Pipeline seems to call same step twice but call is twisted

[Freing Alina]

Dear XNAT experts,

here I am again with a strange pipeline problem. I'm running XNAT 1.6.1 on Mac OS X Mountain Lion. 

The pipeline is supposed to run fslreorient2std on a nifti image, see below for pipeline xml. (The same pipeline syntax worked flawlessly in XNAT 1.5.4.) The pipeline seems to execute the step, there is no error. But the reoriented file isn't created - nothing seems to happen. The executable is called, however, I checked. It is called twice - once correctly as 

"/usr/local/fsl/bin/fslreorient2std /Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr.nii.gz /Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz" 

and once again as 

"/usr/local/fsl/bin/fslreorient2std --version"

The resource xml is also attached. (And "--version" is nowhere in it, this executable doesn't even have that option.) When I manually execute the first call as the correct user via ssh it works nicely (and is only called once), so the problem likely isn't (completely) in fslreorient2std. 

There is nothing in the pipeline log, as the pipeline doesn't notice the step actually fails. It simply fails on the next step, which uses the file created here.

Am I missing something? I have no idea even where to start looking, so I'd be really grateful for any pointers.

Thanks a lot

Alina

#############################

<step id="16" description="Reorient image to FSL standard" >

<resource name="fslreorient2std_ssh" location="ncrc/resource" ssh2Host="my_ip" ssh2User="xnat_user" ssh2Identity="path_to_id_dsa">

<argument id="infile">

<value>^concat('/Volumes/MacintoshHD2/xnat_pipeline_space/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),'/NIFTI/mprage_nifti_inhcorr.nii.gz')^</value>

</argument>

<argument id="outfile">

<value>^concat('/Volumes/MacintoshHD2/xnat_pipeline_space/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),'/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz')^</value>

</argument>

</resource>

</step>

######

<?xml version="1.0" encoding="UTF-8"?>

<pip:Resource xmlns:pip="http://nrg.wustl.edu/pipeline">

        <pip:name>fslreorient2std</pip:name>

        <pip:location>/usr/local/fsl/bin</pip:location>

        <pip:type>Executable</pip:type>

        <pip:description>reorients NIfTI image to FSL standard</pip:description>

        <pip:estimated_time>00:00:01</pip:estimated_time>

        <pip:input>

            <pip:argument id="infile" prefix="" nospace="true">

                <pip:name></pip:name>

                <pip:description>input file</pip:description>

            </pip:argument>

            <pip:argument id="outfile" prefix="" nospace="true">

                <pip:name></pip:name>

                <pip:description>output file</pip:description>

            </pip:argument>

</pip:input>

</pip:Resource>

############################

[John Flavin]

Alina,

Can you attach the contents of your logs directory? There should be three log files, ending with .log, .err, and .xml.

Flavin

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[Mohana Ramaratnam]

Hi Alina,

The pipeline engine has a record of provenance, which includes the version of each of the executables/scrpipts that it invokes. The engine attempts to extract the version by:

First Attempt: PATH_TO_EXECUTABLE -version

Second Attempt (if first fails): PATH_TO_EXECUTABLE --version

Now to your second problem: of fslreorient2std_ssh not generating the output:

Looks like you are doing a SSH, can you skip pipeline engine and directly logon to SSH Host and execute the call 

 "/usr/local/fsl/bin/fslreorient2std /Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr.nii.gz /Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz" 

Do you get the expected result? 

Mohana

[Freing Alina]

Hi Mohana,

thank you for explaining where the "--version" comes from!

Executing the call to fslreorient2std directly yields the expected result, the output file is created.

Alina

----

Dr. rer. nat. Alina Freing
Wissenschaftliche Mitarbeiterin

UNIVERSITÄTSMEDIZIN GÖTTINGEN
GEORG-AUGUST-UNIVERSITÄT
Institut für diagnostische und interventionelle Neuroradiologie
Robert-Koch-Straße 40
37075 Göttingen
Briefpost: 37099 Göttingen
Telefon 0551 / 39-20695
www.universitaetsmedizin-goettingen.de

[Freing Alina]

There are only .log files in my pipeline/logs directory - nothing else. (I think, maybe my log4j system isn't properly initialized….)

Attached is the complete log file for the pipeline in question. (It fails on uploading the reoriented file as the file doesn't exist.)

