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Screensize: 640 x 480 800 x 600 1024 x 768 1280 x 1024 UserName: Password: Format Mode: Basic  Help  Prompt  Format: Font Andale Mono Arial Arial Black Book Antiqua Century Gothic Comic Sans MS Courier New Georgia Impact Lucida Console Script MT Bold Stencil Tahoma Times New Roman Trebuchet MS Verdana   Size 1 2 3 4 5 6   Color Black Red Yellow Pink Green Orange Purple Blue Beige Brown Teal Navy Maroon LimeGreen Message: * HTML is OFF * Forum Code is ON Smilies [quote][i]Originally posted by jimmy.dias[/i] [br]Hi all, Those of you who ran scripts [green]coreg_normalize[/green] or [green]normalize[/green] on Golgi between January 24, 2005 and April 07, 2005 (8:34 a.m), the output BXH file specifies incorrectly that the orientation of the data is in 'LAS' order instead of the correct 'RAS' order. Any processing steps that have been run on the output of [green]coreg_normalize[/green] and [green]normalize[/green] will also have incorrect orientation information in the output BXH files. These headers too will need to be fixed. Orientation snapshot throughout SPM99 pipeline: Assuming an initial orientation of LPI. LPI -> tralign -> LPI LPI -> motioncorrection -> LPI LPI -> LAS -> normalization -> RAS RAS -> smooth -> RAS Data orientation is preserved i.e. output has same orientation as input, when using [green]tralign[/green], [green]smooth[/green], and [green]motioncorrect[/green]. With [green]normalize[/green] and [green]coreg_normalize[/green] however, orientation is not preserved as the input is first reoriented to 'LAS' to match the SPM99 template, and then flipped L-R during SPM99 normalization to finally output a 'RAS' ordered dataset. I'm working on a script that will search the storage servers and fix these incorrect bxh files. In the interim, if you'd like to run any processing/analysis requiring correct orientation information on normalized datasets preprocessed during the above time period do the following: Check orientation by doing the following in MATLAB: [green]getorientation(readmr('run004_01.bxh'))[/green] If orientation is in 'LAS' order, use [green]bxhsetorient[/green] at the Golgi prompt to fix this header. e.g. [purple]bxhsetorient --inplace RAS ncrun004_01.bxh[/purple] Jimmy [/quote]   Check here to include your profile signature. Check here to subscribe to this topic.