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Hi Cécile,
<div class=""><br class="">
</div>
<div class="">I tried to execute the query but there are some variables I don’t know what to set to: </div>
<div class=""><br class="">
</div>
<div class="">$PendingFailSubquery</div>
<div class="">$NewDataSubquery</div>
<div class="">$PendingNewquery</div>
<div class="">$modalities_subquery</div>
<div class="">$left_joins</div>
<div class=""><br class="">
</div>
<div class="">So, I executed the following:</div>
<div class=""><br class="">
</div>
<div class="">===</div>
<div class="">
<div class="">SELECT</div>
<div class=""> p.Name as Site,</div>
<div class=""> c.PSCID as PSCID,</div>
<div class=""> c.CandID as DCCID,</div>
<div class=""> Project.Name as project,</div>
<div class=""> s.Visit_label as visitLabel,</div>
<div class=""> DATE_FORMAT(MIN(pf.Value), '%Y-%m-%d') as First_Acquisition,</div>
<div class=""> FROM_UNIXTIME(MIN(f.InsertTime)) as First_Insertion,</div>
<div class=""> FROM_UNIXTIME(MAX(fqc.QCLastChangeTime)) as Last_QC,</div>
<div class=""> GROUP_CONCAT(DISTINCT OutputType) as Links,</div>
<div class=""> s.ID as sessionID,</div>
<div class=""> GROUP_CONCAT(DISTINCT modality.Scan_type) as sequenceType,</div>
<div class=""> s.CenterID as CenterID,</div>
<div class=""> c.Entity_type as entityType,</div>
<div class=""> s.ProjectID</div>
<div class=""> FROM psc AS p</div>
<div class=""> JOIN session s ON (s.CenterID=p.CenterID)</div>
<div class=""> JOIN candidate c ON (c.CandID=s.CandID)</div>
<div class=""> LEFT JOIN Project ON (s.ProjectID=Project.ProjectID)</div>
<div class=""> JOIN files f ON (f.SessionID=s.ID)</div>
<div class=""> LEFT JOIN files_qcstatus fqc ON (fqc.FileID=f.FileID)</div>
<div class=""> JOIN parameter_file pf ON (f.FileID=pf.FileID)</div>
<div class=""> JOIN parameter_type pt USING (ParameterTypeID)</div>
<div class=""> LEFT JOIN mri_scan_type modality ON</div>
<div class=""> (f.AcquisitionProtocolID=modality.ID)</div>
<div class=""> WHERE</div>
<div class=""> s.Active = 'Y' AND</div>
<div class=""> f.FileType IN ('mnc', 'nii') AND</div>
<div class=""> pt.Name='acquisition_date'</div>
<div class=""> GROUP BY s.ID</div>
<div class=""> ORDER BY c.PSCID, s.Visit_label;</div>
</div>
<div class="">===</div>
<div class=""><br class="">
</div>
<div class="">And I got 34415 rows, here is the last part of it:</div>
<div class=""><br class="">
</div>
<div class="">===</div>
<div class="">
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">| 723-DKC-1 | BGH723308 | 925320 | ADVANCE_ATTAIN | w024 | 2012-05-09 | 2021-03-21 01:26:41 | NULL | ct1unf.0.87,native | 123453 | ct1unf.0.87,flair,mtOFF,mtON,pdw,t1c,t1p,t2w
| 842 | Human | 11 |</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">| 723-DKC-1 | BGH723308 | 925320 | ADVANCE_ATTAIN | w048 | 2012-10-10 | 2021-03-21 01:33:28 | NULL | ct1unf.0.87,native | 127243 | ct1unf.0.87,flair,mtOFF,mtON,pdw,t1c,t1p,t2w
| 842 | Human | 11 |</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">| 723-DKC-1 | BGH723308 | 925320 | ADVANCE_ATTAIN | w096 | 2013-09-17 | 2020-11-25 23:36:42 | NULL | native | 123465 | flair,mtOFF,mtON,pdw,t1c,t1p,t2w
| 842 | Human | 11 |</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; 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: 14px; line-height: normal; font-family: Menlo; color: rgb(0, 0, 0);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">34415 rows in set, 12 warnings (12.43 sec)</span></div>
</div>
<div class="">===</div>
<div class=""><br class="">
</div>
<div class="">I added the name of project where I am uploading BIDS to in the WHERE:</div>
<div class=""><br class="">
</div>
<div class="">===</div>
<div class="">
<div class="">WHERE ...</div>
<div class=""> <span style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0);" class="">AND</span> Project.Name = 'INFORMS'</div>
</div>
<div class="">===</div>
<div class=""><br class="">
</div>
<div class="">I got an empty set. Based on this what should we try?</div>
<div class=""><br class="">
</div>
<div class="">Regarding the Scan_done I manually modified it but I get an error in the web page:</div>
<div class=""><br class="">
</div>
<div class=""><img apple-inline="yes" id="877E5A44-B299-4CDD-9BC0-72D6EB6F5AF9" src="cid:1AE14BA4-BC51-4453-8988-C8B86823A12D" class=""></div>
<div class=""><br class="">
</div>
<div class="">I am happy to do a Zoom call if that helps us move faster.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Alfredo.</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jun 7, 2021, at 4:50 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="">
<div dir="ltr" class="">Hi Alfredo,
<div class=""><br class="">
</div>
<div class="">Interesting. I was expecting to see the Active field set to NULL which would have explained why you do not see anything in the imaging browser. My next theory is that you do not have anything for the parameter_type name 'acquisition_date' which
is very likely to be the case for a BIDS dataset with no date information.</div>
<div class=""><br class="">
</div>
<div class="">Does the following query return anything for you? That is the query that is supposed to return data to the imaging browser (that you can find in