Alina

#######################################

DEBUG main org.nrg.pipeline.utils.PipelineProperties - Initializing the pipeline properties from the specified properties object

DEBUG main org.nrg.pipeline.utils.PipelineProperties - Setting admin email to: alina....@med.uni-goettingen.de

DEBUG main org.nrg.pipeline.utils.PipelineProperties - Setting email ID to: alina....@med.uni-goettingen.de

DEBUG main org.nrg.pipeline.utils.PipelineProperties - Setting SMTP host to: mailout.med.uni-goettingen.de

DEBUG main org.nrg.pipeline.utils.PipelineProperties - Setting REST mail host to: https://10.76.126.189/xnat/data/services/mail/send

FATAL main org.nrg.pipeline.client.XNATPipelineLauncher - Couldnt search for queued workflows

javax.net.ssl.SSLException: hostname in certificate didn't match: <10.76.126.189> != <jonagold.rad-diagno3.med.local>

at org.apache.http.conn.ssl.AbstractVerifier.verify(AbstractVerifier.java:228)

at org.apache.http.conn.ssl.BrowserCompatHostnameVerifier.verify(BrowserCompatHostnameVerifier.java:54)

at org.apache.http.conn.ssl.AbstractVerifier.verify(AbstractVerifier.java:149)

at org.apache.http.conn.ssl.AbstractVerifier.verify(AbstractVerifier.java:130)

at org.apache.http.conn.ssl.SSLSocketFactory.connectSocket(SSLSocketFactory.java:397)

at org.apache.http.impl.conn.DefaultClientConnectionOperator.openConnection(DefaultClientConnectionOperator.java:148)

at org.apache.http.impl.conn.AbstractPoolEntry.open(AbstractPoolEntry.java:150)

at org.apache.http.impl.conn.AbstractPooledConnAdapter.open(AbstractPooledConnAdapter.java:121)

at org.apache.http.impl.client.DefaultRequestDirector.tryConnect(DefaultRequestDirector.java:575)

at org.apache.http.impl.client.DefaultRequestDirector.execute(DefaultRequestDirector.java:425)

at org.apache.http.impl.client.AbstractHttpClient.execute(AbstractHttpClient.java:820)

at org.nrg.xnattools.xml.AbsService.getResponseBody(AbsService.java:87)

at org.nrg.xnattools.xml.XMLSearch.execute(XMLSearch.java:243)

at org.nrg.xnattools.xml.XMLSearch.searchAll(XMLSearch.java:109)

at org.nrg.pipeline.client.XNATPipelineLauncher.isPipelineQueuedOrAwaitingOrOnHold(XNATPipelineLauncher.java:281)

at org.nrg.pipeline.client.XNATPipelineLauncher.launch(XNATPipelineLauncher.java:63)

at org.nrg.pipeline.client.XNATPipelineLauncher.run(XNATPipelineLauncher.java:231)

at org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:221)

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre https://10.76.126.189/xnat/ [https://10.76.126.189/xnat/]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre e34c68f2-4fd2-4d32-8ead-b71e409cb64b [e34c68f2-4fd2-4d32-8ead-b71e409cb64b]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre e34c68f2-4fd2-4d32-8ead-b71e409cb64b [e34c68f2-4fd2-4d32-8ead-b71e409cb64b]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre 1374751475357 [1374751475357]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre mailout.med.uni-goettingen.de [mailout.med.uni-goettingen.de]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre A.Freing [A.Freing]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre /Volumes/MacintoshHD2/XNAT/build/TEST_PROJECT/20130725_132435 [/Volumes/MacintoshHD2/XNAT/build/TEST_PROJECT/20130725_132435]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ALINASXNAT [ALINASXNAT]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre alina....@med.uni-goettingen.de [alina....@med.uni-goettingen.de]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre alina....@stud.uni-goettingen.de [alina....@stud.uni-goettingen.de]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre 4 [4]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre TEST_PROJECT [TEST_PROJECT]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ALINASXNAT_S00001 [ALINASXNAT_S00001]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ALINASXNAT_E00001 [ALINASXNAT_E00001]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ncrc_S00500 [ncrc_S00500]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre 1 [1]

INFO main org.nrg.pipeline.utils.PipelineEngineUtils - Parameter Resolved

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^/Pipeline/parameters/parameter[name='scanids']/values/list^ []

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^/Pipeline/parameters/parameter[name='scanids']/values/unique^ [4]

INFO main org.nrg.pipeline.utils.PipelineEngineUtils - Loop Resolved

INFO main org.nrg.pipeline.utils.PipelineEngineUtils - Output resolved

INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved

INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /common/xnat/pipeline/catalog/ncrc/resource/fslreorient2std_ssh.xml

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^concat('/Volumes/MacintoshHD2/xnat_pipeline_space/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),'/NIFTI/mprage_nifti_inhcorr.nii.gz')^ [/Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr.nii.gz]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^concat('/Volumes/MacintoshHD2/xnat_pipeline_space/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),'/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz')^ [/Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz]

INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /common/xnat/pipeline/catalog/ncrc/resource/fslreorient2std_ssh.xml

INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved

INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /common/xnat/pipeline/catalog/xnat_tools/XnatRestClient_ssh.xml

