[Loris-dev] [LORIS-IPMSA] Series description does not match
Christine Rogers
rogers at bic.mni.mcgill.ca
Thu Dec 20 09:39:30 EST 2018
Hi Alfredo,
Yes, to clarify -- it is best to remove already inserted images/records
before re-running the pipeline, as attempts to load duplicate DICOM
tarballs should give errors, I believe.
If you have QC information already registered for scans you have loaded in
LORIS, this is best to back up very carefully before cleaning and
re-loading images.
Best,
Christine
On Thu, Dec 20, 2018 at 9:23 AM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:
> Hi Christine,
>
>
> If I re-run the insertion pipeline will the "misclassify images" be
> correctly classified or I will have duplicates with different
> classification? I can easily re-run the pipeline but want to make sure I
> won't have duplicates.
>
>
> Thank you very much for your answer.
>
>
> Best,
>
> Alfredo.
> ------------------------------
> *From:* Christine Rogers <rogers at bic.mni.mcgill.ca>
> *Sent:* Wednesday, December 19, 2018 12:59:35 PM
> *To:* Morales Pinzon, Alfredo
> *Cc:* loris-dev at bic.mni.mcgill.ca; aki at mrs.mni.mcgill.ca; Sridar
> Narayanan, Dr.; Marciniak, Andrzej; pistikem at gmail.com; Rozie
> Arnaoutelis, Ms.; douglas.arnold at mcgill.ca; Guttmann, Charles,M.D.
> *Subject:* Re: [Loris-dev] [LORIS-IPMSA] Series description does not match
>
>
> External Email - Use Caution
>
> Hi Alfredo,
> Thanks for your feedback, we'll look to clarify those regex specs in our
> documentation for future releases.
>
> Regarding changing the scan type -- the `files` table has an `
> AcquisitionProtocolID` column which references the mri_scan_type`table's `
> ID` column.
>
> It's possible you may wish to re-run the insertion pipeline to identify
> and generate properly-labelled MINC filenames instead of undertaking manual
> updates in the filesystem and in the database.
>
> Best,
> Christine
>
>
>
> On Tue, Dec 18, 2018 at 11:58 AM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
> Dear LorisDev team,
>
>
> I found the error, the column *series_description_regex* in table
> *mri_protocol* needs to be in a specific format, meaning that the initial
> "/" and ending "/i" must not be placed in the regex string. I replaced "*series_description_regex:
> /^flr$/i*" by "series_description_regex: flr *$" and now I have the
> correct classification when inserting a new image.
>
>
> Now, I just need help with the images that were classified as NA (see my
> previous email), how can I change the type assigned to this images?
>
>
> Additionally, I didn't find any documentation regarding the format of the
> regex that LORIS is expecting, I would be great if we can add it for future
> users. Also, does it make sense to have the last part of the regex hard
> coded as "/i"? Maybe a user would like to use "/x" or other options.
>
>
> Thank you for your help.
>
>
> Best regards,
>
> Alfredo.
> ------------------------------
> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Morales Pinzon, Alfredo
> <AMORALESPINZON at bwh.harvard.edu>
> *Sent:* Monday, December 17, 2018 9:27:28 PM
> *To:* loris-dev at bic.mni.mcgill.ca
> *Cc:* Zografos Caramanos; Sridar Narayanan, Dr.; Marciniak, Andrzej;
> pistikem at gmail.com; Rozie Arnaoutelis; Douglas Arnold, Dr.; Guttmann,
> Charles,M.D.
> *Subject:* [Loris-dev] [LORIS-IPMSA] Series description does not match
>
>
> External Email - Use Caution
>
> Dear LorisDev team,
>
>
> I am batch uploading images (~5000 visits = 15000 MRI images) into LORIS
> but they are not being classified correctly based on the series description
> (series_description_regex in table mri_protocol). Could you help with 2
> things?
>
>
> 1. How can I change the type of an image already inserted? All the images
> inserted, so far around 240, were classified as NA.
