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Raheel, I would think the easiest is to discard the volumes before you do anything else (I do not even convert them). This will both use a more representative volume for realignment and avoid the issue with the non-matching number of volumes in the regressor later-on. The first volume you keep will then be volume 1. Cheers, Marko zafar raheel wrote: > I need help regarding the above matter. In SPM during 1st level analysis > we discard first few slides. > 1. When we define onsets [e.g in time (seconds) not in scan], then we > have to start from beginning e.g. from [0:4:500] or if I am discarding > first 20 sec data then it will be from [21:4:500}. Which one is right? > > 2. In preprocessing, normally we do not discard the initial scans. But > in DESIGN MATRIX, we are using realignment text file with the > regressors. Now in realignment file we have information of all the scans > but in first level analysis we have 10 scans (20 sec data) shorter than > that.Will it will create problem or not? > > In other words, If I am discarding initial scans during first level > analysis, whether I have to discard scans in preprocessing (realignment) > as well or not. > > Secondly whether I have to start onset from 0 or from 21 [If I am > discarding first 20 sec data, means 10 scans (as my TR is 2 sec)] > > Thanks > > Regards > > Raheel -- ____________________________________________________ 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/ ____________________________________________________