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^/Pipeline/parameters/parameter[name='user']/values/unique/text()^ [e34c68f2-4fd2-4d32-8ead-b71e409cb64b]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^/Pipeline/parameters/parameter[name='pwd']/values/unique/text()^ [1374751475357]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre https://jonagold.rad-diagno3.med.local/xnat [https://jonagold.rad-diagno3.med.local/xnat]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^concat('/data/archive/projects/',/Pipeline/parameters/parameter[name='project']/values/unique/text(),'/subjects/',/Pipeline/parameters/parameter[name='subject']/values/unique/text(),'/experiments/',/Pipeline/parameters/parameter[name='xnat_id']/values/unique/text(),'/scans/',/Pipeline/parameters/parameter[name='scanids']/values/unique/text(),'/resources/NIFTI/files/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),'_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz?format=NIFTI')^ [/data/archive/projects/TEST_PROJECT/subjects/ALINASXNAT_S00001/experiments/ALINASXNAT_E00001/scans/4/resources/NIFTI/files/ncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz?format=NIFTI]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre PUT [PUT]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^concat('/Volumes/MacintoshHD2/xnat_pipeline_space/',/Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),'/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz')^ [/Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz]

INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /common/xnat/pipeline/catalog/xnat_tools/XnatRestClient_ssh.xml

INFO main org.nrg.pipeline.task.StepManager - Step attributes resolved

INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /common/xnat/pipeline/catalog/notifications/Notifier.xml

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^/Pipeline/parameters/parameter[name='user']/values/unique/text()^ [e34c68f2-4fd2-4d32-8ead-b71e409cb64b]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^/Pipeline/parameters/parameter[name='pwd']/values/unique/text()^ [1374751475357]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^/Pipeline/parameters/parameter[name='useremail']/values/unique/text()^ [alina....@stud.uni-goettingen.de]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^/Pipeline/parameters/parameter[name='adminemail']/values/unique/text()^ [alina....@med.uni-goettingen.de]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^/Pipeline/parameters/parameter[name='adminemail']/values/unique/text()^ [alina....@med.uni-goettingen.de]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^concat('XNAT update: ', /Pipeline/parameters/parameter[name='sessionId']/values/unique/text(),' NIFTI conversion is now complete.')^ [XNAT update: ncrc_S00500 NIFTI conversion is now complete.]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^/Pipeline/parameters/parameter[name='mailhost']/values/unique/text()^ [mailout.med.uni-goettingen.de]

DEBUG main org.nrg.pipeline.xpath.XPathResolverSaxon - Expre ^concat('Dear ',/Pipeline/parameters/parameter[name='userfullname']/values/unique/text(),',<br> <p> NIFTI conversion is now complete for ', /Pipeline/parameters/parameter[name='sessionId']/values/unique/text(), '<br> <p> XNAT Team.')^ [Dear A.Freing,<br> <p> NIFTI conversion is now complete for ncrc_S00500<br> <p> XNAT Team.]

INFO main org.nrg.pipeline.manager.ResourceManager - Loaded /common/xnat/pipeline/catalog/notifications/Notifier.xml

INFO main org.nrg.pipeline.manager.ExecutionManager - Launching step 0

INFO main org.nrg.pipeline.manager.ExecutionManager - Pipeline executed

INFO main org.nrg.pipeline.manager.ExecutionManager - Launching step 0

FATAL main org.nrg.pipeline.manager.ExecutionManager -  Execution of /usr/local/bin/xnat_tools/XNATRestClient -u e34c68f2-4fd2-4d32-8ead-b71e409cb64b -p ######## -host https://jonagold.rad-diagno3.med.local/xnat -remote /data/archive/projects/TEST_PROJECT/subjects/ALINASXNAT_S00001/experiments/ALINASXNAT_E00001/scans/4/resources/NIFTI/files/ncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz\?format=NIFTI -local /Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz -m PUT at Step[id= 17:] was unsuccesfull

FATAL main org.nrg.pipeline.manager.ExecutionManager -  Execution of /usr/local/bin/xnat_tools/XNATRestClient -u e34c68f2-4fd2-4d32-8ead-b71e409cb64b -p ######## -host https://jonagold.rad-diagno3.med.local/xnat -remote /data/archive/projects/TEST_PROJECT/subjects/ALINASXNAT_S00001/experiments/ALINASXNAT_E00001/scans/4/resources/NIFTI/files/ncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz\?format=NIFTI -local /Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz -m PUT at Step[id= 17:] was unsuccesfull

DEBUG main org.nrg.pipeline.exception.PipelineEngineException -  Execution of /usr/local/bin/xnat_tools/XNATRestClient -u e34c68f2-4fd2-4d32-8ead-b71e409cb64b -p ######## -host https://jonagold.rad-diagno3.med.local/xnat -remote /data/archive/projects/TEST_PROJECT/subjects/ALINASXNAT_S00001/experiments/ALINASXNAT_E00001/scans/4/resources/NIFTI/files/ncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz\?format=NIFTI -local /Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz -m PUT at Step[id= 17:] was unsuccesfull

