I should also note that probtrackx2 finishes in just a few minutes...as if it isn't really engaging in the task.

-Dianne

On Sat, Feb 3, 2018 at 3:41 PM, Dianne Patterson <[log in to unmask]> wrote:

I see what you mean, I am iterating back and forth between the 2 seed masks...I must have grabbed different iterations for my last example (which makes things harder for you...sorry). Here is the first iteration of each of them:

probtrackx --network --mode=seedmask -x subjectrois/atl_r_diff_bin_csf -l -c 0.2 -S 2000 

--steplength=0.5 -P 5000 --stop=subjectrois/unc_r_inv_mask_diff_bin_csf --forcedir -f --opd 

-s dwi/Bed.bedpostX/merged -m dwi/Bed.bedpostX/nodif_brain_mask 

--dir=dwi/unc_r_bip --targetmasks=dwi/unc_r_bip/targets.txt --os2t 

fslstats seeds_to_frontal_orbital_r_diff_bin_csf.nii.gz -V

1791 19070.572266

==============================

probtrackx2 -x subjectrois/atl_r_diff_bin_csf -l -c 0.2 -S 2000 

--steplength=0.5 -P 5000 --stop=subjectrois/unc_r_inv_mask_diff_bin_csf --forcedir -f 

-s dwi/Bed.bedpostX/merged -m dwi/Bed.bedpostX/nodif_brain_mask 

--dir=dwi/unc_r_bip --targetmasks=dwi/unc_r_bip/targets.txt --os2t 

fslstats seeds_to_frontal_orbital_r_diff_bin_csf.nii.gz -V

2 21.296003

=============================

Thank you for spending time helping me with this.

-Dianne

On Sat, Feb 3, 2018 at 1:08 PM, Moises Hernandez <[log in to unmask]> wrote:

mmmm are you using the same seed mask?

-x subjectrois/frontal_orbital_r_diff_bin_csf

-x subjectrois/atl_r_diff_bin_csf

On 3 February 2018 at 15:02, Dianne Patterson <[log in to unmask]> wrote:

Thank you Moises,

Here is the command I am running in probtrackx:

probtrackx --network --mode=seedmask -x subjectrois/frontal_orbital_r_diff_bin_csf -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --stop=subjectrois/unc_r_inv_mask_diff_bin_csf --forcedir -f --opd -s dwi/Bed.bedpostX/merged -m dwi/Bed.bedpostX/nodif_brain_mask --dir=dwi/unc_r_bip --targetmasks=dwi/unc_r_bip/targets.txt --os2t  

I found I cannot simply call probtrackx2 with the same flags, and I've tried various alternative options based on the gui and reading.  I am primarily interested in the seeds-to-target masks that get generated. Clearly I'm doing something very wrong. Here is one of the options I tried in probtrackx2 (but all of the options I've tried have similar results):

probtrackx2 -x subjectrois/atl_r_diff_bin_csf -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --stop=subjectrois/unc_r_inv_mask_diff_bin_csf --forcedir -f --opd -s dwi/Bed.bedpostX/merged -m dwi/Bed.bedpostX/nodif_brain_mask --dir=dwi/unc_r_bip --targetmasks=dwi/unc_r_bip/targets.txt --os2t

(In both cases I have shortened the paths in this email to make the commands easier for us to read)

result using probtrackx command above:

fslstats seeds_to_frontal_orbital_r_diff_bin_csf.nii.gz -V

1791 19070.572266

result using probtrackx2 command above:

fslstats seeds_to_frontal_orbital_r_diff_bin_csf.nii.gz -V

2 21.296003

What am I missing?

Thanks so much,

Dianne

On Sat, Feb 3, 2018 at 12:25 PM, Moises Hernandez <[log in to unmask]> wrote:

Dianne, probtrackx2 has not lost any functionality (what function do you think it has lost?).

It is the opposite, it has added functionality. 

What exact commands (probtrackx & probtrackx) are you using for comparing the results? 

