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It's not quite as simple as that. You'll need to check with your local experts to see which part of the head was acquired first and whether an interleaved sequence was used etc. Once you know this, you can use Display to figure out which slice of the NIfTI image this corresponds to. There is nothing in the NIfTI headers or images that would tell you anything about the order that the slices were acquired in. Best regards, -John On 23 January 2012 16:52, Harold Mouras <[log in to unmask]> wrote: > Thank you very much for these quick and kind responses ! > When moving the crosshair from the bottom to the upper side of the brain for > example on the saggital plan, this third coordinate goes from 0 to 28 (we > hade 28 slices). So, simply, we acquired sequentially from the bottom to the > upper part of the brain, am I right....? > > > > 2012/1/23 John Ashburner <[log in to unmask]> >> >> Just to add something to my previous response... >> >> You can see which is the first slice in an image via the Display >> button. You can identify the first slice by clicking on the corners >> of the volume and looking at the the voxel coordinates. The third >> value is the slice number of that point. >> >> Best regards, >> -John >> >> On 23 January 2012 16:09, Harold Mouras <[log in to unmask]> >> wrote: >> > Dear SPM list, >> > I am beginning to work on data acquired in a new experiment. When >> > looking at >> > DICOM data under osiriX for example, data appeared to have been acquired >> > sequentially from the bottom of the brain. A very first question would >> > be >> > how to be sure of this parameter when looking at the DICOM header ? >> > Moreover, I wondered if the conversion to nifti could have an influence >> > on >> > this in order to plan the slice timing parameters I'll apply in my >> > preprocessing steps. Once the conversion is done, is there any >> > information >> > regarding this parameter in the nifti file header ? >> > Thank you so much in advance, >> > Best regards, >> > Harold >> > >> > >> > -- >> > Harold Mouras >> > Maître de Conférences en Neuroscience >> > Editeur "Socioaffective Neuroscience & Psychology" >> > >> > >> > ------------------------------------------------------------------------- >> > Laboratoire de Neurosciences Fonctionnelles et Pathologies >> > Faculté de médecine >> > 3, rue des Louvels >> > 80036 Amiens, France >> > Téléphone: +33 9 50 48 30 10 >> > [log in to unmask] >> > In french: Website personnal page / Lab page (Amiens) / Lab page (Lille) >> > In english: Website personnal page / Lab page (Amiens) / Lab page >> > (Lille) >> > >> > ------------------------------------------------------------------------- >> > >> > > > > -- > Harold Mouras > Maître de Conférences en Neuroscience > Editeur "Socioaffective Neuroscience & Psychology" > > ------------------------------------------------------------------------- > Laboratoire de Neurosciences Fonctionnelles et Pathologies > Faculté de médecine > 3, rue des Louvels > 80036 Amiens, France > Téléphone: +33 9 50 48 30 10 > [log in to unmask] > In french: Website personnal page / Lab page (Amiens) / Lab page (Lille) > In english: Website personnal page / Lab page (Amiens) / Lab page (Lille) > ------------------------------------------------------------------------- >