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Pieter, If you only need it once, you can apply it to all. When looking in SPM's matlabbatch interface, it does not look like you can implement it there, but you can certainly script it if you hack cg_set_com to accept command line input. Cheers, Marko Pieter Vandemaele wrote: > Hi Marko, > > This is excellent. Can this be executed using matlabbatch? > > Pieter > > Op 29/01/2013 12:00, Marko Wilke schreef: >> Hi Pieter, >> >> so your global orientation looks ok, but your origin seems off. The >> quickest way to correct this (in my humble opinion) is the option >> within vbm8 to reset the origin using the center of mass of the >> largest cluster. Works for me and is (hear, hear :) completely >> automated. Select vbm8, Extended tools, Set origin using center of mass. >> >> Good luck, >> Marko >> >> Pieter Vandemaele wrote: >>> Thanks for the feedback. >>> The screenshots were taken with MRICRON. >>> This is the result with CheckReg in spm. >>> >>> >>> I did not check out all anatomicals, but it would be a huge burden to >>> adjust all subjects manually. >>> I normalised the same data with the Normalisation module and did not >>> have to reorient the images. Normalisation with the Segment module >>> fails. >>> Do you have suggestions to do this fast? >>> Thx >>> >>> Pieter >>> >>> Op 29/01/2013 11:38, Marko Wilke schreef: >>>> Pieter, >>>> >>>> I would expect that they are all looking into the wrong direction :) >>>> but I suggest using spm to check that. If you first call up one of the >>>> templates coming with spm, and then your image, they should look >>>> similar with regard to their overall orientation. If not so, you can >>>> use the pitch, roll, yaw fields to enter multiples (or halves) of pi >>>> to reorient your image. Once you're happy with the result, you can >>>> apply the transformation to all your images, using "reorient images". >>>> This changes the header, so you may want to make sure you have backups >>>> first. >>>> >>>> Cheers, >>>> Marko >>>> >>>> >>>> >>>> Pieter Vandemaele wrote: >>>>> Dear SPM'ers, >>>>> >>>>> I used the Segment module to segment and normalize anatomical scans >>>>> and >>>>> got strange results, see attachments. >>>>> Is this due to the origin localisation? >>>>> What is the easiest way to deal with this? I have 80 subjects so a >>>>> (semi)automatic solution would be ideal. >>>>> >>>>> Best >>>>> >>>>> Pieter >>>> >>> >>> >>> -- >>> Re: Netwerk MR afdeling UZGent >>> >>> *Pieter Vandemaele, *MSc-Ing >>> *GIfMI Site Manager* >>> Ghent Institute for Functional and Metabolic Imaging >>> MR Department -1K12 >>> Ghent University Hospital >>> De Pintelaan 185 >>> 9000 Ghent - BELGIUM >>> >>> [log in to unmask] <mailto:[log in to unmask]> >>> tel: +32 >>> (0)9 332 48 20 >>> http://gifmi.ugent.be fax: +32 (0)9 332 49 69 >>> >>> >>> >>> >> > > > -- > Re: Netwerk MR afdeling UZGent > > *Pieter Vandemaele, *MSc-Ing > *GIfMI Site Manager* > Ghent Institute for Functional and Metabolic Imaging > MR Department -1K12 > Ghent University Hospital > De Pintelaan 185 > 9000 Ghent - BELGIUM > > [log in to unmask] <mailto:[log in to unmask]> tel: +32 > (0)9 332 48 20 > http://gifmi.ugent.be fax: +32 (0)9 332 49 69 > > > > -- ____________________________________________________ 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/ ____________________________________________________