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/derivatives/sub-5167/dwi/Bed.bedpostX

Log directory is: /Exps/Data/BIP_ROTMAN/YC/derivatives/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/derivatives/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]

or 

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

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

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