multivolumeimporter PkModeling

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multivolumeimporter PkModeling

David Fuentes
Hi,

I have multiple sets of 4d DICOM images that I would like to batch process with the PKModeling module using something like:


lib/Slicer-4.3/cli-modules/PkModeling --T1Blood 1600 --T1Tissue 1597 --relaxivity 0.0039 --S0grad 15.0 --fTolerance 1e-4 --gTolerance 1e-4 --xTolerance 1e-5 --epsilon 1e-9 --maxIter 200 --hematocrit 0.4 --aucTimeInterval 90 --computeFpv --usePopAif  --outputKtrans outktrans.nii.gz --outputVe  outVe.nii.gz --outputFpv outfpv.nii.gz --outputMaxSlope outslope.nii.gz --outputAUC outAUC.nii.gz  Data/SampledPhantoms/QINProstate001/Input/QINProstate001-phantom.nrrd

Is there a way to run multivolumeimporter in batch mode to convert DICOM to nrrd ?


thanks,
David


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Re: multivolumeimporter PkModeling

Andrey Fedorov-2
Yes it is possible. Get hints here:

https://github.com/fedorov/PCampReview/blob/master/PCampReviewPreprocessor.py#L116-L151

On Wed, Jul 1, 2015 at 10:22 AM, David Fuentes <[hidden email]> wrote:

> Hi,
>
> I have multiple sets of 4d DICOM images that I would like to batch process
> with the PKModeling module using something like:
>
>
> lib/Slicer-4.3/cli-modules/PkModeling --T1Blood 1600 --T1Tissue 1597
> --relaxivity 0.0039 --S0grad 15.0 --fTolerance 1e-4 --gTolerance 1e-4
> --xTolerance 1e-5 --epsilon 1e-9 --maxIter 200 --hematocrit 0.4
> --aucTimeInterval 90 --computeFpv --usePopAif  --outputKtrans
> outktrans.nii.gz --outputVe  outVe.nii.gz --outputFpv outfpv.nii.gz
> --outputMaxSlope outslope.nii.gz --outputAUC outAUC.nii.gz
> Data/SampledPhantoms/QINProstate001/Input/QINProstate001-phantom.nrrd
>
>
> Is there a way to run multivolumeimporter in batch mode to convert DICOM to
> nrrd ?
>
>
> thanks,
> David
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with
> unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
> 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 Partners Compliance
> HelpLine at
> http://www.partners.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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Re: multivolumeimporter PkModeling

Mehrtash, Alireza
The following gist can be useful (It is supposed that the dicom data are in the following folder hierarchy: patients>studies>series).


Alireza

On Wed, Jul 1, 2015 at 10:41 AM, Andrey Fedorov <[hidden email]> wrote:
Yes it is possible. Get hints here:

https://github.com/fedorov/PCampReview/blob/master/PCampReviewPreprocessor.py#L116-L151

On Wed, Jul 1, 2015 at 10:22 AM, David Fuentes <[hidden email]> wrote:
> Hi,
>
> I have multiple sets of 4d DICOM images that I would like to batch process
> with the PKModeling module using something like:
>
>
> lib/Slicer-4.3/cli-modules/PkModeling --T1Blood 1600 --T1Tissue 1597
> --relaxivity 0.0039 --S0grad 15.0 --fTolerance 1e-4 --gTolerance 1e-4
> --xTolerance 1e-5 --epsilon 1e-9 --maxIter 200 --hematocrit 0.4
> --aucTimeInterval 90 --computeFpv --usePopAif  --outputKtrans
> outktrans.nii.gz --outputVe  outVe.nii.gz --outputFpv outfpv.nii.gz
> --outputMaxSlope outslope.nii.gz --outputAUC outAUC.nii.gz
> Data/SampledPhantoms/QINProstate001/Input/QINProstate001-phantom.nrrd
>
>
> Is there a way to run multivolumeimporter in batch mode to convert DICOM to
> nrrd ?
>
>
> thanks,
> David
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with
> unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
> 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 Partners Compliance
> HelpLine at
> http://www.partners.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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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 Partners Compliance HelpLine at
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Re: multivolumeimporter PkModeling

David Fuentes
In reply to this post by Andrey Fedorov-2
thanks!!

On Wed, Jul 1, 2015 at 9:51 AM, Alireza Mehrtash <[hidden email]> wrote:
The following gist can be useful (It is supposed that the dicom data are in the following folder hierarchy: patients>studies>series).


Alireza

On Wed, Jul 1, 2015 at 10:41 AM, Andrey Fedorov <[hidden email]> wrote:
Yes it is possible. Get hints here:

https://github.com/fedorov/PCampReview/blob/master/PCampReviewPreprocessor.py#L116-L151

On Wed, Jul 1, 2015 at 10:22 AM, David Fuentes <[hidden email]> wrote:
> Hi,
>
> I have multiple sets of 4d DICOM images that I would like to batch process
> with the PKModeling module using something like:
>
>
> lib/Slicer-4.3/cli-modules/PkModeling --T1Blood 1600 --T1Tissue 1597
> --relaxivity 0.0039 --S0grad 15.0 --fTolerance 1e-4 --gTolerance 1e-4
> --xTolerance 1e-5 --epsilon 1e-9 --maxIter 200 --hematocrit 0.4
> --aucTimeInterval 90 --computeFpv --usePopAif  --outputKtrans
> outktrans.nii.gz --outputVe  outVe.nii.gz --outputFpv outfpv.nii.gz
> --outputMaxSlope outslope.nii.gz --outputAUC outAUC.nii.gz
> Data/SampledPhantoms/QINProstate001/Input/QINProstate001-phantom.nrrd
>
>
> Is there a way to run multivolumeimporter in batch mode to convert DICOM to
> nrrd ?
>
>
> thanks,
> David
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with
> unsubscribe as the subject
> http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ
>
>
> 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 Partners Compliance
> HelpLine at
> http://www.partners.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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http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ



_______________________________________________
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http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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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 Partners Compliance HelpLine at
http://www.partners.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.