[Camino-users] camino with HCP data

Fri Dec 13 03:43:02 PST 2013

Hi,

Thank you for your answer.

>
>  We'll take a look into making the necessary adjustments to Camino to
> handle the spatially varying b-value; probably a bit fiddly, but doable.
>  In the meantime, I think you can get a reasonable feel for how well the
> different processing techniques will work by just ignoring the spatial
> variation - not a long term solution though.
>

That sounds good, I am looking forward to the update.

>
>  I see no reason why shredder won't work with longs.  Its three arguments
> are just in bytes, so can't you just use a <chunksize> of 8?
>

I am sorry I am traveling at the moment so I can't reproduce the error
remotely. However I remember that calling the shredder with long arguments
simply resulted in <null> output.

NB. I used an older version of <parallel processing
tutorial><http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Tutorials.ParallelPASTutorial>as
a basis for my scripting. A nice aspect about the tutorial is that the
data is split in several slices with the shredder function, which is
convenient for displaying the reconstruction. That way the <space>
(sometimes also the offset) argument  necessarily has to be >long<.
Naturally this could be overcome by shredding the diffusion data
differently. However 'cat'ing them back together would require some more
tweaking.

With kind regards,

 Emil

>
>  Danny
>
>
>
>
>  On 29 Nov 2013, at 13:58, E.H.J. Nijhuis <emil.nijhuis at gmail.com> wrote:
>
>   Dear Danny and Philip,
>
> thank you very much for your quick and very helpful answer.
>
>  I am aiming to produce streamlines which I can use for a whole brain
> connectivity analysis for the publicly available HCP data (multi shell data
> with b-values of about 0, 1000, 2000 and 3000). With the dataset it was
> possible to estimate FA values in camino but I ran into difficulties when
> processing the data with the PAS approach.
>
> The first thing which was problematic when processing a HCP dataset was
> that the shredder function is not able to accept longs (raw hcp.bfloats are
> rather big >4GB). There was no easy and clean fix to the issue because the
> function uses DataInputStream.read() which cannot accept longs either. I
> overcame the issue by downcasting longs to int somewhere posthoc in the
> source, but that is certainly not robust enough for an actual fix.
>
>  The error considering the lag of b=0 images was with the mesd function
> which I called with the following options:
>
> mesd -schemefile hcp.scheme -filter PAS 1.4 -fastmesd -mepointset 16
> -bgmask hcp.Bchar -maskdatatype ubyte < hcp_SliceX.Bfloat >
> hcp_SliceX.Bdouble
>
>  This resulted in the warning "WARNING: No b=0 data, cannot normalize",
> while the output was essentially blank. I guess if I set the lowest
> b-values to 0 it will work, but given your elaborate answer I now feel
> reluctant to process the data any further because of the caveats with the
> spatially varying b-value and gradient directions.
>
>  Which brings me to my next set of questions:
>
>  1. Are you planning to bring out an update which will be able to process
> the HCP dataset (or more generally datasets with spatially varying
> gradients)?
>  2. If the goal is to produce streamlines for a full brain connectivity
> analysis: what would be your preferred way of processing for a multi-shell
> dataset? (I know it is rather impossible to answer this question properly,
> but I would be very interested in your and others users opinion and advice).
>
>  Thank you a lot for your consideration and expertise.
>
>  With kind regards,
>
>  Emil
>
>
>
> On Mon, Nov 25, 2013 at 5:28 PM, Alexander, Daniel <d.alexander at ucl.ac.uk>wrote:
>
>> What are you trying to do?  Most model fitting routines should work fine
>> without a b=0, but I guess some of the other reconstruction algorithms may
>> demand a b=0 image.  Assuming the low b-value images in the HCP data are
>> b=0, ie set the entries in the schemefile to zero, I would expect to give
>> very similar results to accounting for the slightly non-zero b.
>>
>>  When you say "DSI acquisition", do you really mean DSI, ie a grid of
>> locations in q-space?  HCP use a three-shell HARDI protocol, which is quite
>> different.  Or do you have some special data?
>>
>>  I don't know if anyone has tried processing the standard HCP data using
>> Camino.  Most Camino algorithms should run fine on data acquired with their
>> protocol, although currently Camino doesn't account for the spatially
>> varying b-value and gradient directions in the HCP data.  I am not sure how
>> much of an issue that is in terms of results, but you should at least be
>> able to get an output to look at.
>>
>>  Danny
>>
>>  PS: Please write to camino-users at www.nitrc.org for Camino questions
>> rather than direct to me.  You will get faster and better answers!
>>
>>
>>   On 25 Nov 2013, at 10:06, "E.H.J. Nijhuis" <emil.nijhuis at gmail.com>
>>  wrote:
>>
>>    Dear Daniel,
>>
>>  I recently have attempted to process the diffusion dataset of the human
>> connectome project.
>>
>>  Unfortunately I noticed that camino was unable to process this dataset
>> due to the lag of actual b=0 values (see attached the sample fsl and
>> corresponding camino tables). The small b-value variations are due certain
>> hardware  aspects (see Sotiropoulos et al., Neuroimage 2013).
>>
>>  The lag of actual b0 values results in the following error messages
>> during reconstruction:
>> WARNING: No b=0 data, cannot normalize
>>
>>  Could you please advice me how to best handle the HCP data? Simply round
>> the 'b0'-values? Also, since it is an DSI aquisition protocol, would you
>> still recommend me to use camino?
>>
>>  Thank you a lot for your expertise and consideration.
>>
>>  Yours sincerely,
>>
>>  Emil
>>
>> --
>> ----------------------------------------------
>> Postdoctoral Researcher - MR Techniques in Brain Function
>> *Donders Institute: Centre for Cognitive Neuroimaging*
>>
>> tel  +31 (0)24 36 10885
>> fax +31 (0)24 36 10989
>> web http://www.ru.nl/donders/
>>
>> Postal address:  Trigon 204, P.O. Box 9101, 6500HB Nijmegen, The
>> Netherlands
>> Visiting address: Trigon, Kapittelweg 29, 6525EN Nijmegen, The
>> Netherlands
>>   <bvals><bvecs><hcp100408.scheme>
>>
>>
>>
>
>
> --
> ----------------------------------------------
> Postdoctoral Researcher - MR Techniques in Brain Function
> *Donders Institute: Centre for Cognitive Neuroimaging*
>
> tel  +31 (0)24 36 10885
> fax +31 (0)24 36 10989
> web http://www.ru.nl/donders/
>
> Postal address:  Trigon 204, P.O. Box 9101, 6500HB Nijmegen, The
> Netherlands
> Visiting address: Trigon, Kapittelweg 29, 6525EN Nijmegen, The
> Netherlands
>
>
>

-- 
----------------------------------------------
Postdoctoral Researcher - MR Techniques in Brain Function
*Donders Institute: Centre for Cognitive Neuroimaging*

tel  +31 (0)24 36 10885
fax +31 (0)24 36 10989
web http://www.ru.nl/donders/

Postal address:  Trigon 204, P.O. Box 9101, 6500HB Nijmegen, The Netherlands
Visiting address: Trigon, Kapittelweg 29, 6525EN Nijmegen, The Netherlands
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