Moises.

On 3 February 2018 at 14:10, Dianne Patterson <[log in to unmask]> wrote:

Thank you Michiel, for your suggestion r probtrackx2.  

I have tried the probtrackx2 command as you suggested above both with and without the --opd flag.

Neither is anywhere close to the probtrackx run on the same tract.  The probtrackx run retains a lot of voxels in the two endpoint masks...but probtrackx2 does not retain them (it goes to 0 or 1 voxel retained pretty quickly).

I am surprised to find that probtrackx2 is so different, and that I have apparently lost functionality in probtrackx2 vs probtrackx. I suppose I could continue using probtrackx, but I'd love to understand what is going on here.

Thanks for your time,

Dianne

On Fri, Feb 2, 2018 at 3:33 AM, Michiel Cottaar <[log in to unmask]> wrote:

Hi Dianne,

I suspect that the difference in behaviour is not due to the --mode or even the --network mask, but in the original probtrackx you specify a set of classification targets (through the flags: " --targetmasks=sub-5167/dwi/unc_r_bip/targets.txt --os2t “), however in the new command you choose to output only the path distribution (--opd flag) What happens if you run the probtrackx2 with the same flags as the original probtrackx command, but without the —network or --mode option:

probtrackx2  -x sub-5167/subjectrois/frontal_orbital_r_diff_bin_csf -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --stop=sub-5167/subjectrois/unc_r_inv_mask_diff_bin_csf --forcedir -f --opd -s sub-5167/dwi/Bed.bedpostX/merged -m sub-5167/dwi/Bed.bedpostX/nodif_brain_mask --dir=sub-5167/dwi/unc_r_bip --targetmasks=sub-5167/dwi/unc_r_bip/targets.txt —os2t 

Good luck,

Michiel

On 1 Feb 2018, at 01:30, Dianne Patterson <[log in to unmask]> wrote:

Dear dti experts:

I was hoping to move from probtrackx to probtrackx2, but it seems more complex than I had anticipated:

I can run this command:

probtrackx --network --mode=seedmask -x sub-5167/subjectrois/frontal_orbital_r_diff_bin_csf -l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --stop=sub-5167/subjectrois/unc_r_inv_mask_diff_bin_csf --forcedir -f --opd -s sub-5167/dwi/Bed.bedpostX/merged -m sub-5167/dwi/Bed.bedpostX/nodif_brain_mask --dir=sub-5167/dwi/unc_r_bip --targetmasks=sub-5167/dwi/unc_r_bip/targets.txt --os2t 

probtrackx2  -x sub-5167/dwi/unc_l_bip/masks.txt -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --stop=sub-5167/subjectrois/unc_l_inv_mask_diff_bin_csf.nii.gz --forcedir --opd -s sub-5167/dwi/Bed.bedpostX/merged -m sub-5167/dwi/Bed.bedpostX/nodif_brain_mask --dir=sub-5167/dwi/unc_l_bip

---------------------------------------------

probtrackx2 does not support --mode=seedmask

Is there some equivalent?

In addition, if I remove --mode=seedmask, probtrackx2 complains about --network.  When I remove that as well, probtrackx2 behaves very differently than the original probtrackx command.

I have tried probtrackx2 with and without the bolded flags --onewaycondition  --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 (these are added to the command when I run with the gui).  These also do not seem to make any difference.

============

I was running the original probtrackx command iteratively to look at the resulting size of the two grey matter masks.  I don't understand how to replicate the original behavior with probtrackx2.

Any help would be appreciated.

Thanks,

Dianne

--

Dianne Patterson, Ph.D.

Research Scientist
[log in to unmask]

or 

[log in to unmask]
University of Arizona
Speech and Hearing Science 314

1131 E 2nd Street, Building #71
(Just East of Harvill)

==============

If you don't hear back from me (and you expected to), 

I blame the University's new SPAM filter.

Please write to my gmail account.

==============

Antipiphany: That moment when you realize how little you actually know

==============