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I used flirt. First without and then with the applyxfm arguments. These were my commands: /usr/local/fsl/bin/flirt -in /TEST_DIR/bold_brain.nii -ref /usr/local/fsl/data/standard/MNI152_T1_3mm_brain.nii -out /TEST_DIR /flirt_output.nii -omat /TEST_DIR /flirt_output.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear /usr/local/fsl/bin/flirt -in /TEST_DIR /bold_brain.nii -applyxfm -init /TEST_DIR /flirt_output.mat -out /TEST_DIR /post_flirt_AND_applyxfm.nii.gz -paddingsize 0.0 -interp trilinear -ref /TEST_DIR /flirt_output.nii.gz Perhaps I'll look into FNIRT. I'd feel a lot better nailing this down to a single step. Feels less "noisy" to me. Damion ----- Graduate Student UT Austin | Cognitive Neuroscience DCN Lab <https://labs.la.utexas.edu/church-lang/> On Sun, Oct 9, 2016 at 1:42 PM, Rosalia Dacosta Aguayo <[log in to unmask]> wrote: > Hi Damion, > > I can not tell you with clarity. Which command lines did you use for doing > this? > > I normally use FLIRT and FNIRT. > > Kind regards, > > Rosalia > > El 9 oct. 2016 20:39, "Damion V Demeter" <[log in to unmask]> escribió: > >> Hey Rosalia, >> >> Sorry for the late reply. I don't think I have an easy way to send you >> sample files, but I also think I solved my issue. It feels a little weird, >> but if I run applyxfm with the .mat file and that reference frame (the one >> I was talking about) that flirt created....I get my atlas normalized >> functional image as expected. >> >> It feels clunky and I am worried I'm introducing extra steps, but the >> output passes all visual QA I can think of and looks good. Thoughts on this >> "workflow"? >> >> Damion >> >> ----- >> Graduate Student >> UT Austin | Cognitive Neuroscience >> DCN Lab <https://labs.la.utexas.edu/church-lang/> >> >> On Sat, Oct 8, 2016 at 10:32 PM, Rosalia Dacosta Aguayo < >> [log in to unmask]> wrote: >> >>> Hi Damion, >>> >>> Could you please send me just one subject fmri with its structural as >>> well as the result you got? I will give a look to it but not just now >>> because I am from Spain and here it is 05:30 am esrly in the morning. I >>> will give a look into this in the next few hours. >>> >>> Rosalia >>> >>> El 9 oct. 2016 5:28, "Damion V Demeter" <[log in to unmask]> escribió: >>> >>> Hi Rosalia, >>> >>> My apologies for not giving complete info, I was trying to be concise. >>> Yes, I have a T1 image as well and am using it when running the flirt >>> method. The biggest point of confusion is why my output image (that looks >>> great and is definitely aligned to the atlas; verified by overlay in >>> fslview) is just the single frame reference and not an entire 4d image like >>> the input. >>> >>> Any ideas of what I'm overlooking? Or perhaps, if you have time, could >>> you explain the workflow you'd use to accomplish this? From all I've read, >>> I am doing it correctly, but my output says otherwise. >>> >>> Damion >>> >>> >>> >>> On Oct 8, 2016, at 10:01 PM, Rosalia Dacosta Aguayo <[log in to unmask]> >>> wrote: >>> >>> Hi Damion, do you have structural T1 images for those subjects? A >>> coregistration would be of great help when you have low resolution before >>> MNI registration. >>> >>> Kind regards, >>> >>> Rosalia >>> >>> El 9 oct. 2016 4:55, "Damion Demeter" <[log in to unmask]> escribió: >>> >>>> I have searched the archives and tried a few things I read there, but I >>>> am not having much luck. This feels like a very basic question, but I can't >>>> seem to get it working the way I need. I apologize if this is a repeat >>>> post, but I was not able to find a solution that works for me. >>>> >>>> What I am trying to do: I am trying to register a functional scan to >>>> the MNI atlas. I have successfully done this with flirt (turning off all >>>> smoothing, etc because I only want the transform step), but my output file >>>> is a single frame (reference file?). I have tried to do this with applyxfm >>>> as well, but the image gets moved around and at least one view ends up >>>> chopped off (I'm guessing because the voxel size of the acquired image >>>> isn't the same as the atlas?). >>>> >>>> It's frustrating because this feels like it should be a rather simple >>>> function, but I can't seem to find anything about how to do this transform >>>> without running it through all the steps of FEAT. I'm hoping someone can >>>> point me in the right direction or to the proper tool (or perhaps knows >>>> what I'm doing wrong with FLIRT if that is, indeed, the correct tool to >>>> use). >>>> >>>> Thanks in advance! >>>> >>> >>> >>