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Ok, so what part isn't working? Are you not happy with the result or is it not actually doing anything? If you really want to do things fully manually, you can use the Nudge tool - but it's very unlikely that you're going to get results as good as just using flirt as recommended. On Fri, May 9, 2014 at 3:11 PM, Carola Eleni Hering <[log in to unmask]> wrote: > Yes the labels are correct. I do not yet register the image to the EPI but ony want to bring it in the same orientation, the head is tilted with 30 degrees, but the EPIs are not. > Hope this clarifies it. > > Thank you > > > Am 09.05.2014 um 14:51 schrieb Niels Bergsland <[log in to unmask]>: > >> What do you mean that it's not working - that the registration itself >> is bad or that it's erroring out? >> >> How do the labels look in fslview? Are those correct, with respect to >> the patient anatomy? >> >> On Fri, May 9, 2014 at 12:39 PM, Carola Eleni Hering >> <[log in to unmask]> wrote: >>> Hi Michel, >>> >>> thank you for your fast response. I tried this, but this is not working…. >>> I used as reference image MNI T1 template, for input, my structural wrongly orientated image and then pressed GO. >>> >>> Do you have an idea why this did not work? >>> >>> Thanks a lot, >>> Carola >>> >>> >>> Am 08.05.2014 um 17:44 schrieb Michel Thiebaut de Schotten <[log in to unmask]>: >>> >>>> Hi Carola, >>>> >>>> Why don't you try a simple flirt of your T1 on the average of your movement corrected EPI. >>>> Cheers, >>>> >>>> Michel >>>> >>>> Sent from my iPhone >>>> >>>>> On 8 May 2014, at 16:22, Carola <[log in to unmask]> wrote: >>>>> >>>>> Hi guys, >>>>> >>>>> I would like to manually reorientate my T1 structural non-brain extracted images for each participant. How is this possible in FSL or even FSL view? >>>>> >>>>> At the moment the whole head (structural image) is tilted 30° to the front (pitch) but all my EPI images are in the right orientation. I need this for the non-linear registration. >>>>> >>>>> Could anyone tell me how I can easily reorientate all of the T1 images in the same orientation as the functional ones? >>>>> In SPM it is called: Reorientate current image. Where do I find the same manual reorientation option in FSL? >>>>> >>>>> Thanks a lot, >>>>> Carola >> >> >> >> -- >> Niels Bergsland >> Integration Director >> Buffalo Neuroimaging Analysis Center >> 100 High St. Buffalo NY 14203 >> [log in to unmask] -- Niels Bergsland Integration Director Buffalo Neuroimaging Analysis Center 100 High St. Buffalo NY 14203 [log in to unmask]