<a href="https://secure-web.cisco.com/1weK8jADYBDQk4jpPzRNm8rD0PwVDNCMSqr5yG572iHCS4Y0zqqLqBl9mPaA0wu2sekKrklkT0E-yyzFbYhZ1AepajvvGWnxe688Ok1sCPLPdfeAONPWXzCeqgszXpJ9sgBtvWLUICHxS_J9Ffa7ZOjbld8AX9aUbjG_oYI2dMGGtk_ThMB_SQuneDiRqmTctykQ3dAkWL0sA76pxQnBl3ftDrrfNhBPtIWqATw3ihLuLtYmABCIlnSK4c6I14etC2cOWz4rM78zGhuKp5s0-NMhVRG9h3GS_fcxp9Ltd-TBrjcbTsBuTwN-BmuzRKhZv/https%3A%2F%2Fgithub.com%2Faces%2FLoris%2Fblob%2F23.0-release%2Fmodules%2Fimaging_browser%2Fphp%2Fimagingbrowserrowprovisioner.class.inc" class="">
modules/imaging_browser/php/imagingbrowserrowprovisioner.class.inc</a>).</div>
<div class=""><br class="">
</div>
<div class="">
<table class="gmail-tab-size gmail-highlight gmail-js-file-line-container" style="border-spacing:0px;border-collapse:collapse;color:rgb(36,41,46);font-family:-apple-system,system-ui,"Segoe UI",Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji";font-size:14px">
<tbody style="box-sizing:border-box" class="">
<tr style="box-sizing:border-box" class="">
<td id="gmail-LC177" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">SELECT</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L178" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC178" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">p.Name as Site,</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L179" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC179" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">c.PSCID as PSCID,</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L180" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC180" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">c.CandID as DCCID,</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L181" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC181" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">Project.Name as project,</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L182" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC182" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">s.Visit_label as visitLabel,</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L183" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC183" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">$PendingFailSubquery as Visit_QC_Status,</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L184" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC184" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">DATE_FORMAT(MIN(pf.Value), \"%Y-%m-%d\") as First_Acquisition,</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L185" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC185" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">FROM_UNIXTIME(MIN(f.InsertTime)) as First_Insertion,</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L186" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC186" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">FROM_UNIXTIME(MAX(fqc.QCLastChangeTime)) as Last_QC,</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L187" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC187" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">$NewDataSubquery as New_Data,</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L188" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC188" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">GROUP_CONCAT(DISTINCT OutputType) as Links,</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L189" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC189" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">s.ID as sessionID,</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L190" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC190" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">GROUP_CONCAT(DISTINCT modality.Scan_type) as sequenceType,</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L191" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC191" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">$PendingNewquery as pending,</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L192" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC192" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">$modalities_subquery</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L193" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC193" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">s.CenterID as CenterID,</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L194" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC194" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">c.Entity_type as entityType,</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L195" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC195" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">s.ProjectID</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L196" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC196" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">FROM psc AS p</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L197" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC197" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">JOIN session s ON (s.CenterID=p.CenterID)</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L198" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC198" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">JOIN candidate c ON (c.CandID=s.CandID)</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L199" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC199" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">LEFT JOIN Project ON (s.ProjectID=Project.ProjectID)</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L200" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC200" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">JOIN files f ON (f.SessionID=s.ID)</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L201" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC201" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">LEFT JOIN files_qcstatus fqc ON (fqc.FileID=f.FileID)</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L202" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC202" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">JOIN parameter_file pf ON (f.FileID=pf.FileID)</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L203" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC203" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">JOIN parameter_type pt USING (ParameterTypeID)</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L204" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC204" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">LEFT JOIN mri_scan_type modality ON</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L205" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC205" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">(f.AcquisitionProtocolID=modality.ID)</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L206" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC206" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">$left_joins</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L207" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC207" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">WHERE</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L208" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC208" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">s.Active = 'Y' AND</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L209" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC209" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">f.FileType IN ('mnc', 'nii') AND</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L210" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC210" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">pt.Name='acquisition_date'</span></td>
</tr>
<tr style="box-sizing:border-box" class="">
<td id="gmail-L211" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC211" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">GROUP BY s.ID</span></td>
</tr>
<tr style="box-sizing:border-box;background-color:transparent" class="">
<td id="gmail-L212" class="gmail-js-line-number gmail-blob-num" style="box-sizing:border-box;padding:0px 10px;width:50px;min-width:50px;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;line-height:20px;text-align:right;white-space:nowrap;vertical-align:top">
</td>
<td id="gmail-LC212" class="gmail-js-file-line gmail-blob-code gmail-blob-code-inner" style="box-sizing:border-box;padding:0px 10px;line-height:20px;vertical-align:top;overflow:visible;font-family:SFMono-Regular,Consolas,"Liberation Mono",Menlo,monospace;font-size:12px;white-space:pre">
<span class="gmail-pl-s" style="box-sizing:border-box">ORDER BY c.PSCID, s.Visit_label</span></td>
</tr>
</tbody>
</table>
</div>
</div>
<br class="">
<div class="gmail_quote">
<div class="gmail_attr">If you get an empty result, try removing the following from the WHERE section of the query above:</div>
<div class="gmail_attr"><br class="">
</div>
<div dir="ltr" class="gmail_attr"><span class="gmail-pl-s" style="box-sizing:border-box"> ..... AND</span><span class="gmail-pl-s" style="box-sizing:border-box"> </span></div>
<div dir="ltr" class="gmail_attr"><span class="gmail-pl-s" style="box-sizing:border-box"> pt.Name='acquisition_date'</span><br class="">
</div>
<div dir="ltr" class="gmail_attr"><br class="">
</div>
<div class="gmail_attr">If my second theory is right, you should then see rows returned, in which case you will need to modify the query in the imaging_browser code. </div>
<div class="gmail_attr">Let me know how those go.</div>
<div class="gmail_attr"><br class="">
</div>
<div class="gmail_attr">Regarding the Scan_type, I should probably be populated by the insertion script so this may be a bug on the bids_import scripts specific to the imaging component. In the meantime, you can indeed set the flag to Y for the sessions you
know contain scan data.</div>
<div class="gmail_attr"><br class="">
</div>
<div class="gmail_attr">Hope this helps,</div>
<div class="gmail_attr"><br class="">
</div>
<div class="gmail_attr">Cécile</div>
<div dir="ltr" class="gmail_attr"><br class="">
</div>
<div dir="ltr" class="gmail_attr"><br class="">
</div>
<div dir="ltr" class="gmail_attr">On Mon, Jun 7, 2021 at 12:27 PM Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" 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 style="overflow-wrap: break-word;" class="">Hi Cécile,
<div class=""><br class="">
</div>
<div class="">Thank you for prompt answer. Here is the output of the query:</div>
<div class=""><br class="">
</div>
<div class="">===</div>
<div class="">
