From aliaarefi1997 at gmail.com Tue Dec 4 08:57:14 2018 From: aliaarefi1997 at gmail.com (Ali Aarefi) Date: Tue, 4 Dec 2018 17:27:14 +0330 Subject: [Loris-dev] Instruments API Message-ID: Hello Dear LORIS dev. team, I'm trying to develop a script that automatically insert some information to specifically created instrument instance using restful API.(based on github doc , other doc ) I did use APIs of LORIS for authentication, candidate creation, time point creation and getting candidate and project information successfully. But now, I cannot use "3.3. The candidate instrument data " API (put request). The related part of python script file and its outputs(within the .py file) is attached. Also the used .linst file is attached. Is there any solution to automatically fill an instrument form in loris? Is it possible to write a script that reads from an Excel file and put those into LORIS previously-built instruments using API? Best Regards, Ali -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: loris_Instrument_filler.py Type: text/x-python Size: 1770 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ft.linst Type: application/octet-stream Size: 365 bytes Desc: not available URL: From xavier.lecoursboucher at mcgill.ca Tue Dec 4 13:19:24 2018 From: xavier.lecoursboucher at mcgill.ca (Xavier Lecours Boucher, Mr) Date: Tue, 4 Dec 2018 18:19:24 +0000 Subject: [Loris-dev] Instruments API In-Reply-To: References: Message-ID: Hello, >From what I can see, the instrument name in the linst file is "ft" Can you try the same script with InstrumentName=ft ? When I send a PUT request to an non existant instrument name, I also receive a 405 Thank you - Xavier Lecours ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Ali Aarefi Sent: December 4, 2018 8:57 AM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] Instruments API Hello Dear LORIS dev. team, I'm trying to develop a script that automatically insert some information to specifically created instrument instance using restful API.(based on github doc, other doc) I did use APIs of LORIS for authentication, candidate creation, time point creation and getting candidate and project information successfully. But now, I cannot use "3.3. The candidate instrument data" API (put request). The related part of python script file and its outputs(within the .py file) is attached. Also the used .linst file is attached. Is there any solution to automatically fill an instrument form in loris? Is it possible to write a script that reads from an Excel file and put those into LORIS previously-built instruments using API? Best Regards, Ali -------------- next part -------------- An HTML attachment was scrubbed... URL: From aliaarefi1997 at gmail.com Tue Dec 4 15:12:30 2018 From: aliaarefi1997 at gmail.com (Ali Aarefi) Date: Tue, 4 Dec 2018 23:42:30 +0330 Subject: [Loris-dev] Instruments API In-Reply-To: References: Message-ID: Hello, I tried that script with InstrumentName = "ft". The result was a response with code 500. Thanks for your quick response, - Ali On Tue, Dec 4, 2018, 9:49 PM Xavier Lecours Boucher, Mr < xavier.lecoursboucher at mcgill.ca wrote: > > Hello, > > From what I can see, the instrument name in the linst file is "ft" > > Can you try the same script with InstrumentName=ft ? > > When I send a PUT request to an non existant instrument name, I also > receive a 405 > > Thank you > > - Xavier Lecours > > ------------------------------ > *From:* loris-dev-bounces at bic.mni.mcgill.ca < > loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Ali Aarefi < > aliaarefi1997 at gmail.com> > *Sent:* December 4, 2018 8:57 AM > *To:* loris-dev at bic.mni.mcgill.ca > *Subject:* [Loris-dev] Instruments API > > Hello > > Dear LORIS dev. team, > > I'm trying to develop a script that automatically insert some information > to specifically created instrument instance using restful API.(based on github > doc , other > doc ) > > I did use APIs of LORIS for authentication, candidate creation, time point > creation and getting candidate and project information successfully. But > now, I cannot use "3.3. The candidate instrument data > " > API (put request). > > The related part of python script file and its outputs(within the .py > file) is attached. > Also the used .linst file is attached. > > Is there any solution to automatically fill an instrument form in loris? > Is it possible to write a script that reads from an Excel file and put > those into LORIS previously-built instruments using API? > > Best Regards, > > Ali > -------------- next part -------------- An HTML attachment was scrubbed... URL: From xavier.lecoursboucher at mcgill.ca Wed Dec 5 10:03:10 2018 From: xavier.lecoursboucher at mcgill.ca (Xavier Lecours Boucher, Mr) Date: Wed, 5 Dec 2018 15:03:10 +0000 Subject: [Loris-dev] Instruments API In-Reply-To: References: , Message-ID: Hi Ali, HTTP 500 are returned on server errors. More info about the cause should be available in your server apache error.log I notice that the instrument values part of the filled_form use the question and answers label instead of the keys. Could you try with : filled_form = { 'Meta': { 'Instrument': InstrumentName, 'Visit': VisitLabel, 'Candidate': CandID, 'DDE': boolean }, InstrumentName: { "first_test": "a" } } where the InstrumentName object's key is the question name instead of the question label and the value is the enum key instead of the label. Please let us know of the results. - Xavier ________________________________ From: Ali Aarefi Sent: December 4, 2018 3:12 PM To: Xavier Lecours Boucher, Mr Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] Instruments API Hello, I tried that script with InstrumentName = "ft". The result was a response with code 500. Thanks for your quick response, - Ali On Tue, Dec 4, 2018, 9:49 PM Xavier Lecours Boucher, Mr wrote: Hello, >From what I can see, the instrument name in the linst file is "ft" Can you try the same script with InstrumentName=ft ? When I send a PUT request to an non existant instrument name, I also receive a 405 Thank you - Xavier Lecours ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca

