[Mrtrix-discussion] fibre tracts format

[Donald Tournier]

Hi Philip,

Sounds a bit odd. To narrow things down a bit, could you post the output of
the following:

$ mrinfo dwi.mif
$ mrinfo sf.mif
$ awk '{ if ($0=="END") exit 0; print $0 }' dwi.mif
$ awk '{ if ($0=="END") exit 0; print $0 }' sf.mif
$ ls -l dwi.mif sf.mif

That should give me a bit more info...
Cheers,

Donald.


On 3 June 2010 01:49, Philip G Batchelor <philip.batchelor at kcl.ac.uk> wrote:

>  On 12/03/10 00:38, Donald Tournier wrote:
>
> This message has been archived.  View the original item
> <https://kclev.kcl.ac.uk/EnterpriseVault/ViewMessage.asp?VaultId=1CFCE6957FBD5654F8CCD18F833B7A6301110000kcl-evsite01&SavesetId=730000000000000%7E201003120038120000%7E0%7EE7E2A350A97B45AD91183E4EEB3B887>
> Hi Philip, Sorry, there is currently no documentation on that file
> format... It is quite simple, though. It consists of a text header, followed
> by binary data. The first line of the text header
> Attachments:
>   read_mrtrix_tracks.m
> <https://kclev.kcl.ac.uk/EnterpriseVault/ViewMessage.asp?VaultId=1CFCE6957FBD5654F8CCD18F833B7A6301110000kcl-evsite01&SavesetId=730000000000000%7E201003120038120000%7E0%7EE7E2A350A97B45AD91183E4EEB3B887&AttachmentId=1> (2
> KB)
>
>
>
> Hi
>
> am trying to process some of the Philips DICOM we acquired, in order to
> perform CSD. At the estimate_response stage it crashes, something went wrong
> with 'axes specification' but nore sure what. Here is the sequence of
> operation I go though:
>
>     $ mrconvert -info DICOM/ ./mrtrix-data/dwi.mif
>     [...]
>
>     $ mrconvert dwi.mif -coord 3 0 - | threshold - - | median3D - - |
> median3D - mask.mif
>      [...]
>
>     $ dwi2tensor dwi.mif dti.mif
>     [...]
>
>     $ tensor2FA dti.mif - | mrmult - mask.mif fa.mif
>     $ erode mask.mif - | erode - - | mrmult fa.mif - - | threshold - -abs
> 0.6 sf.mif
>     $ estimate_response dwi.mif sf.mif  response.txt
>
>       estimate_response: incorrect number of axes in axes specification
> "-0,-1,+2,+3"
>       *** glibc detected *** estimate_response: free(): invalid next size
> (fast): 0x000000000194c420 ***
>       ======= Backtrace: =========
>      /lib/libc.so.6(+0x775b6)[0x7f4f4d5065b6]
>     /lib/libc.so.6(cfree+0x73)[0x7f4f4d50ce53]
>     etc...
>
> Am trying to diagnose if I'm doing some basic error, or if there's  a
> problem with the way the axes are read from the DICOMS?
> Any suggestion?
>
> Ph
>



-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://www.nitrc.org/pipermail/mrtrix-discussion/attachments/20100604/4fa80155/attachment.html