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Subject:

R: [SPM] Normalzing FDG-PET images with SPM12

From:

PRESOTTO LUCA <[log in to unmask]>

Reply-To:

PRESOTTO LUCA <[log in to unmask]>

Date:

Tue, 4 Apr 2017 11:41:45 +0000

Content-Type:

text/plain

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Dear Philip,



It's not clear which images you downloaded from ADNI. I guess you downloaded "nr° 3" from your link. Also, calling the files I001.nii to I700.nii doesn't seem a good idea, as you lose which scans were of which subject, the temporal order, who's a control, who's AD and who's an MCI.



Anyway, using ADNI data maybe it would be better to use MRIs for each subject and normalize the data based on T1 images using high res methods. Nonetheless, if you're using old normalize as it seems, you should create one subject for each scan and for each subject use "image to align: Ixxx.nii" and " image to write: Ixxx.nii", 700 times.

You shouldn't receive NaN intensities even if you were doing it giving 700 images to write anyway. Maybe it's the error that John suggested. Even if it sounds weird, as ADNI claims to have the images already oriented in the correct plane.



Cheers,

Luca



-----Messaggio originale-----

Da: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] Per conto di Philip Lin

Inviato: martedì 4 aprile 2017 11:24

A: [log in to unmask]

Oggetto: [SPM] Normalzing FDG-PET images with SPM12



Dear SPM experts,



I've collected about 700 preprocessed FDG-PET images from ADNI (http://adni.loni.usc.edu/). All downloaded images were well preprocessed and be compressed as I001.nii to I700.nii files. The preprocessed procedure were listed in (http://adni.loni.usc.edu/methods/pet-analysis/pre-processing/).



In each image with dimension 160x160x96 and 1.5mm voxel size, we'd like to map voxels to the standard atlas (e.g., Automated Anatomical Labeling) to understand the name of regions. As we known, we need to do a non-linear warping on each image once and it belongs to the "Normalization" step in SPM12. However, in our manipulation with SPM12, how do we specify "image to aling" and how to set "writing options" ?



If we choose "Image to aling" as the I001.nii and "Image to write" as I001.nii to I700.nii, and leave the rest as default, It leads to a prefixed "w" images with NaN intensities.



Philip Lin





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