[Mrtrix-discussion] Inputing own SH coefficents .img file

Wed Sep 11 09:57:50 PDT 2013

Oh thank you that's very useful information, and I was able to solve the
problem of format size.  However, there may be a bug with write_mrtrix.m.
 I simply ran im = read_mrtrix(filename) and then
write_mrtrix(im,new_filename) and there is an error:

Error using fprintf
Function is not defined for 'cell' inputs.

Error in write_mrtrix (line 78)
  fprintf (fid, '\ncomments: %s', image.comments)

Thanks

Evan

On Wed, Sep 11, 2013 at 11:14 AM, Donald Tournier
<d.tournier at brain.org.au>wrote:

> Hi Evan,
>
> I just forgot to mention one more thing: the latest release of MRtrix
> contains Matlab functions to read and write image files in .mif format, in
> the Matlab folder. Probably better than trying to hack an existing Analyze
> image...
>
> Cheers,
> Donald.
> On 11 Sep 2013 20:58, "Donald Tournier" <d.tournier at brain.org.au> wrote:
>
>> Hi Evan,
>>
>> Looks like the file you are generating in Matlab is too small to contain
>> all the data. As you've already noticed, the original size of the dataset
>> is close to 48MB, whereas your file is only about 3MB - I'm guessing it's
>> only one volume out of the 15 required for a lmax 4 file. Not sure why
>> MRtrix didn't catch and report the discrepancy rather than crash, I thought
>> I'd put in checks for that... In any case, your data file is much smaller
>> than expected based on the image header, and this will mean that any
>> attempt to read data past the end of the file will cause an invalid memory
>> access.
>>
>> Hope that helps.
>>
>> Cheers,
>> Donald.
>>  On 11 Sep 2013 06:00, "Evan Schwab" <eschwab3 at jhu.edu> wrote:
>>
>>> Hi,
>>>
>>> Thank you very much in advance.  I am trying to visualize my own ODFs
>>> with my own calculated coefficients for the SH basis.  I create an analyze
>>> file and try to mrconvert to a .mif file but I get a segmentation fault.
>>> Can you please help me to understand what I'm doing wrong? My debugging
>>> process and output is outlined below.
>>>
>>> Thanks so much,
>>>
>>> Evan
>>>
>>>
>>> To debug I did the following:
>>>
>>> 1) I first generate a CSD4.mif file properly by csdeconv.
>>> 2) I mrconvert the CSD4.mif to CSD4.img
>>> 3) I read the analyze file into matlab and replace the .img with my own
>>> 4D coefficient matrix. For debugging purposes I use here a matrix of all
>>> zeros.
>>> 4) Then I write this new matrix as a analyze file with the same header
>>> information as before.
>>> 5) I mrconvert my .img file to a new .mif file (using the -debug flag)
>>>
>>> I get the following output:
>>>
>>> $ mrconvert -info -debug CSD4_clsArray.img CSD4_clsArray.mif
>>> mrconvert [DEBUG]: reading key/value file "/etc/mrtrix.conf"...
>>> mrconvert [INFO]: opening image "CSD4_clsArray.img"...
>>> mrconvert [DEBUG]: preparing file "./CSD4_clsArray.hdr"
>>> mrconvert [DEBUG]: file "./CSD4_clsArray.hdr" mapped at 0x7feb2e267000,
>>> size 348 (read-only)
>>> mrconvert [INFO]: assuming Analyse images are encoded left to right
>>> mrconvert [DEBUG]: preparing file "./CSD4_clsArray.img"
>>> mrconvert [DEBUG]: unmapping file "./CSD4_clsArray.hdr"
>>> mrconvert [DEBUG]: setting up image "CSD4_clsArray.img"...
>>> mrconvert [DEBUG]: sanitising transformation matrix...
>>> mrconvert [DEBUG]: setting up data increments for "CSD4_clsArray.img"...
>>> mrconvert [DEBUG]: data increments initialised with start = 0, stride =
>>> [ 1 112 12544 815360 ]
>>> mrconvert [DEBUG]: mapping image "CSD4_clsArray.img"...
>>> mrconvert [DEBUG]: file "./CSD4_clsArray.img" mapped at 0x7feb2b206000,
>>> size 3261440 (read-only)
>>> mrconvert [DEBUG]: data mapper for image "CSD4_clsArray.img" mapped with
>>> segment size = 12230400 (optimised)
>>> mrconvert [INFO]: creating image "CSD4_clsArray.mif"...
>>> mrconvert [DEBUG]: preparing file "./CSD4_clsArray.mif"
>>> mrconvert [DEBUG]: setting up image "./CSD4_clsArray.mif"...
>>> mrconvert [DEBUG]: sanitising transformation matrix...
>>> mrconvert [DEBUG]: setting up data increments for
>>> "./CSD4_clsArray.mif"...
>>> mrconvert [DEBUG]: data increments initialised with start = 0, stride =
>>> [ 1 112 12544 815360 ]
>>> mrconvert [DEBUG]: mapping image "./CSD4_clsArray.mif"...
>>> mrconvert [DEBUG]: file "./CSD4_clsArray.mif" mapped at 0x7feb2835e000,
>>> size 48921913 (read-write)
>>> mrconvert [DEBUG]: data mapper for image "./CSD4_clsArray.mif" mapped
>>> with segment size = 12230400 (optimised)
>>>
>>>
>>> As well I have the output when I mrconvert the original CSD4.img back to
>>> .mif and the only difference is the line I have labeled as (********)
>>> related to the size of the file.
>>>
>>> $ mrconvert -info -debug CSD4.img CSD42.mif
>>> mrconvert [DEBUG]: reading key/value file "/etc/mrtrix.conf"...
>>> mrconvert [INFO]: opening image "CSD4.img"...
>>> mrconvert [DEBUG]: preparing file "./CSD4.hdr"
>>> mrconvert [DEBUG]: file "./CSD4.hdr" mapped at 0x7f5bcdc81000, size 348
>>> (read-only)
>>> mrconvert [INFO]: assuming Analyse images are encoded left to right
>>> mrconvert [DEBUG]: preparing file "./CSD4.img"
>>> mrconvert [DEBUG]: unmapping file "./CSD4.hdr"
>>> mrconvert [DEBUG]: setting up image "CSD4.img"...
>>> mrconvert [DEBUG]: sanitising transformation matrix...
>>> mrconvert [DEBUG]: setting up data increments for "CSD4.img"...
>>> mrconvert [DEBUG]: data increments initialised with start = 0, stride =
>>> [ 1 112 12544 815360 ]
>>> mrconvert [DEBUG]: mapping image "CSD4.img"...
>>> (********) mrconvert [DEBUG]: file "./CSD4.img" mapped at
>>> 0x7f5bc8095000, size 48921600 (read-only)
>>> mrconvert [DEBUG]: data mapper for image "CSD4.img" mapped with segment
>>> size = 12230400 (optimised)
>>> mrconvert [INFO]: creating image "CSD42.mif"...
>>> mrconvert [DEBUG]: preparing file "./CSD42.mif"
>>> mrconvert [DEBUG]: setting up image "./CSD42.mif"...
>>> mrconvert [DEBUG]: sanitising transformation matrix...
>>> mrconvert [DEBUG]: setting up data increments for "./CSD42.mif"...
>>> mrconvert [DEBUG]: data increments initialised with start = 0, stride =
>>> [ 1 112 12544 815360 ]
>>> mrconvert [DEBUG]: mapping image "./CSD42.mif"...
>>> mrconvert [DEBUG]: file "./CSD42.mif" mapped at 0x7f5bc51ed000, size
>>> 48921913 (read-write)
>>> mrconvert [DEBUG]: data mapper for image "./CSD42.mif" mapped with
>>> segment size = 12230400 (optimised)
>>> mrconvert: copying data... 100%
>>> mrconvert [INFO]: closing image "CSD4.img"...
>>> mrconvert [DEBUG]: unmapping file "./CSD4.img"
>>> mrconvert [INFO]: closing image "./CSD42.mif"...
>>> mrconvert [DEBUG]: unmapping file "./CSD42.mif"
>>>
>>>
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