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
>> ==============
>>
>
>
