Hi,
what do you get if you type
free -m
in the virtual machine?
> Hi Matthew, Attila, and Gwenaelle
>
> Mi VMware player was configured with 6 GB of RAM memory and my host
> machine have 16 GB of RAM. However, it is posible that my guest
> machine (CentOS-32) only uses 1GB by default due to it is a 32-bit
> system... I found the following posts about this problem...
>
> http://vmetc.com/2007/10/28/32-bit-linux-vmware-server-with-more-than-1-gb-of-ram/
>
> http://www.linux.com/feature/119287
>
> Is there any FSL installer over VMware with a 64-bit CentOS ? In the
> FSL download page only appears the 32-bit version, for Windows,
> which not uses the full capabilities of the computer...
>
> Thanks a lot!
>
> Best,
>
> Erick J. Canales-Rodríguez
>
> (+34) 93 652 99 99 ext. 255
>
> Unitat de Recerca, Benito Menni CASM (http://www.hospitalbenitomenni.org/Default.aspx
> )
> Sant Boi del Llobregat (Barcelona), Espanya/España/Spain
>
> Benito Menni Complex assistencial en Salut Mental
>
> De: FSL - FMRIB's Software Library [[log in to unmask]] En nombre de
> Matthew Webster [[log in to unmask]]
> Enviado el: martes, 09 de septiembre de 2008 17:31
> Para: [log in to unmask]
> Asunto: Re: [FSL] FSL-VBM (FAST: Out of memory!)
>
> Hi,
> How much RAM does your virtual machine have? If it's the default
> 1GB and your host machine has plenty of RAM then increasing the VM
> ram could solve your problem - 2GB should probably allow your job to
> complete.
>
> Many Regards
>
> Matthew
>
>> Hi Attila,
>>
>> The problem is with the segmentation process that
>> "fslvbm_2_template" makes implicitely.
>> This function generates a bash to run the "fast" function over all
>> the "FAi_brain" images, and some of them cannot be segmented into
>> probabilistic maps...
>>
>> In particular, I am trying to run a simple segmentation with FAST
>> over only one image (i.e., CONT20_3d_ojo_FAi_brain), with the
>> following instruction:
>>
>> [fsl@localhost FAi]$ /usr/local/fsl/bin/fast -e -ov
>> CONT20_3d_ojo_FAi_brain ;
>>
>> (where -e enable partial volume classification, and -ov allows
>> output partial volume images (one for each class))
>>
>> When I run the above instruction the following message appears:
>>
>> FAST - FMRIB's Automated Segmentation Tool Version 3.53
>> Image: /tmp/fsl_MF9iW5_CONT20_3d_ojo_FAi_brain
>> T1-weighted image
>> Imagesize : 510 x 510 x 178
>> Pixelsize : 0.4688 x 0.4688 x 1
>> Initial K-means segmentation...
>> 8 main iterations ...
>> Estimating PVE...
>> new: Out of Memory!
>>
>> As a result, the segmented images cannot be created. However, this
>> problem occurs only with some of my images, with others the
>> segmentation works accurately.
>> Any ideas about this "Out of Memory" report? It is a problem of my
>> linux virtual machine (VMware player software) or FSL?
>>
>> Thanks a lot,
>>
>> Best regards,
>>
>> Erick J. Canales-Rodríguez
>>
>> (+34) 93 652 99 99 ext. 255
>>
>> Unitat de Recerca, Benito Menni CASM (http://www.hospitalbenitomenni.org/Default.aspx
>> )
>> Sant Boi del Llobregat (Barcelona), Espanya/España/Spain
>>
>> Benito Menni Complex assistencial en Salut Mental
>>
>> De: [log in to unmask] [[log in to unmask]] En nombre de Attila
>> Krajcsi [[log in to unmask]]
>> Enviado el: lunes, 08 de septiembre de 2008 23:03
>> Para: Erick Canales Rodriguez (Benito Menni CASM)
>> Asunto: FSL VBM
>>
>> Hi Erick,
>>
>> Could you find a solution to your problem you've sent to the FSL
>> list?
>>
>> ...
>>
>> I'm not too familiar with FSL yet, but my present idea is that
>> originally I'm using files with .nii extension, and maybe some
>> routines suppose a .nii.gz format. Seems like you had problems with
>> names.
>>
>> And I realized that the VBM tutorial now does not run correctly in
>> 4.1 version (randomise -i GM_mod_merg_s3 -o grot -m GM_mask -d
>> design.mat -t design.con -n 100 -c 2 -V) if you miss the .nii
>> extension that was probably correct in former versions. But maybe
>> I'm on the wrong track.
>>
>> Best,
>> Attila
>>
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>
>
