From waveflux at gmail.com Mon Jan 11 12:26:34 2016 From: waveflux at gmail.com (Tom Beaudry) Date: Mon, 11 Jan 2016 12:26:34 -0500 Subject: [Loris-dev] creating a new instrument Message-ID: Hi guys, I am creating an instrument in php. I've done it before, but for some reason - it doesn't seem to work for me in 15.10. This is what I've done - What am I missing? 1. I modify the templatate, NDB_BVL_Instrument_TEMPLATE.class.inc, and insert my instrument name (Medications) into the appropriate places. I don't modify anything else in the file. 2. I run quickform_parser.php and generate_tables_sql.php. 3. i source the instrument in mysql 4. I add the instrument to the test_name and test_battery tables 5. I create a candidate, a visit, and click on the test that I created and I get a blank screen. The error from the apache log is: [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: include_once(/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc): failed to open stream: Permission denied in /var/www/loris/php/libraries/NDB_Caller.class.inc on line 461 [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: include_once(): Failed opening '/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc' for inclusion (include_path='/PATH/TO/EXTERNAL/LIBRARY/:/var/www/loris/vendor/ pear-pear.php.net/Benchmark:/var/www/loris/vendor/pear-pear.php.net/HTML_Common:/var/www/loris/vendor/pear-pear.php.net/HTML_QuickForm:/var/www/loris/vendor/pear-pear.php.net/Mail:/var/www/loris/vendor/pear-pear.php.net/Pager:.:/usr/share/php:/usr/share/pear:/var/www/loris/project/libraries:/var/www/loris/php/libraries:../project/libraries:../php/libraries:') in /var/www/loris/php/libraries/NDB_Caller.class.inc on line 461 [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: include_once(/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc): failed to open stream: Permission denied in /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 200 [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: include_once(): Failed opening '/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc' for inclusion (include_path='/PATH/TO/EXTERNAL/LIBRARY/:/var/www/loris/vendor/ pear-pear.php.net/Benchmark:/var/www/loris/vendor/pear-pear.php.net/HTML_Common:/var/www/loris/vendor/pear-pear.php.net/HTML_QuickForm:/var/www/loris/vendor/pear-pear.php.net/Mail:/var/www/loris/vendor/pear-pear.php.net/Pager:.:/usr/share/php:/usr/share/pear:/var/www/loris/project/libraries:/var/www/loris/php/libraries:../project/libraries:../php/libraries:') in /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 200 [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Fatal error: Class 'NDB_BVL_Instrument_Medications' not found in /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 203 Thanks! Tom -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Mon Jan 11 12:33:53 2016 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Mon, 11 Jan 2016 12:33:53 -0500 Subject: [Loris-dev] creating a new instrument In-Reply-To: References: Message-ID: Hi Tom, I suspect you're missing just one step -- make your php instrument file apache readable. Try: cd /var/www/loris/project/instruments/ chmod a+r * (You might need to use sudo in order to chmod, depending on your setup.) The good news is this isn't new for 15.10. cheers, Christine On Mon, Jan 11, 2016 at 12:26 PM, Tom Beaudry wrote: > Hi guys, > > I am creating an instrument in php. I've done it before, but for some > reason - it doesn't seem to work for me in 15.10. This is what I've done - > What am I missing? > > 1. I modify the templatate, NDB_BVL_Instrument_TEMPLATE.class.inc, and > insert my instrument name (Medications) into the appropriate places. I > don't modify anything else in the file. > > 2. I run quickform_parser.php and generate_tables_sql.php. > > 3. i source the instrument in mysql > > 4. I add the instrument to the test_name and test_battery tables > > 5. I create a candidate, a visit, and click on the test that I created > and I get a blank screen. > > The error from the apache log is: > > [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: > include_once(/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc): > failed to open stream: Permission denied in > /var/www/loris/php/libraries/NDB_Caller.class.inc on line 461 > [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: > include_once(): Failed opening > '/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc' > for inclusion > (include_path='/PATH/TO/EXTERNAL/LIBRARY/:/var/www/loris/vendor/ > pear-pear.php.net/Benchmark:/var/www/loris/vendor/pear-pear.php.net/HTML_Common:/var/www/loris/vendor/pear-pear.php.net/HTML_QuickForm:/var/www/loris/vendor/pear-pear.php.net/Mail:/var/www/loris/vendor/pear-pear.php.net/Pager:.:/usr/share/php:/usr/share/pear:/var/www/loris/project/libraries:/var/www/loris/php/libraries:../project/libraries:../php/libraries:') > in /var/www/loris/php/libraries/NDB_Caller.class.inc on line 461 > [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: > include_once(/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc): > failed to open stream: Permission denied in > /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 200 > [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: > include_once(): Failed opening > '/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc' > for inclusion > (include_path='/PATH/TO/EXTERNAL/LIBRARY/:/var/www/loris/vendor/ > pear-pear.php.net/Benchmark:/var/www/loris/vendor/pear-pear.php.net/HTML_Common:/var/www/loris/vendor/pear-pear.php.net/HTML_QuickForm:/var/www/loris/vendor/pear-pear.php.net/Mail:/var/www/loris/vendor/pear-pear.php.net/Pager:.:/usr/share/php:/usr/share/pear:/var/www/loris/project/libraries:/var/www/loris/php/libraries:../project/libraries:../php/libraries:') > in /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 200 > [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Fatal error: > Class 'NDB_BVL_Instrument_Medications' not found in > /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 203 > > > Thanks! > Tom > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -- christine.rogers at mcgill.ca LORIS data systems | loris.ca McGill Centre for Integrative Neuroscience| MCIN.ca McConnell Brain Imaging Centre Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Mon Jan 11 12:39:06 2016 From: waveflux at gmail.com (Tom Beaudry) Date: Mon, 11 Jan 2016 12:39:06 -0500 Subject: [Loris-dev] creating a new instrument In-Reply-To: References:

Message-ID: Hi Christine, No i did do that. Any other ideas? Tom On Mon, Jan 11, 2016 at 12:33 PM, Christine Rogers < christine.rogers at mcgill.ca> wrote: > Hi Tom, > > I suspect you're missing just one step -- make your php instrument file > apache readable. > Try: > cd /var/www/loris/project/instruments/ > chmod a+r * > > (You might need to use sudo in order to chmod, depending on your setup.) > The good news is this isn't new for 15.10. > cheers, > Christine > > On Mon, Jan 11, 2016 at 12:26 PM, Tom Beaudry wrote: > >> Hi guys, >> >> I am creating an instrument in php. I've done it before, but for some >> reason - it doesn't seem to work for me in 15.10. This is what I've done - >> What am I missing? >> >> 1. I modify the templatate, NDB_BVL_Instrument_TEMPLATE.class.inc, and >> insert my instrument name (Medications) into the appropriate places. I >> don't modify anything else in the file. >> >> 2. I run quickform_parser.php and generate_tables_sql.php. >> >> 3. i source the instrument in mysql >> >> 4. I add the instrument to the test_name and test_battery tables >> >> 5. I create a candidate, a visit, and click on the test that I created >> and I get a blank screen. >> >> The error from the apache log is: >> >> [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: >> include_once(/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc): >> failed to open stream: Permission denied in >> /var/www/loris/php/libraries/NDB_Caller.class.inc on line 461 >> [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: >> include_once(): Failed opening >> '/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc' >> for inclusion >> (include_path='/PATH/TO/EXTERNAL/LIBRARY/:/var/www/loris/vendor/ >> pear-pear.php.net/Benchmark:/var/www/loris/vendor/pear-pear.php.net/HTML_Common:/var/www/loris/vendor/pear-pear.php.net/HTML_QuickForm:/var/www/loris/vendor/pear-pear.php.net/Mail:/var/www/loris/vendor/pear-pear.php.net/Pager:.:/usr/share/php:/usr/share/pear:/var/www/loris/project/libraries:/var/www/loris/php/libraries:../project/libraries:../php/libraries:') >> in /var/www/loris/php/libraries/NDB_Caller.class.inc on line 461 >> [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: >> include_once(/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc): >> failed to open stream: Permission denied in >> /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 200 >> [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: >> include_once(): Failed opening >> '/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc' >> for inclusion >> (include_path='/PATH/TO/EXTERNAL/LIBRARY/:/var/www/loris/vendor/ >> pear-pear.php.net/Benchmark:/var/www/loris/vendor/pear-pear.php.net/HTML_Common:/var/www/loris/vendor/pear-pear.php.net/HTML_QuickForm:/var/www/loris/vendor/pear-pear.php.net/Mail:/var/www/loris/vendor/pear-pear.php.net/Pager:.:/usr/share/php:/usr/share/pear:/var/www/loris/project/libraries:/var/www/loris/php/libraries:../project/libraries:../php/libraries:') >> in /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 200 >> [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Fatal >> error: Class 'NDB_BVL_Instrument_Medications' not found in >> /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 203 >> >> >> Thanks! >> Tom >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> > > > -- > > christine.rogers at mcgill.ca > LORIS data systems | loris.ca > McGill Centre for Integrative Neuroscience| MCIN.ca > McConnell Brain Imaging Centre > Montreal Neurological Institute > McGill University | Montreal | Canada > -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Mon Jan 11 13:16:46 2016 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Mon, 11 Jan 2016 13:16:46 -0500 Subject: [Loris-dev] creating a new instrument In-Reply-To: <19143_1452533948_5693E8BB_19143_147_1_0ad7e9cb0deb4fe1b4086008ac40b173@EXHUB2010-3.campus.MCGILL.CA> References:

<19143_1452533948_5693E8BB_19143_147_1_0ad7e9cb0deb4fe1b4086008ac40b173@EXHUB2010-3.campus.MCGILL.CA> Message-ID: Hi Tom, Sorry, I read your first email too quickly, and missed the part where you said that you didn't modify anything else inside the template file. It's possible there's a small issue with your php file which is hard to spot, which is why it's failing to open your file /var/www/loris/ project/instruments/NDB_BVL_Instrument_Medications.class.inc Feel free to send me your php instrument file and the *.sql file which was generated for this instrument, or show them to me when you're next stopping by the office. cheers, Christine On Mon, Jan 11, 2016 at 12:39 PM, Tom Beaudry wrote: > Hi Christine, > > No i did do that. > > Any other ideas? > Tom > > On Mon, Jan 11, 2016 at 12:33 PM, Christine Rogers < > christine.rogers at mcgill.ca> wrote: > >> Hi Tom, >> >> I suspect you're missing just one step -- make your php instrument file >> apache readable. >> Try: >> cd /var/www/loris/project/instruments/ >> chmod a+r * >> >> (You might need to use sudo in order to chmod, depending on your setup.) >> The good news is this isn't new for 15.10. >> cheers, >> Christine >> >> On Mon, Jan 11, 2016 at 12:26 PM, Tom Beaudry wrote: >> >>> Hi guys, >>> >>> I am creating an instrument in php. I've done it before, but for some >>> reason - it doesn't seem to work for me in 15.10. This is what I've done - >>> What am I missing? >>> >>> 1. I modify the templatate, NDB_BVL_Instrument_TEMPLATE.class.inc, and >>> insert my instrument name (Medications) into the appropriate places. I >>> don't modify anything else in the file. >>> >>> 2. I run quickform_parser.php and generate_tables_sql.php. >>> >>> 3. i source the instrument in mysql >>> >>> 4. I add the instrument to the test_name and test_battery tables >>> >>> 5. I create a candidate, a visit, and click on the test that I created >>> and I get a blank screen. >>> >>> The error from the apache log is: >>> >>> [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: >>> include_once(/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc): >>> failed to open stream: Permission denied in >>> /var/www/loris/php/libraries/NDB_Caller.class.inc on line 461 >>> [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: >>> include_once(): Failed opening >>> '/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc' >>> for inclusion >>> (include_path='/PATH/TO/EXTERNAL/LIBRARY/:/var/www/loris/vendor/ >>> pear-pear.php.net/Benchmark:/var/www/loris/vendor/pear-pear.php.net/HTML_Common:/var/www/loris/vendor/pear-pear.php.net/HTML_QuickForm:/var/www/loris/vendor/pear-pear.php.net/Mail:/var/www/loris/vendor/pear-pear.php.net/Pager:.:/usr/share/php:/usr/share/pear:/var/www/loris/project/libraries:/var/www/loris/php/libraries:../project/libraries:../php/libraries:') >>> in /var/www/loris/php/libraries/NDB_Caller.class.inc on line 461 >>> [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: >>> include_once(/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc): >>> failed to open stream: Permission denied in >>> /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 200 >>> [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Warning: >>> include_once(): Failed opening >>> '/var/www/loris/project/instruments/NDB_BVL_Instrument_Medications.class.inc' >>> for inclusion >>> (include_path='/PATH/TO/EXTERNAL/LIBRARY/:/var/www/loris/vendor/ >>> pear-pear.php.net/Benchmark:/var/www/loris/vendor/pear-pear.php.net/HTML_Common:/var/www/loris/vendor/pear-pear.php.net/HTML_QuickForm:/var/www/loris/vendor/pear-pear.php.net/Mail:/var/www/loris/vendor/pear-pear.php.net/Pager:.:/usr/share/php:/usr/share/pear:/var/www/loris/project/libraries:/var/www/loris/php/libraries:../project/libraries:../php/libraries:') >>> in /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 200 >>> [Mon Jan 11 12:07:51 2016] [error] [client 192.168.122.1] PHP Fatal >>> error: Class 'NDB_BVL_Instrument_Medications' not found in >>> /var/www/loris/php/libraries/NDB_BVL_Instrument.class.inc on line 203 >>> >>> >>> Thanks! >>> Tom >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >> >> >> -- >> >> christine.rogers at mcgill.ca >> LORIS data systems | loris.ca >> McGill Centre for Integrative Neuroscience| MCIN.ca >> McConnell Brain Imaging Centre >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> > > -- christine.rogers at mcgill.ca LORIS data systems | loris.ca McGill Centre for Integrative Neuroscience| MCIN.ca McConnell Brain Imaging Centre Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From najmeh.khalilimahani at mcgill.ca Mon Jan 25 11:22:44 2016 From: najmeh.khalilimahani at mcgill.ca (Najmeh Khalili-Mahani, Dr) Date: Mon, 25 Jan 2016 11:22:44 -0500 Subject: [Loris-dev] LORIS for CT data? Message-ID: Hi, I was wondering if anyone may have ideas or solutions for expanding LORIS beyond MRI to allow it upload, view and QC CT images (both of brain and non-brain organs) Another related question, would dcm2mnc complain about converting non-brain images to minc and visualizing them with BrainBrowser/JIV? Much thanks Naj -- ================================== Najmeh Khalili-Mahani, PhD Research Associate McGill Centre for Integrative Neuroscience Montreal Neurological Institute McGill University NW-143, 3801 University St. Montreal, QC, H3A 2B4 Office: 514-398-1799 email: najma at bic.mni.mcgill.ca -------------- next part -------------- An HTML attachment was scrubbed... URL: From robert.d.vincent at mcgill.ca Mon Jan 25 11:28:49 2016 From: robert.d.vincent at mcgill.ca (Robert D. Vincent) Date: Mon, 25 Jan 2016 11:28:49 -0500 Subject: [Loris-dev] LORIS for CT data? In-Reply-To: References: Message-ID: Hi, dcm2mnc is flexible about modality and completely ignorant of physiology. I can think of a couple of possible minor issues: First, the spatial reference frame conventions might be different for other substructures (similar to the problems in rat/mouse data, where the head orientation relative to the body is obviously quite different from that of Homo sapiens). Second, our visualization tools make a few "brainlike" assumptions (e.g. assuming that the structure will fit nicely in a cube or sphere). -bert On Mon, Jan 25, 2016 at 11:22 AM, Najmeh Khalili-Mahani, Dr < najmeh.khalilimahani at mcgill.ca> wrote: > Hi, > > I was wondering if anyone may have ideas or solutions for expanding LORIS > beyond MRI to allow it upload, view and QC CT images (both of brain and > non-brain organs) > > Another related question, would dcm2mnc complain about converting > non-brain images to minc and visualizing them with BrainBrowser/JIV? > > Much thanks > Naj > > -- > ================================== > Najmeh Khalili-Mahani, PhD > Research Associate > McGill Centre for Integrative Neuroscience > Montreal Neurological Institute > McGill University > > NW-143, 3801 University St. > Montreal, QC, H3A 2B4 > Office: 514-398-1799 > email: najma at bic.mni.mcgill.ca > -------------- next part -------------- An HTML attachment was scrubbed... URL: