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Hi Cecile,
<div class=""><br class="">
</div>
<div class="">I am now running LORIS-MRI v23.0.3 and LORIS v23.0.2. I am getting the following output for the same command line:</div>
<div class=""><br class="">
</div>
<div class="">Command line</div>
<div class="">===</div>
<div class="">
<div style="margin: 0px; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">perl /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/minc_insertion.pl -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w -mincPath /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc</span></div>
</div>
<div style="margin: 0px; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">===</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""><br class="">
</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Output</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 13px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">===</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-17-32-M9vqyU.log</span></div>
<div style="font-family: Menlo; font-size: 13px; margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures;" class=""><font color="#ff0000" class="">Can't locate object method "selectall_array" via package "DBI::db" at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line
1819.</font></span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series
WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> CandID id: 814099</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> visit_label is: 105ms302w48</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">PSCID is: AZH101303</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> CandID id: 814099</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> visit_label is: 105ms302w48</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">===</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""><br class="">
</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">Log file (</span>/data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-17-32-M9vqyU.log)</div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">===</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">==> Loading file from disk /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 15px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">--> mapping DICOM parameter for /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal; min-height: 15px;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures" class="">--> filters out parameters of length > 1000 for /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc</span></div>
</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">===</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<br class="">
</div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""><br class="">
</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">I think issue is coming from this line:</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""><br class="">
</span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures; caret-color: rgb(0, 0, 0);" class=""><font color="#000000" face="Menlo" size="2" class=""><a href="https://github.com/aces/Loris-MRI/blob/8c7e41549fb10a845caa96f31c8e505ef3adca52/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm#L1819" class="">https://github.com/aces/Loris-MRI/blob/8c7e41549fb10a845caa96f31c8e505ef3adca52/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm#L1819</a></font></span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures; caret-color: rgb(0, 0, 0);" class=""><font color="#000000" face="Menlo" size="2" class=""><br class="">
</font></span></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><font color="#000000" face="Menlo" size="2" class="">Maybe “</font></span><font color="#000000" face="Menlo" size="2" class=""><span style="caret-color: rgb(0, 0, 0);" class="">selectall_array”</span> has
to be replaced by “<span style="caret-color: rgb(0, 0, 0);" class="">selectall_arrayref”?</span></font></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><font color="#000000" face="Menlo" size="2" class=""><span style="caret-color: rgb(0, 0, 0);" class=""><br class="">
</span></font></div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><font color="#000000" face="Menlo" size="2" class=""><span style="caret-color: rgb(0, 0, 0);" class="">Thank you for all your help.</span></font></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""><br class="">
</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Best,</span></div>
<div style="font-family: Menlo; font-size: 13px; color: rgb(0, 0, 0); margin: 0px; font-stretch: normal; line-height: normal;" class="">
Alfredo.</div>
</span></div>
<div class=""><br class="">
</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jan 29, 2021, at 12:57 PM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<p class=""><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;" class=""> External Email - Use Caution </span></p>
<div class=""><br class="webkit-block-placeholder">
</div>
<div dir="ltr" class="">I see. There are significant changes between 22 and 23 on LORIS-MRI (mainly the ability to set specific MRI protocols based on Visit label, Projects or subprojects requiring changes to the MRI protocol tables). However, I do not foresee
any major blocker as to proceed to upgrading to 23.0 for LORIS-MRI.