DEBUG main org.nrg.pipeline.exception.PipelineEngineException - org.nrg.pipeline.exception.PipelineEngineException:  Execution of /usr/local/bin/xnat_tools/XNATRestClient -u e34c68f2-4fd2-4d32-8ead-b71e409cb64b -p ######## -host https://jonagold.rad-diagno3.med.local/xnat -remote /data/archive/projects/TEST_PROJECT/subjects/ALINASXNAT_S00001/experiments/ALINASXNAT_E00001/scans/4/resources/NIFTI/files/ncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz\?format=NIFTI -local /Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz -m PUT at Step[id= 17:] was unsuccesfull

at org.nrg.pipeline.manager.ExecutionManager.execute(ExecutionManager.java:96)

at org.nrg.pipeline.task.StepManager.execute(StepManager.java:166)

at org.nrg.pipeline.manager.PipelineManager.launchPipeline(PipelineManager.java:213)

at org.nrg.pipeline.manager.PipelineManager.launchPipeline(PipelineManager.java:193)

at org.nrg.pipeline.client.XNATPipelineLauncher.launch(XNATPipelineLauncher.java:65)

at org.nrg.pipeline.client.XNATPipelineLauncher.run(XNATPipelineLauncher.java:231)

at org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:221)

DEBUG main org.nrg.pipeline.utils.MailUtils - Sending message with subject: XNAT update: Processing failed for ncrc_S00500

DEBUG main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Setting the REST mail service endpoint to: https://10.76.126.189/xnat/data/services/mail/send

DEBUG main org.springframework.web.client.RestTemplate - Created POST request for "https://10.76.126.189/xnat/data/services/mail/send"

DEBUG main org.springframework.web.client.RestTemplate - Setting request Accept header to [text/plain, */*]

DEBUG main org.springframework.web.client.RestTemplate - Writing [{from=[alina....@med.uni-goettingen.de], to=[alina....@stud.uni-goettingen.de, alina....@med.uni-goettingen.de], subject=[XNAT update: Processing failed for ncrc_S00500], text=[The processing request you submitted for ncrc_S00500 could not be completed at this time. 

 The XNAT technical team is aware of the issue and will notify you when it has been resolved.

 The stdout and the error log files are available as attachments for your perusal.

 We appreciate your patience.  Please contact alina....@med.uni-goettingen.de with questions or concerns. ], html=[<html>The processing request you submitted for ncrc_S00500 could not be completed at this time. <br><br><br> The XNAT technical team is aware of the issue and will notify you when it has been resolved.<br><br><br> The stdout and the error log files are available as attachments for your perusal.<br><br><br> We appreciate your patience.  Please contact alina....@med.uni-goettingen.de with questions or concerns. </html>]}] using [org.springframework.http.converter.FormHttpMessageConverter@5df84008]

DEBUG main httpclient.wire.header - >> "POST /xnat/data/services/mail/send HTTP/1.1[\r][\n]"

DEBUG main httpclient.wire.header - >> "Accept: text/plain, */*[\r][\n]"

DEBUG main httpclient.wire.header - >> "Content-Type: application/x-www-form-urlencoded[\r][\n]"

DEBUG main httpclient.wire.header - >> "Authorization: Basic ZTM0YzY4ZjItNGZkMi00ZDMyLThlYWQtYjcxZTQwOWNiNjRiOjEzNzQ3NTE0NzUzNTc=[\r][\n]"

DEBUG main httpclient.wire.header - >> "User-Agent: Jakarta Commons-HttpClient/3.1[\r][\n]"

DEBUG main httpclient.wire.header - >> "Host: 10.76.126.189[\r][\n]"

DEBUG main httpclient.wire.header - >> "Content-Length: 1065[\r][\n]"

DEBUG main httpclient.wire.header - >> "[\r][\n]"

DEBUG main httpclient.wire.content - >> "from=alina.freing%40med.uni-goettingen.de&to=alina.freing%40stud.uni-goettingen.de&to=alina.freing%40med.uni-goettingen.de&subject=XNAT+update%3A+Processing+failed+for+ncrc_S00500&text=The+processing+request+you+submitted+for+ncrc_S00500+could+not+be+completed+at+this+time.+%0A%0A%0A+The+XNAT+technical+team+is+aware+of+the+issue+and+will+notify+you+when+it+has+been+resolved.%0A%0A%0A+The+stdout+and+the+error+log+files+are+available+as+attachments+for+your+perusal.%0A%0A%0A+We+appreciate+your+patience.++Please+contact+alina.freing%40med.uni-goettingen.de+with+questions+or+concerns.+&html=%3Chtml%3EThe+processing+request+you+submitted+for+ncrc_S00500+could+not+be+completed+at+this+time.+%3Cbr%3E%3Cbr%3E%3Cbr%3E+The+XNAT+technical+team+is+aware+of+the+issue+and+will+notify+you+when+it+has+been+resolved.%3Cbr%3E%3Cbr%3E%3Cbr%3E+The+stdout+and+the+error+log+files+are+available+as+attachments+for+your+perusal.%3Cbr%3E%3Cbr%3E%3Cbr%3E+We+appreciate+your+patience.++Please+contact+alina.freing%40med.uni-goettingen.de+with+questions+or+concerns.+%3C%2Fhtml%3E"

DEBUG main httpclient.wire.header - << "HTTP/1.1 200 OK[\r][\n]"

DEBUG main httpclient.wire.header - << "HTTP/1.1 200 OK[\r][\n]"

