From AMORALESPINZON at BWH.HARVARD.EDU Mon May 10 16:15:02 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 10 May 2021 20:15:02 +0000 Subject: [Loris-dev] BIDS Error Message-ID: <8E375877-D896-4B0E-B0F7-D6BD5565CA67@bwh.harvard.edu> Dear LorisDev team. I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile: https://github.com/aces/Loris-MRI/pull/558/files ) but I?m getting the following error (see all the output below): === ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n === After some debugging I saw that the array subjects in the following line is empty: https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134 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. 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. Looking forward to hearing from you. Best. Alfredo. === /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. warnings.warn("The ability to pass arguments to BIDSLayout that control " Connecting to: database: DATABASE username: USERDATABASE hostname: 111.222.333.444 port : 3306 Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('default_bids_vl',) Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('dataDirBasepath',) Loading the BIDS dataset with BIDS layout library... => BIDS dataset loaded with BIDS layout Grepping candidates from the BIDS layout... Validating the list of participants... ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n === 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Tue May 11 11:36:57 2021 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 11 May 2021 11:36:57 -0400 Subject: [Loris-dev] BIDS Error In-Reply-To: <8E375877-D896-4B0E-B0F7-D6BD5565CA67@bwh.harvard.edu> References: <8E375877-D896-4B0E-B0F7-D6BD5565CA67@bwh.harvard.edu> Message-ID: Hi Alfredo, I do not have access to your dataset but is it possible that there is one or more sub- in the participants.tsv that are different from the sub- used in the directory structure? (a.k.a., folders sub- and filenames that should start with sub-.) 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. I created a PR on LORIS-MRI to elaborate the log from the function you just sent: https://github.com/aces/Loris-MRI/pull/617 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? Let me know how it goes, C?cile > On May 10, 2021, at 4:15 PM, Morales Pinzon, Alfredo wrote: > > Dear LorisDev team. > > I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile: https://github.com/aces/Loris-MRI/pull/558/files ) but I?m getting the following error (see all the output below): > > === > ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n > === > > After some debugging I saw that the array subjects in the following line is empty: > https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134 > > 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. > > 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. > > Looking forward to hearing from you. > > Best. > Alfredo. > > === > /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. > warnings.warn("The ability to pass arguments to BIDSLayout that control " > > Connecting to: > database: DATABASE > username: USERDATABASE > hostname: 111.222.333.444 > port : 3306 > > > Executing query: > SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); > > With arguments: > ('default_bids_vl',) > > > Executing query: > SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); > > With arguments: > ('dataDirBasepath',) > > Loading the BIDS dataset with BIDS layout library... > > => BIDS dataset loaded with BIDS layout > > Grepping candidates from the BIDS layout... > Validating the list of participants... > > ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n > === > > 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. > > Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Tue May 11 11:47:23 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Tue, 11 May 2021 15:47:23 +0000 Subject: [Loris-dev] BIDS Error In-Reply-To: References: <8E375877-D896-4B0E-B0F7-D6BD5565CA67@bwh.harvard.edu> Message-ID: <4286E305-87C3-492A-BE31-0B83CEFD365E@bwh.harvard.edu> Hi Cecile, In my testing dataset I have only one subject, I can share it with you in the LORIS sftp, does that work for you? In the mean time I will diff and pull your PR, and then execute it. I?ll send you the output asap. Best, Alfredo. On May 11, 2021, at 11:36 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, I do not have access to your dataset but is it possible that there is one or more sub- in the participants.tsv that are different from the sub- used in the directory structure? (a.k.a., folders sub- and filenames that should start with sub-.) 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. I created a PR on LORIS-MRI to elaborate the log from the function you just sent: https://github.com/aces/Loris-MRI/pull/617 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? Let me know how it goes, C?cile On May 10, 2021, at 4:15 PM, Morales Pinzon, Alfredo > wrote: Dear LorisDev team. I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile: https://github.com/aces/Loris-MRI/pull/558/files ) but I?m getting the following error (see all the output below): === ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n === After some debugging I saw that the array subjects in the following line is empty: https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134 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. 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. Looking forward to hearing from you. Best. Alfredo. === /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. warnings.warn("The ability to pass arguments to BIDSLayout that control " Connecting to: database: DATABASE username: USERDATABASE hostname: 111.222.333.444 port : 3306 Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('default_bids_vl',) Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('dataDirBasepath',) Loading the BIDS dataset with BIDS layout library... => BIDS dataset loaded with BIDS layout Grepping candidates from the BIDS layout... Validating the list of participants... ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n === 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Tue May 11 12:01:11 2021 From: cecile.madjar at mcin.ca (=?utf-8?Q?C=C3=A9cile_Madjar?=) Date: Tue, 11 May 2021 12:01:11 -0400 Subject: [Loris-dev] BIDS Error In-Reply-To: <4286E305-87C3-492A-BE31-0B83CEFD365E@bwh.harvard.edu> References: <8E375877-D896-4B0E-B0F7-D6BD5565CA67@bwh.harvard.edu> <4286E305-87C3-492A-BE31-0B83CEFD365E@bwh.harvard.edu> Message-ID: <5F1BBE56-5523-4517-ADCF-2A1DB17C952B@mcin.ca> Sounds like a plan. Let me know once it is uploaded and I will ask Nicolas to give me access. Thanks! PS: you can view the diff on the PR and simply copy the code over to your files if easier > On May 11, 2021, at 11:47 AM, Morales Pinzon, Alfredo wrote: > > Hi Cecile, > > In my testing dataset I have only one subject, I can share it with you in the LORIS sftp, does that work for you? > > In the mean time I will diff and pull your PR, and then execute it. I?ll send you the output asap. > > Best, > Alfredo. > >> On May 11, 2021, at 11:36 AM, Cecile Madjar > wrote: >> >> External Email - Use Caution >> >> >> Hi Alfredo, >> >> I do not have access to your dataset but is it possible that there is one or more sub- in the participants.tsv that are different from the sub- used in the directory structure? (a.k.a., folders sub- and filenames that should start with sub-.) >> >> 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. >> >> I created a PR on LORIS-MRI to elaborate the log from the function you just sent: https://github.com/aces/Loris-MRI/pull/617 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? >> >> Let me know how it goes, >> >> C?cile >> >> >>> On May 10, 2021, at 4:15 PM, Morales Pinzon, Alfredo > wrote: >>> >>> Dear LorisDev team. >>> >>> I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile: https://github.com/aces/Loris-MRI/pull/558/files ) but I?m getting the following error (see all the output below): >>> >>> === >>> ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n >>> === >>> >>> After some debugging I saw that the array subjects in the following line is empty: >>> https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134 >>> >>> 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. >>> >>> 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. >>> >>> Looking forward to hearing from you. >>> >>> Best. >>> Alfredo. >>> >>> === >>> /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. >>> warnings.warn("The ability to pass arguments to BIDSLayout that control " >>> >>> Connecting to: >>> database: DATABASE >>> username: USERDATABASE >>> hostname: 111.222.333.444 >>> port : 3306 >>> >>> >>> Executing query: >>> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); >>> >>> With arguments: >>> ('default_bids_vl',) >>> >>> >>> Executing query: >>> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); >>> >>> With arguments: >>> ('dataDirBasepath',) >>> >>> Loading the BIDS dataset with BIDS layout library... >>> >>> => BIDS dataset loaded with BIDS layout >>> >>> Grepping candidates from the BIDS layout... >>> Validating the list of participants... >>> >>> ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n >>> === >>> >>> 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. >>> >>> Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. > > Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Tue May 11 17:37:24 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Tue, 11 May 2021 21:37:24 +0000 Subject: [Loris-dev] BIDS Error In-Reply-To: <5F1BBE56-5523-4517-ADCF-2A1DB17C952B@mcin.ca> References: <8E375877-D896-4B0E-B0F7-D6BD5565CA67@bwh.harvard.edu> <4286E305-87C3-492A-BE31-0B83CEFD365E@bwh.harvard.edu> <5F1BBE56-5523-4517-ADCF-2A1DB17C952B@mcin.ca> Message-ID: Hi C?cile, I just shared the dataset in the sftp in the following path: 2021_05_11/caseCecile_BIDS.zip Additionally, here is the output of the script after adding the prints in the PR 617: === /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. warnings.warn("The ability to pass arguments to BIDSLayout that control " Connecting to: database: DATABASE username: USERDATABASE hostname: 111.222.333.44 port : 3306 Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('default_bids_vl',) Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('dataDirBasepath',) Loading the BIDS dataset with BIDS layout library... => BIDS dataset loaded with BIDS layout Grepping candidates from the BIDS layout... Validating the list of participants... ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n CFTY720D2306.0102.00001is missing from the BIDS Layout List of subjects parsed by the BIDS layout: === Best, Alfredo. On May 11, 2021, at 12:01 PM, C?cile Madjar > wrote: External Email - Use Caution Sounds like a plan. Let me know once it is uploaded and I will ask Nicolas to give me access. Thanks! PS: you can view the diff on the PR and simply copy the code over to your files if easier On May 11, 2021, at 11:47 AM, Morales Pinzon, Alfredo > wrote: Hi Cecile, In my testing dataset I have only one subject, I can share it with you in the LORIS sftp, does that work for you? In the mean time I will diff and pull your PR, and then execute it. I?ll send you the output asap. Best, Alfredo. On May 11, 2021, at 11:36 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, I do not have access to your dataset but is it possible that there is one or more sub- in the participants.tsv that are different from the sub- used in the directory structure? (a.k.a., folders sub- and filenames that should start with sub-.) 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. I created a PR on LORIS-MRI to elaborate the log from the function you just sent: https://github.com/aces/Loris-MRI/pull/617 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? Let me know how it goes, C?cile On May 10, 2021, at 4:15 PM, Morales Pinzon, Alfredo > wrote: Dear LorisDev team. I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile: https://github.com/aces/Loris-MRI/pull/558/files ) but I?m getting the following error (see all the output below): === ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n === After some debugging I saw that the array subjects in the following line is empty: https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134 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. 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. Looking forward to hearing from you. Best. Alfredo. === /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. warnings.warn("The ability to pass arguments to BIDSLayout that control " Connecting to: database: DATABASE username: USERDATABASE hostname: 111.222.333.444 port : 3306 Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('default_bids_vl',) Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('dataDirBasepath',) Loading the BIDS dataset with BIDS layout library... => BIDS dataset loaded with BIDS layout Grepping candidates from the BIDS layout... Validating the list of participants... ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n === 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Tue May 11 18:34:55 2021 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 11 May 2021 18:34:55 -0400 Subject: [Loris-dev] BIDS Error In-Reply-To: References: <8E375877-D896-4B0E-B0F7-D6BD5565CA67@bwh.harvard.edu> <4286E305-87C3-492A-BE31-0B83CEFD365E@bwh.harvard.edu> <5F1BBE56-5523-4517-ADCF-2A1DB17C952B@mcin.ca> Message-ID: Hi Alfredo, It looks like the pybids is not able to read your BIDS dataset, which is why it returns an empty list of subjects. 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? C?cile On Tue, May 11, 2021 at 5:37 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi C?cile, > > I just shared the dataset in the sftp in the following path: > 2021_05_11/caseCecile_BIDS.zip > > Additionally, here is the output of the script after adding the prints in > the PR 617: > > === > /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. > warnings.warn("The ability to pass arguments to BIDSLayout that control " > > Connecting to: > database: DATABASE > username: USERDATABASE > hostname: 111.222.333.44 > port : 3306 > > > Executing query: > SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM > ConfigSettings WHERE Name = %s); > > With arguments: > ('default_bids_vl',) > > > Executing query: > SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM > ConfigSettings WHERE Name = %s); > > With arguments: > ('dataDirBasepath',) > > Loading the BIDS dataset with BIDS layout library... > => BIDS dataset loaded with BIDS layout > > Grepping candidates from the BIDS layout... > Validating the list of participants... > > ERROR: Participant ID mismatch between participants.tsv and raw data found > in the BIDS directory/n > CFTY720D2306.0102.00001is missing from the BIDS Layout > > List of subjects parsed by the BIDS layout: > === > > Best, > Alfredo. > > On May 11, 2021, at 12:01 PM, C?cile Madjar wrote: > > External Email - Use Caution > > Sounds like a plan. Let me know once it is uploaded and I will ask Nicolas > to give me access. > > Thanks! > > PS: you can view the diff on the PR and simply copy the code over to your > files if easier > > On May 11, 2021, at 11:47 AM, Morales Pinzon, Alfredo < > AMORALESPINZON at BWH.HARVARD.EDU> wrote: > > Hi Cecile, > > In my testing dataset I have only one subject, I can share it with you in > the LORIS sftp, does that work for you? > > In the mean time I will diff and pull your PR, and then execute it. I?ll > send you the output asap. > > Best, > Alfredo. > > On May 11, 2021, at 11:36 AM, Cecile Madjar wrote: > > External Email - Use Caution > > Hi Alfredo, > > I do not have access