[Loris-dev] LORIS - Upload nifti and minc
Morales Pinzon, Alfredo
AMORALESPINZON at BWH.HARVARD.EDU
Fri Jan 29 11:44:11 EST 2021
Hi Cecile,
Thank you. This is great.
I will move to v23 regardless of some small issues I had in the migration SQL that don’t impact our project as we are not using the electrophysiology browser or module manager modules.
I’ll test it one I’m in v23 and let you know.
Best,
Alfredo.
On Jan 29, 2021, at 11:09 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
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Hi Alfredo,
I was able to reproduce your bug on version 22.0 of LORIS-MRI and it was maybe present in older versions as well. This was fixed in release 23.0 with better logging information.
I just sent a PR with a fix for 22.0 that you can find here: https://github.com/aces/Loris-MRI/pull/573/files<https://secure-web.cisco.com/1o_hyVjwaWJscvuTnCFM2q5NFsnnPpDEB3tJ03Aey8cGQdSLbtM51LJ-5ulzA1OPNGtiho7fpCaznGroPtMQS5Ds9JjWVMLqjGaK8VogRx4fpWPGuSoOFUwhEwHdbfEP7fM-XFPXg3jJ-U81c381mHOgz8IKdppbEIgOl0QA5Rm3d61z89p5yHUrw9_6ycELjXcFTAzl3bDmQWzX5BXFKJ2SdVcB5skZLIpZPVb7AxzTFisBhAo-qNrjxmtIXfYgzX4q_KjiHIuFLmf_-Zy9zlg/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fpull%2F573%2Ffiles>
That should resolve the issue you were having. Let me know how it goes.
Best,
Cécile
On Fri, Jan 29, 2021 at 1:18 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Cecile,
I tried the script minc_insertion.pl<http://secure-web.cisco.com/17gu-bOY1wRpgyX4EI2L_PmPTOEP6zzoTifAu-ITBpS1FmduGnT99ndduqa9fsDarfSHtytMyvJBkCikVexXZcjp44PUX_jTH8HUBU8BkGxVzBOW2tLt2oTN43FDOArjBus6C3A88PmrdLd9DpA7-AWxKBrepYFAoGaU4cK2-ZbwVAhlj2AbiVERPXrPUOvjfUZRnB_aL0ebBuk3w2Qn0tVsX-YBkfuOkSbb0Pw3aScHAGdwmJZFQIAP3hzqftfoZ_soiFvvHt93F1EC32HE1og/http%3A%2F%2Fminc_insertion.pl> but it seems that the Candidate should not exist before the execution of the script. Is this the case? This would be problematic in order to upload multiple sequences for a given Candidate. This is the error I am getting:
===
$ perl minc_insertion.pl<http://secure-web.cisco.com/17gu-bOY1wRpgyX4EI2L_PmPTOEP6zzoTifAu-ITBpS1FmduGnT99ndduqa9fsDarfSHtytMyvJBkCikVexXZcjp44PUX_jTH8HUBU8BkGxVzBOW2tLt2oTN43FDOArjBus6C3A88PmrdLd9DpA7-AWxKBrepYFAoGaU4cK2-ZbwVAhlj2AbiVERPXrPUOvjfUZRnB_aL0ebBuk3w2Qn0tVsX-YBkfuOkSbb0Pw3aScHAGdwmJZFQIAP3hzqftfoZ_soiFvvHt93F1EC32HE1og/http%3A%2F%2Fminc_insertion.pl> -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w -mincPath /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc
log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log
ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists.
SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303
CandID id: 814099
visit_label is: 105ms302w48
PSCID is: AZH101303
CandID id: 814099
visit_label is: 105ms302w48
Spool message is: ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists
===
Best,
Alfredo.
P.S. The file /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log is not being written.
On Jan 26, 2021, at 4:33 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
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Hi,
Thank you for the clarification. I think I understand better the confusion.