<div class=""><br class="">
</div>
<div class="">Hope this helps,</div>
<div class=""><br class="">
</div>
<div class="">Cécile</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Jan 29, 2021 at 12:15 PM Sridar Narayanan, Dr. <<a href="mailto:sridar.narayanan@mcgill.ca" class="">sridar.narayanan@mcgill.ca</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;" class="">Hi Cecile,
<div class=""><br class="">
</div>
<div class="">I think Alfredo’s plan was to upgrade to 23.0 as soon as the upgrade to 22.0 was completed successfully (since a direct upgrade was not possible). Since 23.0 appears to fix some bugs in 22.0, when would it be most efficient to perform the 22.0
-> 23.0 upgrade? Should Alfredo ensure that 22.0 is functional with all patches applied first, to be safe, or will the upgrade to 23.0 take care of many of these issues?</div>
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class=""><br class="">
</div>
<div class="">Sridar</div>
<div class=""><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Jan 29, 2021, at 11:09 AM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
<br class="">
<div class="">
<div dir="ltr" class="">Hi Alfredo,
<div class=""><br class="">
</div>
<div class="">I was able to reproduce your bug on version 22.0 of LORIS-MRI and it was maybe present in older versions as well. This was fixed in release 23.0 with better logging information.</div>
<div class=""><br class="">
</div>
<div class="">I just sent a PR with a fix for 22.0 that you can find here: <a href="https://secure-web.cisco.com/1g4f8AjQOgqWIsAwkqWCiOmCHzD2rXDAvuqnRmnpBSVe28wjQ1Ycso_XN5QQeVmQTkmBrLxDu00wy3b7b_mzpYMTzh5yyNEYTTzPXaNV1REyVeMp1PNm0EJiRXIx8PCcD2Tw98Ks9Rki5JSfaUmH_qrvzGGoNwcYiFovDADebGANxj2t0V5ZMCoaGgG-wPYl4sugwOpqPiMIbd-061zlGUBA5mf7uIHdlCLzko8yWJN6uXGqzMTXrpsqvdo7WQbmVkF5ekuSNIuCQ6e1ttM7fTQ/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F573%2Ffiles" target="_blank" class="">https://github.com/aces/Loris-MRI/pull/573/files</a></div>
<div class=""><br class="">
</div>
<div class="">That should resolve the issue you were having. Let me know how it goes.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class=""><br class="">
</div>
<div class="">Cécile</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Jan 29, 2021 at 1:18 AM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank" class="">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">Hi Cecile,
<div class=""><br class="">
</div>
<div class="">I tried the script <a href="http://secure-web.cisco.com/1DoH1kQn_ZoaEt8_7ZDW2QX5awXwep3yIUdillxlgWQuhboIi38Rd19WmcPx_77_POJxH11-w1X9x9y0Sxnk7Vnzsablfwld2S2oQAM2AxDU65VyGGFT9OQGt2Jv0Y7R9YCaNdyB_EXmGrUww1crVI-CFaZGVmQd3c04ZKRxb_QVZyPsF0fHct3IZ3HhoyFMAiCxVnRHr1ZxN9VHOB3xCZMg8nAk0BHTbNmxdE7nvWuHf_ZVgn26NcJdx8rNtkURZkV0IrLK8Hs8tcRc2yYW8_A/http%3A%2F%2Fminc_insertion.pl%2F" target="_blank" class="">
minc_insertion.pl</a> but it seems that the Candidate should not exist before the execution of the script. Is this the case? This would be problematic in order to upload multiple sequences for a given Candidate. This is the error I am getting:</div>
<div class=""><br class="">
</div>
<div class="">===</div>
<div class="">
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">$ perl <a href="http://secure-web.cisco.com/1DoH1kQn_ZoaEt8_7ZDW2QX5awXwep3yIUdillxlgWQuhboIi38Rd19WmcPx_77_POJxH11-w1X9x9y0Sxnk7Vnzsablfwld2S2oQAM2AxDU65VyGGFT9OQGt2Jv0Y7R9YCaNdyB_EXmGrUww1crVI-CFaZGVmQd3c04ZKRxb_QVZyPsF0fHct3IZ3HhoyFMAiCxVnRHr1ZxN9VHOB3xCZMg8nAk0BHTbNmxdE7nvWuHf_ZVgn26NcJdx8rNtkURZkV0IrLK8Hs8tcRc2yYW8_A/http%3A%2F%2Fminc_insertion.pl%2F" target="_blank" class="">
minc_insertion.pl</a> -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w -mincPath /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc</span></div>
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""><br class="">
</span></div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><span style="font-variant-ligatures:no-common-ligatures;font-size:11px" class="">
