From sam.payabvash at yale.edu Sat Feb 2 18:58:32 2019 From: sam.payabvash at yale.edu (Payabvash, Sam) Date: Sat, 2 Feb 2019 23:58:32 +0000 Subject: [Loris-dev] Inquiry regarding conversion of DTI in MINC to NIfTI Message-ID: <34A43E11-E3D9-41A7-AF7A-5B9EEC1A029B@yale.edu> Hi, I was wondering if you can kindly help me with conversion of DTI files in MINC format to NIfTI format and extraction of bval and bvec files. I found your LORIS MRI Release v20.1.0 on git hub (https://github.com/aces/Loris-MRI/pull/335); and I followed the instruction on "https://github.com/aces/Loris-MRI" to instal the package on our Ubuntu platform. But can not figure out how to run the "make_niff" function from the MRI.pm in a shell script. The MRI.pm is in the uploadNeuroDB/NeuroDB directory, and I tried : $ perl -MMRI -e 'MRI::make_nii" dti.mnc But it didn't work. I sincerely appreciate your help. Best regards, Sam _____________________________ Sam (Seyedmehdi) Payabvash, MD Assistant Professor of Radiology Yale School of Medicine Email : sam.payabvash at yale.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Mon Feb 4 19:14:34 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Tue, 5 Feb 2019 00:14:34 +0000 Subject: [Loris-dev] [IPMSA] MRI batch uploader cannot handle visits labels with "_" Message-ID: Dear LORIS-dev team, In the IPMSA project for the first time we are using visit labels for the MRI visits including the character "_" in the visit label, for instance ADDTC_1. This however cannot be handle by the MRI batch uploader because it uses the first part the name as visit label, in the previous example it uses "ADDTC" which is not a valid visit label. I can help modifying the code where the split using "_" is used (if this is used) but need indications on where to do it. Here is the log from the file log_batch_imageuploader_YYY12345_123456_ADDTC_1.txt (I modified the PSCID to be YYY12345, the CandidateId to be 123456, and the path to the project to the location of loris to /XXX/): --------------------------------------------------------------------------------------- Running now the following command: /XXX/bin/mri/uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 8299 /XXX/YYY12345_123456_ADDTC_1.tar.gz -verbose /XXX/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-17-7-AkVEyo /XXX/data/tarchive -clobber -database -profile prod -verbose Source: /tmp/ImagingUpload-17-7-AkVEyo Target: /XXX/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-17-7-AkVEyo You are creating a tar with the following command: tar -cf /XXX/data/tarchive/ImagingUpload-17-7-AkVEyo.tar ImagingUpload-17-7-AkVEyo getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-17-7-AkVEyo * Archive target location : /XXX/data/tarchive/DCM_2011-02-17_ImagingUpload-17-7-AkVEyo.tar * Name of creating host : 132.206.178.78 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-02-04 17:07:43 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 6ca6a6e5c3a77bb8a15dc1eeae3147a7 ImagingUpload-17-7-AkVEyo.tar * md5sum for DICOM tarball gzipped : eda7f62c570818aa0d96a73ded441345 ImagingUpload-17-7-AkVEyo.tar.gz * md5sum for complete archive : 79d919f5676aadeea91762a4a07c165e DCM_2011-02-17_ImagingUpload-17-7-AkVEyo.tar Adding archive info into database Removing temporary files from target location Done adding archive info into database /XXX/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod /XXX/data/tarchive/DCM_2011-02-17_ImagingUpload-17-7-AkVEyo.tar -verbose md5sum /XXX/data/tarchive/DCM_2011-02-17_ImagingUpload-17-7-AkVEyo.tar PSCID is: YYY12345 CandID id: 123456 visit_label is: ADDTC candidate id 123456 => No Visit labelVisit label does not exist Set newVisitNo = 5 and centerID = 316 PSCID is: YYY12345 CandID id: 123456 visit_label is: ADDTC Number of MINC files that will be considered for inserting into the database: 5 --------------------------------------------------------------------------------------- Let me know if the issue is clear and if you need more information. We have more than 20 visit label with "_" in the name. Best, Alfredo. P.S. We previously modified the name of the visit label to replace the character "-" with "_" because the API cannot handle "-" in the url. 