[Camino-users] Re:Camino-users Digest, Vol 22, Issue 1

Tue Apr 2 19:09:19 PDT 2013

Hello, professor,I am very grateful for your kind help. Since I was using Camino to do multi fiber tractography, and tutorial I refered to was on this website http://cmic.cs.ucl.ac.uk/camino/index.php?n=Tutorials.MultiFibreTractography .I found that the codes  there were still using oogl and .img format, did I use your old tutorial website on this subject?

Thanks again for your help!

At 2013-04-03 03:00:09,camino-users-request at www.nitrc.org wrote:
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>Today's Topics:
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>   1. ask for help on track (=?GBK?B?wt7otL2/?=)
>   2. Re: ask for help on track (Philip A Cook)
>   3. Expanded NIfTI support since r1175 (Philip A Cook)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 2 Apr 2013 14:45:09 +0800 (CST)
>From: =?GBK?B?wt7otL2/?= <lujiaoluo1990 at 126.com>
>Subject: [Camino-users] ask for help on track
>To: camino-users at www.nitrc.org
>Message-ID:
>	<7fd45c62.24d4b.13dc97dfc90.Coremail.lujiaoluo1990 at 126.com>
>Content-Type: text/plain; charset="gbk"
>
>Hello, I was using this code below to do fiber tracking:
> track -inputmodel dt -seedfile lADT_FA.hdr -outputroot A_DT -outputtracts oogl < A_DT.Bdouble
>but it gave a warning below:
>" tools.CL_Initializer checkParsing
>WARNING: WARNING: couldn't parse arg 6: '-outputtracts'
>tools.CL_Initializer checkParsing
>WARNING: WARNING: couldn't parse arg 7: 'oogl'  "
>What can I do to sovle this problem?
>Thanks in advance!
>
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>Message: 2
>Date: Tue, 2 Apr 2013 11:43:46 -0400
>From: Philip A Cook <cookpa at mail.med.upenn.edu>
>Subject: Re: [Camino-users] ask for help on track
>To: ??? <lujiaoluo1990 at 126.com>
>Cc: camino-users at www.nitrc.org
>Message-ID: <5992233F-F096-40FB-B74A-9C93FA3CAF97 at mail.med.upenn.edu>
>Content-Type: text/plain; charset=utf-8
>
>Hi,
>
>The OOGL output was removed some time ago, we use VTK now. We are moving away from Analyze also, in favor of NIFTI, but Analyze still works.
>
>    track -inputmodel dt -seedfile lADT_FA.hdr -outputroot A_DT < A_DT.Bdouble | vtkstreamlines > tracts.vtk
>
>Older versions of Camino (before r1020) support OOGL. 
>
>
>On Apr 2, 2013, at 2:45 AM, ç½—ç’å¨‡ wrote:
>
>> Hello, I was using this code below to do fiber tracking:
>>  track -inputmodel dt -seedfile lADT_FA.hdr -outputroot A_DT -outputtracts oogl < A_DT.Bdouble
>> but it gave a warning below:
>> " tools.CL_Initializer checkParsing
>> WARNING: WARNING: couldn't parse arg 6: '-outputtracts'
>> tools.CL_Initializer checkParsing
>> WARNING: WARNING: couldn't parse arg 7: 'oogl'  "
>> What can I do to sovle this problem? 
>> Thanks in advance!
>> 
>> 
>> 
>> _______________________________________________
>> Camino-users mailing list
>> Camino-users at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/camino-users
>
>
>
>------------------------------
>
>Message: 3
>Date: Tue, 2 Apr 2013 11:55:06 -0400
>From: Philip A Cook <cookpa at mail.med.upenn.edu>
>Subject: [Camino-users] Expanded NIfTI support since r1175
>To: camino-users at www.nitrc.org
>Message-ID: <064DC9C4-7A21-433F-B183-E7568BDC72E4 at mail.med.upenn.edu>
>Content-Type: text/plain; charset=us-ascii
>
>Hi,
>
>Most apps should now support output to an nii file, and should accept nii input. I have tested some common use cases but it is still fairly new code so please let me know if there are any problems. Backwards compatibility is preserved for people handling raw data.
>
>Example:
>
>  track -inputfile dwi4D.nii.gz
>
>  dtfit dwi4D.nii.gz schemefile | fa -header dwi4D.nii.gz -outputfile fa.nii.gz
>
>Using large nii input files will require more memory as the entire file is read in and re-ordered on the fly, but it can be more convenient.
>
>
>Vector data can be written to a 4D NIFTI file. One possibly confusing thing, if you do
>
>  dtfit dwi4D.nii.gz schemefile -outputfile dt.nii.gz
>
>You will get the 8-component Camino output in nii vector form, not a DT image. To get a DT image, do
>
>    dtfit dwi4D.nii.gz schemefile | dt2nii -header dwi4D.nii.gz -outputroot dt_
>
>To convert vector data to 3D nii images, call voxel2image.
>
>
>Vector data can also be read, eg
>
>  modelfit -model pospos ... -outputfile twoDT.nii.gz
>
>  dteig -inputfile twoDT.nii.gz -inputmodel multitensor > eig.Bdouble
>
>
>
>There is one special case, allowing input of tensors when DT input is expected. 
>
>Example:
>
>  track -inputmodel dt -inputfile dtitk_dt.nii.gz ...
>
>will read a NIFTI_SYMMATRIX correctly, though obviously there's no exit code etc. This is therefore equivalent to
>
>  nii2dt -inputfile dtitk_dt.nii.gz |  track -inputmodel dt ...
>
>Meanwhile, 
>
>  dtfit data.nii.gz scheme -outputfile caminodt.nii.gz
>
>  dteig -inputfile caminodt.nii.gz -outputfile eig.nii.gz 
>
>will read the standard Camino output (8 components) and produce a NIFTI output.
>
>image2voxel will convert any of these files back to voxel order if needed. 
>
>
>
>
>
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>End of Camino-users Digest, Vol 22, Issue 1
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