DEBUG main httpclient.wire.header - << "Date: Thu, 25 Jul 2013 11:25:02 GMT[\r][\n]"

DEBUG main httpclient.wire.header - << "Server: Apache/2.2.22 (Unix) DAV/2 mod_jk/1.2.37 mod_ssl/2.2.22 OpenSSL/0.9.8x[\r][\n]"

DEBUG main httpclient.wire.header - << "Set-Cookie: JSESSIONID=1BB4DA52F47BCF9B3EAEB597692480F4; Path=/xnat/; Secure; HttpOnly[\r][\n]"

DEBUG main httpclient.wire.header - << "Set-Cookie: SESSION_EXPIRATION_TIME="0,900000"; Version=1; Path=/[\r][\n]"

DEBUG main httpclient.wire.header - << "Accept-Ranges: bytes[\r][\n]"

DEBUG main httpclient.wire.header - << "Content-Length: 2[\r][\n]"

DEBUG main httpclient.wire.header - << "Vary: Accept-Encoding,User-Agent[\r][\n]"

DEBUG main httpclient.wire.header - << "MS-Author-Via: DAV[\r][\n]"

DEBUG main httpclient.wire.header - << "X-Frame-Options: SameOrigin[\r][\n]"

DEBUG main httpclient.wire.header - << "Content-Type: text/plain;charset=ISO-8859-1[\r][\n]"

DEBUG main httpclient.wire.header - << "[\r][\n]"

DEBUG main org.springframework.web.client.RestTemplate - POST request for "https://10.76.126.189/xnat/data/services/mail/send" resulted in 200 (OK)

DEBUG main org.springframework.web.client.RestTemplate - Reading [java.lang.String] as "text/plain;charset=ISO-8859-1" using [org.springframework.http.converter.StringHttpMessageConverter@3790835a]

DEBUG main httpclient.wire.content - << "OK"

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found the following response from https://10.76.126.189/xnat/data/services/mail/send: [200] OK

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Date with values: [Thu, 25 Jul 2013 11:25:02 GMT]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Server with values: [Apache/2.2.22 (Unix) DAV/2 mod_jk/1.2.37 mod_ssl/2.2.22 OpenSSL/0.9.8x]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Set-Cookie with values: [JSESSIONID=1BB4DA52F47BCF9B3EAEB597692480F4; Path=/xnat/; Secure; HttpOnly, SESSION_EXPIRATION_TIME="0,900000"; Version=1; Path=/]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Accept-Ranges with values: [bytes]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Content-Length with values: [2]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Vary with values: [Accept-Encoding,User-Agent]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: MS-Author-Via with values: [DAV]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: X-Frame-Options with values: [SameOrigin]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Content-Type with values: [text/plain;charset=ISO-8859-1]

DEBUG main org.nrg.pipeline.utils.MailUtils - Message sent OK.

DEBUG main org.nrg.pipeline.utils.MailUtils - Sending message with subject: XNAT update: Processing failed for ncrc_S00500

DEBUG main org.springframework.web.client.RestTemplate - Created POST request for "https://10.76.126.189/xnat/data/services/mail/send"

DEBUG main org.springframework.web.client.RestTemplate - Setting request Accept header to [text/plain, */*]

DEBUG main org.springframework.web.client.RestTemplate - Writing [{from=[alina....@med.uni-goettingen.de], to=[alina....@med.uni-goettingen.de], subject=[XNAT update: Processing failed for ncrc_S00500], text=[The processing request you submitted for ncrc_S00500 could not be completed at this time. 

 The XNAT technical team is aware of the issue and will notify you when it has been resolved.

 The stdout and the error log files are available as attachments for your perusal.

 We appreciate your patience.  Please contact alina....@med.uni-goettingen.de with questions or concerns. 

 Pipeline:  

/common/xnat/pipeline/catalog/ncrc/fslreorient_only.xml

 Cause:  

org.nrg.pipeline.exception.PipelineEngineException: Unable to complete pipeline  Execution of /usr/local/bin/xnat_tools/XNATRestClient -u e34c68f2-4fd2-4d32-8ead-b71e409cb64b -p ######## -host https://jonagold.rad-diagno3.med.local/xnat -remote /data/archive/projects/TEST_PROJECT/subjects/ALINASXNAT_S00001/experiments/ALINASXNAT_E00001/scans/4/resources/NIFTI/files/ncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz\?format=NIFTI -local /Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz -m PUT at Step[id= 17:] was unsuccesfull  Execution of /usr/local/bin/xnat_tools/XNATRestClient -u e34c68f2-4fd2-4d32-8ead-b71e409cb64b -p ######## -host https://jonagold.rad-diagno3.med.local/xnat -remote /data/archive/projects/TEST_PROJECT/subjects/ALINASXNAT_S00001/experiments/ALINASXNAT_E00001/scans/4/resources/NIFTI/files/ncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz\?format=NIFTI -local /Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz -m PUT at Step[id= 17:] was unsuccesfull

at org.nrg.pipeline.manager.PipelineManager.launchPipeline(PipelineManager.java:226)

at org.nrg.pipeline.manager.PipelineManager.launchPipeline(PipelineManager.java:193)

at org.nrg.pipeline.client.XNATPipelineLauncher.launch(XNATPipelineLauncher.java:65)

at org.nrg.pipeline.client.XNATPipelineLauncher.run(XNATPipelineLauncher.java:231)

at org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:221)

