Sending a large amount of studies (8TB) to dcm4chee with STORESCU

Clédio Moreira Paiva

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Sep 15, 2019, 10:26:43 PM9/15/19

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Hello

i have a problem with one of my dcm4chee servers. The main disk (a kingston SSD) has bad sectors, and i lost the integrity of the database (i have backups, but the backups are also currupted).

But my storage HDD is OK, so i have all the images saved and healthy. This server has 3 years of studies. its a 8TB HDD.

I think that I can replace the database's corrupted SSD, reinstall the system and send the images to the server again, using the STORESCU TOOL from dcm4chee toolkit.

But it is a very large amout of images to send (8TB). I think that STORESCU has a limit to scan subfolders, and even if I send separetely the Years folder, I think that is just "too much" to STORESCU tool ... Even sending MONTHs folder separately I think that can be too much .. .

How can I proceed in this scenario? Whats the reliable way to send these studies to server, and be sure that each study was sent correctly?

Thanks!

Udara M Pathirage - උදාර පතිරගේ

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Sep 15, 2019, 11:21:01 PM9/15/19

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Hi Dear

I got your point. First of all, can I know which DCM4CHE version currently you are using? Bye

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Clédio Moreira Paiva

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Sep 15, 2019, 11:32:44 PM9/15/19

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Hello, im using dcm4chee 2.x on the faulty server. But if there is a trick to do it on the newer version, i can set-up a dcm4chee-5x, no problem !

Thanks !

Em segunda-feira, 16 de setembro de 2019 00:21:01 UTC-3, Udara escreveu:

Hi Dear

I got your point. First of all, can I know which DCM4CHE version currently you are using? Bye

>>Best Regards From
Maj Udara Pathirage
Master of IT, UCSC, Colombo | BSc in ENCM, Kelaniya | Dip. IT, NIBM | MCS(SL) | MBCS CITP (UK) | SNOMED CT

On Mon, Sep 16, 2019 at 7:56 AM Clédio Moreira Paiva <cled...@gmail.com> wrote:

Hello

i have a problem with one of my dcm4chee servers. The main disk (a kingston SSD) has bad sectors, and i lost the integrity of the database (i have backups, but the backups are also currupted).

But my storage HDD is OK, so i have all the images saved and healthy. This server has 3 years of studies. its a 8TB HDD.

I think that I can replace the database's corrupted SSD, reinstall the system and send the images to the server again, using the STORESCU TOOL from dcm4chee toolkit.

But it is a very large amout of images to send (8TB). I think that STORESCU has a limit to scan subfolders, and even if I send separetely the Years folder, I think that is just "too much" to STORESCU tool ... Even sending MONTHs folder separately I think that can be too much .. .

How can I proceed in this scenario? Whats the reliable way to send these studies to server, and be sure that each study was sent correctly?

Thanks!

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Udara M Pathirage - උදාර පතිරගේ

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Sep 15, 2019, 11:44:12 PM9/15/19

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Hi,

Thanks for the information. If you are using dcm4chee 2.X and hope to transfer your images to the same version, you can follow he step in this

https://udara-research.blogspot.com/2019/08/how-to-backup-restore-studies-images.html

If you may find any issues, contact me..

Bye

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Clédio Moreira Paiva

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Sep 15, 2019, 11:56:23 PM9/15/19

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Hi

thank you for your quick response! but i read your blog, and your tutorial ... its great if i had the database backup file "pacsdb.sql" ... but the point is right there ... the main SSD of my server is currupted. i lost the Database, i cant just export the database to a sql file and then restore it ... i have just the dicom image dir (the storage dir is healthy) ... so i need to send this HUGE (8TB) dicom image folder to the new server, using some tool like STORESCU from dcm4che toolkit ....

Thank you!

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Udara M Pathirage - උදාර පතිරගේ

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Sep 16, 2019, 12:01:29 AM9/16/19

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Ah, I got your point. But I think you may not be able to access to your 8TB data without having its corresponding MySQL database. As per my knowledge, you have to have the database in order to retrieve data from the dcm4chee then it opens relevant images from the 8TB storage...

I have no idea other than that. I'm sorry..

Bye

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LOG

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Sep 16, 2019, 10:36:33 AM9/16/19

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In both Dcm4chee versions is possible to create entries in the database for a list of dicom files

To do it in Arc light version take a look at next link:

https://groups.google.com/forum/#!topic/dcm4che/jCpmAVoegZQ

Alvaro G [Andor]

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Sep 16, 2019, 10:54:40 AM9/16/19

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Hola Clédio,

(I forgot to answer the list too, Clédio will see this message as a duplicate, sorry)

It's true, you can't feed the whole disk to the tool because it will choke, you have to divide your migration in parts in two ways:

First, I would do the migration month by month, beginning by the files received more recently (which probably are the ones you might need right now). So if you have your DICOM storage partitioned the "traditional" dcm4chee way (/storage/year/month/day...) I would go to the latest month you have in storage, lets say, /dicom/2019/09
Second, I would feed the storescu or dcmsnd tool using the 'xargs' tool. Xargs is a tool that will get a lot of filenames through its input, and, as output, run a tool with this filenames as parameters as many times as needed.

Lets see an example:

find /dicom/2019/09 -type f -print0| xargs -0 /storescu -c DCM4CHEE@localhost:11112

The first part of the command is the one that will define the parameters for the second. In this case it'll look for all the files in the /dicom/2019/09 path.
The second part of the command takes the output of the first command and pass it as a parameter to the "storescu" command.

But, if you have thousands of files on that path, and you pass them as a parameter, that would overflow the shell and the app, so what xargs will do is only passing enough filenames as parameter to not overflow the shell, then run the command again with another bunch of files, then again...

Instead of giving control to xargs for the number of parameters, you could use the option '-n' to tell exactly how many parameters to pass on each run. So, the final example that will let you understand it better:

find /dicom/2019/09 -type f -print0| xargs -0 -n 10 /storescu -c DCM4CHEE@localhost:11112

I you had, lets say, a hundred files on that path, xargs would the storescu tool ten times, passing ten files as a parameter each time.

Start with a small directory, then begin migrating month by month.

PS: The '-print0' and '-0' options are there to avoid problems with paths containing spaces

PPS: Go to the mailing list archive and search for 'xargs' to find more examples

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Clédio Moreira Paiva

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Sep 16, 2019, 9:55:58 PM9/16/19

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Hi Andor, Thank you for your detailed explanation ! I will try it, and i will search more about xargs on the discussion board. Thanks !

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Clédio Moreira Paiva

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Sep 16, 2019, 9:57:23 PM9/16/19

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Hi, LOG, thank you for show me the way, i will search about it ! Thanks !

Clédio Moreira Paiva

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Dec 20, 2019, 8:34:44 PM12/20/19

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Andor, thank you very much, you saved my life ! I can resend my entire 8TB disk with your trick with xargs. I create an shell script that make this task more easy. i will realease this script in forum, maybe help somebody. thanks again !

Em segunda-feira, 16 de setembro de 2019 11:54:40 UTC-3, andor escreveu:

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