You can insert MINC files without having to insert DICOM files by running the minc_insertion.pl<http://secure-web.cisco.com/1CRWLdhPK0QJwqPsDM4eN1sMctn09UpUmGm1ZACvkTVa4MFcegyiYHM-gnd66amN903PeYLfAWQNIvPTZ5yOnEPThk8ksAOROmQS3eWh0U8d8V8e7OzW5hcKgr-r-hohMmcc-QL9o2-pieYi2wKVTxk6Jp1FIcAvYVtg88EIZDsttuCveFvjbvwcs__pZDy8Et4MwQsmqkvt6Oc74cpqzwx4rBRYvkaEN1XHX8VHjpAYfYevk7OMqQ5atJ7rvdQX7Wnce-Y6YMEjf3TzlKPLILg/http%3A%2F%2Fminc_insertion.pl> script with the -force option. Basically, the force option will bypass checks to see if there are DICOMs to attach the file to.
minc_insertion.pl<http://secure-web.cisco.com/1CRWLdhPK0QJwqPsDM4eN1sMctn09UpUmGm1ZACvkTVa4MFcegyiYHM-gnd66amN903PeYLfAWQNIvPTZ5yOnEPThk8ksAOROmQS3eWh0U8d8V8e7OzW5hcKgr-r-hohMmcc-QL9o2-pieYi2wKVTxk6Jp1FIcAvYVtg88EIZDsttuCveFvjbvwcs__pZDy8Et4MwQsmqkvt6Oc74cpqzwx4rBRYvkaEN1XHX8VHjpAYfYevk7OMqQ5atJ7rvdQX7Wnce-Y6YMEjf3TzlKPLILg/http%3A%2F%2Fminc_insertion.pl> -profile <name of your profile file, typically prod> -mincPath <path to your MINC file> -force -create_minc_pics
For the NIfTI files alone, because of the nature of that file format (no header information like MINC...), you will have to specify a lot of the information when calling the script imaging_non_minc_insertion.pl<http://secure-web.cisco.com/1ANFDRFiRPX99wUpC1gLtmUEZUofuWa1YZIPvpt87N85cQ5aLcJwJ9Smm-wYcByOM8Od5Xjlo9-tl0ZQJY7JJ27g0DbjPQbPN_QnnSHs9CqrVFjFlbxUVjECyQKBTq0uT8IQOCtU-B9Il0lt9aY3N1aQFBd6GvX2BeQVz7KQjcRNZT9uFGQ5UUd_7hTAP4isf2q5V8InvWEmEgkYKTrZvOSEe-eXGvSk-6HvLP2LKIs_OHhCR0S-b_aO2sFFoQkvgyDg1FdVGN7K5vNrFFJu3QQ/http%3A%2F%2Fimaging_non_minc_insertion.pl> (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... Basically all the columns of the files table). It needs to be associated with an upload_id for the logging in the database but the upload_id does not necessarily need to be DICOM files. It could be a zipped archive of all the NIfTI files of the session uploaded for example. Then you would just need to create a little wrapper script to run imaging_non_minc_insertion.pl<http://secure-web.cisco.com/1ANFDRFiRPX99wUpC1gLtmUEZUofuWa1YZIPvpt87N85cQ5aLcJwJ9Smm-wYcByOM8Od5Xjlo9-tl0ZQJY7JJ27g0DbjPQbPN_QnnSHs9CqrVFjFlbxUVjECyQKBTq0uT8IQOCtU-B9Il0lt9aY3N1aQFBd6GvX2BeQVz7KQjcRNZT9uFGQ5UUd_7hTAP4isf2q5V8InvWEmEgkYKTrZvOSEe-eXGvSk-6HvLP2LKIs_OHhCR0S-b_aO2sFFoQkvgyDg1FdVGN7K5vNrFFJu3QQ/http%3A%2F%2Fimaging_non_minc_insertion.pl> on the loaded NIfTI files.
Does that clarify the steps?
Thanks!
Cécile
On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. <sridar.narayanan at mcgill.ca<mailto:sridar.narayanan at mcgill.ca>> wrote:
Hi Cecile,
Just to clarify, many import issues seem to stem from problems with the implementation of dcm2mnc used by Loris. These DICOM files can be successfully converted to MINC and NifTI with other tools, and so we were wondering if it would be possible to import MRI data into Loris as MINC & NifTI files instead of importing the DICOMs. Alternatively, we could convert these files to BIDS and import that instead of DICOM. The important point is whether we can avoid importing DICOM for new scan/participant instances, but import only BIDS or MINC + NiFTI data and generate a new Loris ID from this. We are not asking about attaching a MINC or NifTI file to an existing record, which we know can be done (e.g. for label files associated with the images).
Thanks,
Sridar
On Jan 25, 2021, at 5:01 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
Hi Alfredo,
I am a bit confused by your email. The two perl scripts I mentioned last week do not require the data to be organized in BIDS to insert them. Did you look into them?