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""><font face="Menlo" class="">
<div style="margin:0px;font-stretch:normal;line-height:normal" class="">log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class="">ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists.</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""> SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series
WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""> CandID id: 814099</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""> visit_label is: 105ms302w48</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class="">PSCID is: AZH101303</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""> CandID id: 814099</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class=""> visit_label is: 105ms302w48</div>
<div style="margin:0px;font-stretch:normal;line-height:normal" class="">Spool message is: ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists</div>
</font></div>
</span></div>
<div class="">===</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Alfredo.</div>
<div class=""><br class="">
</div>
<div class="">P.S. The file <span style="font-family:Menlo;font-size:11px" class="">/data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log is not being </span><font face="Menlo" class=""><span style="font-size:11px" class="">written.</span></font><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Jan 26, 2021, at 4:33 PM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
<br class="">
<div class="">
<p class=""><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)" class=""> External Email - Use Caution </span></p>
<div class=""><br class="">
</div>
<div dir="ltr" class="">Hi,
<div class=""><br class="">
</div>
<div class="">Thank you for the clarification. I think I understand better the confusion.</div>
<div class=""><br class="">
</div>
<div class="">You can insert MINC files without having to insert DICOM files by running the
<a href="http://secure-web.cisco.com/1CRWLdhPK0QJwqPsDM4eN1sMctn09UpUmGm1ZACvkTVa4MFcegyiYHM-gnd66amN903PeYLfAWQNIvPTZ5yOnEPThk8ksAOROmQS3eWh0U8d8V8e7OzW5hcKgr-r-hohMmcc-QL9o2-pieYi2wKVTxk6Jp1FIcAvYVtg88EIZDsttuCveFvjbvwcs__pZDy8Et4MwQsmqkvt6Oc74cpqzwx4rBRYvkaEN1XHX8VHjpAYfYevk7OMqQ5atJ7rvdQX7Wnce-Y6YMEjf3TzlKPLILg/http%3A%2F%2Fminc_insertion.pl" target="_blank" class="">
minc_insertion.pl</a> script with the -force option. Basically, the force option will bypass checks to see if there are DICOMs to attach the file to.</div>
<div class=""><br class="">
</div>
<div class=""><a href="http://secure-web.cisco.com/1CRWLdhPK0QJwqPsDM4eN1sMctn09UpUmGm1ZACvkTVa4MFcegyiYHM-gnd66amN903PeYLfAWQNIvPTZ5yOnEPThk8ksAOROmQS3eWh0U8d8V8e7OzW5hcKgr-r-hohMmcc-QL9o2-pieYi2wKVTxk6Jp1FIcAvYVtg88EIZDsttuCveFvjbvwcs__pZDy8Et4MwQsmqkvt6Oc74cpqzwx4rBRYvkaEN1XHX8VHjpAYfYevk7OMqQ5atJ7rvdQX7Wnce-Y6YMEjf3TzlKPLILg/http%3A%2F%2Fminc_insertion.pl" target="_blank" class="">minc_insertion.pl</a>
-profile <name of your profile file, typically prod> -mincPath <path to your MINC file> -force -create_minc_pics</div>
<div class=""><br class="">
</div>
<div class="">For the NIfTI files alone, because of the nature of that file format (no header information like MINC...), you will have to specify a lot of the information when calling the script <a href="http://secure-web.cisco.com/1ANFDRFiRPX99wUpC1gLtmUEZUofuWa1YZIPvpt87N85cQ5aLcJwJ9Smm-wYcByOM8Od5Xjlo9-tl0ZQJY7JJ27g0DbjPQbPN_QnnSHs9CqrVFjFlbxUVjECyQKBTq0uT8IQOCtU-B9Il0lt9aY3N1aQFBd6GvX2BeQVz7KQjcRNZT9uFGQ5UUd_7hTAP4isf2q5V8InvWEmEgkYKTrZvOSEe-eXGvSk-6HvLP2LKIs_OHhCR0S-b_aO2sFFoQkvgyDg1FdVGN7K5vNrFFJu3QQ/http%3A%2F%2Fimaging_non_minc_insertion.pl" target="_blank" class="">imaging_non_minc_insertion.pl</a>
(output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... Basically all the columns of the files table). It needs to be associated with an upload_id for the logging in the database but the upload_id does not necessarily need to be DICOM files.
