Unable to run antsRegistrationSyN.sh

[ksreeniv]

I am trying to run antsRegistrationSyN.sh and I keep getting the following error.

[user31 ~]$ antsRegistrationSyN.sh (even if calling including the full path I get the same error)


--------------------------------------------------------------------------------------
Error locating ANTS
--------------------------------------------------------------------------------------
It seems that the ANTSPATH environment variable is not set. Please add the ANTSPATH
variable. This can be achieved by editing the .bash_profile in the home directory.
Add:

ANTSPATH=/home/yourname/bin/ants/

Or the correct location of the ANTS binaries.

Alternatively, edit this script ( antsRegistrationSyN.sh ) to set up this parameter correctly.

I did search the forums and found some similar issues. From my understanding, the path not being defined properly can cause several issues. In my case, the files are being found, which I interpret as paths being defined correctly. (Using older version as that is what is currently present on the HPC cluster)

[user31 ~]$ which ANTS
/software/ants/2.3.4/bin/ANTS

[user31 ~]$ which antsRegistration
/software/ants/2.3.4/bin/antsRegistration

[user31 ~]$ which antsRegistrationSyN.sh
/software/ants/2.3.4/bin/antsRegistrationSyN.sh

[user31 ~]$ echo $PATH
/software/ants/2.3.4/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/opt/ibutils/bin:/hpc/usertools:/opt/zeek/bin:/home/user31/.local/bin:/home/user31/bin

[user31 ~]$ echo $ANTSPATH
/software/ants/2.3.4/bin/

When I execute ANTS and antsRegistration they run just fine (please see below), but antsRegistrationSyN errors out (as shown above).

[user31 ~]$ ANTS -h

COMMAND: 
       ANTS

OPTIONS: 
       -x, --mask-image maskFileName
       -m, --image-metric 
       -o, --output-naming 
       --R 
       -i, --number-of-iterations 
       --Restrict-Deformation 
       -v, --verbose 
       --use-all-metrics-for-convergence_

[user31 ~]$ antsRegistration

COMMAND: 
     antsRegistration
          This program is a user-level registration application meant to utilize classes 
          in ITK v4.0 and later. The user can specify any number of "stages" where a stage 
          consists of a transform; an image metric; and iterations, shrink factors, and 
          smoothing sigmas for each level. Note that explicitly setting the 
          dimensionality, metric, transform, output, convergence, shrink-factors, and 
          smoothing-sigmas parameters is mandatory.

OPTIONS: 

I am not sure what I am doing wrong and would greatly appreciate some help/guidance. I am very sorry if I have missed a similar post. Thank you.

-Karthik

[gdevenyi]

The error is pretty clear:

It seems that the ANTSPATH environment variable is not set. Please add the ANTSPATH
variable. This can be achieved by editing the .bash_profile in the home directory.
Add:

ANTSPATH=/home/yourname/bin/ants/

ANTSPATH is not PATH. ANTSPATH is the internal variable the developers decided to use to override the global PATH inside ants-supplied scripts.

[ksreeniv]

Thank you for the response. I do understand that the ANTSPATH and PATH are not the same. I did not directly append the location of the binary files to the PATH variable. I first defined ANTSPATH (which points to the binaries) and then appended my ANTSPATH to the PATH. If I print ANTSPATH and it will display the path to my binary folder.

[user31 ~]$ echo $PATH
/software/ants/2.3.4/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/opt/ibutils/bin:/hpc/usertools:/opt/zeek/bin:/home/user31/.local/bin:/home/user31/bin

[user31 ~]$ echo $ANTSPATH
/software/ants/2.3.4/bin/

[cookpa]

This is the test that's failing, assuming that your copy of the script is not modified.

ANTs/Scripts/antsRegistrationSyN.sh

Lines 32 to 35 in 12cfa66

	if [[ ${#ANTSPATH} -le 3 ]];
	then
	setPath >&2
	fi

Are you doing all this interactively? Can you run

echo $ANTSPATH
${ANTSPATH}antsRegistrationSyN.sh

[ksreeniv]

Yes, I was trying to make sure the ANTs module was loaded properly. I also tried the above commands (from one of the previous posts) and it didn't work for antsRegistrationSyN.sh. Output below

[user31 ~]$ echo $ANTSPATH
/software/ants/2.3.4/bin/
[user31 ~]$ ${ANTSPATH}antsRegistrationSyN.sh

--------------------------------------------------------------------------------------
Error locating ANTS
--------------------------------------------------------------------------------------
It seems that the ANTSPATH environment variable is not set. Please add the ANTSPATH
variable. This can be achieved by editing the .bash_profile in the home directory.
Add:

ANTSPATH=/home/yourname/bin/ants/

Or the correct location of the ANTS binaries.

Alternatively, edit this script ( antsRegistrationSyN.sh ) to set up this parameter correctly.

Having no issues with the other two

[user31 ~]$ ${ANTSPATH}antsRegistration

COMMAND: 
     antsRegistration
          This program is a user-level registration application meant to utilize classes 
          in ITK v4.0 and later. The user can specify any number of "stages" where a stage 
          consists of a transform; an image metric; and iterations, shrink factors, and 
          smoothing sigmas for each level. Note that explicitly setting the 
          dimensionality, metric, transform, output, convergence, shrink-factors, and 
          smoothing-sigmas parameters is mandatory. 

OPTIONS: 

[user31 ~]$ ${ANTSPATH}ANTS
 call ANTS -h or ANTS --help 

sidenote: I faced the same error above when I tried running antsRegistrationSyN.sh on my computer using a python script (subprocess module). However, I did not face any issues when I ran antsRegistrationSyN.sh directly in the terminal.

[cookpa]

[user31 ~]$ echo $ANTSPATH
/software/ants/2.3.4/bin/
[user31 ~]$ ${ANTSPATH}antsRegistrationSyN.sh

--------------------------------------------------------------------------------------
Error locating ANTS
--------------------------------------------------------------------------------------

Something in your environment is stopping this check from working:

if [[ ${#ANTSPATH} -le 3 ]]; 
   then 
     setPath >&2 
   fi 

To isolate the test, make this a runnable script:

#!/bin/bash

if [[ ${#ANTSPATH} -le 3 ]]; 
   then 
     echo "bashopts are [ $- ]"
     echo "ANTSPATH is [ $ANTSPATH ], and the test failed on length [ ${#ANTSPATH} ]"
   fi 

[ksreeniv]

This is the output after running the above

[jiq7635@quser21 ~]$ sh test_ver1.sh 
enter code
enter loop

bashopts are [ hB ]
ANTSPATH is [  ], and the test failed on length [ 0 ]

Went on to further check again and the ANTSPATH variable was not exported and thus not being passed down to env. Thank you both and my sincere apologies for having wasted your time and for any inconvenience.