> on behalf of Ali Aarefi > Sent: December 4, 2018 8:57 AM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] Instruments API Hello Dear LORIS dev. team, I'm trying to develop a script that automatically insert some information to specifically created instrument instance using restful API.(based on github doc, other doc) I did use APIs of LORIS for authentication, candidate creation, time point creation and getting candidate and project information successfully. But now, I cannot use "3.3. The candidate instrument data" API (put request). The related part of python script file and its outputs(within the .py file) is attached. Also the used .linst file is attached. Is there any solution to automatically fill an instrument form in loris? Is it possible to write a script that reads from an Excel file and put those into LORIS previously-built instruments using API? Best Regards, Ali -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Mon Dec 10 16:29:46 2018 From: waveflux at gmail.com (Tom Beaudry) Date: Mon, 10 Dec 2018 16:29:46 -0500 Subject: [Loris-dev] importing tables into an instrument Message-ID: Hi Guys, I have a large table that I want to insert into LORIS (see my attachment). This is the data for 1 participant. The number of rows can vary from patient to patient. I was wondering if anyone has experience with this or has a good idea as to how I can import this data into LORIS. This is a tricky problem since LORIS saves instrument data where each row represent a candidate, and each column is single value, where I essentially want this value to be a table in my use case. I also would want a solution that would allow / make it possible for a DQT to be able to extract this data. Is this possible, or should i just upload an excel / csv file for the candidate instead because it's outside of the scope of LORIS. Thanks, Tom -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Sample Data.xlsx Type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet Size: 1378510 bytes Desc: not available URL: From leigh.ibis at gmail.com Mon Dec 10 17:15:41 2018 From: leigh.ibis at gmail.com (Leigh MacIntyre) Date: Mon, 10 Dec 2018 17:15:41 -0500 Subject: [Loris-dev] importing tables into an instrument In-Reply-To: References: Message-ID: Hi Tom, Sruthy, please correct me if I am wrong but this looks to me like it would be very similar to the DTI Prep upload you have set up? L Sent from my iPhone > On Dec 10, 2018, at 4:29 PM, Tom Beaudry wrote: > > Hi Guys, > > I have a large table that I want to insert into LORIS (see my attachment). This is the data for 1 participant. The number of rows can vary from patient to patient. > > I was wondering if anyone has experience with this or has a good idea as to how I can import this data into LORIS. This is a tricky problem since LORIS saves instrument data where each row represent a candidate, and each column is single value, where I essentially want this value to be a table in my use case. I also would want a solution that would allow / make it possible for a DQT to be able to extract this data. > > Is this possible, or should i just upload an excel / csv file for the candidate instead because it's outside of the scope of LORIS. > > Thanks, > Tom > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev From sruthy.mcin at gmail.com Tue Dec 11 10:35:47 2018 From: sruthy.mcin at gmail.com (Sruthy Mathew) Date: Tue, 11 Dec 2018 10:35:47 -0500 Subject: [Loris-dev] importing tables into an instrument In-Reply-To: References:

Message-ID: Hi Tom, As Leigh mentioned, IBIS has a similar instrument called DTI Prep, which parses excel data (each row represent data of different candidates) and stores the data in the database. Let me know when you have time for a quick chat regarding this :) Thanks, Sruthy On Mon, Dec 10, 2018 at 5:15 PM Leigh MacIntyre wrote: > Hi Tom, > > Sruthy, please correct me if I am wrong but this looks to me like it would > be very similar to the DTI Prep upload you have set up? > > L > > Sent from my iPhone > > > On Dec 10, 2018, at 4:29 PM, Tom Beaudry wrote: > > > > Hi Guys, > > > > I have a large table that I want to insert into LORIS (see my > attachment). This is the data for 1 participant. The number of rows can > vary from patient to patient. > > > > I was wondering if anyone has experience with this or has a good idea as > to how I can import this data into LORIS. This is a tricky problem since > LORIS saves instrument data where each row represent a candidate, and each > column is single value, where I essentially want this value to be a table > in my use case. I also would want a solution that would allow / make it > possible for a DQT to be able to extract this data. > > > > Is this possible, or should i just upload an excel / csv file for the > candidate instead because it's outside of the scope of LORIS. > > > > Thanks, > > Tom > > > > _______________________________________________ > > Loris-dev mailing list > > Loris-dev at bic.mni.mcgill.ca > > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Mon Dec 17 21:27:28 2018 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Tue, 18 Dec 2018 02:27:28 +0000 Subject: [Loris-dev] [LORIS-IPMSA] Series description does not match Message-ID: Dear LorisDev team, I am batch uploading images (~5000 visits = 15000 MRI images) into LORIS but they are not being classified correctly based on the series description (series_description_regex in table mri_protocol). Could you help with 2 things? 1. How can I change the type of an image already inserted? All the images inserted, so far around 240, were classified as NA. 2. Could you tell me if I am missing something in the series_description_regex in table mri_protocol? Here is what I have in the table mri_protocol and mri_scan_type, and a screenshot (attached) of one of the inserted images in LORIS: ----------------------------------------------------------------------------- mysql> select * from mri_protocol \G; *************************** 1. row *************************** ID: 1004 Center_name: ZZZZ ScannerID: 0 Scan_type: 41 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^flr$/i *************************** 2. row *************************** ID: 1005 Center_name: ZZZZ ScannerID: 0 Scan_type: 1001 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^pdw$/i *************************** 3. row *************************** ID: 1007 Center_name: ZZZZ ScannerID: 0 Scan_type: 1002 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^t2w$/i *************************** 4. row *************************** ID: 1009 Center_name: ZZZZ ScannerID: 0 Scan_type: 1003 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^t1c$/i *************************** 5. row *************************** ID: 1010 Center_name: ZZZZ ScannerID: 0 Scan_type: 1004 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^t1p$/i *************************** 6. row *************************** ID: 1011 Center_name: ZZZZ ScannerID: 0 Scan_type: 1005 