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Dear Matthew,

I tried doing that and it worked though sometimes error messages still appear. However some tracks did not appear when i overlaid it on top of the structural image though it was open on fslview. Is it a threshold issue or a something went wrong during the tracking? 

This was the output in terminal:

neuros-iMac-2:~/Desktop] neuro% rm -rf /Users/neuro/Desktop/PD_PATIENTS/2/KSK_TENSOR32DIRECTIONS/KSK_OUTPUT/KSK_bedpostx.bedpostX/2PPNright

mkdir -p /Users/neuro/Desktop/PD_PATIENTS/2/KSK_TENSOR32DIRECTIONS/KSK_OUTPUT/KSK_bedpostx.bedpostX/2PPNright

133 125 87 (mm) -> 0.479357 235.023 283.833 (voxels)

/Users/neuro/Downloads/fsl/bin/probtrackx2 --simple --seedref=/Users/neuro/Desktop/PD_PATIENTS/2/KSK_TENSOR32DIRECTIONS/KSK_OUTPUT/KSK_bedpostx.bedpostX/s004a1001_brain.nii.gz -o 2PPNright -x /Users/neuro/Desktop/PD_PATIENTS/2/KSK_TENSOR32DIRECTIONS/KSK_OUTPUT/KSK_bedpostx.bedpostX/2PPNright/fdt_coordinates.txt  -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --xfm=/Users/neuro/Desktop/PD_PATIENTS/2/KSK_TENSOR32DIRECTIONS/KSK_OUTPUT/KSK_bedpostx.bedpostX/xfms/str2diff.mat --forcedir --opd -s /Users/neuro/Desktop/PD_PATIENTS/2/KSK_TENSOR32DIRECTIONS/KSK_OUTPUT/KSK_bedpostx.bedpostX/merged -m /Users/neuro/Desktop/PD_PATIENTS/2/KSK_TENSOR32DIRECTIONS/KSK_OUTPUT/KSK_bedpostx.bedpostX/nodif_brain_mask  --dir=/Users/neuro/Desktop/PD_PATIENTS/2/KSK_TENSOR32DIRECTIONS/KSK_OUTPUT/KSK_bedpostx.bedpostX/2PPNright

Log directory is: /Users/neuro/Desktop/PD_PATIENTS/2/KSK_TENSOR32DIRECTIONS/KSK_OUTPUT/KSK_bedpostx.bedpostX/2PPNright

Running in simple mode

Load bedpostx samples

1_1

1_2

1_3

2_1

2_2

2_3

 

nfibres  : 2

nsamples : 50

 

Done loading samples.

 

time spent tracking: 1 seconds

 

save results

finished

Done!


Thanks.


Best regards,

Isobel French

Academic Coordinator and Research Officer
Neurosurgery Research Unit, Division of Neurosurgery
Department of Surgery, Faculty of Medicine
University Malaya

Suite 15 T8-4a 
Level 4, Menara Timur
University of Malaya Medical Center

016-7937605
03-79493138

On Tue, Jan 12, 2016 at 8:21 PM, Matthew Webster <[log in to unmask]> wrote:
Hello,
  Yes - once you have generated the transforms, you can run probtrackx to generate outputs in non-diffusion space ( e.g. structural or standard ).

Kind Regards
Matthew

Dear Matthew,

Does that mean that I should register the images first before using PROBTRACKX to get the track i want to look at? 

Thanks.


Best regards,

Isobel French

Academic Coordinator and Research Officer
Neurosurgery Research Unit, Division of Neurosurgery
Department of Surgery, Faculty of Medicine
University Malaya

Suite 15 T8-4a 
Level 4, Menara Timur
University of Malaya Medical Center

016-7937605
03-79493138

On Mon, Jan 11, 2016 at 7:32 PM, Matthew Webster <[log in to unmask]> wrote:
Hello Isobel,
The Fdt GUI has an option for registration, that I think should do what you want.

Kind Regards
Matthew


Dear Matthew,

Which gui are you referring to? I tried converting images through applywarp from diffusion to structural and structural to diffusion as instructed in the practical. After that I used PROBTRACKX to obtain tracks from a structural space through non-linear seed space. Converting the images were successful though to what extent I'm not sure. However when I tried obtaining the tracks from the non-linear seed space the image was 'out of range' in fslview (i am unable to attach the image as the file size exceeded the maximum size). 

What could be the problem to this? 

Tqvm.

Best regards,

Isobel French