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LAI does indeed mean left, anterior, inferior. This encodes the location of the first voxel in the file, as well as the ordering of the directions. This order will depend on the file format converter you used, and it may be perfectly correct. How are you displaying the images? If you use the Display button of SPM, the PET.nii template should face upwards and to the left the same as the various MRI templates. After the appropriate reorientation, your own image should be facing similarly. The thing to be careful of though is whether left and right are correct. This is not something that I'd be able to tell you with any confidence. Best regards, -John On 17 February 2012 18:15, David Andel <[log in to unmask]> wrote: > Thanks a lot Bas, Donals, and John for your helpful answers! > > Now I am reorienting my old images to fit the PET.nii template from SPM8. > My original Analyze 7.5 images are "RPI Left-handed" and so is the PET.nii > template. > However, my images look up (transverse) and to the right (sagittal), whereas > the PET.nii template looks down and to the left. > After reorienting my images using a yaw of pi (or -pi; or a pitch and roll > of pi (or -pi) each) I receive the same orientation, but now my images are > said by spm_orientations to be "LAI Left-handed". > I assume RPI means right, posterior, inferior, and LAI means left, anterior, > inferior. > I guess this is a problem, isn't it? > Is there a way to reorient my images correctly in SPM or do I have to use > third-party software (I have used Pmod in the past). > Just tested with Pmod where I reorder the slices "top to bottom" and this > way the images fit and still are "RPI Left-handed". > I mean, yes, I have a solution, but is there a way to do the same in SPM as > well? > > Thanks, > David > > > On 17.02.2012 17:23, Neggers, S.F.W. wrote: >> >> Hi Donald, David, >> >> Donald: I remember how you learned about *.mat files in spm8, that >> was after a question from me about 4D data ;-) >> >> *.mat files are only used for 4D data in spm8 as far as im aware of. >> For realigning (not reslicing) oir coregistering or manually >> displacing 3D time series data I never get *.mat files as used to be >> the case in spm2 and earlier. It is not needed for 3D data as this >> info is in the header per image. >> >> David: I guess you can reuse your old data right away. When doing it >> anew, take care that your images roughly match the MNI template before >> starting. There is no such thing anymore as an 'origin' in nifti files >> that is actually used. Things work different for nii data. >> >> That does NOT mean, in general, that you do not have to manually >> align your images anymore in spm5/8. It is STILL needed (just not with >> origin setting anymore). As Donald said, your images need to >> approximately match MNI before doing any further preprocessing. >> >> When you are lucky your old Analyze 7.5 format data is already close >> to MNI as you aligned them already by using mat files (in spm99), but >> i cant tell without inspecting them. My other remark about raw format >> means that, for most institutes/scanners ive seen, conversion from >> Dicom or other raw scanner format to nifti yields files that are often >> close enough to MNI to start right away. But dont COUNT on it. >> >> Finally: take proper care about flipping L/R too when using analyze >> images in SPM8. In Analyze images, this information about image >> handedness is not stored in the image header, you need to tell SPM. >> For nifti, this is less of an issue as handedness is encoded in the >> header. >> >> Actually, SPM8 can, in my experience, handle quite a difference >> between starting positions of images automatically during >> coregistration/normalization. Indeed, when orientation is off by 10-20 >> degrees, and location by several cm, your usually fine and SPM will >> succeed in matching scans to eachother or the template. With bigger >> differences this might fail. But ALWAYS check your results to make >> sure, there are no guarantees. >> >> Good luck, >> >> Bas >> >> >> >> ________________________________ >> From: MCLAREN, Donald [[log in to unmask]] >> Sent: Friday, February 17, 2012 4:15 PM >> To: Neggers, S.F.W. >> Cc: [log in to unmask] >> Subject: Re: [SPM] setting origin to ac >> >> Bas/David, >> >> For fMRI data, SPM8 still relies on the *.mat files. The reason for >> this is that the nifti file can only have 1 transformation matrix in >> it (I learned this about a month ago). If you remove the *.mat files >> from a directory and display the images, you will notice that they >> shift. The classic example is motion correction. After you motion >> correct the data, you have a mat file. If you remove the mat file, you >> undo the motion correction. >> >> As for reading analyze 7.5 files. This shouldn't be a problem. I've >> read these files into SPM8 without any problems. >> >> If you try to use old SPM.mat files, you will have some issues as the >> contents of the header that is read by SPM5/8 has changed. >> >> Best Regards, Donald McLaren >> ================= >> D.G. McLaren, Ph.D. >> Postdoctoral Research Fellow, GRECC, Bedford VA >> Research Fellow, Department of Neurology, Massachusetts General Hospital >> and >> Harvard Medical School >> Office: (773) 406-2464 >> ===================== >> This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED >> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is >> intended only for the use of the individual or entity named above. If the >> reader of the e-mail is not the intended recipient or the employee or >> agent >> responsible for delivering it to the intended recipient, you are hereby >> notified that you are in possession of confidential and privileged >> information. Any unauthorized use, disclosure, copying or the taking of >> any >> action in reliance on the contents of this information is strictly >> prohibited and may be unlawful. If you have received this e-mail >> unintentionally, please immediately notify the sender via telephone at >> (773) >> 406-2464 or email. >> >> >> >> On Fri, Feb 17, 2012 at 10:05 AM, S.F.W. Neggers >> <[log in to unmask]<mailto:[log in to unmask]>> wrote: >> Hi David, >> >> Let's assume you used data in Analyze 7.5 format in spm99. Is that >> correct? >> >> SPM8 uses the Nifti format, no *mat files are required anymore as the >> voxel-to-world mapping (that was stored in the mat-file for spm99 and >> spm2) is now saved in the nifti file header directly. The origin is >> also implicitely 'stored' in the voxel to world matrix. There is no >> explicit origin anymore for Nifti data. >> >> Your task is now much more general: make sure all your images are >> roughly in correspondance with the template you want to eventually >> register all your data to (usually an MNI template). >> >> I never tried it, but perhaps spm8 can read Analyze images, and write >> results out in correct nii? Then you'd be done. >> >> When that doesnt work: the information about the correct >> displacements is already in your Aanalyze + mat files, so you might be >> able to write a conversion script that converts your Analyze files to >> nifti taking into account the *mat files (and saving the appropriate >> voxel-2-world matrix in the nii headers). That would save you the >> hassle. Perhaps such a script is already out there? >> >> On another note: most raw formats (Dicom, PAR/REC) can be converted >> to nifti nowadays, creating images already that are in quite good >> correspondance with MNI, and there is no need anymore for manual >> realignment. At least that is how it is for us. This will strongly >> depend on your pipeline from the scanner to your computer. And of >> course you would need the old raw scanner data. >> >> Good luck, >> >> Bas >> >> >> >> >> >> >> Op 17-02-12 15:28, David Andel schreef: >> >> Dear SMPers >> >> I have analysed a number of scans years ago in SPM99. >> For this purpose I have set the origin to the anterior commissure >> manually for each scan. >> >> Now I want to reanalyse the whole study in SMP8 again. >> Is there a way to apply the origins set in SPM99 for each scan now in >> SPM8 so that I don't have to manually redo all this? >> That would save me quite some time. >> I guess this must be stored in some of the *.mat files, doesn't it? >> >> Thank you and best regards, >> David >> >> >> >> -- >> -------------------------------------------------- >> Dr. S.F.W. Neggers >> Division of Brain Research >> Rudolf Magnus Institute for Neuroscience >> Utrecht University Medical Center >> >> Visiting : Heidelberglaan 100, 3584 CX Utrecht >> Room B.01.1.03 >> Mail : Huispost B01.206, P.O. 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