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 cecile.madjar at mcin.ca Tue Feb 5 10:49:13 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 5 Feb 2019 10:49:13 -0500 Subject: [Loris-dev] [IPMSA] MRI batch uploader cannot handle visits labels with "_" In-Reply-To: References: Message-ID: Dear Alfredo, As a convention, we try to avoid using "_" or "-" in our visit labels (or IDs or scan types) since the "_" (or "-") could be used on filenames to separate PSCID, DCCID, VisitLabels and ScanTypes. In your case, your Visit label could probably be renamed ADDTC1 to remove the underscore. If it is absolutely vital to have "_" in your visit labels, you just need to modify the if statement in the function getSubjectIDs of your prod file. I tried running a dataset with an underscore in the visit label on my sandbox and the dataset was attached to the correct visit label with the underscore. Here is the modification of the if statement I did to the prod file: if ($patientName=~ /([^_]+)_(\d+)_([A-Z]+_\d+)/) { $subjectID{'PSCID'} = NeuroDB::MRI::my_trim($1); $subjectID{'CandID'} = NeuroDB::MRI::my_trim($2); $subjectID{'visitLabel'} = NeuroDB::MRI::my_trim($3); } However, I cannot guaranty you won't regret having "_" in your names later on as I am not sure 100% that it would not break other things down the line. I believe the CCNA group are using "_" in their visit labels and it added a few complications for them. I'll let them comment on this since they have more experience with this than I. Hope this helps! C?cile On Mon, Feb 4, 2019 at 7:14 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LORIS-dev team, > > In the IPMSA project for the first time we are using visit labels for the > MRI visits including the character "_" in the visit label, for instance > ADDTC_1. This however cannot be handle by the MRI batch uploader because > it uses the first part the name as visit label, in the previous example it > uses "ADDTC" which is not a valid visit label. I can help modifying the > code where the split using "_" is used (if this is used) but need > indications on where to do it. > > Here is the log from the > file log_batch_imageuploader_YYY12345_123456_ADDTC_1.txt (I modified the > PSCID to be YYY12345, the CandidateId to be 123456, and the path to the > project to the location of loris to /XXX/): > > > > --------------------------------------------------------------------------------------- > Running now the following command: /XXX/bin/mri/uploadNeuroDB/ > imaging_upload_file.pl -profile prod -upload_id 8299 > /XXX/YYY12345_123456_ADDTC_1.tar.gz -verbose > > /XXX/bin/mri/dicom-archive/dicomTar.pl /tmp/ImagingUpload-17-7-AkVEyo > /XXX/data/tarchive -clobber -database -profile prod -verbose > Source: /tmp/ImagingUpload-17-7-AkVEyo > Target: /XXX/data/tarchive > > Testing for database connectivity. > Database is available. > > You will archive the dir : ImagingUpload-17-7-AkVEyo > > You are creating a tar with the following command: > tar -cf /XXX/data/tarchive/ImagingUpload-17-7-AkVEyo.tar > ImagingUpload-17-7-AkVEyo > > > getting md5sums and gzipping!! > > * Taken from dir : /tmp/ImagingUpload-17-7-AkVEyo > * Archive target location : > /XXX/data/tarchive/DCM_2011-02-17_ImagingUpload-17-7-AkVEyo.tar > * Name of creating host : 132.206.178.78 > * Name of host OS : Linux > * Created by user : lorisadmin > * Archived on : 2019-02-04 17:07:43 > * dicomSummary version : 1 > * dicomTar version : 1 > * md5sum for DICOM tarball : 6ca6a6e5c3a77bb8a15dc1eeae3147a7 > ImagingUpload-17-7-AkVEyo.tar > * md5sum for DICOM tarball gzipped : eda7f62c570818aa0d96a73ded441345 > ImagingUpload-17-7-AkVEyo.tar.gz > * md5sum for complete archive : 79d919f5676aadeea91762a4a07c165e > DCM_2011-02-17_ImagingUpload-17-7-AkVEyo.tar > > Adding archive info into database > > Removing temporary files from target location > > > Done adding archive info into database > > /XXX/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod > /XXX/data/tarchive/DCM_2011-02-17_ImagingUpload-17-7-AkVEyo.tar -verbose > md5sum /XXX/data/tarchive/DCM_2011-02-17_ImagingUpload-17-7-AkVEyo.tar > PSCID is: YYY12345 > CandID id: 123456 > visit_label is: ADDTC > candidate id 123456 > > => No Visit labelVisit label does not exist > Set newVisitNo = 5 and