[Loris-dev] LORIS - Upload nifti and minc

Fri Jan 29 11:09:22 EST 2021

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
>>>> http://www.massgeneralbrigham.org/complianceline
>>>> <http://secure-web.cisco.com/1q-ePyFea6WSQhWdpXg0cjjf5QxojMXFKfAvUcNMmHc3nbTBr6tyvmxq4uxx2thoPu2hDka6euZtG_leaa4zs5d6QFuDtb0IrJ8LCr8swig6pX4KV4wjFMEfVo3JUZcic2kgUX05QhOpnoIOG6IZzE_t8oGtK4USGu9tK45YzxhhD_ce5CG4UuWKyeCBl7HNIkHmZhhQx1aW2E9WjajKNr2fhONfo04Nfm6jAM9pJU2KLorfShzI_QTcJZ0GOICzHln6VhTBHNNBBXGj7L7H7AQ/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>>>> . 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
>>>> <https://secure-web.cisco.com/144wJ9PqeZERh-MgDDtF93WU9P1mkq_XgAq2hpkoO3ydxQ3-xdKLSm5vtJtKx2tbFWdAt3GmfBjLxHXeIPmaphG9eead6kEPmC8T-ZmYt0pLEo4iqoEiSrCWB2MgsekUYaH9VhwTMArdjZTMjBejiTpDrESQ7-NfsdKWY77Iopa0YHZFT1FfdbK-xUC9Z2DNelIPelCSHWJl0dXw3D-_sUgqFMhObnEl2_uAD42U8msu-5Um48htLbOUyC1tn2RUteL8LKWCIYyx_yYxHhl0KAQ/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-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
>>> <http://secure-web.cisco.com/1OSlhjjV74N3AA1H_KC8JOM2-Dytks19qSUt0wYfQRZJgDLpq6rl5UWl6M8ompG6KnWEVMcfjqbVY8ce0rCYefT1WAbs1Sk9Ik8Z8ulBZ6RrQKMIc0qMPE-1RJXBjy9wDcGr9DQXCALDTSEBFDCgtcY2QMuC5x-lKK2SgLOrjUWswv99UdtbxH06sH6Uy03f7tDGhWtPh9vl3O7tcb9YhlvqlT6tKqcUPeEMUPm0TzMEMZS_TufJzfBvP8dpKZbL-dkJVzuwqcQDhRFOqOEnDWA/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>>> . 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.
>>>
>>
>>
> 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.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20210129/1a8330c2/attachment-0001.html>