That would be rather hard to do. You might as well install Michael Hanke's
debian/ubuntu packages:
http://apsy.gse.uni-magdeburg.de/main/index.psp?sec=1&page=hanke/fsl&lang=en
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Hege Erdal
Sent: Friday, June 20, 2008 7:40 AM
To: [log in to unmask]
Subject: Re: [FSL] Problems with mfast
I have now tried to use a mask from one of the images to distract the brain
of the other image, but it still gives me that error-message. What does the
error-message mean? Do anybody know?
And how do I install FAST4 on a Ubuntu-machine without installing all of
fsl?
Hege
On Thu, 19 Jun 2008 08:40:10 +1000, Steve Smith <[log in to unmask]>
wrote:
>Hi,
>
>I'm not sure - maybe you don't have good correspondence between the
>masking of the two pre-aligned images. I would recommend trying FAST4
>though as we are moving over to that in general.
>
>Cheers.
>
>
>On 18 Jun 2008, at 18:59, Hege Erdal wrote:
>
>> Hi,
>> I'm new with fsl, and have just installed fsl on my Ubuntu.
>> I'm trying to use mfast, have used Bet to extract out non-tissue,
>> but in a
>> most cases, I get the error-message. I'm using mfast on a t1 and a
>> t2 picture.
>>
>> /usr/share/fsl/bin/mfast -s 2 -c 3 -od
>> /media/LaCie/NIFTI-format/Dykkar_Bo_nei/Dykkar_Bo_brain
>> /media/LaCie/NIFTI-format/Dykkar_Bo_nei/Dykkar_Bo_brain
>> /media/LaCie/NIFTI-format/Dykkar_Bo_nei/Dykkar_Bo2_brain.nii.gz
>> No convergence in 30 SVDCMP iterations
>>
>> MFAST - Multispectral FAST Version 3.53
>>
>> Channel 0: /tmp/fsl_ASbhq4_Dykkar_Bo
>> Channel 1: /tmp/fsl_ASbhq4_Dykkar_Bo2
>> Imagesize : 256 x 256 x 19
>> Pixelsize : 0.898438 x 0.898438 x 6.65
>>
>> Slice is too thick, 2D segmentation will be performed!
>> initial segmentation by KMeans....
>> 4 main iterations ...
>>
>> Matrix Inverse: Not invertable!
>>
>> Finished
>>
>> In the rest of the cases I get
>>
>> /usr/share/fsl/bin/mfast -s 2 -c 3 -od
>> /media/LaCie/NIFTI-format/Dykkar_Df/Dykkar_Df_brain
>> /media/LaCie/NIFTI-format/Dykkar_Df/Dykkar_Df_brain
>> /media/LaCie/NIFTI-format/Dykkar_Df/Dykkar_Df2_brain.nii.gz
>> 313577.5 681402.9 485882.3 1480862.8
>>
>>
>> MFAST - Multispectral FAST Version 3.53
>>
>> Channel 0: /tmp/fsl_5nFAIf_Dykkar_Df_brain
>> Channel 1: /tmp/fsl_5nFAIf_Dykkar_Df2_brain
>> Imagesize : 256 x 256 x 19
>> Pixelsize : 0.898438 x 0.898438 x 6.65
>>
>> Slice is too thick, 2D segmentation will be performed!
>> initial segmentation by KMeans....
>> 4 main iterations ...
>>
>> Segmentation done successfully!
>>
>> Calculation time 51 seconds!
>>
>> Write segmentation image /tmp/fsl_5nFAIf.fastout/QQQQQ_seg.hdr
>> Successfully!
>>
>> Class: tissue 0 tissue 1 tissue 2
total
>> Volume:
>> Finished
>>
>>
>> Do you have any idea what I can do to fix this? I ran the fsl
>> evaluation,
>> and it said that the tests passed. I think maybe there might be
>> something
>> wrong with the brain extraction, cause when I tried to use an another
>> computer with mfast, it all worked out fine.
>>
>> Thanks,
>> Hege
>>
>
>
>---------------------------------------------------------------------------
>Stephen M. Smith, Professor of Biomedical Engineering
>Associate Director, Oxford University FMRIB Centre
>
>FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>+44 (0) 1865 222726 (fax 222717)
>[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>---------------------------------------------------------------------------
>=========================================================================
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