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">mysql> SELECT CandID, Visit_label, Active, Scan_done, CenterID, ProjectID, SubprojectID FROM session WHERE Visit_label = 'screening' AND CandID=207019;</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">+--------+-------------+--------+-----------+----------+-----------+--------------+</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">| CandID | Visit_label | Active | Scan_done | CenterID | ProjectID | SubprojectID |</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">+--------+-------------+--------+-----------+----------+-----------+--------------+</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">| 207019 | screening | Y | NULL | 843 | 12 | 2 |</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">+--------+-------------+--------+-----------+----------+-----------+--------------+</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo;" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">1 row in set (0.00 sec)</span></div>
</div>
<div class="">===<br class="">
<div class=""><br class="">
</div>
<div class="">I guess the “Scan_done” should be ‘Y’ instead of ’NULL’. Is this something that the BIDS importing script should take care of? Is the fix as simple as just setting Scan_done to ‘Y’?</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Alfredo.</div>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On Jun 6, 2021, at 4:48 PM, Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@BWH.HARVARD.EDU" target="_blank" class="">AMORALESPINZON@BWH.HARVARD.EDU</a>> wrote:</div>
<br class="">
<div class="">
<div style="overflow-wrap: break-word;" class="">Hi Cécile,
<div class=""><br class="">
</div>
<div class="">We managed to insert the candidates and the visits, and create the specific file names for BIDS before actually launching the BIDS script. The script finally worked, however I don’t see the images in LORIS. I am adding down below the bids log
insertion. Is there something additional I need to do to be able to see the images? In the web site I see the candidate and the visit but the column “Imaging Scan Done” is marked with a question mark (see attachment).</div>
<div class=""><br class="">
</div>
<div class="">===</div>
<div class="">
<div class="">/PROJECT/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.6/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early
as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument.</div>
<div class=""> warnings.warn("The ability to pass arguments to BIDSLayout that control "</div>
<div class=""><br class="">
</div>
<div class="">Connecting to:</div>
<div class=""> database: DATABASE</div>
<div class=""> username: USERNAME</div>
<div class=""> hostname: 111.222.333440</div>
<div class=""> port : 1234</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ('default_bids_vl',)</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ('dataDirBasepath',)</div>
<div class=""><br class="">
</div>
<div class="">AMP::bids_dir: /DATA/CAND_A/bids</div>
<div class="">Loading the BIDS dataset with BIDS layout library...</div>
<div class=""><br class="">
</div>
<div class="">AMP::bids_config: /PROJECT/bin/mri/python/lib/bids.json</div>
<div class="">root: /DATA/CAND_A/bids</div>
<div class="">target:: /DATA/CAND_A/bids/dataset_description.json</div>
<div class=""> => BIDS dataset loaded with BIDS layout</div>
<div class=""><br class="">
</div>
<div class="">Grepping candidates from the BIDS layout...</div>
<div class="">Validating the list of participants...</div>
<div class="">subjects: ['207019']</div>
<div class=""> => Passed validation of the list of participants</div>
<div class=""><br class="">
</div>
<div class=""> => List of participants found:</div>
<div class=""> 207019</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Grepping list of sessions from the BIDS layout...</div>
<div class=""> => List of sessions found:</div>
<div class=""><br class="">
</div>
<div class=""> 207019: screening</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Grepping the different modalities from the BIDS layout...</div>
<div class=""> => Done grepping the different modalities from the BIDS layout</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT * FROM candidate WHERE PSCID = %s</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ('207019',)</div>
<div class="">Executing query:</div>
<div class=""> SELECT SubprojectID FROM subproject WHERE title = %s</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ['Experimental']</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT * FROM session WHERE CandID = %s AND Visit_label = %s</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ('622350', 'screening')</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT * FROM candidate WHERE PSCID = %s</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ('207019',)</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT SubprojectID FROM subproject WHERE title = %s</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ['Experimental']</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT * FROM session WHERE CandID = %s AND Visit_label = %s</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ('622350', 'screening')</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT type FROM ImagingFileTypes</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ('248248fb303a762548e0be602b0b6bd6c6f33b4c860898c69faa8273be7a80f6d93b6413ec3bbeaadf22005fac04b07e9c08487e7b0a6690f64c2781d77d69b4',)</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT type FROM ImagingFileTypes</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ('b16bc029ea1cb8271a0728785d04eddaaa66e4d89c09e990552667b3c5598d17cee045b5b4ee3480dc2b8e08b5b05ca4e53c57f50b13b26f6467b9e4f455d09e',)</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT type FROM ImagingFileTypes</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ('44346136db049d0faf867a34d57d5714803a320b070013da0e1cf66e064f4dc9db92533f8aa8caaafcb78ce141c5444c5b8f8dc6b1d1c7dac530a4c2375eedcd',)</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT type FROM ImagingFileTypes</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ('ee91658a67d7d96007f6f0c625cceb700c9fa5bbecf34cea3cae8f1445a6efce5f735b2ab68d26717a6aaa418808b3d8fb30b03e03ae1982b0eeed834429d081',)</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT type FROM ImagingFileTypes</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Executing query:</div>
