Hi Erick,
this FAST problem is apparently well known and somebody is dealing with it right now. Keep in touch!
Gwenaelle
--- En date de : Mar 9.9.08, Erick Canales Rodriguez (Benito Menni CASM) <[log in to unmask]> a écrit :
> De: Erick Canales Rodriguez (Benito Menni CASM) <[log in to unmask]>
> Objet: Re: [FSL] FSL-VBM (FAST: Out of memory!)
> À: [log in to unmask]
> Date: Mardi 9 Septembre 2008, 9h29
> 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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