-
YES, THEY HAVE ABSOLUTELY THE SAME FILENAME.
I have even checked the warp files and they seems to be ok!
this is strange because when I set FMRIB as the target, then tbss_non_FA works but not when I set the most typical subject in the study as the target.
Any idea will be highly appreciated!
Best
/Kami
--- On Tue, 4/19/11, Tejasvi Gundapuneedi <[log in to unmask]> wrote:
From: Tejasvi Gundapuneedi <[log in to unmask]>
Subject: Re: [FSL] Fw: [FSL] tbss_non_FA
To: [log in to unmask]
Date: Tuesday, April 19, 2011, 7:05 PM
Are the names of the MD data files same as that of the FA files names?
I got this error when the file names did not
match.
-Thanks
On Tue, Apr 19, 2011 at 1:35 PM, kambiz rakhshan <[log in to unmask]> wrote:
Thanks Mathew for the tips but actually the problem was before applying the warp to the MD images so it was at :
f
or f in `$FSLDIR/bin/imglob *_*` ;
so i change it to
for f in `$FSLDIR/bin/imglob *_FA.nii.gz` ; do
but another problem occurs (see bellow). I don't have any idea of what's going one but the registration was perfect for FA.Do you have any suggestion?
Many thanks
/Kami
ERROR (nifti_image_read): failed to find header file for '../MD/B2503.70.dti'
** ERROR: nifti_image_open(../MD/B2503.70.dti): bad header info
Error: failed to open file ../MD/B2503.70.dti
ERROR: Could not open image ../MD/B2503.70.dti
Image Exception : #22 :: Failed to read volume ../MD/B2503.70.dti
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
B2504.30.dti
** ERROR
(nifti_image_read): failed to find header file for '../MD/B2504.30.dti'
** ERROR: nifti_image_open(../MD/B2504.30.dti): bad header info
Error: failed to open file ../MD/B2504.30.dti
ERROR: Could not open image ../MD/B2504.30.dti
Image Exception : #22 :: Failed to read volume ../MD/B2504.30.dti
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
B2504.35.dti
** ERROR (nifti_image_read): failed to find header file for '../MD/B2504.35.dti'
** ERROR: nifti_image_open(../MD/B2504.35.dti): bad header info
Error: failed to open file ../MD/B2504.35.dti
ERROR: Could not open image ../MD/B2504.35.dti
Image Exception : #22 :: Failed to read volume ../MD/B2504.35.dti
terminate called after throwing an instance of 'RBD_COMMON::BaseException'
Aborted
B2504.60.dti
--- On Tue, 4/19/11, Matthew Webster <[log in to unmask]> wrote:
From: Matthew Webster <[log in to unmask]>
Subject: Re: [FSL] Fw: [FSL] tbss_non_FA
To: "kambiz rakhshan" <[log in to unmask]>
Date: Tuesday, April 19, 2011, 7:28 AM
Hello,
Since you're at the last stage of tbss_non_FA, it might be best to create the all_MD image by hand... e.g. ( assuming your controls and patients images begin with CON and PAT )
fslmerge -t firstOutput `$FSLDIR/bin/imglob CON*_to_target_${ALTIM}.nii.gz`
fslmerge -t secondOutput `$FSLDIR/bin/imglob PAT*_to_target_${ALTIM}.nii.gz`
fslmerge -t ../stats/all_MD firstOutput secondOutput
then you can create the skeleton needed by randomise:
cd ../stats
fslmaths all_MD -mas mean_FA_mask all_MD
thresh=`cat thresh.txt`
tbss_skeleton -i mean_FA -p $thresh
mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA all_MD_skeletonised -a all_MD
Matt
> Dear FSL experts,
>
> I posted the following message a while ago but haven't received any response yet. I am kind of stuck and not able to go forward.I will appreciate if somebody can help me through?
>
> Thanks in Advance!
> /Kami
>
> --- On Fri, 4/15/11, kambiz rakhshan <[log in to unmask]> wrote:
>
>
> I have tried to apply tbss_non_FA to my MD images (N= 287 subjects to normalize to the most typical subject in the study) and I carefully followed the steps given in TBSS manual, however, there seems to be too many files that causes the program to crash. I have also tried to change the tbss_non_FA as it was recommended
:
>
> ${FSLDIR}/bin/fslmerge -t ../stats/all_$ALTIM `$FSLDIR/bin/imglob *_to_target_${ALTIM}.*`
>
> in $FSLDIR/bin/tbss_non_FA
>
> to read:
>
> ${FSLDIR}/bin/fslmerge -t ../stats/all_$ALTIM `$FSLDIR/bin/imglob *_to_target_${ALTIM}.nii.gz`
>
> I did this simply by changing a line in gedit program using a diplay function by right-clicking on tbss_non_FA but the error still persists (SEE BELLOW)!
>
> What can I do to get ride of this error or perhaps I didn't change the noted line appropriately?
>
> I will greatly appreciate if somebody help me !
> Kami
>
>
>
> using pre-chosen registration target: target
> upsampling alternative images into standard space
> /usr/share/fsl/4.1/bin/tbss_non_FA: 95: /usr/share/fsl/4.1/bin/imglob: Argument list too long
> merging all upsampled MD images into
single 4D image
>
> Usage: fslmerge <-x/y/z/t/a> <output> <file1 file2 .......>
> -t : concatenate images in time
> -x : concatenate images in the x direction
> -y : concatenate images in the y direction
> -z : concatenate images in the z direction
> -a : auto-choose: single slices -> volume, volumes -> 4D (time series)
> ** ERROR (nifti_image_read): failed to find header file for 'all_MD'
> ** ERROR: nifti_image_open(all_MD): bad header info
>
--
Regards,
Tejasvi.Gundapuneedi
214-315-6766