<div class=""> SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s</div>
<div class=""><br class="">
</div>
<div class="">With arguments:</div>
<div class=""> ('749c00e5aa64583c91f29672b228b9d89e691cef7d8f3380eefbc1fee466bd3d987fd7178001f0e4f63684a50e139a7bb8ed197981d1588ffc4dfc4eed8278b8',)</div>
</div>
<div class="">===</div>
<div class=""><br class="">
</div>
<div class="">Thank you for your help.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Alfredo.</div>
<div class=""><br class="">
</div>
<div class=""><span id="gmail-m_3600118325310015018cid:5D3A3868-20A3-45CC-B1D8-FE1F6FAADE66" class=""><Screen Shot 2021-06-06 at 4.44.57 PM.png></span><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On May 13, 2021, at 10:08 AM, 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="">The requirement of not having any special characters in the Participant ID or Session ID comes from BIDS and the libraries used to parse the BIDS dataset before insertion into LORIS. </div>
<div class=""><br class="">
</div>
<div class="">On the LORIS front: </div>
<div class="">
<ul class="">
<li class="">the ID used next to sub-<ID> will be used for the PSCID field of the candidate table (the CandID field being automatically generated as 6 random digits by the insertion script).</li><li class="">the ID used next to ses-<ID> will be used for the visit label field of the session table</li></ul>
<div class="">There might be another solution for you: modifying the file <a href="https://secure-web.cisco.com/1GvLDW-g8RekA6xfXzTQGS9x-cvm3VJ64Me4gEy4E2Yh3_J_-W9ZJiP9DEv9M9oH_JN3CJGEaRyJUvOCUzrNqMXl0tpX8TJ_Cfrs5JA9p_ICYgDGAU_HcPRpK0aHBkRHCW9mHZTixcIoY9EEim1Tt4JhQWyQlJpaTKY-bd1bc5O1lxwHz6sj4nGQ5bXFiDLYRP4Y8DWJzxYpm8EMaj_QYRiVdUOwHiSGfVGMouhDDMYYwBHrEEdV1Ompf5QRyVkSSAJaGL2Q3tSABSa8USdVkOQ/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fmain%2Fpython%2Flib%2Fbids.json" target="_blank" class="">https://github.com/aces/Loris-MRI/blob/main/python/lib/bids.json</a>
so that it matches the string used for your data. You would need to modify the pattern for subject and session in that file to match what you have. In theory, once done, pybids should be able to read your dataset. </div>
<div class=""><br class="">
</div>
<div class="">Hope this helps,</div>
<div class=""><br class="">
</div>
<div class="">Cécile</div>
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, May 13, 2021 at 9:47 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 Cécile,
<div class=""><br class="">
</div>
<div class="">
<blockquote type="cite" class="">
<div dir="ltr" class="">
<div class="">Is it possible to modify your IDs to be alphanumerical?</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
It is possible but puts more burden on our side as every single file now has to be modified. What would be best format for LORIS for the user ids (e.g., six digits) and the visit labels (e.g., alphanumerical without dash)? I just want to make sure we are compliant
with LORIS requirements before modifying the bids files.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Alfredo.<br class="">
<div class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On May 11, 2021, at 6:34 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="">It looks like the pybids is not able to read your BIDS dataset, which is why it returns an empty list of subjects.</div>
<div class=""><br class="">
</div>
<div class="">I just tried on the python terminal to load your dataset on pybids and it does not find any subject or visit. This is probably due to the name of the subject that contains special characters. That will also be problematic for the session label
of your dataset. I guess subjects in BIDS should remain alphanumerical only. Is it possible to modify your IDs to be alphanumerical?</div>
<div class=""><br class="">
</div>
<div class="">Cécile</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, May 11, 2021 at 5:37 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 Cécile,
<div class=""><br class="">
</div>
<div class="">I just shared the dataset in the sftp in the following path: 2021_05_11/caseCecile_BIDS.zip</div>
<div class=""><br class="">
</div>
<div class="">Additionally, here is the output of the script after adding the prints in the PR 617:</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="">/PROJECT/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.6/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is
likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and