to your dataset but is it possible that there is one > or more sub- in the participants.tsv that are different from the > sub- used in the directory structure? (a.k.a., folders sub- and > filenames that should start with sub-.) > > 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. > > I created a PR on LORIS-MRI to elaborate the log from the function you > just sent: https://github.com/aces/Loris-MRI/pull/617 > 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? > > Let me know how it goes, > > C?cile > > > On May 10, 2021, at 4:15 PM, Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > > Dear LorisDev team. > > I am running the BIDS uploading functionality of LORIS (from this PR > suggested by Cecile: https://github.com/aces/Loris-MRI/pull/558/files > ) > but I?m getting the following error (see all the output below): > > === > ERROR: Participant ID mismatch between participants.tsv and raw data found > in the BIDS directory/n > === > > After some debugging I saw that the array subjects in the following line > is empty: > > https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134 > > > 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. > > 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. > > Looking forward to hearing from you. > > Best. > Alfredo. > > === > /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. > warnings.warn("The ability to pass arguments to BIDSLayout that control " > > Connecting to: > database: DATABASE > username: USERDATABASE > hostname: 111.222.333.444 > port : 3306 > > > Executing query: > SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM > ConfigSettings WHERE Name = %s); > > With arguments: > ('default_bids_vl',) > > > Executing query: > SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM > ConfigSettings WHERE Name = %s); > > With arguments: > ('dataDirBasepath',) > > Loading the BIDS dataset with BIDS layout library... > > => BIDS dataset loaded with BIDS layout > > Grepping candidates from the BIDS layout... > Validating the list of participants... > > ERROR: Participant ID mismatch between participants.tsv and raw data found > in the BIDS directory/n > === > > 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 Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.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. > > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > > 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 Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.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. > > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > > > > 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 Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.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. > > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Thu May 13 09:47:44 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Thu, 13 May 2021 13:47:44 +0000 Subject: [Loris-dev] BIDS Error In-Reply-To: References: <8E375877-D896-4B0E-B0F7-D6BD5565CA67@bwh.harvard.edu> <4286E305-87C3-492A-BE31-0B83CEFD365E@bwh.harvard.edu> <5F1BBE56-5523-4517-ADCF-2A1DB17C952B@mcin.ca> Message-ID: Hi C?cile, Is it possible to modify your IDs to be alphanumerical? 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. Best, Alfredo. On May 11, 2021, at 6:34 PM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, It looks like the pybids is not able to read your BIDS dataset, which is why it returns an empty list of subjects. 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? C?cile On Tue, May 11, 2021 at 5:37 PM Morales Pinzon, Alfredo > wrote: Hi C?cile, I just shared the dataset in the sftp in the following path: 2021_05_11/caseCecile_BIDS.zip Additionally, here is the output of the script after adding the prints in the PR 617: === /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. warnings.warn("The ability to pass arguments to BIDSLayout that control " Connecting to: database: DATABASE username: USERDATABASE hostname: 111.222.333.44 port : 3306 Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('default_bids_vl',) Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('dataDirBasepath',) Loading the BIDS dataset with BIDS layout library... => BIDS dataset loaded with BIDS layout Grepping candidates from the BIDS layout... Validating the list of participants... ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n CFTY720D2306.0102.00001is missing from the BIDS Layout List of subjects parsed by the BIDS layout: === Best, Alfredo. On May 11, 2021, at 12:01 PM, C?cile Madjar > wrote: External Email - Use Caution Sounds like a plan. Let me know once it is uploaded and I will ask Nicolas to give me access. Thanks! PS: you can view the diff on the PR and simply copy the code over to your files if easier On May 11, 2021, at 11:47 AM, Morales Pinzon, Alfredo > wrote: Hi Cecile, In my testing dataset I have only one subject, I can share it with you in the LORIS sftp, does that work for you? In the mean time I will diff and pull your PR, and then execute it. I?ll send you the output asap. Best, Alfredo. On May 11, 2021, at 11:36 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, I do not have access to your dataset but is it possible that there is one or more sub- in the participants.tsv that are different from the sub- used in the directory structure? (a.k.a., folders sub- and filenames that should start with sub-.) 