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Mark, I am afraid my complete lack of computer skills is going to show, but here is what I put in (with no results): fslswapdim KALBFLEISCH_5295_36_1_7_ep2d_pace_moco_3DFilter_20080107_0001.nii -x y -z KALBFLEISCH_5295_36_1_7_ep2d_pace_moco_3DFilter_20080107_0001_swapped I also tried it without the .nii, but no result that way either. I know if has to be something in my typing or understanding of command line (which is none- I am learning as I go), can you see what I am doing wrong? Thanks, Emily ----- Original Message ----- From: Mark Jenkinson <[log in to unmask]> Date: Friday, February 15, 2008 1:30 pm Subject: Re: [FSL] reorientation > No. > If you know scripting you can do it with a little script. > Otherwise, just run it one at a time. > Make doubly sure that you backup and check that the first result > is OK before doing the rest though, as otherwise it is a great waste! > > All the best, > Mark > > > On 15 Feb 2008, at 18:26, Emily T Stoneham wrote: > > > Ahhh! I get it :) so, there is no way to do this for all files > at > > one time, then? > > > > Emily > > ----- Original Message ----- > > From: Mark Jenkinson <[log in to unmask]> > > Date: Friday, February 15, 2008 1:26 pm > > Subject: Re: [FSL] reorientation > > > >> Hi, > >> > >> You need to run this command once (separately) for every image, > >> either structural or functional, that you want to change. > >> Remember to make a backup first! > >> > >> The filenames are in the command. > >> I put in the "origdata" and "swappeddata" as examples. > >> > >> If you have an image file called "functional_run2.nii.gz" and > >> you want to change its orientation (stop it being upside down) > >> then you would run: > >> > >> fslswapdim functional_run2 -x y -z functional_run2_swapped > >> > >> to create a new image file called "functional_run2_swapped.nii.gz". > >> You can use whatever names you like though. > >> > >> Make sure you look at the output in fslview to see if it has worked > >> before doing this to any other files. > >> > >> All the best, > >> Mark > >> > >> > >> > >> On 15 Feb 2008, at 18:19, Emily T Stoneham wrote: > >> > >>> Mark, when you say 'use the right filenames' how do I put those > >> in > >>> the command? Also, do I list all of them, or is the folder name > >>> sufficient? > >>> > >>> ----- Original Message ----- > >>> From: Mark Jenkinson <[log in to unmask]> > >>> Date: Friday, February 15, 2008 1:14 pm > >>> Subject: Re: [FSL] reorientation > >>> > >>>> Hi, > >>>> > >>>> Yes, cd into the directory then type the command I said (using > the>>>> right filenames for your data). > >>>> It should not take very long even with a big dataset (lots of > >>>> timepoints). > >>>> If it is taking more than 5 minutes then something has probably > >>>> gone > >>>> wrong. > >>>> Of course the time can depend on the speed of your > machine/network/>>>> disk storage and how > >>>> many users are doing things. > >>>> It will not print any special message though when it works. > >>>> It will simply give you a fresh prompt (like cd would do). > >>>> > >>>> All the best, > >>>> Mark > >>>> > >>>> > >>>> > >>>> On 15 Feb 2008, at 18:08, Emily T Stoneham wrote: > >>>> > >>>>> Mark, > >>>>> I assume I cd to the folder then put in the message (this is > >>>>> what I have done)? Will it tell me when it is finished (it is > >>>>> taking a long time, but I assume that is because there are a lot > >>>> of > >>>>> files)? > >>>>> > >>>>> Thanks, > >>>>> Emily > >>>>> > >>>>> ----- Original Message ----- > >>>>> From: Mark Jenkinson <[log in to unmask]> > >>>>> Date: Friday, February 15, 2008 12:31 pm > >>>>> Subject: Re: [FSL] reorientation > >>>>> > >>>>>> Hi, > >>>>>> > >>>>>> There is no GUI option, but you can play about with fslswapdim > >>>> on the > >>>>>> command line to do it (run from the Terminal application). > Just>>>> make>> sure you keep a backup of the original and do *not* > keep any > >>>> output>> where fslswapdim has printed a message about left/right > >>>> flips, as > >>>>>> this > >>>>>> is quite dangerous. > >>>>>> > >>>>>> If you have a standard axial scan (that looks like the standard > >>>>>> brain in > >>>>>> orientation in fslview, except for being upside down in the > >>>>>> sagittal and > >>>>>> coronal views) then the following command should work: > >>>>>> > >>>>>> fslswapdim origdata -x y -z swappeddata > >>>>>> > >>>>>> All the best, > >>>>>> Mark > >>>>>> > >>>>>> > >>>>>> > >>>>>> On 15 Feb 2008, at 16:46, Emily Stoneham wrote: > >>>>>> > >>>>>>> Hello! > >>>>>>> > >>>>>>> When I do an initial look at the functional images (289 > to a > >>>>>>> run), the sagittals are all upside down. > >>>>>>> is there a way to fix all of them at once using the FSL GUI > >> (I am > >>>>>> > >>>>>>> on a Mac)? > >>>>>>> > >>>>>>> Thanks, > >>>>>>> Emily > >>>>>>> > >>>>>> > >>>>>> <estoneha.vcf> > >>>> > >>>> <estoneha.vcf> > >> > >> <estoneha.vcf> >