It could be a zipped archive of all the NIfTI files of the session uploaded for example. Then you would just need to create a little wrapper script to run
<a href="http://secure-web.cisco.com/1ANFDRFiRPX99wUpC1gLtmUEZUofuWa1YZIPvpt87N85cQ5aLcJwJ9Smm-wYcByOM8Od5Xjlo9-tl0ZQJY7JJ27g0DbjPQbPN_QnnSHs9CqrVFjFlbxUVjECyQKBTq0uT8IQOCtU-B9Il0lt9aY3N1aQFBd6GvX2BeQVz7KQjcRNZT9uFGQ5UUd_7hTAP4isf2q5V8InvWEmEgkYKTrZvOSEe-eXGvSk-6HvLP2LKIs_OHhCR0S-b_aO2sFFoQkvgyDg1FdVGN7K5vNrFFJu3QQ/http%3A%2F%2Fimaging_non_minc_insertion.pl" target="_blank" class="">
imaging_non_minc_insertion.pl</a> on the loaded NIfTI files.</div>
<div class=""><br class="">
</div>
<div class="">Does that clarify the steps? </div>
<div class=""><br class="">
</div>
<div class="">Thanks!</div>
<div class=""><br class="">
</div>
<div class="">Cécile</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. <<a href="mailto:sridar.narayanan@mcgill.ca" target="_blank" class="">sridar.narayanan@mcgill.ca</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">Hi Cecile,
<div class=""><br class="">
</div>
<div class="">Just to clarify, many import issues seem to stem from problems with the implementation of dcm2mnc used by Loris. These DICOM files can be successfully converted to MINC and NifTI with other tools, and so we were wondering if it would be possible
to import MRI data into Loris as MINC & NifTI files <u class="">instead of</u> importing the DICOMs. Alternatively, we could convert these files to BIDS and import that instead of DICOM. The important point is whether we can
<u class="">avoid importing DICOM</u> for new scan/participant instances, but import only BIDS or MINC + NiFTI data and generate a new Loris ID from this. We are not asking about attaching a MINC or NifTI file to an existing record, which we know can be done
(e.g. for label files associated with the images).</div>
<div class=""><br class="">
</div>
<div class="">Thanks,</div>
<div class=""><br class="">
</div>
<div class="">Sridar</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Jan 25, 2021, at 5:01 PM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
<br class="">
<div class="">
<div dir="ltr" class="">Hi Alfredo,
<div class=""><br class="">
</div>
<div class="">I am a bit confused by your email. The two perl scripts I mentioned last week do not require the data to be organized in BIDS to insert them. Did you look into them?</div>
<div class=""><br class="">
</div>
<div class="">Sorry, maybe I am missing something.</div>
<div class=""><br class="">
</div>
<div class="">Cécile</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank" class="">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">Hi Cecile,
<div class=""><br class="">
</div>
<div class="">Thank you for your answer. I am sorry I was not enough specific regarding what we are looking for. We are actually looking for a solution to avoid importing the “raw” images in minc and nifti images instead of DICOM. We are having a lot of issues
importing DICOM (~1.700 visits with issues) and we want to explore options for uploading the original images (e.g., t1) using minc and nifti without them being in BIDS formar.</div>
<div class=""><br class="">
</div>
