Dear mark ,
Thanks for your reply , I was just making sure if my
procedure is correct.I can see standard data (Which comes with fsl) in
3D but not mine.It gives blank screen.
Regards
sunil .
On Sun, Jan 27, 2013 at 6:39 AM, Mark Jenkinson
<[log in to unmask]> wrote:
> 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
--
Sunil Koundal
Senior Research Fellow
NMR Research Centre
INMAS, DRDO
DELHI-54
Mobile number -+919910969525
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