pass it to the BIDSLayout via the `indexer` argument.</span></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=""> warnings.warn("The ability to pass arguments to BIDSLayout that control "</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</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="">Connecting to:</span></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=""> database: DATABASE</span></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=""> username: USERDATABASE</span></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=""> hostname: 111.222.333.44</span></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=""> port : 3306</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</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="">Executing query:</span></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=""> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</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="">With arguments:</span></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=""> ('default_bids_vl',)</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</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="">Executing query:</span></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=""> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</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="">With arguments:</span></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=""> ('dataDirBasepath',)</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class="">
<br class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span></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="">Loading the BIDS dataset with BIDS layout library...</span></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=""> => BIDS dataset loaded with BIDS layout</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</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="">Grepping candidates from the BIDS layout...</span></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="">Validating the list of participants...</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</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="">ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n</span></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="">CFTY720D2306.0102.00001is missing from the BIDS Layout</span></div>
<div style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</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="">List of subjects parsed by the BIDS layout:</span></div>
</div>
<div class="">===</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Alfredo.</div>
<div class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On May 11, 2021, at 12:01 PM, Cécile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
<br class="">
<div 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>
Sounds like a plan. Let me know once it is uploaded and I will ask Nicolas to give me access.
<div class=""><br class="">
</div>
<div class="">Thanks!</div>
<div class=""><br class="">
</div>
<div class="">PS: you can view the diff on the PR and simply copy the code over to your files if easier<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On May 11, 2021, at 11:47 AM, Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@BWH.HARVARD.EDU" target="_blank" class="">AMORALESPINZON@BWH.HARVARD.EDU</a>> wrote:</div>
<br class="">
<div class="">
<div class="">Hi Cecile,
<div class=""><br class="">
</div>
<div class="">In my testing dataset I have only one subject, I can share it with you in the LORIS sftp, does that work for you?</div>
<div class=""><br class="">
</div>
<div class="">In the mean time I will diff and pull your PR, and then execute it. I’ll send you the output asap.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Alfredo. </div>
<div class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On May 11, 2021, at 11:36 AM, Cecile Madjar <<a href="mailto:cecile.madjar@mcin.ca" target="_blank" class="">cecile.madjar@mcin.ca</a>> wrote:</div>
<br class="">
<div class="">
<p style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" 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 style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
<br class="">
</div>
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline" class="">Hi
Alfredo,</span>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
<br class="">
</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
I do not have access to your dataset but is it possible that there is one or more sub-<ID> in the participants.tsv that are different from the sub-<ID> used in the directory structure? (a.k.a., folders sub-<ID> and filenames that should start with sub-<ID>.)</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
<br class="">
</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
This function is specifically cross checking the list provided in the participants.tsv file and the information gathered by the BIDSLayout library that read your BIDS dataset.</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
<br class="">
</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
I created a PR on LORIS-MRI to elaborate the log from the function you just sent: <a href="https://secure-web.cisco.com/17BHyJzFWfexg2et-D1qxjFw7-MsSpwCyZsKHDjuQa1Iruj-GV8fZRnaNOQe7rTfFaljPkHD9E0Kch6nwzSvbbe_48vUcKT3ozGDvxPfpe248W0Nml3EbqwefqTQo6V0gIBseIrXtJ4qwpUnrLVYpwZQyTPaDCbkm_NqrpLrBeXaHi-m5KCVluJqMYsb1DZBrqFL_XKJiIevFuiValC7eTehDRbTek9A5RvYsPN6hDTzEHFPQfCzzRD6W_iQSp80c_PbAKgxDUVLU2cePcP45pg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F617" target="_blank" class="">https://github.com/aces/Loris-MRI/pull/617</a> Maybe
try adding the print statement in the diff of the PR to your code and rerun to get a better idea of what is going on?</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
<br class="">
</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
Let me know how it goes,</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
<br class="">
</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
Cécile</div>
<div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none" class="">
<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On May 10, 2021, at 4:15 PM, Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@bwh.harvard.edu" target="_blank" class="">AMORALESPINZON@bwh.harvard.edu</a>> wrote:</div>
<br class="">
<div class="">
<div class="">
<div class="">Dear LorisDev team.</div>
<div class=""><br class="">
</div>
<div class="">I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile:<span class=""> </span><a href="https://secure-web.cisco.com/1eWQtSLH8tHTpC1qsinKLnr4amf7Vdt1MLFNigX4jKdNz2mAoHV9ejLLcHZh1a0CUaUlzZMYTU9qzLaUEYYpyP1cl5UCR8e02WTmdMZUKXBNDeD8-cV2O5yTv8cgci7szP_MIGsvZ7FCjhqVmibPUnMFYbs6uYHGXZHOB5MsouWYLRHh89rJtQaFS8DOg4jfbwjp1bxwnO4FyuD3aKRv17dw9zoczaaXWnkbXXr87i6NQKYmA1NXhjM570IkyzSKuq-dlKj94vTZIlAChD5aFeg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F558%2Ffiles" target="_blank" class="">https://github.com/aces/Loris-MRI/pull/558/files</a> )
but I’m getting the following error (see all the output below):</div>
<div class=""><br class="">
</div>
<div class="">===</div>
<div class="">
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n</span></div>
</div>
<div class="">===</div>
<div class=""><br class="">
</div>
<div class="">After some debugging I saw that the array subjects in the following line is empty:</div>
<a href="https://secure-web.cisco.com/1sAIMc1N1U7sTpJYVEGfljx8iP9AUjxof1GeCQwNPKhd82OAXEZmdHoYu7n3Uq8jLaO-quBK1igoIw9Oo7d5JVNCfb3MNy6u-cvR2KkL-rfKwSOW_ovP_V5YKydvDMoE1ltw4MO29keFq-JiTymIk8Wm8TbXeHKxF2njboK6-6bctzRI-5K2tWwz82zUZyzDxyFdn4zXPqI8AihHeuWQQG3GOGgPSbRP-GOUfwbu2eVmvL_P_ldZetO1qjKowic0Gqnt-a9XN_8GORD5BLNlxTw/https%3A%2F%2Fgithub.com%2Flaemtl%2FLoris-MRI%2Fblob%2F3742522fa46b0ee2b9e384e30650a0c1f425c7af%2Fpython%2Flib%2Fbidsreader.py%23L134" target="_blank" class="">https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134</a>
<div class=""><br class="">
</div>
<div class="">I thought the issue was that we have symbolic links in our folder structure but after setting a testing example I am getting the same exact error.</div>
<div class=""><br class="">
</div>
<div class="">Any ideas why this is happening? The error does not help much. I’m happy to share the testing case, with all the BIDS structure to a LORIS developer, if this is helpful.</div>
<div class=""><br class="">
</div>
<div class="">Looking forward to hearing from you.</div>
<div class=""><br class="">
</div>
<div class="">Best.</div>
<div class="">Alfredo.</div>
<div class=""><br class="">
</div>
<div class="">===</div>
<div class="">
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">/PROJECT/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.6/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is
likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and
pass it to the BIDSLayout via the `indexer` argument.</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> warnings.warn("The ability to pass arguments to BIDSLayout that control "</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">Connecting to:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> database: DATABASE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> username: USERDATABASE</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> hostname: 111.222.333.444</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> port : 3306</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">Executing query:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">With arguments:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> ('default_bids_vl',)</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">Executing query:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">With arguments:</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> ('dataDirBasepath',)</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px" class="">
<br class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">Loading the BIDS dataset with BIDS layout library...</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px" class="">
<br class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""> => BIDS dataset loaded with BIDS layout</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">Grepping candidates from the BIDS layout...</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">Validating the list of participants...</span></div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo;min-height:16px" class="">
<span style="font-variant-ligatures:no-common-ligatures" class=""></span><br class="">
</div>
<div style="margin:0px;font-stretch:normal;font-size:14px;line-height:normal;font-family:Menlo" class="">
<span style="font-variant-ligatures:no-common-ligatures" class="">ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n</span></div>
</div>
<div class="">===</div>
<div class=""><br class="">
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