], html=[<html>The processing request you submitted for ncrc_S00500 could not be completed at this time. <br><br><br> The XNAT technical team is aware of the issue and will notify you when it has been resolved.<br><br><br> The stdout and the error log files are available as attachments for your perusal.<br><br><br> We appreciate your patience.  Please contact alina....@med.uni-goettingen.de with questions or concerns. <br><br><br> Pipeline:  <br><br>/common/xnat/pipeline/catalog/ncrc/fslreorient_only.xml<br><br><br> Cause:  <br><br>org.nrg.pipeline.exception.PipelineEngineException: Unable to complete pipeline  Execution of /usr/local/bin/xnat_tools/XNATRestClient -u e34c68f2-4fd2-4d32-8ead-b71e409cb64b -p ######## -host https://jonagold.rad-diagno3.med.local/xnat -remote /data/archive/projects/TEST_PROJECT/subjects/ALINASXNAT_S00001/experiments/ALINASXNAT_E00001/scans/4/resources/NIFTI/files/ncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz\?format=NIFTI -local /Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz -m PUT at Step[id= 17:] was unsuccesfull  Execution of /usr/local/bin/xnat_tools/XNATRestClient -u e34c68f2-4fd2-4d32-8ead-b71e409cb64b -p ######## -host https://jonagold.rad-diagno3.med.local/xnat -remote /data/archive/projects/TEST_PROJECT/subjects/ALINASXNAT_S00001/experiments/ALINASXNAT_E00001/scans/4/resources/NIFTI/files/ncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz\?format=NIFTI -local /Volumes/MacintoshHD2/xnat_pipeline_space/ncrc_S00500/NIFTI/mprage_nifti_inhcorr_stdorient.nii.gz -m PUT at Step[id= 17:] was unsuccesfull

at org.nrg.pipeline.manager.PipelineManager.launchPipeline(PipelineManager.java:226)

at org.nrg.pipeline.manager.PipelineManager.launchPipeline(PipelineManager.java:193)

at org.nrg.pipeline.client.XNATPipelineLauncher.launch(XNATPipelineLauncher.java:65)

at org.nrg.pipeline.client.XNATPipelineLauncher.run(XNATPipelineLauncher.java:231)

at org.nrg.pipeline.client.XNATPipelineLauncher.main(XNATPipelineLauncher.java:221)

</html>]}] using [org.springframework.http.converter.FormHttpMessageConverter@5df84008]

DEBUG main httpclient.wire.header - >> "POST /xnat/data/services/mail/send HTTP/1.1[\r][\n]"

DEBUG main httpclient.wire.header - >> "Accept: text/plain, */*[\r][\n]"

DEBUG main httpclient.wire.header - >> "Content-Type: application/x-www-form-urlencoded[\r][\n]"

DEBUG main httpclient.wire.header - >> "Authorization: Basic ZTM0YzY4ZjItNGZkMi00ZDMyLThlYWQtYjcxZTQwOWNiNjRiOjEzNzQ3NTE0NzUzNTc=[\r][\n]"

DEBUG main httpclient.wire.header - >> "User-Agent: Jakarta Commons-HttpClient/3.1[\r][\n]"

DEBUG main httpclient.wire.header - >> "Host: 10.76.126.189[\r][\n]"

DEBUG main httpclient.wire.header - >> "Content-Length: 4784[\r][\n]"

DEBUG main httpclient.wire.header - >> "[\r][\n]"

