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Dear FSL group,
I have now set up and run the iterating probtrackx2 routine on a virtual
ubuntu machine with 32 GB of ram.
Once again, it bombs with a memory error, though perhaps more informative
that the mac output. I have attached the error.

I will try this with more ram and see if it behaves correctly.

-Dianne

On Sun, Feb 18, 2018 at 5:43 PM, Dianne Patterson <[log in to unmask]> wrote:

> Thankyou Moises,
>
> I think if what you said was true, then the procedure would not run on any
> machines.
> Once probtrackx2 crashes, it subsequently complains that it cannot find
> the images
> that would have been created if probtrackx2 had run successfully.
> Thanks,
>
> Dianne
>
> On Sun, Feb 18, 2018 at 2:54 PM, Moises Hernandez <[log in to unmask]>
> wrote:
>
>> Hi Dianne,
>> In this case, I think some of your variables or write permissions are
>> wrong:
>>
>> "Could not open image ..."
>> "No such file or directory..."
>>
>> Moises
>>
>> On 18 February 2018 at 16:19, Dianne Patterson <[log in to unmask]>
>> wrote:
>>
>>> I tried creating a new user on the 2013 mac pro that bombed on
>>> probtrackx2 with the malloc error under my login.
>>>
>>> The new user had the minimum .bashrc necessary to find fsl and call my
>>> scripts.  It also bombed after a couple of iterations of protrackx2, but
>>> with a different error message (near the bottom, bolded).  I have left in
>>> the messages for the first couple of iterations to demonstrate that it is
>>> working initially, but only bombs later.  Please tell me if there are any
>>> specific tests I should be running that I am not thinking of.
>>>
>>> Thanks in advance,
>>>
>>> -Dianne
>>>
>>> save results
>>>
>>> finished
>>>
>>> size of old seed mask is
>>>
>>> 1755 18687.242188
>>>
>>> size of new seed mask is
>>>
>>> 1627 17324.298828
>>>
>>> run 2nd bip round
>>>
>>> seed is /Exps/Data/BIP_ROTMAN/YC/derivatives/sub-5167/dwi/unc_r_bip/
>>> roi_B_1
>>>
>>> target is /Exps/Data/BIP_ROTMAN/YC/derivatives/sub-5167/dwi/unc_r_bip/
>>> roi_A_2
>>>
>>> /Exps/Data/BIP_ROTMAN/YC/sub-5167
>>>
>>> BipSub thinks bedpost dir is /Exps/Data/BIP_ROTMAN/YC/deriv
>>> atives/sub-5167/dwi/Bed.bedpostX
>>>
>>> Log directory is: /Exps/Data/BIP_ROTMAN/YC/deriv
>>> atives/sub-5167/dwi/unc_r_bip
>>>
>>> Running in seedmask mode
>>>
>>> load seeds
>>>
>>> done.
>>>
>>> Load bedpostx samples
>>>
>>> 1_1
>>>
>>> 1_2
>>>
>>> 1_3
>>>
>>> 2_1
>>>
>>> 2_2
>>>
>>> 2_3
>>>
>>> 3_1
>>>
>>> 3_2
>>>
>>> 3_3
>>>
>>>
>>> nfibres  : 3
>>>
>>> nsamples : 50
>>>
>>>
>>> Done loading samples.
>>>
>>> Volume seeds
>>>
>>> volume 1
>>>
>>>
>>> time spent tracking: 1242 seconds
>>>
>>>
>>> save results
>>>
>>> */usr/local/bip/bip.sh: line 55:  2385 Segmentation fault: 11
>>> probtrackx2 -x ${seed} -l -c 0.2 -S 2000 --steplength=0.5 -P 5000
>>> --stop=${inv} --forcedir --opd -s ${BEDPOST}/merged -m
>>> ${BEDPOST}/nodif_brain_mask --dir=${tract_dir}
>>> --targetmasks=${tract_dir}/targets.txt --os2t*
>>>
>>> *size of old seed mask is*
>>>
>>> *1647 17537.259766*
>>>
>>> size of new seed mask is
>>>
>>> Image Exception : #22 :: ERROR: Could not open image
>>> /Exps/Data/BIP_ROTMAN/YC/derivatives/sub-5167/dwi/unc_r_bip/seeds*
>>>
>>> cp: /Exps/Data/BIP_ROTMAN/YC/derivatives/sub-5167/dwi/unc_r_bip/seeds*:
>>> No such file or directory
>>>
>>> Cannot open volume /Exps/Data/BIP_ROTMAN/YC/deriv
>>> atives/sub-5167/dwi/unc_r_bip/roi_B_2 for reading!
>>>
>>> Image Exception : #22 :: ERROR: Could not open image
>>> /Exps/Data/BIP_ROTMAN/YC/derivatives/sub-5167/dwi/unc_r_bip/roi_B_2
>>>
>>> increment i and j
>>>
>>> i is 2
>>>
>>> j is 3
>>>
>>> unc_r
>>>
>>> /usr/local/bip/bip.sh: line 197: [: too many arguments
>>>
>>>
>>> --
>>> Dianne Patterson, Ph.D.
>>> Research Scientist
>>> [log in to unmask] <[log in to unmask]>
>>> or
>>> [log in to unmask]
>>> University of Arizona
>>> Speech and Hearing Science 314
>>> 1131 E 2nd Street, Building #71
>>> <https://maps.google.com/?q=1131+E+2nd+Street,+Building+%2371&entry=gmail&source=g>
>>> (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
>>> ==============
>>>
>>
>>
>