centerID = 316 > PSCID is: YYY12345 > CandID id: 123456 > visit_label is: ADDTC > > Number of MINC files that will be considered for inserting into the > database: 5 > > --------------------------------------------------------------------------------------- > > Let me know if the issue is clear and if you need more information. We > have more than 20 visit label with "_" in the name. > > Best, > Alfredo. > > P.S. We previously modified the name of the visit label to replace the > character "-" with "_" because the API cannot handle "-" in the url. > > 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 > 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 Feb 19 18:04:13 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Tue, 19 Feb 2019 23:04:13 +0000 Subject: [Loris-dev] [IPMSA project] LORIS missing updates in assign_missing_instruments.php Message-ID: Dear LORIS-dev team, In the IPMSA project we are batch inserting the clinical data. I am following the steps suggested by Rida, that I successfully used for a first study but now I am stuck in one of the steps. In that step I call the script "assign_missing_instruments.php" to assign missing instruments in the system. Using the script without the option "confirm", the output is telling me that only 1053 out of the expected 32338 visits are going to be created. Could you help understanding where is the problem or if the script I am missing something? What I can see is that script is only generating the changes for 2 out the new 83 visit labels. Here is the steps I have for the uploading process of clinical data, I am stuck in step number 8: 1. Generate the labels of the visits in the system (successfully done - 83 new visit labels) a. Modify the file config.xml b. Run the script "php populate_visit_windows.php" 2. Populate the table "test_battery" (successfully done: 678 new entries were added.) a. For each visit a set of instruments is assigned. 3. Check the state of tables - session: 31027 rows - flad: 275176 rows 4. Create the visits using the LORIS-API (successfully done: 32345 visits were created.) - table "session" has now "63372" rows (32345 = 31027 previous rows + 32345 new rows) 5. Check state of "session" table (17246 entries are "In progress") - select count(*) from session where Visit='In Progress'; 6. Hack the session table (successfully done: 32345 rows were updated ) a. Update each new row in the session table (32345 new rows) like this: UPDATE session SET Visit='In Progress',Scan_done='N',Current_stage='Visit',Date_stage_change='2010-12-24',Date_visit='2010-12-24' WHERE Visit_label='VISIT_LABEL' AND CandID=123456; 7. Check state of "session" table (49584 entries are "In progress", 49584 = 17246 old entries + 32338 new entries) [7 entries were not updated for missing date] - select count(*) from session where Visit='In Progress'; 8. Run php assign missing instruments - When running assign_missing_instruments.php with no arguments I get 1053 changes but I should get 32338 changes. The changes are pointing to only 2 out of the new 83 visit labels. 9. Insert instrument-visit information 10. Add "Candidate" information Thank you very much for help. Let me know if you need more details from my side. 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 rolando.acosta at cnbp.ca Wed Feb 20 11:02:56 2019 From: rolando.acosta at cnbp.ca (Rolando Acosta) Date: Wed, 20 Feb 2019 11:02:56 -0500 Subject: [Loris-dev] Issue with password reset on LORIS 20.1.0 and LORIS 20.2.0 In-Reply-To: References: Message-ID: Hi loris-dev team, About a month ago at CHU Sainte-Justine we did a fresh installation of LORIS 20.1.0. We noticed at that time that the password recovery mechanism wasn't sending the recovery email to the user (Home Page -> Login (module) -> click on "Forgot your password?"). We upgraded to LORIS 20.2.0 and the issue seems persist for us. I'm wondering if somebody else have a similar issue. The strange thing is that for LORIS 19 is working fine. Thank you very much in advance for the help you can provide us, Rolando Acosta Canadian Neonatal Brain Platform (CHU Sainte-Justine) -------------- next part -------------- An HTML attachment was scrubbed... URL: From rogers at bic.mni.mcgill.ca Thu Feb 21 10:38:55 2019 