Normalise to MNI
This step creates modulated warped tissue class images based on the final/6th Dartel Template created in the last step. This is the step I am most unclear about.
Select according to= what is the difference between "Few Subjects" and "Many Subjects"? The manual specifies "Many Subjects" being ideal for VBM, so is "Few Subjects" ideal for EPI data?
Flow Fields= each of the 6 u_rc*.nii for a subject, correct? How would this change if I had multiple subjects I was running at once- would I just list 1-6 for each individual, with all subjects together?
Images= not sure what I need here to select here. It seems to me I would want to select my epi data, i.e. the realigned/slice time corrected images, but the manual just mentions the c1*.nii files. I am a bit confused about what exactly is being normalized to MNI space here.
Finally, the manual says the output of this step will be a bunch of smwc1*.nii files, but I am not clear what these are supposed to be, and how they will fit in with the rest of the processing/analysis stream. If I am to include my epi images, will the output be my epi data normalised to MNI based on the segmentation parameters determined from New Segment/Dartel template? Also, am I to understand that there is smoothing done in this final step of normalisation, or should I add a module following this step to smooth the output images?
Any help on these matters would be greatly appreciated! I apologize for the excessively long e-mail.
Best,
Heather
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