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. I created a PR on LORIS-MRI to elaborate the log from the function you just sent: https://github.com/aces/Loris-MRI/pull/617 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? Let me know how it goes, C?cile On May 10, 2021, at 4:15 PM, Morales Pinzon, Alfredo > wrote: Dear LorisDev team. I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile: https://github.com/aces/Loris-MRI/pull/558/files ) but I?m getting the following error (see all the output below): === ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n === After some debugging I saw that the array subjects in the following line is empty: https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134 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. 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. Looking forward to hearing from you. Best. Alfredo. === /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. warnings.warn("The ability to pass arguments to BIDSLayout that control " Connecting to: database: DATABASE username: USERDATABASE hostname: 111.222.333.444 port : 3306 Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('default_bids_vl',) Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('dataDirBasepath',) Loading the BIDS dataset with BIDS layout library... => BIDS dataset loaded with BIDS layout Grepping candidates from the BIDS layout... Validating the list of participants... ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n === 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Thu May 13 10:08:15 2021 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Thu, 13 May 2021 10:08:15 -0400 Subject: [Loris-dev] BIDS Error In-Reply-To: References: <8E375877-D896-4B0E-B0F7-D6BD5565CA67@bwh.harvard.edu> <4286E305-87C3-492A-BE31-0B83CEFD365E@bwh.harvard.edu> <5F1BBE56-5523-4517-ADCF-2A1DB17C952B@mcin.ca>

Message-ID: Hi Alfredo, 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. On the LORIS front: - the ID used next to sub- 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). - the ID used next to ses- will be used for the visit label field of the session table There might be another solution for you: modifying the file https://github.com/aces/Loris-MRI/blob/main/python/lib/bids.json 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. Hope this helps, C?cile On Thu, May 13, 2021 at 9:47 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi C?cile, > > Is it possible to modify your IDs to be alphanumerical? > > > 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. > > Best, > Alfredo. > > On May 11, 2021, at 6:34 PM, Cecile Madjar wrote: > > External Email - Use Caution > > Hi Alfredo, > > It looks like the pybids is not able to read your BIDS dataset, which is > why it returns an empty list of subjects. > > 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? > > C?cile > > On Tue, May 11, 2021 at 5:37 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Hi C?cile, >> >> I just shared the dataset in the sftp in the following path: >> 2021_05_11/caseCecile_BIDS.zip >> >> Additionally, here is the output of the script after adding the prints in >> the PR 617: >> >> === >> /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. >> warnings.warn("The ability to pass arguments to BIDSLayout that control >> " >> >> Connecting to: >> database: DATABASE >> username: USERDATABASE >> hostname: 111.222.333.44 >> port : 3306 >> >> >> Executing query: >> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM >> ConfigSettings WHERE Name = %s); >> >> With arguments: >> ('default_bids_vl',) >> >> >> Executing query: >> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM >> ConfigSettings WHERE Name = %s); >> >> With arguments: >> ('dataDirBasepath',) >> >> Loading the BIDS dataset with BIDS layout library... >> => BIDS dataset loaded with BIDS layout >> >> Grepping candidates from the BIDS layout... >> Validating the list of participants... >> >> ERROR: Participant ID mismatch between participants.tsv and raw data >> found in the BIDS directory/n >> CFTY720D2306.0102.00001is missing from the BIDS Layout >> >> List of subjects parsed by the BIDS layout: >> === >> >> Best, >> Alfredo. >> >> On May 11, 2021, at 12:01 PM, C?cile Madjar >> wrote: >> >> External Email - Use Caution >> >> Sounds like a plan. Let me know once it is uploaded and I will ask >> Nicolas to give me access. >> >> Thanks! >> >> PS: you can view the diff on the PR and simply copy the code over to your >> files if easier >> >> On May 11, 2021, at 11:47 AM, Morales Pinzon, Alfredo < >> AMORALESPINZON at BWH.HARVARD.EDU> wrote: >> >> Hi Cecile, >> >> In my testing dataset I have only one subject, I can share it with you in >> the LORIS sftp, does that work for you? >> >> In the mean time I will diff and pull your PR, and then execute it. I?ll >> send you the output asap. >> >> Best, >> Alfredo. >> >> On May 11, 2021, at 11:36 AM, Cecile Madjar >> wrote: >> >> External Email - Use Caution >> >> Hi Alfredo, >> >> I do not have access to your dataset but is it possible that there is one >> or more sub- in the participants.tsv that are different from the >> sub- used in the directory structure? (a.k.a., folders sub- and >> filenames that should start with sub-.) >> >> 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. >> >> I created a PR on LORIS-MRI to elaborate the log from the function you >> just sent: https://github.com/aces/Loris-MRI/pull/617 >> 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? >> >> Let me know how it goes, >> >> C?cile >> >> >> On May 10, 2021, at 4:15 PM, Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >> Dear LorisDev team. >> >> I am running the BIDS uploading functionality of LORIS (from this PR >> suggested by Cecile: https://github.com/aces/Loris-MRI/pull/558/files >> ) >> but I?m getting the following error (see all the output below): >> >> === >> ERROR: Participant ID mismatch between participants.tsv and raw data >> found in the BIDS directory/n >> === >> >> After some debugging I saw that the array subjects in the following line >> is empty: >> >> https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134 >> >> >> 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. >> >> 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. >> >> Looking forward to hearing from you. >> >> Best. >> Alfredo. >> >> === >> /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. >> warnings.warn("The ability to pass arguments to BIDSLayout that control >> " >> >> Connecting to: >> database: DATABASE >> username: USERDATABASE >> hostname: 111.222.333.444 >> port : 3306 >> >> >> Executing query: >> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM >> ConfigSettings WHERE Name = %s); >> >> With arguments: >> ('default_bids_vl',) >> >> >> Executing query: >> SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM >> ConfigSettings WHERE Name = %s); >> >> With arguments: >> ('dataDirBasepath',) >> >> Loading the BIDS dataset with BIDS layout library... >> >> => BIDS dataset loaded with BIDS layout >> >> Grepping candidates from the BIDS layout... >> Validating the list of participants... >> >> ERROR: Participant ID mismatch between participants.tsv and raw data >> found in the BIDS directory/n >> === >> >> 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 Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.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. >> >> Please note that this e-mail is not secure (encrypted). If you do not >> wish to continue communication over unencrypted e-mail, please notify the >> sender of this message immediately. Continuing to send or respond to >> e-mail after receiving this message means you understand and accept this >> risk and wish to continue to communicate over unencrypted e-mail. >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> >> 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 Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.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. >> >> Please note that this e-mail is not secure (encrypted). If you do not >> wish to continue communication over unencrypted e-mail, please notify the >> sender of this message immediately. Continuing to send or respond to >> e-mail after receiving this message means you understand and accept this >> risk and wish to continue to communicate over unencrypted e-mail. >> >> >> >> 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 Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.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. >> >> Please note that this e-mail is not secure (encrypted). If you do not >> wish to continue communication over unencrypted e-mail, please notify the >> sender of this message immediately. Continuing to send or respond to >> e-mail after receiving this message means you understand and accept this >> risk and wish to continue to communicate over unencrypted e-mail. >> > > 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 Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.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. > > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. 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Message-ID: Hi Alfredo and Pisti, The BIDS specification is here: https://bids-specification.readthedocs.io/en/stable/02-common-principles.html Hyphens are considered alphanumeric characters, and underscores are used to separate entities. Periods are not allowed, so if there are files or directory names containing periods, that may be the issue. Sridar From: Cecile Madjar Date: Thursday, May 13, 2021 at 10:08 AM To: "Morales Pinzon, Alfredo" Cc: "loris-dev at bic.mni.mcgill.ca" , "Douglas Arnold, Dr." , "Sridar Narayanan, Dr." , Rozie Arnaoutelis , "Guttmann Charles,M.D." , Istv?n ?kos M?rocz , Samson Antel Subject: Re: [Loris-dev] BIDS Error Hi Alfredo, 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. On the LORIS front: * the ID used next to sub- 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). * the ID used next to ses- will be used for the visit label field of the session table There might be another solution for you: modifying the file https://github.com/aces/Loris-MRI/blob/main/python/lib/bids.json 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. Hope this helps, C?cile On Thu, May 13, 2021 at 9:47 AM Morales Pinzon, Alfredo > wrote: Hi C?cile, Is it possible to modify your IDs to be alphanumerical? 