Hi,
Sorry, I don't really understand your question.
What do you mean by rotated "slightly left or right"?
What do you what to do?
And what has this got to do with your original question about 3D rendering in FSLView?
All the best,
Mark
On 25 Jan 2013, at 07:06, sunil koundal <[log in to unmask]> wrote:
> Dear Rosalia and Mark,
> This is what i am doing .
> i have 5 subjects (6,7,8,9,10),
> after i run tbss_2_reg -t sunil , i found my images were rotated
> slightly left or right. so can i rotate it using fsl ? kindly guide me
> , if these steps are ok and how to proceed further for voxelwise stats
>
> Regards
> sunil
> [nmrsu@localhost ~]$ cd Desktop/tbss
> [nmrsu@localhost sg48]$ ls
>
> 6.nii.gz 7.nii.gz 8.nii.gz 9.nii.gz 10.nii.gz
> [nmrsu@localhost tbss]$ tbss_1_preproc 6 7 8 9 10
> processing 10
> processing 6
> processing 7
> processing 8
> processing 9
> Now running "slicesdir" to generate report of all input images
> Finished. To view, point your web browser at
> file:/home/nmrsu/Desktop/tbss/FA/slicesdir/index.html
> now i have copied target brain(sunil) to tbss dirls
>
> [nmrsu@localhost tbss]$ ls
> FA origdata sunil.nii.gz
> [nmrsu@localhost tbss]$ tbss_2_reg -t sunil
> 10_FA_to_target
> 6_FA_to_target
> 7_FA_to_target
> 8_FA_to_target
> 9_FA_to_target
> 9683
> [nmrsu@localhost tbss]$ tbss_3_postreg -S
> using pre-chosen target for registration
> affine-registering target to MNI152 space
> transforming (and upsampling) all FA images into MNI152 space
> 10_FA
> 6_FA
> 7_FA
> 8_FA
> 9_FA
> merging all upsampled FA images into single 4D image
> creating valid mask and mean FA
> skeletonising mean FA
> [nmrsu@localhost tbss]$ tbss_4_prestats 0.2
> creating skeleton mask using threshold 0.2
> creating skeleton distancemap (for use in projection search)
> projecting all FA data onto skeleton
> [nmrsu@localhost tbss]$ cd stats
> [nmrsu@localhost stats]$ ls
> all_FA.nii.gz mean_FA_skeleton_mask_dst.nii.gz
> all_FA_skeletonised.nii.gz mean_FA_skeleton_mask.nii.gz
> mean_FA_mask.nii.gz mean_FA_skeleton.nii.gz
> mean_FA.nii.gz thresh.txt
>
>
>
> [nmrsu@localhost tbss]$ cd FA
> [nmrsu@localhost FA]$ ls
> 10_FA_mask.nii.gz 8_FA_mask.nii.gz
> 10_FA.nii.gz 8_FA.nii.gz
> 10_FA_to_target.log 8_FA_to_target.log
> 10_FA_to_target.mat 8_FA_to_target.mat
> 10_FA_to_target.nii.gz 8_FA_to_target.nii.gz
> 10_FA_to_target_warp.msf 8_FA_to_target_warp.msf
> 10_FA_to_target_warp.nii.gz 8_FA_to_target_warp.nii.gz
> 6_FA_mask.nii.gz 9_FA_mask.nii.gz
> 6_FA.nii.gz 9_FA.nii.gz
> 6_FA_to_target.log 9_FA_to_target.log
> 6_FA_to_target.mat 9_FA_to_target.mat
> 6_FA_to_target.nii.gz 9_FA_to_target.nii.gz
> 6_FA_to_target_warp.msf 9_FA_to_target_warp.msf
> 6_FA_to_target_warp.nii.gz 9_FA_to_target_warp.nii.gz
> 7_FA_mask.nii.gz best.msf
> 7_FA.nii.gz slicesdir
> 7_FA_to_target.log target_mask.nii.gz
> 7_FA_to_target.mat target.nii.gz
> 7_FA_to_target.nii.gz target_to_MNI152.mat
> 7_FA_to_target_warp.msf target_to_MNI152.nii.gz
> 7_FA_to_target_warp.nii.gz tbss_logs
>
>
> On Wed, Jan 23, 2013 at 4:49 PM, Rosalia Dacosta Aguayo
> <[log in to unmask]> wrote:
>> Hi Sunil,
>>
>> Normally they recommend to set a threshold of 0.2.
>>
>> If you read carefully this link:
>> http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TBSS/UserGuide#Testing_left_vs._right_in_TBSS
>>
>> You will find that the right command for the for step is: tbss_4_prestats
>> 0.2
>>
>> 1. Did you set this threshold when you run the four step?
>>
>> 2. Have you well installed the 3D viewer?
>>
>> 3. Another sources: Think there are other possibilities to look an image in
>> 3D, for example, Free Surfer...
>>
>> Peace,
>>
>> Rosalia.
>>
>
>
>
> --
> Sunil Koundal
> Senior Research Fellow
> NMR Research Centre
> INMAS, DRDO
> DELHI-54
> Mobile number -+919910969525
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