Hello,
As Michiel suggested it might be a good idea to look at your three intermediate images:
tract_norm_MNI.nii.gz
tract_norm_thr01_mask.nii.gz
tract_norm_thr05_mask_MNI.nii.gz
in order to see at what point your tracts dissapear.
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 30 Jun 2018, at 12:38, Dev vasu <[log in to unmask]> wrote:
>
> Dear Sir,
>
> I have changed the script, when i look at fdt_paths.nii.gz i see the tracks, i think there is some problem with thresholding, but i am not sure, what is the problem with thresholding.
>
> could you please suggest me some steps post probtrackx analysis to know if i have done some thing wrong.
>
>
> Thanks
> Vasudev
>
> On Sat, Jun 30, 2018 at 12:41 PM, Michiel Cottaar <[log in to unmask]> wrote:
> Dear Vasudev,
>
> When you look at the original fdt_paths.nii.gz do you see any tracts? If so, could you have a look at the intermediate files and check at what point these tracts disappear? That would make it a bit easier to pin-point what the problem would be. One thing I did notice in the script is that the thresholding fslmaths command produces a file called “tract_norm_thr01_mask.nii.gz”. This should probably be “tract_norm_thr05_mask.nii.gz”, because the threshold is set to 0.05 and in the next line that is the filename you use.
>
> Best wishes,
> Michiel
>
>> On 26 Jun 2018, at 15:04, Dev vasu <[log in to unmask]> wrote:
>>
>>
>>
>>
>> Dear all,
>>
>> I have written a small script for thresholding fdt_paths.nii.gz, i am incurring a problem in which i could not find any tracks originating from seed and terminating at the termination mask.
>>
>>
>> I have provided segmented custom seed masks with way points and termination masks ( in MNI space )
>>
>>
>>
>>
>> warpimg=`pwd -P`/bedpostX/xfms/diff2standard_warp.nii.gz
>> refMNI=/FSL/fsl_5.0.3/fsl/data/standard/MNI152_T1_2mm
>> fslmaths fdt_paths.nii.gz -div `cat waytotal` tract_norm.nii.gz
>> applywarp -i tract_norm.nii.gz -r ${refMNI} -w ${warpimg} -o tract_norm_MNI.nii.gz
>> fslmaths tract_norm.nii.gz -thr 0.05 -bin tract_norm_thr01_mask.nii.gz
>> applywarp -i tract_norm_thr05_mask.nii.gz -r ${refMNI} -w ${warpimg} -o tract_norm_thr05_mask_MNI.nii.gz
>> fslmaths tract_norm_thr05_mask_MNI.nii.gz -thr 0.5 -bin tract_norm_thr05_mask_MNI.nii.gz
>>
>> Could you please suggest me if the procedure in which i threshold is incorrect or if there is any problem in my approach that i usually end up with either artifacts or no tracks originating at seed and terminating at termination mask, although waytotal indicates around 478 tracks.
>>
>>
>> Thanks
>> Vasudev
>>
>>
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