Problem importing large files in Slicer

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Problem importing large files in Slicer

O'Callaghan, Paul 2

I have just completed scanning of bone samples using a synchrotron. The results of which consist of approximately 2000 slices each of a single tiff. I created a single stack tif using ImageJ, but unfortunately I cannot get slicer to recognise it as a 3D stack. The filesize of the stack is approximately 50Gbytes.

 

When I load the stack by dragging the file into the 3D window or by import data. Slicer just seems to register the file as 1 single slice. Is there any other way of reconstructing the 3D volume? Or is the file too big?

 

My computer is an I5 with 8GBytes of RAM fitted with a solid state drive. I’m running Slicer 4.62 on a linux Ubuntu platform.

 

Many thanks

 

Paul O’Callaghan.

 

Dr Paul O’Callaghan

Research Fellow | School of Life Sciences | London South Bank University | 103 Borough Road, London, SE1 0AA

t: +44 (0)20 7815 7949  | e: [hidden email]



 

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Re: Problem importing large files in Slicer

Murat Maga

I never tried to load a single 3D tiff file into slicer. I am not sure if it accepts that. However, you can load your original stack directly into slicer. Just drag one of the 2D tiff slices and then expand the options for load data and uncheck ‘single slice’. That will load your image stack as a volume, instead of a single file.

 

However, you will run of memory. You can’t fit 50GB dataset into 8GB memory. I don’t think Slicer has any out-of-memory dataset support for this kind of datasets.

 

You can look into options of reducing the dataset out of slicer.  Cropping field of view, downsampling by 2 (or more) in each axis (you can do that in ImageJ) are all options to load entire datasets. Or consider looking at chunks of your dataset at full resolution (if that’s acceptable).

 

M

 

From: slicer-users [mailto:[hidden email]] On Behalf Of O'Callaghan, Paul 2
Sent: Thursday, March 23, 2017 9:34 AM
To: SPL Slicer Users <[hidden email]>
Subject: [slicer-users] Problem importing large files in Slicer

 

I have just completed scanning of bone samples using a synchrotron. The results of which consist of approximately 2000 slices each of a single tiff. I created a single stack tif using ImageJ, but unfortunately I cannot get slicer to recognise it as a 3D stack. The filesize of the stack is approximately 50Gbytes.

 

When I load the stack by dragging the file into the 3D window or by import data. Slicer just seems to register the file as 1 single slice. Is there any other way of reconstructing the 3D volume? Or is the file too big?

 

My computer is an I5 with 8GBytes of RAM fitted with a solid state drive. I’m running Slicer 4.62 on a linux Ubuntu platform.

 

Many thanks

 

Paul O’Callaghan.

 

Dr Paul O’Callaghan

Research Fellow | School of Life Sciences | London South Bank University | 103 Borough Road, London, SE1 0AA

t: +44 (0)20 7815 7949  | e: [hidden email]

 

 

Become what you want to be

lsbu.ac.uk | Twitter | Facebook | Instagram

 

Copyright in this email and in any attachments belongs to London South Bank University. This email, and its attachments if any, may be confidential or legally privileged and is intended to be seen only by the person to whom it is addressed. If you are not the intended recipient, please note the following: (1) You should take immediate action to notify the sender and delete the original email and all copies from your computer systems; (2) You should not read copy or use the contents of the email nor disclose it or its existence to anyone else. The views expressed herein are those of the author(s) and should not be taken as those of London South Bank University, unless this is specifically stated. London South Bank University is a company limited by guarantee registered in England and Wales. The following details apply to London South Bank University: Company number - 00986761; Registered office and trading address - 103 Borough Road London SE1 0AA; VAT number - 778 1116 17 Email address - [hidden email]


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Re: Problem importing large files in Slicer

Hollister Herhold
In reply to this post by O'Callaghan, Paul 2
The way to do this (or the way I do it with similar datasets) is to import the TIFF stack into ImageJ, preferably as a virtual stack so as to use less memory, and then export it as an NRRD file. This can then be imported into slicer as a volume. 

You’ll probably need to set the voxel size in the “Volumes” module so your dimensions and rulers work correctly.

8GB really isn’t sufficient to process this dataset, though. You could consider using ImageJ to chop out areas you’re not interested in before importing into slicer.

Hope this helps.

-Hollister


On Mar 23, 2017, at 12:34 PM, O'Callaghan, Paul 2 <[hidden email]> wrote:

I have just completed scanning of bone samples using a synchrotron. The results of which consist of approximately 2000 slices each of a single tiff. I created a single stack tif using ImageJ, but unfortunately I cannot get slicer to recognise it as a 3D stack. The filesize of the stack is approximately 50Gbytes.
 
