[Camino-users] [External] Re: Problem Converting DWI Data

[Cook, Philip]

Thanks Michael.

 You also have the option of reading in the DWI data directly as NIFTI, eg

  wdtfit 4Ddwi_b1000.nii.gz dwi.scheme -outputfile dt.Bdouble

You'll still need to increase the available RAM to do this.

On Dec 3, 2018, at 7:36 AM, Michael Dayan <mdayan.research at gmail.com<mailto:mdayan.research at gmail.com>> wrote:

Hi Maedeh,

You are running out of memory. You have to increase it by changing the maximum value with the following command:

export CAMINO_HEAP_SIZE=2000

where 2000 = 2000 Mb and can be set to whatever maximum amount of RAM you want Camino to use (within the amount of RAM you have obviously).

You can do it as a one off by typing this command in your terminal, or set it permanently by writing it in your <HOME_DIR>/.bashrc file (for the changes to take effect you will need to refresh your current terminal with the new bash settings by typing source ~/.bashrc, or you can just start a new terminal).

Best,

Michael

On Sun, Dec 2, 2018 at 5:15 PM maedeh khalilian <maedeh.kh73 at gmail.com<mailto:maedeh.kh73 at gmail.com>> wrote:
Dear Camino experts,
I want to reconstruct my DWI image to  create dt.Bdouble in order to do a tractography.
But when I run the command below:
image2voxel -4dimage 4Ddwi_b1000.nii.gz -outputfile dwi.Bfloat
I see the error below and the created dt.Bdouble is empty !!
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
    at data.ScannerOrderDataSource.init(ScannerOrderDataSource.java:169)
    at data.ScannerOrderDataSource.<init>(ScannerOrderDataSource.java:134)
    at data.ScannerOrderScaledDataSource.<init>(ScannerOrderScaledDataSource.java:52)
    at imaging.Nifti1Dataset.getImageDataSource(Nifti1Dataset.java:2312)
    at apps.ImageToVoxel.execute(ImageToVoxel.java:104)
    at apps.EntryPoint.main(EntryPoint.java:293)

I dunno where the problem is from.
let me know if  my scheme file and DWI image is necessary for checking.
I would be grateful if u could help me.
Cheers
Maedeh

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