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

[maedeh khalilian]

Dear Michael and Philip,
You were right and I just did it successfully.
Thank u very much.
Cheers,
Maedeh,


On Mon, Dec 3, 2018 at 7:43 PM Cook, Philip <cookpa at pennmedicine.upenn.edu>
wrote:

> 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>
> 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>
> 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
>>
>> _______________________________________________
>> Camino-users mailing list
>> Camino-users at www.nitrc.org
>> https://www.nitrc.org/mailman/listinfo/camino-users
>>
> _______________________________________________
> Camino-users mailing list
> Camino-users at www.nitrc.org
> https://www.nitrc.org/mailman/listinfo/camino-users
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.nitrc.org/pipermail/camino-users/attachments/20181204/c5ecd8b1/attachment.html>