Wei,

This is due to a bug in ShapeWorksGroom.  I've fixed some bugs with the crop tool recently.  Are you using the most recent git changes?  If so, is there any way you can point us to your data?

Thanks,

Alan

On Tue, Jun 24, 2014 at 3:50 PM, Wei Liu <weiliu620@gmail.com> wrote:

Dear Shapeworks users, 

I started to run ShapeWorksGroom on some real data. I have 5 binary segmentation images, each with size 512x512xZ, where Z varies from 200 to 350. I got "failed to allocate memory" errors that I attached at the end of this email. It seems the error happened when auto_cropping the second volume. I tried both the ShapeWorksGroom binary built with "OMP" on and off, and get the same error. When observing the memory usage while the code is running, I didn't see a point where memory is used up. My input volumes are all in char,  in case the internal data structure depends on the input data. 

Did I miss anything? I appreciate your help. 

 Here is the output with the errors:

===============================

weiliu@lando:/scratch/experiments/shapeworks> /scratch/packages/shapeworks.git/build/ShapeWorksGroom/ShapeWorksGroom lung.preprocess1.xml isolate hole_fill center auto_crop

isolate

PE105.nii.gz

PE900.nii.gz

PE908.nii.gz

PE916.nii.gz

PE919.nii.gz

hole_fill

PE105DT.nii.gz

PE900DT.nii.gz

PE908DT.nii.gz

PE916DT.nii.gz

PE919DT.nii.gz

center

PE105DT.nii.gz

origin = [-200.9, -156.5, -228.75]

new origin = [-183, -183, -110.312]

PE900DT.nii.gz

origin = [-172.2, -201.4, -285]

new origin = [-173.5, -173.5, -156.25]

PE908DT.nii.gz

origin = [-173.6, -200, -305]

new origin = [-200, -200, -153.125]

PE916DT.nii.gz

origin = [-126, -119.8, -262.25]

new origin = [-140.5, -140.5, -130.625]

PE919DT.nii.gz

origin = [-198.8, -206.5, -298.5]

new origin = [-220, -220, -160.625]

 --------------- 

1 0 0 -22.3928

0 1 0 37.8377

0 0 1 -123.706

0 0 0 1

1 0 0 66.0496

0 1 0 -35.3846

0 0 1 -132.132

0 0 0 1

1 0 0 18.8881

0 1 0 1.02713

0 0 1 -151.533

0 0 0 1

1 0 0 5.90316

0 1 0 13.3788

0 0 1 -136.408

0 0 0 1

1 0 0 18.3276

0 1 0 30.1235

0 0 1 -132.154

0 0 0 1

auto_crop

WARNING!  Assumes objects are centered in each image!

reading PE105DT.nii.gz

ImageRegion (0x7fffe48f4210)

  Dimension: 3

  Index: [75, 132, 8]

  Size: [366, 240, 344]

reading PE900DT.nii.gz

ImageRegion (0x7fffe48f4210)

  Dimension: 3

  Index: [145, 96, 34]

  Size: [197, 296, 187]

reading PE908DT.nii.gz

ImageRegion (0x7fffe48f4210)

  Dimension: 3

  Index: [84, 110, 33]

  Size: [380, 270, 197]

reading PE916DT.nii.gz

ImageRegion (0x7fffe48f4210)

  Dimension: 3

  Index: [27, 116, 4]

  Size: [457, 276, 204]

reading PE919DT.nii.gz

ImageRegion (0x7fffe48f4210)

  Dimension: 3

  Index: [100, 137, 12]

  Size: [299, 207, 239]

crop size is [468, 330, 354]

cropping PE105DT.nii.gz

thisidx = [0, 0, 0]

thissz = [512, 512, 353]

lb = 18446744072788810304

lb = 65534

lb = 2

WARNING: In /scratch/packages/InsightToolkit-3.20.1/Code/Common/itkImageBase.txx, line 289

Image (0x11832a0): Not executing UpdateOutputData due to zero pixel condition RequestedRegion:ImageRegion (0x1183480)

  Dimension: 3

  Index: [0, 0, 0]

  Size: [0, 512, 353]

 BufferedRegion: ImageRegion (0x11834b8)

  Dimension: 3

  Index: [0, 0, 0]

  Size: [512, 512, 353]

itk::ExceptionObject (0x7f2928000c90)

Location: "TElement* itk::ImportImageContainer<TElementIdentifier, TElement>::AllocateElements(itk::ImportImageContainer<TElementIdentifier, TElement>::ElementIdentifier) const [with TElementIdentifier = long unsigned int; TElement = unsigned char; itk::ImportImageContainer<TElementIdentifier, TElement>::ElementIdentifier = long unsigned int]" 

File: /scratch/packages/InsightToolkit-3.20.1/Code/Common/itkImportImageContainer.txx

Line: 188

Description: Failed to allocate memory for image.

==========================================

And here is the xml file I used:

==============================

<?xml version="1.0" ?>

<!-- Preprocessing parameters 1 for Torus example -->

<!-- Value of background pixels in the image -->

<background> 0.0 </background>

 <!-- Value of foreground pixels in the image -->

<foreground> 1.0 </foreground> 

<!-- Number of background pixels to pad the edges of the cropped volume -->

<pad> 10 </pad> 

<!-- filename to store transforms generated during preprocessing -->        

<transform_file> lung.translations </transform_file> 

                              

<!-- Output progress information -->

<verbose> 1 </verbose>      

<!-- Set of input files to process -->

<inputs>          

PE105.nii.gz

PE900.nii.gz

PE908.nii.gz

PE916.nii.gz

PE919.nii.gz

</inputs>

<!-- Output filenames to use -->

<outputs>           

PE105DT.nii.gz

PE900DT.nii.gz

PE908DT.nii.gz

PE916DT.nii.gz

PE919DT.nii.gz

</outputs>

===============================