Yes the second stage of tbss_deproject assumes that your stats
directory is called "stats"
Saad.
On 3 Jul 2008, at 13:03, Agnieszka Burzynska wrote:
> Hi,
> I tried to de-project my tbss data. First, I used tbss_deproject xx
> 1 and it
> worked. Next, I tried tbss_depoject xx 2, but the only new files I
> find in
> my FAi directory are subject_FAi_to_target_nonlinear_inv.nii.
>
> I want to deproject the whole skeleton, called SKEL.nii. I will be
> very
> grateful if you can have a look on the commands before and outputs
> and help
> me figure out what went wrong. My stats directory has a modified
> name (stats
> 25), can this cause the problem for option 2 but not for option 1?
>
> Thanks!
> Aga
>
>
> -----------------
> tbss_deproject SKEL.nii 2
>
> /usr/local/fsl/bin/tbss_deproject: line 1: sl#!/bin/sh: No such
> file or
> directory
> de-projecting <skeleton-space-image> into all_FA (nonlinearly aligned)
> subject space
> output will be SKEL_to_all_FA
> processing subject1_FAi:
> BOUND = (0.505558,2.12219) (0,0.779109) (-0.808892,0.820176)
> BOUND = (0,0.462407) (-0.172311,0.383608) (-0.302999,0.428936)
> BOUND = (0.110172,0.506126) (0,0.383608) (-0.176276,0.38572)
> BOUND = (0.100894,0.457127) (0,0.354172) (-0.161431,0.373548)
> BOUND = (0.0952364,0.425322) (0,0.334708) (-0.152378,0.36181)
> BOUND = (0.095717,0.406732) (0,0.32005) (-0.153147,0.35798)
> BOUND = (0.0945744,0.390617) (0,0.308534) (-0.151319,0.353759)
> BOUND = (0.0971113,0.38118) (0,0.299277) (-0.155378,0.355612)
> BOUND = (0.0994486,0.374525) (0,0.291736) (-0.159118,0.359585)
> BOUND = (0.1059,0.374119) (0,0.285507) (-0.169441,0.372069)
> ***************************************************
> The following COMPULSORY options have not been set:
> -w,--warp filename for warp transform (volume)
> -o,--out filename for output (warped) image
> ***************************************************
>
> applywarp (Version 1.2)
> Copyright(c) 2001, University of Oxford (Mark Jenkinson)
>
> Usage:
> applywarp -i invol -o outvol -r refvol -w warpvol
>
> Compulsory arguments (You MUST set one or more of):
> -i,--in filename of input image (to be warped)
> -w,--warp filename for warp transform (volume)
> -o,--out filename for output (warped) image
>
> Optional arguments (You may optionally specify one or more of):
> -r,--ref filename for reference image
> --abs treat warp field as absolute: x' = w(x)
> --rel treat warp field as relative: x' = x + w(x)
> --premat filename for pre-transform (affine matrix)
> --postmat filename for post-transform (affine matrix)
> -m,--mask filename for mask image (in reference space)
> --interp interpolation method {nn,trilinear,sinc}
> -v,--verbose switch on diagnostic messages
> -h,--help display this message
>
> Usage: /usr/local/fsl/bin/imrm <list of image names to remove>
> NB: filenames can be basenames or not
>
------------------------------------------------------------------------
---
Saad Jbabdi,
Postdoctoral Research Assistant,
Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222545 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~saad
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