Trying to run the script --> line 189: ASHS_WORK: parameter null or not set

[Pau Packard Blasco]

Hi,

I just downloaded and installed the latest version of fast-ashs for MacOs (ashs-fastashs-20170915) and the last version of the U Penn Atlas for fast-ashs (ashs_atlas_upennpmc_20170810).

I have T2 image a voxel resolution of 0.39*0.39*2, and a T1 with a 1*1*1 resolution, which should be within the resolution range of the atlas right?

I am running the script from Terminal on my standalone MacOS X Yosemite. I followed the tutorial Getting Started and everything seemed to work. The only difference is that when I checked the T2 images direction I used the 'darwin' instead of 'linux' with my bash shell Mac Os Terminal, so like this:

> /Users/Pau/Documents/Pau_Work/FMRI_SILTM/ashs/ashs-1.0.0/ext/Darwin/bin/c3d S12238_20181123_001_017_t2_tse_cor_512_p2_2mm.nii -info

My problem is that I can't seem to get the segmentation running properly.

First I go to where I have my T2 and T1 images and where I want the output to go:

> cd /Users/Pau/Documents/Pau_Work/FMRI_SILTM/ashs/Processed_data

Then I try to get the script running like so:

> nohup $ASHS_ROOT/bin/ashs_main.sh -I subj12238 -a $ASHS_ROOT/ashs_atlas_upennpmc_20170810 -g y_S12238_20181123_001_016_t1_mpr_ns_sag_p2_1_0_iso.nii -f S12238_20181123_001_017_t2_tse_cor_512_p2_2mm.nii -w /Users/Pau/Documents/Pau_Work/FMRI_SILTM/ashs/Processed_data/subj12238 &

I  always get the following message:

ASHS_WORK: parameter null or not set

That's the only thing that appears on the nohup.out file it produces. It's seems odd because then the script doesn't seem to do anything else, even if I let it run for a while, but I don't get an Exit message unless I actually press 'ctrl + C'.

So it seems the problem is when it tries to convert the working directory to the absolute path.

I tried with different paths and directories but I always get the same message.

Any ideas about what I should try next or where I went wrong?

Thanks in advance,

Pau Alexander Packard,  Ph.D.
Department of Psychology
University of Luebeck
Maria-Goeppert-Str. 9a
D-23562 Luebeck, Germany
Building MFC VIII, 1. OG, Raum 1
Phone: +49 451 3101 3606
Fax:   +49 451 3101 3604

[Paul Yushkevich]

Hi Pau

Have you tried the cloud-based version: https://sites.google.com/view/ashs-dox/cloud-ashs/overview?authuser=0

It may be easier to test out a dataset than running on the Mac.

I have to see what's going on with that ASHS_WORK error, perhaps it's a Mac bug?

Thanks!
Paul

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

[Pau Alexander Packard]

Thanks for the tip! Someone sent me the web link to the older ASHS website: https://sites.google.com/site/hipposubfields/home, so I hadn't even seen the new website with the cloud-ashs instructions. I'll try the cloud version and see what happens.

[joue.ni...@gmail.com]

Hi,

I'm piggybacking on Pau's message because I am also getting a very similar error in my nohup.out:

<$ASHS_ROOT>/bin/ashs_main.sh: line 193: ASHS_WORK: parameter null or not set

I am running the latest fastashs v.2.0.0 under Debian 9.13, and the confusing thing is that I have gotten ASHS to run with no problems on the same system before -- and I'm using the same scripts, but it's been a while. I have the environment variable ASHS_ROOT set in my .bashrc (my default shell is BASH), and have it added to my path and both exported.

Any help or leads to help me troubleshoot very much appreciated!!

Gina

[joue.ni...@gmail.com]

I figured out the source of the message/my error -- my script basically wasn't calling ashs_main.sh correctly.

Here are the details in case others run into the same error.

I had a commented line in my call to ashs_main.sh via nohup (I had switches on separate lines and chained with "\"):

 nohup nice -n $niceness $ASHS_ROOT/bin/ashs_main.sh -P -I $subj \

#  some comment that screws up the call

           -a $ashs_atlas \
           -g $f_T1 \
           -f $f_T2 \
           -w $soutd > ${logf}.log 2> ${logf}.err &

This caused the rest of the switches to be ignored/treated like a new command so the ashs_main.sh looked like it was improperly called. Although the nohup.out "ASHS_WORK: parameter null or not set" message was opaque, the standard error output gave a bit more informative message: " -a: command not found".