From: rogers at bic.mni.mcgill.ca (Christine Rogers) Date: Thu, 21 Feb 2019 10:38:55 -0500 Subject: [Loris-dev] Issue with password reset on LORIS 20.1.0 and LORIS 20.2.0 In-Reply-To: References: Message-ID: Hi Rolando, Just to confirm -- Is your upgraded LORIS successfully sending other email notifications (e.g. for new User Accounts, Doc Repo notifications) ? It would be helpful to confirm if it's just this module/feature we should look into, vs general email issues. Thanks, Christine On Wed, Feb 20, 2019 at 11:03 AM Rolando Acosta wrote: > Hi loris-dev team, > > About a month ago at CHU Sainte-Justine we did a fresh installation of > LORIS 20.1.0. We noticed at that time that the password recovery mechanism > wasn't sending the recovery email to the user (Home Page -> Login (module) > -> click on "Forgot your password?"). We upgraded to LORIS 20.2.0 and the > issue seems persist for us. I'm wondering if somebody else have a similar > issue. The strange thing is that for LORIS 19 is working fine. > > Thank you very much in advance for the help you can provide us, > > Rolando Acosta > Canadian Neonatal Brain Platform (CHU Sainte-Justine) > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.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 rolando.acosta at cnbp.ca Thu Feb 21 11:24:53 2019 From: rolando.acosta at cnbp.ca (Rolando Acosta) Date: Thu, 21 Feb 2019 11:24:53 -0500 Subject: [Loris-dev] Issue with password reset on LORIS 20.1.0 and LORIS 20.2.0 In-Reply-To: References: Message-ID: Hi Christine, Thank you very much the quick address of the issue. It's very appreciated. Yes, the upgraded LORIS is successfully sending other email notifications. The "Edit User" module (MainMenu -> Admin -> User Accounts -> Click on one of the usernames on the table -> Edit User -> check "Send email to user" -> Save) is doing it without issues. Cheers, Rolando. On Thu, Feb 21, 2019 at 10:39 AM Christine Rogers wrote: > Hi Rolando, > > Just to confirm -- Is your upgraded LORIS successfully sending other email > notifications (e.g. for new User Accounts, Doc Repo notifications) ? > It would be helpful to confirm if it's just this module/feature we should > look into, vs general email issues. > Thanks, > Christine > > On Wed, Feb 20, 2019 at 11:03 AM Rolando Acosta > wrote: > >> Hi loris-dev team, >> >> About a month ago at CHU Sainte-Justine we did a fresh installation of >> LORIS 20.1.0. We noticed at that time that the password recovery mechanism >> wasn't sending the recovery email to the user (Home Page -> Login (module) >> -> click on "Forgot your password?"). We upgraded to LORIS 20.2.0 and the >> issue seems persist for us. I'm wondering if somebody else have a similar >> issue. The strange thing is that for LORIS 19 is working fine. >> >> Thank you very much in advance for the help you can provide us, >> >> Rolando Acosta >> Canadian Neonatal Brain Platform (CHU Sainte-Justine) >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.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 ccna at mcin.ca Thu Feb 21 11:29:47 2019 From: ccna at mcin.ca (zia mohades) Date: Thu, 21 Feb 2019 11:29:47 -0500 Subject: [Loris-dev] ccna login In-Reply-To: References: Message-ID: Hi Alain, Thank you for your email. We'll investigate this and we'll get back to you shortly. Also, in the future, please kindly send all your CCNA related issues/concerns only to ccna at mcin.ca since loris-dev at bic.mni.mcgill.ca mailing list is solely intended for LORIS developers' related issues. Thank you On Thu, Feb 21, 2019 at 11:06 AM Berthiaume, Alain wrote: > I can't seem to reset my password. > > Is my account still active? > > Al > > > > ------------------------------ > *From:* Berthiaume, Alain > *Sent:* February 21, 2019 11:03 AM > *To:* Mouna Safi-Harab; Laura Thompson > *Subject:* Re: BRI6429_221270_Initial_MRI > > > Hi Mouna, > > I can't seem to reset my password. > > Is my account still active? > > Al > ------------------------------ > *From:* Mouna Safi-Harab > *Sent:* June 7, 2018 5:33:07 PM > *To:* Berthiaume, Alain > *Subject:* Re: BRI6429_221270_Initial_MRI > > Thanks! second upload seems to have gone through. > > - Mouna > > On Thu, Jun 7, 2018 at 2:43 PM, Berthiaume, Alain > wrote: > > i