[Loris-dev] LORIS - Upload nifti and minc

Fri Jan 29 12:57:01 EST 2021

I see. There are significant changes between 22 and 23 on LORIS-MRI (mainly
the ability to set specific MRI protocols based on Visit label, Projects or
subprojects requiring changes to the MRI protocol tables). However, I do
not foresee any major blocker as to proceed to upgrading to 23.0 for
LORIS-MRI.

Hope this helps,

Cécile

On Fri, Jan 29, 2021 at 12:15 PM Sridar Narayanan, Dr. <
sridar.narayanan at mcgill.ca> wrote:

> Hi Cecile,
>
> I think Alfredo’s plan was to upgrade to 23.0 as soon as the upgrade to
> 22.0 was completed successfully (since a direct upgrade was not possible).
> Since 23.0 appears to fix some bugs in 22.0, when would it be most
> efficient to perform the 22.0 -> 23.0 upgrade? Should Alfredo ensure that
> 22.0 is functional with all patches applied first, to be safe, or will the
> upgrade to 23.0 take care of many of these issues?
>
> Thanks,
>
> Sridar
>
>
> On Jan 29, 2021, at 11:09 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
> 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
>
> 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> wrote:
>
>> Hi Cecile,
>>
>> I tried the script minc_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 -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> wrote:
>>
>>         External Email - Use Caution
>>
>> 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> 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>
>>> 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> 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>
>>>> wrote:
>>>>
>>>>         External Email - Use Caution
>>>>
>>>> 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> 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.
>>>>> 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
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>>>>> . 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
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>>>>>
>>>>
>>>> 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
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>>>
>>>
>> 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.
>>
>
>
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