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Just out of curiosity, what happens if you try running it on a non-image file? (just to see if it gives you some type of error). By the way, running it without any arguments gives you the usage of the command, right? On Thursday, May 15, 2014, Matyáš <[log in to unmask]> wrote: > Hi, > > I'm not sure how to use the wrapper version but I tried these two commands: > /usr/lib/fsl/4.1/fslreorient2std T1.nii > /usr/lib/fsl/5.0/fslreorient2std T1.nii > > and both ended without any output. I think I have installed all properly, > but I will try to reinstall fsl completely. > > Output for : ls $FSLDIR/data/standard > > matyas@matyas-workstation:~$ ls $FSLDIR/data/standard > avg152T1_brain.nii.gz > avg152T1.nii.gz > FMRIB58_FA-skeleton_1mm.nii.gz > FMRIB58_FA_1mm.nii.gz > LowerCingulum_1mm.nii.gz > MNI152lin_T1_1mm_brain.nii.gz > MNI152lin_T1_1mm.nii.gz > MNI152lin_T1_1mm_subbr_mask.nii.gz > MNI152lin_T1_2mm_brain_mask.nii.gz > MNI152lin_T1_2mm_brain.nii.gz > MNI152lin_T1_2mm.nii.gz > MNI152_T1_0.5mm.nii.gz > MNI152_T1_1mm_brain_mask_dil.nii.gz > MNI152_T1_1mm_brain_mask.nii.gz > MNI152_T1_1mm_brain.nii.gz > MNI152_T1_1mm_first_brain_mask.nii.gz > MNI152_T1_1mm_Hipp_mask_dil8.nii.gz > MNI152_T1_1mm.nii.gz > MNI152_T1_2mm_brain_mask_deweight_eyes.nii.gz > MNI152_T1_2mm_brain_mask_dil.nii.gz > MNI152_T1_2mm_brain_mask_dil1.nii.gz > MNI152_T1_2mm_brain_mask.nii.gz > MNI152_T1_2mm_brain.nii.gz > MNI152_T1_2mm_b0.nii.gz > MNI152_T1_2mm_edges.nii.gz > MNI152_T1_2mm_eye_mask.nii.gz > MNI152_T1_2mm_LR-masked.nii.gz > MNI152_T1_2mm.nii.gz > MNI152_T1_2mm_skull.nii.gz > MNI152_T1_2mm_strucseg.nii.gz > MNI152_T1_2mm_strucseg_periph.nii.gz > MNI152_T1_2mm_VentricleMask.nii.gz > tissuepriors > > Thank you for yours suggestions, > > All the best, > Matyas > > > Dne 14.5.2014 17:56, Mark Jenkinson napsal(a): > > Hi, > > Actually you can run it without a second argument, in which case it > displays a transformation matrix that could be used to achieve the > reorientation, but without altering the original image. So it should be > possible to run it in this mode, and this is how it is used inside fsl_anat. > > So Matyas - I would check what Matt suggested, and make sure that you > have all the necessary components of FSL installed. For instance, what > happens when you do: > ls $FSLDIR/data/standard > ? > > All the best, > Mark > > > On 14 May 2014, at 16:39, Michael Dwyer <[log in to unmask]> wrote: > > Hi Matyas, you have to specify an output filename -- so fslresorient2std > T1.nii T1_reodient.nii, not just fslreorient2std T1.nii. > > > On Wed, May 14, 2014 at 9:31 AM, Matyáš <[log in to unmask]> wrote: > > Hi, > > There is no error message from fslreorient2std, but there is no output > either (I tried to call it alone like this: fslreorient2std T1.nii - and > there was no output to terminal). The thing with convert_xfm is that in > fsl_anat script it first run fslreorient2std, this should provide > T1_std2orig.mat (or I think it should), and this is input for convert_xfm > in the fsl_anat pipeline (convert_xfm -omat T1_std2orig.mat -inverse > T1_orig2std.mat) - and this ends with "Cannot read input-matrix" error. > > I installed it with Neurodebian as you said, but I has version 4.1. also > installed on my PC, so maybe this could do some problems. > > > > > Dne 14.5.2014 15:17, Mark Jenkinson napsal(a): > > Hi, > > I have not heard of this before, and it is very concerning. > How does the convert_xfm error relate to fslreorient2std (as the latter > does not call convert_xfm)? > > If you just run fslreorient2std on its own, do you get an error message? > > And did you install FSL via NeuroDebian, or some other way? > > All the best, > Mark > > > > On 14 May 2014, at 15:02, Matyáš <[log in to unmask]> wrote: > > Hi all, > > I want to ask if anyone has experienced that fslreorient2std doesn't > provide any output in Ubuntu 12.04 or above (I'm using fsl 5.0.6). I wanted > to try fsl_anat script for my structural data, but in first step of this > script it exits with error message that convert_xfm could not read > T1_std2orig.mat and after while I found out that this is problem of > fslreorient2std. It does the same on my laptop with Ubuntu 14.04. Any idea > why this is > > -- Niels Bergsland Integration Director Buffalo Neuroimaging Analysis Center 100 High St. Buffalo NY 14203 [log in to unmask]