Sorry, maybe I am missing something.
Cécile
On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Hi Cecile,
Thank you for your answer. I am sorry I was not enough specific regarding what we are looking for. We are actually looking for a solution to avoid importing the “raw” images in minc and nifti images instead of DICOM. We are having a lot of issues importing DICOM (~1.700 visits with issues) and we want to explore options for uploading the original images (e.g., t1) using minc and nifti without them being in BIDS formar.
Do you have scripts for this?
Best,
Alfredo.
On Jan 19, 2021, at 1:59 PM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:
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Hi Alfredo,
Very sorry for the late reply. In short, yes, it is possible to do both.
It is possible to insert MINC files in LORIS by using the LORIS-MRI script called minc_insertion.pl<https://secure-web.cisco.com/1h8RHj_R4mnovi1vzHjXIG7OriE5SmwPXivIa6upEGgUmO0oyYw5rNJDqM2MdvPGvTNW0VgU36iIDos755qEXc2ZLdcGpGZQRfXLN_QGCSHqe5_pR8SPcRCLVkIkUT9JFyTm2tgFJomSHtiCakjIicPSDvv5QaC2BEX0O8gPHeY_UrixP8DhG29aU9BwThbmfsNCgJS9rWE8hkKiSJu3dXUWYZuz3SELo6A5cEG3a0urWWaEYKsL-uNUUQlpn-dLXHjrf4KywfR-f_8XtyxHIrA/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fmain%2FuploadNeuroDB%2Fminc_insertion.pl> in the uploadNeuroDB folder. If you run perl minc_insertion.pl<http://secure-web.cisco.com/13jgtqDYN7Gf_vgFThFhtlVEFqhsVru-JRquRrfzp92y9hcK9koGa9r9E_RCEHuDzqw9ZQq4eWBdGe5cbbKU8_yrxXgz98kTVTBySSdwUF3dgAiL6ls9glxHxeHwLfR-M9U6DLj3ePJR758eO7Ukl-KBwGCnH1TTfOmLDAPWxs4ABKnOnHa0AHFN4qsRIDO6BMvq5wK_o-G0mjUXNUyb7jkUjg-xsaAHbLYjZ1X15d3pWFi0jmNTPfm57PC77a41n7xp5Ae2Ji6UtzrGAczTtBg/http%3A%2F%2Fminc_insertion.pl> -h; you will see the explanation on how to run the script.
Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called imaging_non_minc_insertion.pl<https://secure-web.cisco.com/11rMDfTbsxeYelAro9qFHffjunl6PQySl-cFRkp1QAl_sinKZ_2ULH-80TnkR2omX6h5c78cX8Vvl4xgml5nGxkii9oOTjLtfmZO4NsBu-w2Dxh2E5l5p4rjx9RKrSRQak24h8B8rvl1sVWzkBe5qftWBHEd1FCLV4ptJPdCzV7xqJf3fMCIGfs77Mk6WCmGBhuL0FPSHDnWmRRvXzXAT5wH5eAUsHI3_2F8yAh25Hpvd-t9vttu-mAGU_XbLNQXQf2DNBFxGjThITPI2ptn38Q/https%3A%2F%2Fgithub.com%2Faces%2FLoris-MRI%2Fblob%2Fmain%2FuploadNeuroDB%2Fimaging_non_minc_insertion.pl> in the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl<http://secure-web.cisco.com/1JUwbjz4V-PmM1LkrSIDPw4ydwAZ7otVSJadvo40dcrQMsYYfCLZsWRbpIcZwOZ3-TV3DyLARQX4Fp7-IHGmufed_LFzA0ah5UuJSegiZBGWQE9RiKXU6LxPe9xHqMfhyirSZF4zFetUaHoOtn5Pa9lFbV5o2FFI95zKG4NrmEX-HgUA_dMYmHrIFagQBzH_uujh-hUSiWM7Hvbf_d_KanWYNOrmkjAoe07MI18KuH0XsY5Gmhap81i-fVggYZHLthuCTL9_Dpky-ZNaeiyOlZw/http%3A%2F%2Fimaging_non_minc_insertion.pl> should give you all the information you need in order to run the script.
Hope this helps,
Cécile
On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LorisDev team,
Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format?
Best regards,
Alfredo.
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