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. Best, Alfredo. On May 11, 2021, at 6:34 PM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, It looks like the pybids is not able to read your BIDS dataset, which is why it returns an empty list of subjects. 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? C?cile On Tue, May 11, 2021 at 5:37 PM Morales Pinzon, Alfredo > wrote: Hi C?cile, I just shared the dataset in the sftp in the following path: 2021_05_11/caseCecile_BIDS.zip Additionally, here is the output of the script after adding the prints in the PR 617: === /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. warnings.warn("The ability to pass arguments to BIDSLayout that control " Connecting to: database: DATABASE username: USERDATABASE hostname: 111.222.333.44 port : 3306 Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('default_bids_vl',) Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('dataDirBasepath',) Loading the BIDS dataset with BIDS layout library... => BIDS dataset loaded with BIDS layout Grepping candidates from the BIDS layout... Validating the list of participants... ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n CFTY720D2306.0102.00001is missing from the BIDS Layout List of subjects parsed by the BIDS layout: === Best, Alfredo. On May 11, 2021, at 12:01 PM, C?cile Madjar > wrote: External Email - Use Caution Sounds like a plan. Let me know once it is uploaded and I will ask Nicolas to give me access. Thanks! PS: you can view the diff on the PR and simply copy the code over to your files if easier On May 11, 2021, at 11:47 AM, Morales Pinzon, Alfredo > wrote: Hi Cecile, In my testing dataset I have only one subject, I can share it with you in the LORIS sftp, does that work for you? In the mean time I will diff and pull your PR, and then execute it. I?ll send you the output asap. Best, Alfredo. On May 11, 2021, at 11:36 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, I do not have access to your dataset but is it possible that there is one or more sub- in the participants.tsv that are different from the sub- used in the directory structure? (a.k.a., folders sub- and filenames that should start with sub-.) 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. I created a PR on LORIS-MRI to elaborate the log from the function you just sent: https://github.com/aces/Loris-MRI/pull/617 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? Let me know how it goes, C?cile On May 10, 2021, at 4:15 PM, Morales Pinzon, Alfredo > wrote: Dear LorisDev team. I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile: https://github.com/aces/Loris-MRI/pull/558/files ) but I?m getting the following error (see all the output below): === ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n === After some debugging I saw that the array subjects in the following line is empty: https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134 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. 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. Looking forward to hearing from you. Best. Alfredo. === /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. warnings.warn("The ability to pass arguments to BIDSLayout that control " Connecting to: database: DATABASE username: USERDATABASE hostname: 111.222.333.444 port : 3306 Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('default_bids_vl',) Executing query: SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s); With arguments: ('dataDirBasepath',) Loading the BIDS dataset with BIDS layout library... => BIDS dataset loaded with BIDS layout Grepping candidates from the BIDS layout... Validating the list of participants... ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n === 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. The information in this e-mail is intended only for the person to whom it is addressed. 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URL: From AMORALESPINZON at BWH.HARVARD.EDU Thu May 27 16:59:52 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Thu, 27 May 2021 20:59:52 +0000 Subject: [Loris-dev] Can't assign users to a new project Message-ID: Dear LorisDev team, I just created a new project using the web interface of LORIS but I cannot assign users to that new project because it is not listed in the project list in the edit user section. I can see all the previous projects except the new one. Any ideas why this might be happening? Is there something in the database I should double check? I am running LORIS v23.0.2. Best, 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. From joh17964 at umn.edu Fri May 28 15:44:44 2021 From: joh17964 at umn.edu (Eli Johnson) Date: Fri, 28 May 2021 14:44:44 -0500 Subject: [Loris-dev] Can't assign users to a new project In-Reply-To: References: Message-ID: Hi Alfredo, You can manually add the user to a project in the user_project_rel table. Once you add the relationship for the admin account you will see it appear as an option in the project selection box of the user_accounts module. Dev team, can new projects be automatically added to the Superuser admin account? I have been manually adding new ones so they appear in the user_accounts project selection boxes. I believe this was automatically done before the v23 update. Best, Eli Eli Johnson Developer/Data Manager Institute of Child Development University of Minnesota joh17964 at umn.edu On Fri, May 28, 2021 at 11:00 AM wrote: > Send Loris-dev mailing list submissions to > loris-dev at bic.mni.mcgill.ca > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > or, via email, send a message with subject or body 'help' to > loris-dev-request at bic.mni.mcgill.ca > > You can reach the person managing the list at > loris-dev-owner at bic.mni.mcgill.