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^mtOFF$/i *************************** 7. row *************************** ID: 1012 Center_name: ZZZZ ScannerID: 0 Scan_type: 1006 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^mtON$/i *************************** 8. row *************************** ID: 1013 Center_name: ZZZZ ScannerID: 0 Scan_type: 1000 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: NULL 8 rows in set (0.00 sec) ----------------------------------------------------------------------------- mysql> select * from mri_scan_type; +------+--------------+ | ID | Scan_type | +------+--------------+ | 40 | fMRI | | 41 | flair | | 44 | t1 | | 45 | t2 | | 46 | pd | | 47 | mrs | | 48 | dti | | 49 | t1relx | | 50 | dct2e1 | | 51 | dct2e2 | | 52 | scout | | 53 | tal_msk | | 54 | cocosco_cls | | 55 | clean_cls | | 56 | em_cls | | 57 | seg | | 58 | white_matter | | 59 | gray_matter | | 60 | csf_matter | | 61 | nlr_masked | | 62 | pve | | 999 | unknown | | 1000 | NA | | 1001 | pdw | | 1002 | t2w | | 1003 | t1c | | 1004 | t1p | | 1005 | mtOFF | | 1006 | mtON | +------+--------------+ ----------------------------------------------------------------------------- Thank you for any help. Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2018-12-17 at 9.17.59 PM.png Type: image/png Size: 163638 bytes Desc: Screen Shot 2018-12-17 at 9.17.59 PM.png URL: From AMORALESPINZON at bwh.harvard.edu Tue Dec 18 11:58:20 2018 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Tue, 18 Dec 2018 16:58:20 +0000 Subject: [Loris-dev] [LORIS-IPMSA] Series description does not match In-Reply-To: References: Message-ID: Dear LorisDev team, I found the error, the column series_description_regex in table mri_protocol needs to be in a specific format, meaning that the initial "/" and ending "/i" must not be placed in the regex string. I replaced "series_description_regex: /^flr$/i" by "series_description_regex: flr *$" and now I have the correct classification when inserting a new image. Now, I just need help with the images that were classified as NA (see my previous email), how can I change the type assigned to this images? Additionally, I didn't find any documentation regarding the format of the regex that LORIS is expecting, I would be great if we can add it for future users. Also, does it make sense to have the last part of the regex hard coded as "/i"? Maybe a user would like to use "/x" or other options. Thank you for your help. Best regards, Alfredo. ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Morales Pinzon, Alfredo Sent: Monday, December 17, 2018 9:27:28 PM To: loris-dev at bic.mni.mcgill.ca Cc: Zografos Caramanos; Sridar Narayanan, Dr.; Marciniak, Andrzej; pistikem at gmail.com; Rozie Arnaoutelis; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: [Loris-dev] [LORIS-IPMSA] Series description does not match External Email - Use Caution Dear LorisDev team, I am batch uploading images (~5000 visits = 15000 MRI images) into LORIS but they are not being classified correctly based on the series description (series_description_regex in table mri_protocol). Could you help with 2 things? 1. How can I change the type of an image already inserted? All the images inserted, so far around 240, were classified as NA. 2. Could you tell me if I am missing something in the series_description_regex in table mri_protocol? Here is what I have in the table mri_protocol and mri_scan_type, and a screenshot (attached) of one of the inserted images in LORIS: ----------------------------------------------------------------------------- mysql> select * from mri_protocol \G; *************************** 1. row *************************** ID: 1004 Center_name: ZZZZ ScannerID: 0 Scan_type: 41 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^flr$/i *************************** 2. row *************************** ID: 1005 Center_name: ZZZZ ScannerID: 0 Scan_type: 1001 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^pdw$/i *************************** 3. row *************************** ID: 1007 Center_name: ZZZZ ScannerID: 0 Scan_type: 1002 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^t2w$/i *************************** 4. row *************************** ID: 1009 Center_name: ZZZZ ScannerID: 0 Scan_type: 1003 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^t1c$/i *************************** 5. row *************************** ID: 1010 Center_name: ZZZZ ScannerID: 0 Scan_type: 1004 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^t1p$/i *************************** 6. row *************************** ID: 1011 Center_name: ZZZZ ScannerID: 0 Scan_type: 1005 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^mtOFF$/i *************************** 7. row *************************** ID: 1012 Center_name: ZZZZ ScannerID: 0 Scan_type: 1006 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^mtON$/i *************************** 8. row *************************** ID: 1013 Center_name: ZZZZ ScannerID: 0 Scan_type: 1000 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: NULL 8 rows in set (0.00 sec) ----------------------------------------------------------------------------- mysql> select * from mri_scan_type; +------+--------------+ | ID | Scan_type | +------+--------------+ | 40 | fMRI | | 41 | flair | | 44 | t1 | | 45 | t2 | | 46 | pd | | 47 | mrs | | 48 | dti | | 49 | t1relx | | 50 | dct2e1 | | 51 | dct2e2 | | 52 | scout | | 53 | tal_msk | | 54 | cocosco_cls | | 55 | clean_cls | | 56 | em_cls | | 57 | seg | | 58 | white_matter | | 59 | gray_matter | | 60 | csf_matter | | 61 | nlr_masked | | 62 | pve | | 999 | unknown | | 1000 | NA | | 1001 | pdw | | 1002 | t2w | | 1003 | t1c | | 1004 | t1p | | 1005 | mtOFF | | 1006 | mtON | +------+--------------+ ----------------------------------------------------------------------------- Thank you for any help. Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From rogers at bic.mni.mcgill.ca Wed Dec 19 12:59:35 2018 From: rogers at bic.mni.mcgill.ca (Christine Rogers) Date: Wed, 19 Dec 2018 12:59:35 -0500 Subject: [Loris-dev] [LORIS-IPMSA] Series description does not match In-Reply-To: References: Message-ID: Hi Alfredo, Thanks for your feedback, we'll look to clarify those regex specs in our documentation for future releases. Regarding changing the scan type -- the `files` table has an ` AcquisitionProtocolID` column which references the mri_scan_type`table's `ID` column. It's possible you may wish to re-run the insertion pipeline to identify and generate properly-labelled MINC filenames instead of undertaking manual updates in the filesystem and in the database. Best, Christine On Tue, Dec 18, 2018 at 11:58 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team, > > > I found the error, the column *series_description_regex* in table > *mri_protocol* needs to be in a specific format, meaning that the initial > "/" and ending "/i" must not be placed in the regex string. I replaced "*series_description_regex: > /^flr$/i*" by "series_description_regex: flr *$" and now I have the > correct classification when inserting a new image. > > > Now, I just need help with the images that were classified as NA (see my > previous email), how can I change the type assigned to this images? > > > Additionally, I didn't find any documentation regarding the format of the > regex that LORIS is expecting, I would be great if we can add it for future > users. Also, does it make sense to have the last part of the regex hard > coded as "/i"? Maybe a user would like to use "/x" or other options. > > > Thank you for your help. > > > Best regards, > > Alfredo. > ------------------------------ > *From:* loris-dev-bounces at bic.mni.mcgill.ca < > loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo > > *Sent:* Monday, December 17, 2018 9:27:28 PM > *To:* loris-dev at bic.mni.mcgill.ca > *Cc:* Zografos Caramanos; Sridar Narayanan, Dr.; Marciniak, Andrzej; > pistikem at gmail.com; Rozie Arnaoutelis; Douglas Arnold, Dr.; Guttmann, > Charles,M.D. > *Subject:* [Loris-dev] [LORIS-IPMSA] Series description does not match > > > External Email - Use Caution > > Dear LorisDev team, > > > I am batch uploading images (~5000 visits = 15000 MRI images) into LORIS > but they are not being classified correctly based on the series description > (series_description_regex in table mri_protocol). Could you help with 2 > things? > > > 1. How can I change the type of an image already inserted? All the images > inserted, so far around 240, were classified as NA. > > > 2. Could you tell me if I am missing something in the series_description_regex > in table mri_protocol? Here is what I have in the table mri_protocol and > mri_scan_type, and a screenshot (attached) of one of the inserted images in > LORIS: > > > > ----------------------------------------------------------------------------- > > mysql> select * from mri_protocol \G; > *************************** 1. row *************************** > ID: 1004 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 41 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^flr$/i > *************************** 2. row *************************** > ID: 1005 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1001 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^pdw$/i > *************************** 3. row *************************** > ID: 1007 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1002 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^t2w$/i > *************************** 4. row *************************** > ID: 1009 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1003 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^t1c$/i > *************************** 5. row *************************** > ID: 1010 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1004 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^t1p$/i > *************************** 6. row *************************** > ID: 1011 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1005 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^mtOFF$/i > *************************** 7. row *************************** > ID: 1012 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1006 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^mtON$/i > *************************** 8. row *************************** > ID: 1013 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1000 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: NULL > 8 rows in set (0.00 sec) > > > ----------------------------------------------------------------------------- > > > mysql> select * from mri_scan_type; > +------+--------------+ > | ID | Scan_type | > +------+--------------+ > | 40 | fMRI | > | 41 | flair | > | 44 | t1 | > | 45 | t2 | > | 46 | pd | > | 47 | mrs | > | 48 | dti | > | 49 | t1relx | > | 50 | dct2e1 | > | 51 | dct2e2 | > | 52 | scout | > | 53 | tal_msk | > | 54 | cocosco_cls | > | 55 | clean_cls | > | 56 | em_cls | > | 57 | seg | > | 58 | white_matter | > | 59 | gray_matter | > | 60 | csf_matter | > | 61 | nlr_masked | > | 62 | pve | > | 999 | unknown | > | 1000 | NA | > | 1001 | pdw | > | 1002 | t2w | > | 1003 | t1c | > | 1004 | t1p | > | 1005 | mtOFF | > | 1006 | mtON | > +------+--------------+ > > > ----------------------------------------------------------------------------- > > > Thank you for any help. > > > Best regards, > > Alfredo. > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Thu Dec 20 09:23:08 2018 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Thu, 20 Dec 2018 14:23:08 +0000 Subject: [Loris-dev] [LORIS-IPMSA] Series description does not match In-Reply-To: References: , Message-ID: Hi Christine, If I re-run the insertion pipeline will the "misclassify images" be correctly classified or I will have duplicates with different classification? I can easily re-run the pipeline but want to make sure I won't have duplicates. Thank you very much for your answer. Best, Alfredo. ________________________________ From: Christine Rogers Sent: Wednesday, December 19, 2018 12:59:35 PM To: Morales Pinzon, Alfredo Cc: loris-dev at bic.mni.mcgill.ca; aki at mrs.mni.mcgill.ca; Sridar Narayanan, Dr.; Marciniak, Andrzej; pistikem at gmail.com; Rozie Arnaoutelis, Ms.; douglas.arnold at mcgill.ca; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [LORIS-IPMSA] Series description does not match External Email - Use Caution Hi Alfredo, Thanks for your feedback, we'll look to clarify those regex specs in our documentation for future releases. Regarding changing the scan type -- the `files` table has an `AcquisitionProtocolID` column which references the mri_scan_type`table's `ID` column. It's possible you may wish to re-run the insertion pipeline to identify and generate properly-labelled MINC filenames instead of undertaking manual updates in the filesystem and in the database. Best, Christine On Tue, Dec 18, 2018 at 11:58 AM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, I found the error, the column series_description_regex in table mri_protocol needs to be in a specific format, meaning that the initial "/" and ending "/i" must not be placed in the regex string. I replaced "series_description_regex: /^flr$/i" by "series_description_regex: flr *$" and now I have the correct classification when inserting a new image. Now, I just need help with the images that were classified as NA (see my previous email), how can I change the type assigned to this images? Additionally, I didn't find any documentation regarding the format of the regex that LORIS is expecting, I would be great if we can add it for future users. Also, does it make sense to have the last part of the regex hard coded as "/i"? Maybe a user would like to use "/x" or other options. Thank you for your help. Best regards, Alfredo. ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca

> on behalf of Morales Pinzon, Alfredo > Sent: Monday, December 17, 2018 9:27:28 PM To: loris-dev at bic.mni.mcgill.ca Cc: Zografos Caramanos; Sridar Narayanan, Dr.; Marciniak, Andrzej; pistikem at gmail.com; Rozie Arnaoutelis; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: [Loris-dev] [LORIS-IPMSA] Series description does not match External Email - Use Caution Dear LorisDev team, I am batch uploading images (~5000 visits = 15000 MRI images) into LORIS but they are not being classified correctly based on the series description (series_description_regex in table mri_protocol). Could you help with 2 things? 1. How can I change the type of an image already inserted? All the images inserted, so far around 240, were classified as NA. 2. Could you tell me if I am missing something in the series_description_regex in table mri_protocol? Here is what I have in the table mri_protocol and mri_scan_type, and a screenshot (attached) of one of the inserted images in LORIS: ----------------------------------------------------------------------------- mysql> select * from mri_protocol \G; *************************** 1. row *************************** ID: 1004 Center_name: ZZZZ ScannerID: 0 Scan_type: 41 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^flr$/i *************************** 2. row *************************** ID: 1005 Center_name: ZZZZ ScannerID: 0 Scan_type: 1001 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^pdw$/i *************************** 3. row *************************** ID: 1007 Center_name: ZZZZ ScannerID: 0 Scan_type: 1002 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^t2w$/i *************************** 4. row *************************** ID: 1009 Center_name: ZZZZ ScannerID: 0 Scan_type: 1003 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^t1c$/i *************************** 5. row *************************** ID: 1010 Center_name: ZZZZ ScannerID: 0 Scan_type: 1004 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^t1p$/i *************************** 6. row *************************** ID: 1011 Center_name: ZZZZ ScannerID: 0 Scan_type: 1005 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^mtOFF$/i *************************** 7. row *************************** ID: 1012 Center_name: ZZZZ ScannerID: 0 Scan_type: 1006 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^mtON$/i *************************** 8. row *************************** ID: 1013 Center_name: ZZZZ ScannerID: 0 Scan_type: 1000 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: NULL 8 rows in set (0.00 sec) ----------------------------------------------------------------------------- mysql> select * from mri_scan_type; +------+--------------+ | ID | Scan_type | +------+--------------+ | 40 | fMRI | | 41 | flair | | 44 | t1 | | 45 | t2 | | 46 | pd | | 47 | mrs | | 48 | dti | | 49 | t1relx | | 50 | dct2e1 | | 51 | dct2e2 | | 52 | scout | | 53 | tal_msk | | 54 | cocosco_cls | | 55 | clean_cls | | 56 | em_cls | | 57 | seg | | 58 | white_matter | | 59 | gray_matter | | 60 | csf_matter | | 61 | nlr_masked | | 62 | pve | | 999 | unknown | | 1000 | NA | | 1001 | pdw | | 1002 | t2w | | 1003 | t1c | | 1004 | t1p | | 1005 | mtOFF | | 1006 | mtON | +------+--------------+ ----------------------------------------------------------------------------- Thank you for any help. Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From rogers at bic.mni.mcgill.ca Thu Dec 20 09:39:30 2018 From: rogers at bic.mni.mcgill.ca (Christine Rogers) Date: Thu, 20 Dec 2018 09:39:30 -0500 Subject: [Loris-dev] [LORIS-IPMSA] Series description does not match In-Reply-To: References:

Message-ID: Hi Alfredo, Yes, to clarify -- it is best to remove already inserted images/records before re-running the pipeline, as attempts to load duplicate DICOM tarballs should give errors, I believe. If you have QC information already registered for scans you have loaded in LORIS, this is best to back up very carefully before cleaning and re-loading images. Best, Christine On Thu, Dec 20, 2018 at 9:23 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Christine, > > > If I re-run the insertion pipeline will the "misclassify images" be > correctly classified or I will have duplicates with different > classification? I can easily re-run the pipeline but want to make sure I > won't have duplicates. > > > Thank you very much for your answer. > > > Best, > > Alfredo. > ------------------------------ > *From:* Christine Rogers > *Sent:* Wednesday, December 19, 2018 12:59:35 PM > *To:* Morales Pinzon, Alfredo > *Cc:* loris-dev at bic.mni.mcgill.ca; aki at mrs.mni.mcgill.ca; Sridar > Narayanan, Dr.; Marciniak, Andrzej; pistikem at gmail.com; Rozie > Arnaoutelis, Ms.; douglas.arnold at mcgill.ca; Guttmann, Charles,M.D. > *Subject:* Re: [Loris-dev] [LORIS-IPMSA] Series description does not match > > > External Email - Use Caution > > Hi Alfredo, > Thanks for your feedback, we'll look to clarify those regex specs in our > documentation for future releases. > > Regarding changing the scan type -- the `files` table has an ` > AcquisitionProtocolID` column which references the mri_scan_type`table's ` > ID` column. > > It's possible you may wish to re-run the insertion pipeline to identify > and generate properly-labelled MINC filenames instead of undertaking manual > updates in the filesystem and in the database. > > Best, > Christine > > > > On Tue, Dec 18, 2018 at 11:58 AM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > > Dear LorisDev team, > > > I found the error, the column *series_description_regex* in table > *mri_protocol* needs to be in a specific format, meaning that the initial > "/" and ending "/i" must not be placed in the regex string. I replaced "*series_description_regex: > /^flr$/i*" by "series_description_regex: flr *$" and now I have the > correct classification when inserting a new image. > > > Now, I