DEBUG main httpclient.wire.content - >> "from=alina.freing%40med.uni-goettingen.de&to=alina.freing%40med.uni-goettingen.de&subject=XNAT+update%3A+Processing+failed+for+ncrc_S00500&text=The+processing+request+you+submitted+for+ncrc_S00500+could+not+be+completed+at+this+time.+%0A%0A%0A+The+XNAT+technical+team+is+aware+of+the+issue+and+will+notify+you+when+it+has+been+resolved.%0A%0A%0A+The+stdout+and+the+error+log+files+are+available+as+attachments+for+your+perusal.%0A%0A%0A+We+appreciate+your+patience.++Please+contact+alina.freing%40med.uni-goettingen.de+with+questions+or+concerns.+%0A%0A%0A+Pipeline%3A++%0A%0A%2Fcommon%2Fxnat%2Fpipeline%2Fcatalog%2Fncrc%2Ffslreorient_only.xml%0A%0A%0A+Cause%3A++%0A%0Aorg.nrg.pipeline.exception.PipelineEngineException%3A+Unable+to+complete+pipeline++Execution+of+%2Fusr%2Flocal%2Fbin%2Fxnat_tools%2FXNATRestClient+-u+e34c68f2-4fd2-4d32-8ead-b71e409cb64b+-p+%23%23%23%23%23%23%23%23+-host+https%3A%2F%2Fjonagold.rad-diagno3.med.local%2Fxnat+-remote+%2Fdata%2Farchive%2Fprojects%2FTEST_PROJECT%2Fsubjects%2FALINASXNAT_S00001%2Fexperiments%2FALINASXNAT_E00001%2Fscans%2F4%2Fresources%2FNIFTI%2Ffiles%2Fncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz%5C%3Fformat%3DNIFTI+-local+%2FVolumes%2FMacintoshHD2%2Fxnat_pipeline_space%2Fncrc_S00500%2FNIFTI%2Fmprage_nifti_inhcorr_stdorient.nii.gz+-m+PUT+at+Step%5Bid%3D+17%3A%5D+was+unsuccesfull++Execution+of+%2Fusr%2Flocal%2Fbin%2Fxnat_tools%2FXNATRestClient+-u+e34c68f2-4fd2-4d32-8ead-b71e409cb64b+-p+%23%23%23%23%23%23%23%23+-host+https%3A%2F%2Fjonagold.rad-diagno3.med.local%2Fxnat+-remote+%2Fdata%2Farchive%2Fprojects%2FTEST_PROJECT%2Fsubjects%2FALINASXNAT_S00001%2Fexperiments%2FALINASXNAT_E00001%2Fscans%2F4%2Fresources%2FNIFTI%2Ffiles%2Fncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz%5C%3Fformat%3DNIFTI+-local+%2FVolumes%2FMacintoshHD2%2Fxnat_pipeline_space%2Fncrc_S00500%2FNIFTI%2Fmprage_nifti_inhcorr_stdorient.nii.gz+-m+PUT+at+Step%5Bid%3D+17%3A%5D+was+unsuccesfull%0A%09at+org.nrg.pipeline.manager.PipelineManager.launchPipeline%28PipelineManager.java%3A226%29%0A%09at+org.nrg.pipeline.manager.PipelineManager.launchPipeline%28PipelineManager.java%3A193%29%0A%09at+org.nrg.pipeline.client.XNATPipelineLauncher.launch%28XNATPipelineLauncher.java%3A65%29%0A%09at+org.nrg.pipeline.client.XNATPipelineLauncher.run%28XNATPipelineLauncher.java%3A231%29%0A%09at+org.nrg.pipeline.client.XNATPipelineLauncher.main%28XNATPipelineLauncher.java%3A221%29%0A&html=%3Chtml%3EThe+processing+request+you+submitted+for+ncrc_S00500+could+not+be+completed+at+this+time.+%3Cbr%3E%3Cbr%3E%3Cbr%3E+The+XNAT+technical+team+is+aware+of+the+issue+and+will+notify+you+when+it+has+been+resolved.%3Cbr%3E%3Cbr%3E%3Cbr%3E+The+stdout+and+the+error+log+files+are+available+as+attachments+for+your+perusal.%3Cbr%3E%3Cbr%3E%3Cbr%3E+We+appreciate+your+patience.++Please+contact+alina.freing%40med.uni-goettingen.de+with+questions+or+concerns.+%3Cbr%3E%3Cbr%3E%3Cbr%3E+Pipeline%3A++%3Cbr%3E%3Cbr%3E%2Fcommon%2Fxnat%2Fpipeline%2Fcatalog%2Fncrc%2Ffslreorient_only.xml%3Cbr%3E%3Cbr%3E%3Cbr%3E+Cause%3A++%3Cbr%3E%3Cbr%3Eorg.nrg.pipeline.exception.PipelineEngineException%3A+Unable+to+complete+pipeline++Execution+of+%2Fusr%2Flocal%2Fbin%2Fxnat_tools%2FXNATRestClient+-u+e34c68f2-4fd2-4d32-8ead-b71e409cb64b+-p+%23%23%23%23%23%23%23%23+-host+https%3A%2F%2Fjonagold.rad-diagno3.med.local%2Fxnat+-remote+%2Fdata%2Farchive%2Fprojects%2FTEST_PROJECT%2Fsubjects%2FALINASXNAT_S00001%2Fexperiments%2FALINASXNAT_E00001%2Fscans%2F4%2Fresources%2FNIFTI%2Ffiles%2Fncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz%5C%3Fformat%3DNIFTI+-local+%2FVolumes%2FMacintoshHD2%2Fxnat_pipeline_space%2Fncrc_S00500%2FNIFTI%2Fmprage_nifti_inhcorr_stdorient.nii.gz+-m+PUT+at+Step%5Bid%3D+17%3A%5D+was+unsuccesfull++Execution+of+%2Fusr%2Flocal%2Fbin%2Fxnat_tools%2FXNATRestClient+-u+e34c68f2-4fd2-4d32-8ead-b71e409cb64b+-p+%23%23%23%23%23%23%23%23+-host+https%3A%2F%2Fjonagold.rad-diagno3.med.local%2Fxnat+-remote+%2Fdata%2Farchive%2Fprojects%2FTEST_PROJECT%2Fsubjects%2FALINASXNAT_S00001%2Fexperiments%2FALINASXNAT_E00001%2Fscans%2F4%2Fresources%2FNIFTI%2Ffiles%2Fncrc_S00500_MPRAGE_NIFTI_INHCORR_STDORIENT.nii.gz%5C%3Fformat%3DNIFTI+-local+%2FVolumes%2FMacintoshHD2%2Fxnat_pipeline_space%2Fncrc_S00500%2FNIFTI%2Fmprage_nifti_inhcorr_stdorient.nii.gz+-m+PUT+at+Step%5Bid%3D+17%3A%5D+was+unsuccesfull%0A%09at+org.nrg.pipeline.manager.PipelineManager.launchPipeline%28PipelineManager.java%3A226%29%0A%09at+org.nrg.pipeline.manager.PipelineManager.launchPipeline%28PipelineManager.java%3A193%29%0A%09at+org.nrg.pipeline.client.XNATPipelineLauncher.launch%28XNATPipelineLauncher.java%3A65%29%0A%09at+org.nrg.pipeline.client.XNATPipelineLauncher.run%28XNATPipelineLauncher.java%3A231%29%0A%09at+org.nrg.pipeline.client.XNATPipelineLauncher.main%28XNATPipelineLauncher.java%3A221%29%0A%3C%2Fhtml%3E"