<div class="">Do you have scripts for this?</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Alfredo.<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Jan 19, 2021, at 1:59 PM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
<br class="">
<div class="">
<p class=""><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)" class=""> External Email - Use Caution </span></p>
<div class=""><br class="">
</div>
<div dir="ltr" class="">Hi Alfredo,
<div class=""><br class="">
</div>
<div class="">Very sorry for the late reply. In short, yes, it is possible to do both.</div>
<div class=""><br class="">
</div>
<div class="">It is possible to insert MINC files in LORIS by using the LORIS-MRI script called
<a href="https://secure-web.cisco.com/1h8RHj_R4mnovi1vzHjXIG7OriE5SmwPXivIa6upEGgUmO0oyYw5rNJDqM2MdvPGvTNW0VgU36iIDos755qEXc2ZLdcGpGZQRfXLN_QGCSHqe5_pR8SPcRCLVkIkUT9JFyTm2tgFJomSHtiCakjIicPSDvv5QaC2BEX0O8gPHeY_UrixP8DhG29aU9BwThbmfsNCgJS9rWE8hkKiSJu3dXUWYZuz3SELo6A5cEG3a0urWWaEYKsL-uNUUQlpn-dLXHjrf4KywfR-f_8XtyxHIrA/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fmain%2FuploadNeuroDB%2Fminc_insertion.pl" target="_blank" class="">
minc_insertion.pl</a> in the uploadNeuroDB folder. If you run perl <a href="http://secure-web.cisco.com/13jgtqDYN7Gf_vgFThFhtlVEFqhsVru-JRquRrfzp92y9hcK9koGa9r9E_RCEHuDzqw9ZQq4eWBdGe5cbbKU8_yrxXgz98kTVTBySSdwUF3dgAiL6ls9glxHxeHwLfR-M9U6DLj3ePJR758eO7Ukl-KBwGCnH1TTfOmLDAPWxs4ABKnOnHa0AHFN4qsRIDO6BMvq5wK_o-G0mjUXNUyb7jkUjg-xsaAHbLYjZ1X15d3pWFi0jmNTPfm57PC77a41n7xp5Ae2Ji6UtzrGAczTtBg/http%3A%2F%2Fminc_insertion.pl" target="_blank" class="">
minc_insertion.pl</a> -h; you will see the explanation on how to run the script.</div>
<div class=""><br class="">
</div>
<div class="">Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called
<a href="https://secure-web.cisco.com/11rMDfTbsxeYelAro9qFHffjunl6PQySl-cFRkp1QAl_sinKZ_2ULH-80TnkR2omX6h5c78cX8Vvl4xgml5nGxkii9oOTjLtfmZO4NsBu-w2Dxh2E5l5p4rjx9RKrSRQak24h8B8rvl1sVWzkBe5qftWBHEd1FCLV4ptJPdCzV7xqJf3fMCIGfs77Mk6WCmGBhuL0FPSHDnWmRRvXzXAT5wH5eAUsHI3_2F8yAh25Hpvd-t9vttu-mAGU_XbLNQXQf2DNBFxGjThITPI2ptn38Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fmain%2FuploadNeuroDB%2Fimaging_non_minc_insertion.pl" target="_blank" class="">
imaging_non_minc_insertion.pl</a> in the same uploadNeuroDB folder. Running perl <a href="http://secure-web.cisco.com/1JUwbjz4V-PmM1LkrSIDPw4ydwAZ7otVSJadvo40dcrQMsYYfCLZsWRbpIcZwOZ3-TV3DyLARQX4Fp7-IHGmufed_LFzA0ah5UuJSegiZBGWQE9RiKXU6LxPe9xHqMfhyirSZF4zFetUaHoOtn5Pa9lFbV5o2FFI95zKG4NrmEX-HgUA_dMYmHrIFagQBzH_uujh-hUSiWM7Hvbf_d_KanWYNOrmkjAoe07MI18KuH0XsY5Gmhap81i-fVggYZHLthuCTL9_Dpky-ZNaeiyOlZw/http%3A%2F%2Fimaging_non_minc_insertion.pl" target="_blank" class="">
imaging_non_minc_insertion.pl</a> should give you all the information you need in order to run the script.</div>
<div class=""><br class="">
</div>
<div class="">Hope this helps,</div>
<div class=""><br class="">
</div>
<div class="">Cécile</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank" class="">AMORALESPINZON@bwh.harvard.edu</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Dear LorisDev team,<br class="">
<br class="">
Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format?<br class="">
<br class="">
Best regards,<br class="">
Alfredo.<br class="">
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