just need help with the images that were classified as NA (see my > previous email), how can I change the type assigned to this images? > > > Additionally, I didn't find any documentation regarding the format of the > regex that LORIS is expecting, I would be great if we can add it for future > users. Also, does it make sense to have the last part of the regex hard > coded as "/i"? Maybe a user would like to use "/x" or other options. > > > Thank you for your help. > > > Best regards, > > Alfredo. > ------------------------------ > *From:* loris-dev-bounces at bic.mni.mcgill.ca < > loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo > > *Sent:* Monday, December 17, 2018 9:27:28 PM > *To:* loris-dev at bic.mni.mcgill.ca > *Cc:* Zografos Caramanos; Sridar Narayanan, Dr.; Marciniak, Andrzej; > pistikem at gmail.com; Rozie Arnaoutelis; Douglas Arnold, Dr.; Guttmann, > Charles,M.D. > *Subject:* [Loris-dev] [LORIS-IPMSA] Series description does not match > > > External Email - Use Caution > > Dear LorisDev team, > > > I am batch uploading images (~5000 visits = 15000 MRI images) into LORIS > but they are not being classified correctly based on the series description > (series_description_regex in table mri_protocol). Could you help with 2 > things? > > > 1. How can I change the type of an image already inserted? All the images > inserted, so far around 240, were classified as NA. > > > 2. Could you tell me if I am missing something in the series_description_regex > in table mri_protocol? Here is what I have in the table mri_protocol and > mri_scan_type, and a screenshot (attached) of one of the inserted images in > LORIS: > > > > ----------------------------------------------------------------------------- > > mysql> select * from mri_protocol \G; > *************************** 1. row *************************** > ID: 1004 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 41 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^flr$/i > *************************** 2. row *************************** > ID: 1005 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1001 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^pdw$/i > *************************** 3. row *************************** > ID: 1007 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1002 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^t2w$/i > *************************** 4. row *************************** > ID: 1009 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1003 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^t1c$/i > *************************** 5. row *************************** > ID: 1010 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1004 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^t1p$/i > *************************** 6. row *************************** > ID: 1011 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1005 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^mtOFF$/i > *************************** 7. row *************************** > ID: 1012 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1006 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^mtON$/i > *************************** 8. row *************************** > ID: 1013 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1000 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: NULL > 8 rows in set (0.00 sec) > > > ----------------------------------------------------------------------------- > > > mysql> select * from mri_scan_type; > +------+--------------+ > | ID | Scan_type | > +------+--------------+ > | 40 | fMRI | > | 41 | flair | > | 44 | t1 | > | 45 | t2 | > | 46 | pd | > | 47 | mrs | > | 48 | dti | > | 49 | t1relx | > | 50 | dct2e1 | > | 51 | dct2e2 | > | 52 | scout | > | 53 | tal_msk | > | 54 | cocosco_cls | > | 55 | clean_cls | > | 56 | em_cls | > | 57 | seg | > | 58 | white_matter | > | 59 | gray_matter | > | 60 | csf_matter | > | 61 | nlr_masked | > | 62 | pve | > | 999 | unknown | > | 1000 | NA | > | 1001 | pdw | > | 1002 | t2w | > | 1003 | t1c | > | 1004 | t1p | > | 1005 | mtOFF | > | 1006 | mtON | > +------+--------------+ > > > ----------------------------------------------------------------------------- > > > Thank you for any help. > > > Best regards, > > Alfredo. > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Thu Dec 20 09:46:58 2018 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Thu, 20 Dec 2018 14:46:58 +0000 Subject: [Loris-dev] [LORIS-IPMSA] Series description does not match In-Reply-To: References:

, Message-ID: Hi Christine, That sounds great. Where can I find the documentation for removing inserted images/records? So far we don't have QC information. Best, Alfredo. ________________________________ From: Christine Rogers Sent: Thursday, December 20, 2018 9:39 AM To: Morales Pinzon, Alfredo Cc: loris-dev at bic.mni.mcgill.ca; aki at mrs.mni.mcgill.ca; Sridar Narayanan, Dr.; Marciniak, Andrzej; Istv?n ?kos M?rocz; Rozie Arnaoutelis, Ms.; douglas.arnold at mcgill.ca; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [LORIS-IPMSA] Series description does not match External Email - Use Caution Hi Alfredo, Yes, to clarify -- it is best to remove already inserted images/records before re-running the pipeline, as attempts to load duplicate DICOM tarballs should give errors, I believe. If you have QC information already registered for scans you have loaded in LORIS, this is best to back up very carefully before cleaning and re-loading images. Best, Christine On Thu, Dec 20, 2018 at 9:23 AM Morales Pinzon, Alfredo > wrote: Hi Christine, If I re-run the insertion pipeline will the "misclassify images" be correctly classified or I will have duplicates with different classification? I can easily re-run the pipeline but want to make sure I won't have duplicates. Thank you very much for your answer. Best, Alfredo. ________________________________ From: Christine Rogers > Sent: Wednesday, December 19, 2018 12:59:35 PM To: Morales Pinzon, Alfredo Cc: loris-dev at bic.mni.mcgill.ca; aki at mrs.mni.mcgill.ca; Sridar Narayanan, Dr.; Marciniak, Andrzej; pistikem at gmail.com; Rozie Arnaoutelis, Ms.; douglas.arnold at mcgill.ca; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] [LORIS-IPMSA] Series description does not match External Email - Use Caution Hi Alfredo, Thanks for your feedback, we'll look to clarify those regex specs in our documentation for future releases. Regarding changing the scan type -- the `files` table has an `AcquisitionProtocolID` column which references the mri_scan_type`table's `ID` column. It's