DEBUG main httpclient.wire.header - << "HTTP/1.1 200 OK[\r][\n]"

DEBUG main httpclient.wire.header - << "HTTP/1.1 200 OK[\r][\n]"

DEBUG main httpclient.wire.header - << "Date: Thu, 25 Jul 2013 11:25:12 GMT[\r][\n]"

DEBUG main httpclient.wire.header - << "Server: Apache/2.2.22 (Unix) DAV/2 mod_jk/1.2.37 mod_ssl/2.2.22 OpenSSL/0.9.8x[\r][\n]"

DEBUG main httpclient.wire.header - << "Set-Cookie: JSESSIONID=DB1C293D5B97C3A5D5C1451789AD3E0F; Path=/xnat/; Secure; HttpOnly[\r][\n]"

DEBUG main httpclient.wire.header - << "Set-Cookie: SESSION_EXPIRATION_TIME="0,900000"; Version=1; Path=/[\r][\n]"

DEBUG main httpclient.wire.header - << "Accept-Ranges: bytes[\r][\n]"

DEBUG main httpclient.wire.header - << "Content-Length: 2[\r][\n]"

DEBUG main httpclient.wire.header - << "Vary: Accept-Encoding,User-Agent[\r][\n]"

DEBUG main httpclient.wire.header - << "MS-Author-Via: DAV[\r][\n]"

DEBUG main httpclient.wire.header - << "X-Frame-Options: SameOrigin[\r][\n]"

DEBUG main httpclient.wire.header - << "Content-Type: text/plain;charset=ISO-8859-1[\r][\n]"

DEBUG main httpclient.wire.header - << "[\r][\n]"

DEBUG main org.springframework.web.client.RestTemplate - POST request for "https://10.76.126.189/xnat/data/services/mail/send" resulted in 200 (OK)

DEBUG main org.springframework.web.client.RestTemplate - Reading [java.lang.String] as "text/plain;charset=ISO-8859-1" using [org.springframework.http.converter.StringHttpMessageConverter@3790835a]

DEBUG main httpclient.wire.content - << "OK"

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found the following response from https://10.76.126.189/xnat/data/services/mail/send: [200] OK

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Date with values: [Thu, 25 Jul 2013 11:25:12 GMT]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Server with values: [Apache/2.2.22 (Unix) DAV/2 mod_jk/1.2.37 mod_ssl/2.2.22 OpenSSL/0.9.8x]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Set-Cookie with values: [JSESSIONID=DB1C293D5B97C3A5D5C1451789AD3E0F; Path=/xnat/; Secure; HttpOnly, SESSION_EXPIRATION_TIME="0,900000"; Version=1; Path=/]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Accept-Ranges with values: [bytes]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Content-Length with values: [2]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Vary with values: [Accept-Encoding,User-Agent]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: MS-Author-Via with values: [DAV]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: X-Frame-Options with values: [SameOrigin]

INFO main org.nrg.mail.services.impl.RestBasedMailServiceImpl - Found header: Content-Type with values: [text/plain;charset=ISO-8859-1]

DEBUG main org.nrg.pipeline.utils.MailUtils - Message sent OK.

[Freing Alina]

To provide some "closure" to this matter, if somebody else is seeing something of this sort: the problem was with Mountain Lion, neither with XNAT nor fslreorient2std. For remote login, Mountain Lion doesn't source .bash_profile anymore, but now sources .bashrc. So $FSLDIR wasn't set properly. No idea why I couldn't see any error messages, though, fsl should have reported failure. Anyway, now it works :)!

Alina