[Mrtrix-discussion] fibre tracts format

[Donald Tournier]

OK, I'm really stumped... The only place in the code where that error
message could have come from is in accessing the image for an MRtrix format
(.mif) file. The "mrinfo" commands that you ran also will have run through
those sections of code, but neither of them crashed... The actual headers
for both images look fine to me. Guess we're going to have to dig deeper...

By the way, I doubt that the extra 34th volume is the issue, although you
might need to deal with that separately - more on that later.

For now, let's try this. Copy these commands into a terminal (and amend as
required), and then copy/paste the entire terminal session and post it back
here:

# build debug version of code:
$ cd <MRtrix source folder>
$ ./build clean
$ ./build -debug
$ export PATH=`pwd`/bin:$PATH
$ export LD_LIBRARY_PATH=`pwd`/lib

# check that you're running the freshly built version (build date should be
today):
$ mrinfo --version

# first cut:
$ cd <your data folder>
$ estimate_response dwi.mif sf.mif  response.txt -debug

# debugger output:
$ gdb --args dwi.mif sf.mif  response.txt -debug
(gdb) run
(gdb) bt full

If after all this, I still can't figure it out, you might want to send me
the data so I can have a look at it...


Back to the extra 34th dataset issue: it shouldn't affect the CSD and
tracking processes directly, but it will affect the DT calculations. That
will affect the estimate_response stage, since it uses the highest FA voxels
as 'single-fibre' voxels, and uses the primary eigenvector as the primary
orientation. So you'll need to take care of that manually. Here's how:

# extract the DW scheme from the DWI:
$ mrinfo dwi.mif -grad encoding.b

# remove the last volume from the DWI:
$ mrconvert dwi.mif -coord 3 0:32 dwi2.mif

# remove the last line from the encoding file:
$ head -n 33 encoding.b > encoding2.b

# use the amended DWI and encoding files whenever requried, e.g.:
$ dwi2tensor dwi2.mif -grad encoding2.b dti.mif


OK, that should do for now...
Cheers,

Donald.




On 5 June 2010 01:50, Philip G Batchelor <philip.batchelor at kcl.ac.uk> wrote:

>  Hi
>
> thanks, output is attached, I see it has recognised the data as being DTI
> which is good. On the other hand, it's a 32 directions scan with one b=0,
> and I see
> dim: 112,112,60*,34*
>
> could it be that it has fallen foul of the cheeky 34th dataset which
> Philips add, an isotropic DW image? caused issues with quite a few of our
> codes, ppl always forget about it.
>
> Ph
>
>
> On 04/06/10 05:54, Donald Tournier wrote:
>
> 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
>
>
>


-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078
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