[Mrtrix-discussion] fibre tracts format

[Philip G Batchelor]

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 This message has been archived.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
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