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
------------------------------------------------------------------------
---
-