cleaned up the directories on the re-upload. It was just post > processing done here. > > thanks > > Al > ------------------------------ > *From:* Mouna Safi-Harab > *Sent:* June 7, 2018 2:12:46 PM > *To:* Berthiaume, Alain > *Cc:* Isabelle Chouinard > *Subject:* Re: BRI6429_221270_Initial_MRI > > I just checked; you have an extra space in the Visit Label (between > Initial and the MRI part). > > But also, just out of curiosity, when I open the zip, there is all these > directories in it such as localizers and ADD (please see screenshot), is > this expected? > > > > Thanks, > > Mouna > > On Thu, Jun 7, 2018 at 12:59 PM, Berthiaume, Alain > wrote: > > i double check and i don't see the error, could you be more specific? > > thanks > > Al > ------------------------------ > *From:* Mouna Safi-Harab > *Sent:* June 7, 2018 12:15:04 PM > *To:* Berthiaume, Alain > *Cc:* Isabelle Chouinard > *Subject:* BRI6429_221270_Initial_MRI > > Hi Alain, > > Can you please re-upload the scan for the candidate above? The PatientName > header in the DICOMs did not match exactly BRI6429_221270_Initial_MRI > > Thanks, > > - Mouna > ------------------------------ > > Confidentiality Statement - The contents of this email, as well as what?s > attached, are to be used only by the person meant to receive it. The email > may contain private or privileged information. If you are not the person > meant to receive it, by law you cannot read, use, disclose, copy, or send > this email or any of its contents. If you received this email by mistake, > let the sender know right away, and delete the email and what?s attached, > as well as any copies you have. Also, if you think the email is spam or is > sales-like and you don?t want to receive any more, let the sender know > right away. You may also report the email to the Information and Privacy > Office (infoprivacyoffice at toh.ca). Thank you. > > > > Avis de confidentialit? ? Seule la personne ? qui ce courriel est destin? > peut en utiliser le contenu et ses pi?ces jointes. Ce courriel peut > contenir des renseignements confidentiels ou prot?g?s. Si vous n??tes pas > le destinataire du courriel, il vous est interdit par la loi d?en lire, > utiliser, divulguer, copier ou envoyer le contenu. Si vous avez re?u ce > courriel par erreur, avisez-en imm?diatement l?exp?diteur et supprimez le > courriel et ses pi?ces jointes et toute copie que vous poss?dez. Par > ailleurs, si vous croyez que ce courriel est du pourriel ou du mat?riel de > vente et que vous ne voulez plus recevoir de courriels semblables, > informez-en imm?diatement l?exp?diteur. Vous pouvez aussi signaler ce > courriel au Bureau de la protection de la vie priv?e et de l?information ( > info.privee at lho.ca). Merci. > ------------------------------ > > > ------------------------------ > > Confidentiality Statement - The contents of this email, as well as what?s > attached, are to be used only by the person meant to receive it. The email > may contain private or privileged information. If you are not the person > meant to receive it, by law you cannot read, use, disclose, copy, or send > this email or any of its contents. If you received this email by mistake, > let the sender know right away, and delete the email and what?s attached, > as well as any copies you have. Also, if you think the email is spam or is > sales-like and you don?t want to receive any more, let the sender know > right away. You may also report the email to the Information and Privacy > Office (infoprivacyoffice at toh.ca). Thank you. > > > > Avis de confidentialit? ? Seule la personne ? qui ce courriel est destin? > peut en utiliser le contenu et ses pi?ces jointes. Ce courriel peut > contenir des renseignements confidentiels ou prot?g?s. Si vous n??tes pas > le destinataire du courriel, il vous est interdit par la loi d?en lire, > utiliser, divulguer, copier ou envoyer le contenu. Si vous avez re?u ce > courriel par erreur, avisez-en imm?diatement l?exp?diteur et supprimez le > courriel et ses pi?ces jointes et toute copie que vous poss?dez. Par > ailleurs, si vous croyez que ce courriel est du pourriel ou du mat?riel de > vente et que vous ne voulez plus recevoir de courriels semblables, > informez-en imm?diatement l?exp?diteur. Vous pouvez aussi signaler ce > courriel au Bureau de la protection de la vie priv?e et de l?information ( > info.privee at lho.ca). Merci. > ------------------------------ > > > ------------------------------ > > Confidentiality Statement - The contents of this email, as well as what?s > attached, are to be used only by the person meant to receive it. The email > may contain private or privileged information. If you are not the person > meant to receive it, by law you cannot read, use, disclose, copy, or send > this email or any of its contents. If you received this email by mistake, > let the sender know right away, and delete the email and what?s attached, > as well as any copies you have. Also, if you think the email is spam or is > sales-like and you don?t want to receive any more, let the sender know > right away. You may also report the email to the Information and Privacy > Office (infoprivacyoffice at toh.ca). Thank you. > > > > Avis de confidentialit? ? Seule la personne ? qui ce courriel est destin? > peut en utiliser le contenu et ses pi?ces jointes. Ce courriel peut > contenir des renseignements confidentiels ou prot?g?s. Si vous n??tes pas > le destinataire du courriel, il vous est interdit par la loi d?en lire, > utiliser, divulguer, copier ou envoyer le contenu. Si vous avez re?u ce > courriel par erreur, avisez-en imm?diatement l?exp?diteur et supprimez le > courriel et ses pi?ces jointes et toute copie que vous poss?dez. Par > ailleurs, si vous croyez que ce courriel est du pourriel ou du mat?riel de > vente et que vous ne voulez plus recevoir de courriels semblables, > informez-en imm?diatement l?exp?diteur. Vous pouvez aussi signaler ce > courriel au Bureau de la protection de la vie priv?e et de l?information ( > info.privee at lho.ca). Merci. > ------------------------------ > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: BRI6429.png Type: image/png Size: 24824 bytes Desc: not available URL: From john.saigle at mcin.ca Mon Feb 25 14:52:42 2019 From: john.saigle at mcin.ca (John Saigle) Date: Mon, 25 Feb 2019 14:52:42 -0500 Subject: [Loris-dev] Issue with password reset on LORIS 20.1.0 and LORIS 20.2.0 In-Reply-To: References: Message-ID: Hi Rolando, We've confirmed the issue on our side and are working on a fix. Thanks for helping us out by reporting the bug. All the best, John On Thu, Feb 21, 2019 at 11:25 AM Rolando Acosta wrote: > Hi Christine, > > Thank you very much the quick address of the issue. It's very appreciated. > > Yes, the upgraded LORIS is successfully sending other email notifications. > The "Edit User" module (MainMenu -> Admin -> User Accounts -> Click on one > of the usernames on the table -> Edit User -> check "Send email to user" -> > Save) is doing it without issues. > > Cheers, > Rolando. > > > On Thu, Feb 21, 2019 at 10:39 AM Christine Rogers < > rogers at bic.mni.mcgill.ca> wrote: > >> Hi Rolando, >> >> Just to confirm -- Is your upgraded LORIS successfully sending other >> email notifications (e.g. for new User Accounts, Doc Repo notifications) ? >> It would be helpful to confirm if it's just this module/feature we should >> look into, vs general email issues. >> Thanks, >> Christine >> >> On Wed, Feb 20, 2019 at 11:03 AM Rolando Acosta >> wrote: >> >>> Hi loris-dev team, >>> >>> About a month ago at CHU Sainte-Justine we did a fresh installation of >>> LORIS 20.1.0. We noticed at that time that the password recovery mechanism >>> wasn't sending the recovery email to the user (Home Page -> Login (module) >>> -> click on "Forgot your password?"). We upgraded to LORIS 20.2.0 and the >>> issue seems persist for us. I'm wondering if somebody else have a similar >>> issue. The strange thing is that for LORIS 19 is working fine. >>> >>> Thank you very much in advance for the help you can provide us, >>> >>> Rolando Acosta >>> Canadian Neonatal Brain Platform (CHU Sainte-Justine) >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.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 >> > _______________________________________________ > 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 cecile.madjar at gmail.com Mon Feb 25 15:15:09 2019 From: cecile.madjar at gmail.com (Cecile Madjar) Date: Mon, 25 Feb 2019 15:15:09 -0500 Subject: [Loris-dev] Inquiry regarding conversion of DTI in MINC to NIfTI In-Reply-To: <34A43E11-E3D9-41A7-AF7A-5B9EEC1A029B@yale.edu> References: <34A43E11-E3D9-41A7-AF7A-5B9EEC1A029B@yale.edu> Message-ID: Hi Sam, So sorry for the delay in the reply. For some reason I never received your email. Are you trying to create the .bval and .bvec files of already registered MINC files into LORIS? If so, there is a tool that was created in that PR ( https://github.com/aces/Loris-MRI/pull/335) called create_nifti_bval_bvec.pl that can be found in the tools directory of LORIS-MRI. This script would create all the required bval and bvec files for the DWI files present in your LORIS instance. Run "create_nifti_bval_bvec.pl -h" to print out the help of that script that lists the options you can use to run the script. Hope this helps. Let me know how this goes or if you have any questions. C?cile On Sat, Feb 2, 2019 at 6:58 PM Payabvash, Sam wrote: > Hi, > > I was wondering if you can kindly help me with conversion of DTI files in > MINC format to NIfTI format and extraction of bval and bvec files. > > I found your LORIS MRI Release v20.1.0 on git hub ( > https://github.com/aces/Loris-MRI/pull/335); and I followed the > instruction on "https://github.com/aces/Loris-MRI" to instal the package > on our Ubuntu platform. > > But can not figure out how to run the "make_niff" function from the MRI.pm > in a shell script. > The MRI.pm is in the uploadNeuroDB/NeuroDB directory, and I tried : > > $ perl -MMRI -e 'MRI::make_nii" dti.mnc > > But it didn't work. > > I sincerely appreciate your help. > > Best regards, > Sam > > _____________________________ > Sam (Seyedmehdi) Payabvash, MD > Assistant Professor of Radiology > Yale School of Medicine > Email : sam.payabvash at yale.edu > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rolando.acosta at cnbp.ca Mon Feb 25 15:42:16 2019 From: rolando.acosta at cnbp.ca (Rolando Acosta) Date: Mon, 25 Feb 2019 15:42:16 -0500 Subject: [Loris-dev] Issue with password reset on LORIS 20.1.0 and LORIS 20.2.0 In-Reply-To: References: Message-ID: Hi John, Thank you very much for the update. I appreciate very much loris-dev work and support. Best, Rolando. On Mon, Feb 25, 2019 at 2:52 PM John Saigle wrote: > Hi Rolando, > > We've confirmed the issue on our side and are working on a fix. Thanks for > helping us out by reporting the bug. > > All the best, > John > > On Thu, Feb 21, 2019 at 11:25 AM Rolando Acosta > wrote: > >> Hi Christine, >> >> Thank you very much the quick address of the issue. It's very appreciated. >> >> Yes, the upgraded LORIS is successfully sending other email >> notifications. The "Edit User" module (MainMenu -> Admin -> User Accounts >> -> Click on one of the usernames on the table -> Edit User -> check "Send >> email to user" -> Save) is doing it without issues. >> >> Cheers, >> Rolando. >> >> >> On Thu, Feb 21, 2019 at 10:39 AM Christine Rogers < >> rogers at bic.mni.mcgill.ca> wrote: >> >>> Hi Rolando, >>> >>> Just to confirm -- Is your upgraded LORIS successfully sending other >>> email notifications (e.g. for new User Accounts, Doc Repo notifications) ? >>> It would be helpful to confirm if it's just this module/feature we >>> should look into, vs general email issues. >>> Thanks, >>> Christine >>> >>> On Wed, Feb 20, 2019 at 11:03 AM Rolando Acosta >>> wrote: >>> >>>> Hi loris-dev team, >>>> >>>> About a month ago at CHU Sainte-Justine we did a fresh installation of >>>> LORIS 20.1.0. We noticed at that time that the password recovery mechanism >>>> wasn't sending the recovery email to the user (Home Page -> Login (module) >>>> -> click on "Forgot your password?"). We upgraded to LORIS 20.2.0 and the >>>> issue seems persist for us. I'm wondering if somebody else have a similar >>>> issue. The strange thing is that for LORIS 19 is working fine. >>>> >>>> Thank you very much in advance for the help you can provide us, >>>> >>>> Rolando Acosta >>>> Canadian Neonatal Brain Platform (CHU Sainte-Justine) >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.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 >>> >> _______________________________________________ >> 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: