Hi - we use several different hardware flavours of 64-bit linux
desktop / cluster nodes and have had pretty much NO problems
installing linux and getting FSL to work. If you'd like a list of the
exact linux flavours we used we can send this info.
Cheers.
On 10 Sep 2007, at 09:10, Wen, Wei wrote:
> Thanks Steve.
>
> You are right on getting a 64-bit machine. But to sort out hardware
> compatibility issue is a struggle! Anyway, will take your advice to
> get a
> new machine.
>
> Thanks a lot!
> WW
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> Of Steve Smith
> Sent: Monday, 10 September 2007 5:57 PM
> To: [log in to unmask]
> Subject: Re: [FSL] tbss_3
>
> Hi - yes and no:
>
> You should be able to make this work by only merging some of the
> images at a time (also you might change the merge command to use
> avwmerge++). But then you would need to run certain steps in parallel
> and some with the data fully combined - you'll have to play quite a
> bit with the tbss scripts to do this. At the end you will have to
> combine all the data to do the stats in randomise, and you are very
> likely to run into the same problem then.
>
> I would also suggest that you might cut down the field-of view once
> everything is sampled into standard space - but given the huge number
> of subjects that you have this probably won't cut things down enough.
>
> In short - if you're prepared to get stuck into amending all the TBSS
> scripts you might be able to make this work - but might get stuck at
> the end with the randomise call. (Note that the new version of
> randomise, which would be compatible with all your preprocessing
> using FSL 3.3, can be run to use a lot less RAM than the old version
> - but I bet it still will require too much for this number of
> subjects).
>
> In short - it will be much easier to just find a 64-bit machine -
> they're not expensive and increasingly neuroimaging analysis needs it!
>
> Cheers.
>
>
>
>
> On 10 Sep 2007, at 08:29, Wen, Wei wrote:
>
>> Hi Steve,
>>
>> Is there a workaround please?
>>
>>
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>> Behalf
>> Of Steve Smith
>> Sent: Monday, 10 September 2007 5:16 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] tbss_3
>>
>> Hi,
>>
>>
>> On 10 Sep 2007, at 04:24, Wen, Wei wrote:
>>
>>> Hi Steve and FSLers,
>>>
>>>
>>>
>>> When I was doing tbss_3, I had the following error messages (after
>>> individual normalization). Is there a solution or we have to do it
>>> with a 64-bit system due to the large file size it was trying to
>>> generate?
>>
>> That's right - that's the solution.
>>
>> Cheers.
>>
>>
>>
>>> (over 280 scans and each is about 14MB)? (I am using tbss v1.0 )
>>>
>>>
>>>
>>> Many thanks and regards,
>>>
>>>
>>> Wei Wen, Sydney Australia
>>>
>>>
>>>
>>>
>>>
>>> ====================================================================
>>> =
>>> =
>>> =====
>>>
>>> merging all upsampled FA images into single 4D image
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> ** ERROR: nifti_read_buffer: attempted to read into NULL buffer
>>>
>>> /usr/local/fsl/bin/tbss_3_postreg: line 82: 6884 Segmentation
>>> fault ${FSLDIR}/bin/avwmerge -t ../stats/all_FA `$FSLDIR/bin/
>>> imglob -oneperimage *_nonlinear_hr.*`
>>>
>>> ** ERROR: nifti_image_read(all_FA): can't open header file
>>>
>>> ** ERROR: nifti_image_open(all_FA): bad header info
>>>
>>> Error: failed to open file all_FA
>>>
>>> Error:: FslCloneHeader: Null pointer passed for FSLIO
>>>
>>> creating mean FA
>>>
>>> ** ERROR: nifti_image_read(all_FA): can't open header file
>>>
>>> ** ERROR: nifti_image_open(all_FA): bad header info
>>>
>>> Error: failed to open file all_FA
>>>
>>> Error:: FslGetIntensityScaling: Null pointer passed for FSLIO
>>>
>>> skeletonising mean FA
>>>
>>> ** ERROR: nifti_image_read(mean_FA): can't open header file
>>>
>>> ** ERROR: nifti_image_open(mean_FA): bad header info
>>>
>>> Error: failed to open file mean_FA
>>>
>>> ERROR: Could not open image mean_FA
>>>
>>> Image Exception : #22 :: Failed to read volume mean_FA
>>>
>>> terminate called after throwing an instance of
>>> 'RBD_COMMON::Exception'
>>>
>>> /usr/local/fsl/bin/tbss_3_postreg: line 90: 6904
>>> Aborted ${FSLDIR}/bin/tbss_skeleton -i mean_FA -o
>>> mean_FA_skeleton
>>>
>>> now view mean_FA_skeleton to check whether the default threshold of
>>> 2000 needs changing, when running:
>>>
>>> tbss_4_prestats [threshold]
>>>
>>> -
>>>
>>
>>
>> ---------------------------------------------------------------------
>> -
>> --
>> ---
>> 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
>> ---------------------------------------------------------------------
>> -
>> --
>> ---
>>
>>
>>
>> -
>
>
> ----------------------------------------------------------------------
> --
> ---
> 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
> ----------------------------------------------------------------------
> --
> ---
>
>
>
> -
------------------------------------------------------------------------
---
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
------------------------------------------------------------------------
---