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Loris-dev digest..." > Today's Topics: > > 1. Can't assign users to a new project (Morales Pinzon, Alfredo) > > > > ---------- Forwarded message ---------- > From: "Morales Pinzon, Alfredo" > To: "loris-dev at bic.mni.mcgill.ca" > Cc: Rozie Arnaoutelis , Sridar Narayanan < > sridar.narayanan at mcgill.ca>, "Douglas Arnold, Dr." < > douglas.arnold at mcgill.ca>, "Guttmann, Charles, M.D." < > guttmann at bwh.harvard.edu> > Bcc: > Date: Thu, 27 May 2021 20:59:52 +0000 > Subject: [Loris-dev] Can't assign users to a new project > Dear LorisDev team, > > I just created a new project using the web interface of LORIS but I cannot > assign users to that new project because it is not listed in the project > list in the edit user section. I can see all the previous projects except > the new one. > > Any ideas why this might be happening? Is there something in the database > I should double check? > > I am running LORIS v23.0.2. > > Best, > 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 Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.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. > Please note that this e-mail is not secure (encrypted). If you do not > wish to continue communication over unencrypted e-mail, please notify the > sender of this message immediately. Continuing to send or respond to > e-mail after receiving this message means you understand and accept this > risk and wish to continue to communicate over unencrypted e-mail. > > > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Mon May 31 08:47:08 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Mon, 31 May 2021 08:47:08 -0400 Subject: [Loris-dev] Can't assign users to a new project In-Reply-To: References: Message-ID: I don't believe it was ever automatically done. It was likely done as part of a one-time upgrade script when the relation was introduced, but since it's an SQL table there would need to be a time for the insert to be run. - Dave On Fri, May 28, 2021 at 3:45 PM Eli Johnson wrote: > Hi Alfredo, > > You can manually add the user to a project in the user_project_rel table. > Once you add the relationship for the admin account you will see it appear > as an option in the project selection box of the user_accounts module. > > Dev team, can new projects be automatically added to the Superuser admin > account? I have been manually adding new ones so they appear in the > user_accounts project selection boxes. I believe this was automatically > done before the v23 update. > > Best, > Eli > > Eli Johnson > Developer/Data Manager > Institute of Child Development > University of Minnesota > joh17964 at umn.edu > > > On Fri, May 28, 2021 at 11:00 AM > wrote: > >> Send Loris-dev mailing list submissions to >> loris-dev at bic.mni.mcgill.ca >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> or, via email, send a message with subject or body 'help' to >> loris-dev-request at bic.mni.mcgill.ca >> >> You can reach the person managing the list at >> loris-dev-owner at bic.mni.mcgill.ca >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Loris-dev digest..." >> Today's Topics: >> >> 1. Can't assign users to a new project (Morales Pinzon, Alfredo) >> >> >> >> ---------- Forwarded message ---------- >> From: "Morales Pinzon, Alfredo" >> To: "loris-dev at bic.mni.mcgill.ca" >> Cc: Rozie Arnaoutelis , Sridar Narayanan < >> sridar.narayanan at mcgill.ca>, "Douglas Arnold, Dr." < >> douglas.arnold at mcgill.ca>, "Guttmann, Charles, M.D." < >> guttmann at bwh.harvard.edu> >> Bcc: >> Date: Thu, 27 May 2021 20:59:52 +0000 >> Subject: [Loris-dev] Can't assign users to a new project >> Dear LorisDev team, >> >> I just created a new project using the web interface of LORIS but I >> cannot assign users to that new project because it is not listed in the >> project list in the edit user section. I can see all the previous projects >> except the new one. >> >> Any ideas why this might be happening? Is there something in the database >> I should double check? >> >> I am running LORIS v23.0.2. >> >> Best, >> 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 Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.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. >> Please note that this e-mail is not secure (encrypted). If you do not >> wish to continue communication over unencrypted e-mail, please notify the >> sender of this message immediately. Continuing to send or respond to >> e-mail after receiving this message means you understand and accept this >> risk and wish to continue to communicate over unencrypted e-mail. >> >> >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: