Hi both -
Matt is completely right about this - upsampling the data causes all
sorts of problems (and breaks some of the assumptions of the
tractorgaphy algorithm). It is NOT advised either for tractography or
TBSS.
There is one other way that you could have got these numbers if your
data is not upsampled. That is if your nodif_brain_mask is in a high
resolution space, but your data is not.
if you do fslinfo on your data itself, and the numbers are the same
as this then there is nothing we can do I'm afraid.
If the fslinfo numbers for data are smaller, but the numbers for
nodif_brain_mask are the same as this, then you can replace
nodif_brain_mask by the correct mask in diffusion space and re-run
bedpostX (which will take MUCH less time than before!)
Cheers
T
On 12 Mar 2008, at 02:54, Matt Glasser wrote:
> This is a great example of why you don't want to interpolate your
> data (on
> the scanner or otherwise) for tractography. Your data is stored in
> float 32
> format, which means 32 bits per pixel (or 4 bytes). To find at
> least how
> much RAM you would need to run probtrackx multiply by the
> dimensions of the
> image: 4*256*240*140*50=1.65GB. Now, there are six "merged" files
> you have
> to load for probtrackx, so the total RAM that you have to have just to
> complete the loading process is 9.89GB (if you don't include any
> other use
> for the probtrackx exe itself, or the operating system). If your
> data were
> not interpolated, the footprint would be 1.24GB. I believe it is
> possible
> to "deinterpolate" data, but I don't have experience with that.
> Although
> files are smaller on your disk because of compression, they must be
> loaded
> into RAM uncompressed.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf
> Of James Sheehan
> Sent: Tuesday, March 11, 2008 10:19 PM
> To: [log in to unmask]
> Subject: Re: [FSL] ProbtrackX Memory Allocation
>
> Here is the result for th1samples and th2samples.
> Thank you!
> # fslinfo /root/Desktop/control/subject100.bedpostX/
> merged_th1samples.nii.gz
>
> data_type FLOAT32
> dim1 256
> dim2 240
> dim3 144
> dim4 50
> datatype 16
> pixdim1 1.0000000000
> pixdim2 1.0000000000
> pixdim3 1.0000000000
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1+
> #
> # fslinfo /root/Desktop/control/subject100.bedpostX/
> merged_th2samples.nii.gz
>
> data_type FLOAT32
> dim1 256
> dim2 240
> dim3 144
> dim4 50
> datatype 16
> pixdim1 1.0000000000
> pixdim2 1.0000000000
> pixdim3 1.0000000000
> pixdim4 1.0000000000
> cal_max 0.0000
> cal_min 0.0000
> file_type NIFTI-1+
> #
>
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