possible you may wish to re-run the insertion pipeline to identify and generate properly-labelled MINC filenames instead of undertaking manual updates in the filesystem and in the database. Best, Christine On Tue, Dec 18, 2018 at 11:58 AM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, I found the error, the column series_description_regex in table mri_protocol needs to be in a specific format, meaning that the initial "/" and ending "/i" must not be placed in the regex string. I replaced "series_description_regex: /^flr$/i" by "series_description_regex: flr *$" and now I have the correct classification when inserting a new image. Now, I just need help with the images that were classified as NA (see my previous email), how can I change the type assigned to this images? Additionally, I didn't find any documentation regarding the format of the regex that LORIS is expecting, I would be great if we can add it for future users. Also, does it make sense to have the last part of the regex hard coded as "/i"? Maybe a user would like to use "/x" or other options. Thank you for your help. Best regards, Alfredo. ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca

> on behalf of Morales Pinzon, Alfredo > Sent: Monday, December 17, 2018 9:27:28 PM To: loris-dev at bic.mni.mcgill.ca Cc: Zografos Caramanos; Sridar Narayanan, Dr.; Marciniak, Andrzej; pistikem at gmail.com; Rozie Arnaoutelis; Douglas Arnold, Dr.; Guttmann, Charles,M.D. Subject: [Loris-dev] [LORIS-IPMSA] Series description does not match External Email - Use Caution Dear LorisDev team, I am batch uploading images (~5000 visits = 15000 MRI images) into LORIS but they are not being classified correctly based on the series description (series_description_regex in table mri_protocol). Could you help with 2 things? 1. How can I change the type of an image already inserted? All the images inserted, so far around 240, were classified as NA. 2. Could you tell me if I am missing something in the series_description_regex in table mri_protocol? Here is what I have in the table mri_protocol and mri_scan_type, and a screenshot (attached) of one of the inserted images in LORIS: ----------------------------------------------------------------------------- mysql> select * from mri_protocol \G; *************************** 1. row *************************** ID: 1004 Center_name: ZZZZ ScannerID: 0 Scan_type: 41 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^flr$/i *************************** 2. row *************************** ID: 1005 Center_name: ZZZZ ScannerID: 0 Scan_type: 1001 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^pdw$/i *************************** 3. row *************************** ID: 1007 Center_name: ZZZZ ScannerID: 0 Scan_type: 1002 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^t2w$/i *************************** 4. row *************************** ID: 1009 Center_name: ZZZZ ScannerID: 0 Scan_type: 1003 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^t1c$/i *************************** 5. row *************************** ID: 1010 Center_name: ZZZZ ScannerID: 0 Scan_type: 1004 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^t1p$/i *************************** 6. row *************************** ID: 1011 Center_name: ZZZZ ScannerID: 0 Scan_type: 1005 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^mtOFF$/i *************************** 7. row *************************** ID: 1012 Center_name: ZZZZ ScannerID: 0 Scan_type: 1006 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: /^mtON$/i *************************** 8. row *************************** ID: 1013 Center_name: ZZZZ ScannerID: 0 Scan_type: 1000 TR_range: NULL TE_range: NULL TI_range: NULL slice_thickness_range: NULL FoV_x_range: NULL FoV_y_range: NULL FoV_z_range: NULL xspace_range: NULL yspace_range: NULL zspace_range: NULL xstep_range: NULL ystep_range: NULL zstep_range: NULL time_range: NULL series_description_regex: NULL 8 rows in set (0.00 sec) ----------------------------------------------------------------------------- mysql> select * from mri_scan_type; +------+--------------+ | ID | Scan_type | +------+--------------+ | 40 | fMRI | | 41 | flair | | 44 | t1 | | 45 | t2 | | 46 | pd | | 47 | mrs | | 48 | dti | | 49 | t1relx | | 50 | dct2e1 | | 51 | dct2e2 | | 52 | scout | | 53 | tal_msk | | 54 | cocosco_cls | | 55 | clean_cls | | 56 | em_cls | | 57 | seg | | 58 | white_matter | | 59 | gray_matter | | 60 | csf_matter | | 61 | nlr_masked | | 62 | pve | | 999 | unknown | | 1000 | NA | | 1001 | pdw | | 1002 | t2w | | 1003 | t1c | | 1004 | t1p | | 1005 | mtOFF | | 1006 | mtON | +------+--------------+ ----------------------------------------------------------------------------- Thank you for any help. Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From rogers at bic.mni.mcgill.ca Thu Dec 20 11:25:03 2018 From: rogers at bic.mni.mcgill.ca (Christine Rogers) Date: Thu, 20 Dec 2018 11:25:03 -0500 Subject: [Loris-dev] [LORIS-IPMSA] Series description does not match In-Reply-To: References:

Message-ID: Hi Alfredo, This documentation is available in the github.com/aces/Loris-MRI repo within the docs/ directory, for example: https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md#rerunning-the-imaging-pipeline It contains recommendations for how to carefully remove imaging file records before re-running the pipeline. (Please note this link above points to the "minor" branch in this repo - you will want to ensure the documentation you are consulting matches the release/branch of your codebase.) Best, Christine On Thu, Dec 20, 2018 at 9:47 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Christine, > > > That sounds great. Where can I find the documentation for removing > inserted images/records? So far we don't have QC information. > > > Best, > > Alfredo. > > > > ------------------------------ > *From:* Christine Rogers > *Sent:* Thursday, December 20, 2018 9:39 AM > *To:* Morales Pinzon, Alfredo > *Cc:* loris-dev at bic.mni.mcgill.ca; aki at mrs.mni.mcgill.ca; Sridar > Narayanan, Dr.; Marciniak, Andrzej; Istv?n ?kos M?rocz; Rozie Arnaoutelis, > Ms.; douglas.arnold at mcgill.ca; Guttmann, Charles,M.D. > *Subject:* Re: [Loris-dev] [LORIS-IPMSA] Series description does not match > > > External Email - Use Caution > > Hi Alfredo, > > Yes, to clarify -- it is best to remove already inserted images/records > before re-running the pipeline, as attempts to load duplicate DICOM > tarballs should give errors, I believe. > If you have QC information already registered for scans you have loaded in > LORIS, this is best to back up very carefully before cleaning and > re-loading images. > Best, > Christine > > On Thu, Dec 20, 2018 at 9:23 AM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > > Hi Christine, > > > If I re-run the insertion pipeline will the "misclassify images" be > correctly classified or I will have duplicates with different > classification? I can easily re-run the pipeline but want to make sure I > won't have duplicates. > > > Thank you very much for your answer. > > > Best, > > Alfredo. > ------------------------------ > *From:* Christine Rogers > *Sent:* Wednesday, December 19, 2018 12:59:35 PM > *To:* Morales Pinzon, Alfredo > *Cc:* loris-dev at bic.mni.mcgill.ca; aki at mrs.mni.mcgill.ca; Sridar > Narayanan, Dr.; Marciniak, Andrzej; pistikem at gmail.com; Rozie > Arnaoutelis, Ms.; douglas.arnold at mcgill.ca; Guttmann, Charles,M.D. > *Subject:* Re: [Loris-dev] [LORIS-IPMSA] Series description does not match > > > External Email - Use Caution > > Hi Alfredo, > Thanks for your feedback, we'll look to clarify those regex specs in our > documentation for future releases. > > Regarding changing the scan type -- the `files` table has an ` > AcquisitionProtocolID` column which references the mri_scan_type`table's ` > ID` column. > > It's possible you may wish to re-run the insertion pipeline to identify > and generate properly-labelled MINC filenames instead of undertaking manual > updates in the filesystem and in the database. > > Best, > Christine > > > > On Tue, Dec 18, 2018 at 11:58 AM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > > Dear LorisDev team, > > > I found the error, the column *series_description_regex* in table > *mri_protocol* needs to be in a specific format, meaning that the initial > "/" and ending "/i" must not be placed in the regex string. I replaced "*series_description_regex: > /^flr$/i*" by "series_description_regex: flr *$" and now I have the > correct classification when inserting a new image. > > > Now, I just need help with the images that were classified as NA (see my > previous email), how can I change the type assigned to this images? > > > Additionally, I didn't find any documentation regarding the format of the > regex that LORIS is expecting, I would be great if we can add it for future > users. Also, does it make sense to have the last part of the regex hard > coded as "/i"? Maybe a user would like to use "/x" or other options. > > > Thank you for your help. > > > Best regards, > > Alfredo. > ------------------------------ > *From:* loris-dev-bounces at bic.mni.mcgill.ca < > loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo > > *Sent:* Monday, December 17, 2018 9:27:28 PM > *To:* loris-dev at bic.mni.mcgill.ca > *Cc:* Zografos Caramanos; Sridar Narayanan, Dr.; Marciniak, Andrzej; > pistikem at gmail.com; Rozie Arnaoutelis; Douglas Arnold, Dr.; Guttmann, > Charles,M.D. > *Subject:* [Loris-dev] [LORIS-IPMSA] Series description does not match > > > External Email - Use Caution > > Dear LorisDev team, > > > I am batch uploading images (~5000 visits = 15000 MRI images) into LORIS > but they are not being classified correctly based on the series description > (series_description_regex in table mri_protocol). Could you help with 2 > things? > > > 1. How can I change the type of an image already inserted? All the images > inserted, so far around 240, were classified as NA. > > > 2. Could you tell me if I am missing something in the series_description_regex > in table mri_protocol? Here is what I have in the table mri_protocol and > mri_scan_type, and a screenshot (attached) of one of the inserted images in > LORIS: > > > > ----------------------------------------------------------------------------- > > mysql> select * from mri_protocol \G; > *************************** 1. row *************************** > ID: 1004 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 41 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^flr$/i > *************************** 2. row *************************** > ID: 1005 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1001 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^pdw$/i > *************************** 3. row *************************** > ID: 1007 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1002 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^t2w$/i > *************************** 4. row *************************** > ID: 1009 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1003 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^t1c$/i > *************************** 5. row *************************** > ID: 1010 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1004 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^t1p$/i > *************************** 6. row *************************** > ID: 1011 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1005 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^mtOFF$/i > *************************** 7. row *************************** > ID: 1012 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1006 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: /^mtON$/i > *************************** 8. row *************************** > ID: 1013 > Center_name: ZZZZ > ScannerID: 0 > Scan_type: 1000 > TR_range: NULL > TE_range: NULL > TI_range: NULL > slice_thickness_range: NULL > FoV_x_range: NULL > FoV_y_range: NULL > FoV_z_range: NULL > xspace_range: NULL > yspace_range: NULL > zspace_range: NULL > xstep_range: NULL > ystep_range: NULL > zstep_range: NULL > time_range: NULL > series_description_regex: NULL > 8 rows in set (0.00 sec) > > > ----------------------------------------------------------------------------- > > > mysql> select * from mri_scan_type; > +------+--------------+ > | ID | Scan_type | > +------+--------------+ > | 40 | fMRI | > | 41 | flair | > | 44 | t1 | > | 45 | t2 | > | 46 | pd | > | 47 | mrs | > | 48 | dti | > | 49 | t1relx | > | 50 | dct2e1 | > | 51 | dct2e2 | > | 52 | scout | > | 53 | tal_msk | > | 54 | cocosco_cls | > | 55 | clean_cls | > | 56 | em_cls | > | 57 | seg | > | 58 | white_matter | > | 59 | gray_matter | > | 60 | csf_matter | > | 61 | nlr_masked | > | 62 | pve | > | 999 | unknown | > | 1000 | NA | > | 1001 | pdw | > | 1002 | t2w | > | 1003 | t1c | > | 1004 | t1p | > | 1005 | mtOFF | > | 1006 | mtON | > +------+--------------+ > > > ----------------------------------------------------------------------------- > > > Thank you for any help. > > > Best regards, > > Alfredo. > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: