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):

[log in to unmask]" type="cite"> 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 happening?

Thank you,

Matyas

--

Michael G. Dwyer, Ph.D.

Assistant Professor of Neurology and Biomedical Informatics
Director of Technical Imaging Development
Buffalo Neuroimaging Analysis Center

University at Buffalo
100 High St. Buffalo NY 14203
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(716) 859-7065