DICOM is a medical format the MRI produces. They can come in different specifics, but it is common to get one dicom per slice in anatomical scans, or per TR in fMRI data. Nifti is a format designed for 3D or 4D files. 

For realignment I presume you mean normalizing to the MNI template? The problem (presumably) is that the origin of the images (the point labeled 0,0,0) is not near the AC. one thing to try is to use the coregister function. This has worked for me in the past to get an approximate first pass. 

Alternately you can use the display function, and reset the origin to the AC. You can apply this transform to many files. So you can do it on one person and apply it to the rest, and it MIGHT work OK. For a small data set I would advise to do each individually, but this may not be feasible if you have one of the larger AFNI data sets. If you do this, check the results carefully. 

Best of luck, 

Colin Hawco, PhD
Neuranalysis Consulting
Neuroimaging analysis and consultation
www.neuranalysis.com
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-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Bermal Harman
Sent: August-25-17 12:20 PM
To: [log in to unmask]
Subject: [SPM] SPM12

Dear Sir/Madam
I am doing my research on AD detection through applying image processing algorithms on sMRI data. I use SPM12 for preprocessing steps, yet i am not able to realign the nifti data that i dowloaded from the ADNI website. SPM12 allows up to 4cm translation and 15degrees rotation. Since the translations for x-y-z directions are more than 100cm, the algorithm dont work for realignment. I would like to ask how can i download the data which are not translated more tha 3cm for all x-y-z directions?
Is there a way that can limit this range? I use the parameters given below:
• fMri or Mri
• MRI scans were acquired using a 3T
• T1-weighted scanner(Simens)
• Acquisition Plane = Sagittal
•Matrix Z= 177 pixels
• Mfg model= skyra
• Slice Thichness = 1.2mm
• TE/ TR= 2.98ms/ 2300ms
 
 
Additionally, I tried to dowload data in DICOM format(for one scan there are 100 scans in DICOM format) and convert them into NIFTI format (one-by-one for each DICOM data). However, when i dowload the same data in nii(MIFTI) format, in this case i dowload only 4 nii data, whereas it is 110 in DICOM ones. What is the reason behind this?
I would appreciate your help a lot.