 |
 |
Dear Christopher, the i,j,k space sizes of my images go through 18 in one of the 3 dim and 768 in the other 2. But this flips to from k to j-space when I open the different file. So when I open in MricroN the axial, I´ve got a 3D image with 18 slices (slice thickness 5 mm) in the z-coordinate and with nearly 768x768 voxels on the y and x-coordinates (7687x768x18), and so on when I open a sagittal 3D slice, it is 18x768x768. When opened in FSLView, they are 255x255x21 and 21x255x255 respectively. Actually I´m not sure of the scan parameters of my images apart from the thickness. would it be any possibility of merging these two images and getting a decent 3D nifty? Regards Blas -----Ursprüngliche Nachricht----- Von: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] Im Auftrag von Watson, Christopher Gesendet: Donnerstag, 26. Januar 2012 15:52 An: [log in to unmask] Betreff: Re: [SPM] WG: [SPM] T1 data suitability for VBM What were your scan parameters? Maybe the resolution is poor in all but one orientation, and that's why it looks bad in the other orientations. ________________________________________ From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Marko Wilke [[log in to unmask]] Sent: Thursday, January 26, 2012 7:36 AM To: [log in to unmask] Subject: Re: [SPM] WG: [SPM] T1 data suitability for VBM Hi Couto, for starters, I would suggest you try another DICOM converter (maybe the one coming with spm...) to see if you still have these issues. Also, one of the reasons you only have "nice" data in one dimension may be that you do not have a 3D acquisition and that the other images represent reformatted versions of that, but I can't tell from a distance. In any case, as a rule of thumb I would say that, if the data does not look good to the naked eye, it is not likely to be suitable for a VBM analysis :) Cheers, Marko Couto, Blas wrote: > -----Ursprüngliche Nachricht----- > Von: Couto, Blas > Gesendet: Donnerstag, 26. Januar 2012 12:17 > An: [log in to unmask] > Betreff: WG: [SPM] T1 data suitability for VBM > > Dear Christopher, > > thanks for your response. I do want the not- o* and not- co* images, though while doing the conversion, besides this two types of files, I have as output 3 other .nii which contains slices. However, this slices happens to be of good quality in just one of the orientations (e.g sagittal) but not in the other 2, and so on with the three files.nii. Would you have any idea why this is working so? And why I do not have a single 3D volume with the 3 orientations of suitable (or at least similar) quality of voxel? > > Thankyou in advance, again. > Kind regards, > Blas Couto > > -----Ursprüngliche Nachricht----- > Von: Chris Watson [mailto:[log in to unmask]] > Gesendet: Mittwoch, 25. Januar 2012 20:05 > An: Couto, Blas > Cc: [log in to unmask] > Betreff: Re: [SPM] T1 data suitability for VBM > > I believe you want the image that is not the o* or co* image. On my system, the output filename is the study protocol that is entered on the scanner, so it would output e.g. > STUDY.nii > oSTUDY.nii > coSTUDY.nii > > Couto, Blas wrote: >> >> Dear collegues, >> >> >> >> I have a sample data of structural MRIs, and I would like to try a >> VBM analysis. However, while converting DICOM files to nifti (using >> Chris Rorden´s software dcm2nii ), my output files are 2 or more .nii >> containing either sagital, coronal or axial T1 oriented slices. I >> would like to know if they are all/either suitable for SPM VBM analysis? >> >> >> >> Thank you all in advance. >> >> Best regards, >> >> >> >> Blas Couto >> >> >> >> >> >> _________________________________________________________ >> >> *Juan Blas Marcos Couto, M.D.* >> >> *Researcher* >> >> *Laboratory of Experimental Psychology& Neuroscience* >> >> *Institute of Cognitive Neurology (INECO)& CONICET* >> >> *Pacheco de Melo 1854/60 (C1126AAB) >> Buenos Aires, Argentina >> Phone/Fax: +54 (11) 4812-0010* >> >> >> > -- ____________________________________________________ PD Dr. med. Marko Wilke Facharzt für Kinder- und Jugendmedizin Leiter, Experimentelle Pädiatrische Neurobildgebung Universitäts-Kinderklinik Abt. III (Neuropädiatrie) Marko Wilke, MD, PhD Pediatrician Head, Experimental Pediatric Neuroimaging University Children's Hospital Dept. III (Pediatric Neurology) Hoppe-Seyler-Str. 1 D - 72076 Tübingen, Germany Tel. +49 7071 29-83416 Fax +49 7071 29-5473 [log in to unmask] http://www.medizin.uni-tuebingen.de/kinder/epn ____________________________________________________