>
>
> 2. Could you tell me if I am missing something in the series_description_regex
> in table mri_protocol? Here is what I have in the table mri_protocol and
> mri_scan_type, and a screenshot (attached) of one of the inserted images in
> LORIS:
>
>
>
> -----------------------------------------------------------------------------
>
> mysql> select * from mri_protocol \G;
> *************************** 1. row ***************************
> ID: 1004
> Center_name: ZZZZ
> ScannerID: 0
> Scan_type: 41
> TR_range: NULL
> TE_range: NULL
> TI_range: NULL
> slice_thickness_range: NULL
> FoV_x_range: NULL
> FoV_y_range: NULL
> FoV_z_range: NULL
> xspace_range: NULL
> yspace_range: NULL
> zspace_range: NULL
> xstep_range: NULL
> ystep_range: NULL
> zstep_range: NULL
> time_range: NULL
> series_description_regex: /^flr$/i
> *************************** 2. row ***************************
> ID: 1005
> Center_name: ZZZZ
> ScannerID: 0
> Scan_type: 1001
> TR_range: NULL
> TE_range: NULL
> TI_range: NULL
> slice_thickness_range: NULL
> FoV_x_range: NULL
> FoV_y_range: NULL
> FoV_z_range: NULL
> xspace_range: NULL
> yspace_range: NULL
> zspace_range: NULL
> xstep_range: NULL
> ystep_range: NULL
> zstep_range: NULL
> time_range: NULL
> series_description_regex: /^pdw$/i
> *************************** 3. row ***************************
> ID: 1007
> Center_name: ZZZZ
> ScannerID: 0
> Scan_type: 1002
> TR_range: NULL
> TE_range: NULL
> TI_range: NULL
> slice_thickness_range: NULL
> FoV_x_range: NULL
> FoV_y_range: NULL
> FoV_z_range: NULL
> xspace_range: NULL
> yspace_range: NULL
> zspace_range: NULL
> xstep_range: NULL
> ystep_range: NULL
> zstep_range: NULL
> time_range: NULL
> series_description_regex: /^t2w$/i
> *************************** 4. row ***************************
> ID: 1009
> Center_name: ZZZZ
> ScannerID: 0
> Scan_type: 1003
> TR_range: NULL
> TE_range: NULL
> TI_range: NULL
> slice_thickness_range: NULL
> FoV_x_range: NULL
> FoV_y_range: NULL
> FoV_z_range: NULL
> xspace_range: NULL
> yspace_range: NULL
> zspace_range: NULL
> xstep_range: NULL
> ystep_range: NULL
> zstep_range: NULL
> time_range: NULL
> series_description_regex: /^t1c$/i
> *************************** 5. row ***************************
> ID: 1010
> Center_name: ZZZZ
> ScannerID: 0
> Scan_type: 1004
> TR_range: NULL
> TE_range: NULL
> TI_range: NULL
> slice_thickness_range: NULL
> FoV_x_range: NULL
> FoV_y_range: NULL
> FoV_z_range: NULL
> xspace_range: NULL
> yspace_range: NULL
> zspace_range: NULL
> xstep_range: NULL
> ystep_range: NULL
> zstep_range: NULL
> time_range: NULL
> series_description_regex: /^t1p$/i
> *************************** 6. row ***************************
> ID: 1011
> Center_name: ZZZZ
> ScannerID: 0
> Scan_type: 1005
> TR_range: NULL
> TE_range: NULL
> TI_range: NULL
> slice_thickness_range: NULL
> FoV_x_range: NULL
> FoV_y_range: NULL
> FoV_z_range: NULL
> xspace_range: NULL
> yspace_range: NULL
> zspace_range: NULL
> xstep_range: NULL
> ystep_range: NULL
> zstep_range: NULL
> time_range: NULL
> series_description_regex: /^mtOFF$/i
> *************************** 7. row ***************************
> ID: 1012
> Center_name: ZZZZ
> ScannerID: 0
> Scan_type: 1006
> TR_range: NULL
> TE_range: NULL
> TI_range: NULL
> slice_thickness_range: NULL
> FoV_x_range: NULL
> FoV_y_range: NULL
> FoV_z_range: NULL
> xspace_range: NULL
> yspace_range: NULL
> zspace_range: NULL
> xstep_range: NULL
> ystep_range: NULL
> zstep_range: NULL
> time_range: NULL
> series_description_regex: /^mtON$/i
> *************************** 8. row ***************************
> ID: 1013
> Center_name: ZZZZ
> ScannerID: 0
> Scan_type: 1000
> TR_range: NULL
> TE_range: NULL
> TI_range: NULL
> slice_thickness_range: NULL
> FoV_x_range: NULL
> FoV_y_range: NULL
> FoV_z_range: NULL
> xspace_range: NULL
> yspace_range: NULL
> zspace_range: NULL
> xstep_range: NULL
> ystep_range: NULL
> zstep_range: NULL
> time_range: NULL
> series_description_regex: NULL
> 8 rows in set (0.00 sec)
>
>
> -----------------------------------------------------------------------------
>
>
> mysql> select * from mri_scan_type;
> +------+--------------+
> | ID | Scan_type |
> +------+--------------+
> | 40 | fMRI |
> | 41 | flair |
> | 44 | t1 |
> | 45 | t2 |
> | 46 | pd |
> | 47 | mrs |
> | 48 | dti |
> | 49 | t1relx |
> | 50 | dct2e1 |
> | 51 | dct2e2 |
> | 52 | scout |
> | 53 | tal_msk |
> | 54 | cocosco_cls |
> | 55 | clean_cls |
> | 56 | em_cls |
> | 57 | seg |
> | 58 | white_matter |
> | 59 | gray_matter |
> | 60 | csf_matter |
> | 61 | nlr_masked |
> | 62 | pve |
> | 999 | unknown |
> | 1000 | NA |
> | 1001 | pdw |
> | 1002 | t2w |
> | 1003 | t1c |
> | 1004 | t1p |
> | 1005 | mtOFF |
> | 1006 | mtON |
> +------+--------------+
>
>
> -----------------------------------------------------------------------------
>
>
> Thank you for any help.
>
>
> Best regards,
>
> Alfredo.
>
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>
>
> --
>
> christine.rogers at mcgill.ca
> McGill Centre for Integrative Neuroscience | MCIN.ca
> Montreal Neurological Institute
> McGill University | Montreal | Canada
>
--
christine.rogers at mcgill.ca
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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