When I load the stack by dragging the file into the 3D window or by import data. Slicer just seems to register the file as 1 single slice. Is there any other way of reconstructing the 3D volume? Or is the file too big?
 
My computer is an I5 with 8GBytes of RAM fitted with a solid state drive. I’m running Slicer 4.62 on a linux Ubuntu platform.
 
Many thanks
 
Paul O’Callaghan.
 
Dr Paul O’Callaghan
Research Fellow | School of Life Sciences | London South Bank University | 103 Borough Road, London, SE1 0AA
t: +44 (0)20 7815 7949  | e: [hidden email]


 
Become what you want to be
 
Copyright in this email and in any attachments belongs to London South Bank University. This email, and its attachments if any, may be confidential or legally privileged and is intended to be seen only by the person to whom it is addressed. If you are not the intended recipient, please note the following: (1) You should take immediate action to notify the sender and delete the original email and all copies from your computer systems; (2) You should not read copy or use the contents of the email nor disclose it or its existence to anyone else. The views expressed herein are those of the author(s) and should not be taken as those of London South Bank University, unless this is specifically stated. London South Bank University is a company limited by guarantee registered in England and Wales. The following details apply to London South Bank University: Company number - 00986761; Registered office and trading address - 103 Borough Road London SE1 0AA; VAT number - 778 1116 17 Email address - [hidden email] _______________________________________________
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Re: Problem importing large files in Slicer

Andras Lasso-2

For robust visualization and processing I usually recommend 5x more physical memory and 10x more virtual memory space than the size of your data set. If you don’t have that much physical memory everything will still work but slower.

 

You can downsample large data sets and/or crop to a region of interest to reduce their size.

 

Andras

 

From: slicer-users [mailto:[hidden email]] On Behalf Of Hollister Herhold
Sent: March 23, 2017 15:20
To: O'Callaghan, Paul 2 <[hidden email]>; SPL Slicer Users <[hidden email]>
Subject: Re: [slicer-users] Problem importing large files in Slicer

 

The way to do this (or the way I do it with similar datasets) is to import the TIFF stack into ImageJ, preferably as a virtual stack so as to use less memory, and then export it as an NRRD file. This can then be imported into slicer as a volume. 

 

You’ll probably need to set the voxel size in the “Volumes” module so your dimensions and rulers work correctly.

 

8GB really isn’t sufficient to process this dataset, though. You could consider using ImageJ to chop out areas you’re not interested in before importing into slicer.

 

Hope this helps.

 

-Hollister

 

 

On Mar 23, 2017, at 12:34 PM, O'Callaghan, Paul 2 <[hidden email]> wrote:

 

I have just completed scanning of bone samples using a synchrotron. The results of which consist of approximately 2000 slices each of a single tiff. I created a single stack tif using ImageJ, but unfortunately I cannot get slicer to recognise it as a 3D stack. The filesize of the stack is approximately 50Gbytes.

 

When I load the stack by dragging the file into the 3D window or by import data. Slicer just seems to register the file as 1 single slice. Is there any other way of reconstructing the 3D volume? Or is the file too big?

 

My computer is an I5 with 8GBytes of RAM fitted with a solid state drive. I’m running Slicer 4.62 on a linux Ubuntu platform.

 

Many thanks

 

Paul O’Callaghan.

 

Dr Paul O’Callaghan

Research Fellow | School of Life Sciences | London South Bank University | 103 Borough Road, London, SE1 0AA

t: +44 (0)20 7815 7949  | e: [hidden email]




 

Become what you want to be

 

Copyright in this email and in any attachments belongs to London South Bank University. This email, and its attachments if any, may be confidential or legally privileged and is intended to be seen only by the person to whom it is addressed. If you are not the intended recipient, please note the following: (1) You should take immediate action to notify the sender and delete the original email and all copies from your computer systems; (2) You should not read copy or use the contents of the email nor disclose it or its existence to anyone else. The views expressed herein are those of the author(s) and should not be taken as those of London South Bank University, unless this is specifically stated. London South Bank University is a company limited by guarantee registered in England and Wales. The following details apply to London South Bank University: Company number - 00986761; Registered office and trading address - 103 Borough Road London SE1 0AA; VAT number - 778 1116 17 Email address - [hidden email] _______________________________________________
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[hidden email] with unsubscribe as the subject
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