Hi Michael,
How I can install the new version of the Debian package? It is necesary to install again the fsl, or only replace some functions?
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: FSL - FMRIB's Software Library [[log in to unmask]] En nombre de Michael Hanke [[log in to unmask]]
Enviado el: jueves, 02 de octubre de 2008 13:25
Para: [log in to unmask]
Asunto: Re: [FSL] Problems with FSL-VBM in a Debian Linux machine?
Hi,
this is most likely caused by a bug in Debian package, that was fixed
earlier this week. Are you running the latest package version?
Cheers,
Michael
On Thu, Oct 02, 2008 at 12:47:14PM +0200, Erick Canales Rodriguez (Benito Menni CASM) wrote:
> Hi FSL programmers,
>
> I have some questions about FSL-VBM. I am trying to run my analysis following the instructions from the FSL-VBM home page but there are some errors in my results. In particular, in the two first steps of the algorithm (fslvbm_1_bet and/or fslvbm_2_template) the template image is not created.
>
> I detected the cause of my errors...the algorithm requires to open some images that are not created
>
> Due to I obtain the same type of error for all of my images, I will explain in detail the analysis corresponding to only one image...for example, "CONT20_3d.nii.gz"
>
>
> The first step in the FSL-VBM analysis is
>
> fslvbm_1_bet -b, or alternatively, fslvbm_1_bet -N
>
> When I run the above function I obtain the following:
>
> 1) A new folder "struc" with a copy of the original image, with the new name "CONT20_3d.nii.gz_struc.nii.gz".
>
> 2) The brain extracted image (bet), which is created under the name "CONT20_3d.nii.gz_struc.nii.gz_brain.nii.gz"
>
>
> The second step in the FSL-VBM analysis is
>
> fslvbm_2_template –a, or alternatively, fslvbm_2_template -n
>
> This program generates a script "fslvbm2a" to perform, in a first step, the segmentation of the image...with "fast". Due to my errors are located inside this process, I revised the fslvbm2a script created in my analysis, which generates the following instructions:
>
> /usr/share/fsl/bin/fast -R 0.3 -H 0.1 CONT20_3d_ojo.nii.gz_struc.nii.gz_brain;
> /usr/share/fsl/bin/immv CONT20_3d_ojo.nii.gz_struc.nii.gz_brain_pve_1 CONT20_3d_ojo.nii.gz_struc.nii.gz_GM
>
> /usr/share/fsl/bin/fast -R 0.3 -H 0.1 CONT20_3d_ojo.nii.gz_struc.nii.gz_brain.nii.gz_brain;
> /usr/share/fsl/bin/immv CONT20_3d_ojo.nii.gz_struc.nii.gz_brain.nii.gz_brain_pve_1 CONT20_3d_ojo.nii.gz_struc.nii.gz_brain.nii.gz_GM
>
> The first part of the above instructions performs in a correct way; the "fast" function is capable to run the segmentation of the image "CONT20_3d_ojo.nii.gz_struc.nii.gz_brain". However, the second part of the codes does not work because the image
> "CONT20_3d_ojo.nii.gz_struc.nii.gz_brain.nii.gz_brain" does not exist.
>
> To see the cause of this problem I revised the "fslvbm_2_template" program, specially the sentences that generate the names of the images that will be computed with fast,
>
> This procedure is achieved by means of the following instructions inside "fslvbm_2_template":
>
> ### segmentation
> /bin/rm -f fslvbm2a
> for g in `$FSLDIR/bin/imglob *_struc.*` ; do
> echo $g
> echo "$FSLDIR/bin/fast -R 0.3 -H 0.1 ${g}_brain ; \
> $FSLDIR/bin/immv ${g}_brain_pve_1 ${g}_GM" >> fslvbm2a
> done
>
> As I understand this code makes the "fast" analysis with all the images with the string "_struct". The problem with this fact is that the images
> "CONT20_3d.nii.gz_struc.nii.gz" and "CONT20_3d.nii.gz_struc.nii.gz_brain.nii.gz" will be selected by "imglob", and therefore, the "fslvbm2a" script will be created to perform the segmentation on the images "CONT20_3d.nii.gz_struc.nii.gz_brain.nii.gz" and "CONT20_3d_ojo.nii.gz_struc.nii.gz_brain.nii.gz_brain". The problem is that the second image does not exist, as a consequence, the soft reports errors...
>
> In my opinion only the image "CONT20_3d.nii.gz_struc.nii.gz_brain.nii.gz" must be computed in the above analysis. This is correct?
> This can be done by a simple modification of the above instructions, for example:
>
> ### segmentation
> /bin/rm -f fslvbm2a
> for g in `$FSLDIR/bin/imglob *brain.*` ; do
> echo $g
> echo "$FSLDIR/bin/fast -R 0.3 -H 0.1 ${g} ; \
> $FSLDIR/bin/immv ${g}_brain_pve_1 ${g}_GM" >> fslvbm2a
> done
>
> Any opinion about this?
> There are similar reported problems in the fsl soft (4.1) compiled under a Debian (64bit) Linux machine?
>
> All the above explanation was developed with a single image, when more images are included the same error is reported for each of them.
>
> Many thanks
>
> 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
>
> ________________________________
> Este mensaje se dirige exclusivamente a su destinatario y puede contener información privilegiada o confidencial. Si no es vd. el destinatario indicado, queda notificado de que la utilización, divulgación y/o copia sin autorización está prohibida en virtud de la legislación vigente. Si ha recibido este mensaje por error, le rogamos que nos lo comunique inmediatamente por esta misma vía y proceda a su destrucción.
>
> Aquest missatge va dirigit exclusivament al seu destinatari i pot contenir informació privilegiada o confidencial. Si vosté no és el destinatari indicat, li notifiquem que la utilització, divulgació i/o còpia sense autorització està prohibida en virtud de la legislació vigent. Si ha rebut aquest missatge per error, li preguem que ens ho comuniqui el més aviat possible.
--
GPG key: 1024D/3144BE0F Michael Hanke
http://apsy.gse.uni-magdeburg.de/hanke
ICQ: 48230050
|