<div dir="ltr"><font color="#000000" face="arial, helvetica, sans-serif">Hi Philip,</font><div><font color="#000000" face="arial, helvetica, sans-serif"><br></font></div><div><font color="#000000" face="arial, helvetica, sans-serif">Thanks for your reply and it is really helpful.</font></div><div><font color="#000000" face="arial, helvetica, sans-serif">I have use split4dnii to split NIFTI format tensor to 6 components (lower triangle), and they are automatically named as</font></div><div><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif">0001.nii.gz 0002.nii.gz 0003.nii.gz 0004.nii.gz 0005.nii.gz 0006.nii.gz.</font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif"><br></font></p><p style="margin:0px;line-height:normal"><font face="arial, helvetica, sans-serif"><font color="#000000">To use DTITK function to fit tensor, I need to know the what the number </font><font color="#000000">represent.</font></font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif"><br></font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif">Does 0001 represent dxx, </font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif"> 0002 represent dxx, </font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif"> 0003 represent day, </font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif"> 0004 represent dzx,</font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif"> 0005 represent dzy,</font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif"> 0006 represent dzz ?</font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif"><br></font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif">The meaning for the tensor components is very important for me to do next process.</font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif"><br></font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif">Thanks for your patience and help,</font></p><p style="margin:0px;line-height:normal"><font color="#000000" face="arial, helvetica, sans-serif">Xiaoping</font></p><p style="margin:0px;font-size:18px;line-height:normal;font-family:Menlo;color:rgb(255,59,29)"><br></p><p style="margin:0px;font-size:18px;line-height:normal;font-family:Menlo;color:rgb(255,59,29)"><br></p></div></div><div class="gmail_extra"><br><div class="gmail_quote">2016-08-05 15:17 GMT-07:00 Philip A Cook <span dir="ltr"><<a href="mailto:cookpa@mail.med.upenn.edu" target="_blank">cookpa@mail.med.upenn.edu</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
1. Camino's raw data format is upper triangular, but dt2nii will write tensors with lower triangular elements, as specified by NIFTI. These should work with DTI-TK. You will have to do other pre-processing, see the DTI-TK documentation here<br>
<br>
<a href="http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.BeforeReg" rel="noreferrer" target="_blank">http://dti-tk.sourceforge.net/<wbr>pmwiki/pmwiki.php?n=<wbr>Documentation.BeforeReg</a><br>
<br>
<br>
<br>
2. If you want the components back you can call split4dnii, which will split 4D or 5D nii into 3D images.<br>
<br>
<br>
3. I don't recommend using analyzedti or any Analyze files, they are obsolete now. With NIFTI:<br>
<br>
dtfit data.nii.gz mask.nii.gz | dt2nii -header mask.nii.gz -outputroot myDT_<br>
<br>
This will make<br>
<br>
myDT_dt.nii.gz<br>
myDT_exitcode.nii.gz<br>
myDT_lnS0.nii.gz<br>
<br>
You can then do<br>
<br>
fa -inputfile myDT_dt.nii.gz -outputfile myDT_fa.nii.gz<br>
md -inputfile myDT_dt.nii.gz -outputfile myDT_md.nii.gz<br>
<br>
If you want the full eigen system, things are a little trickier, but you can use voxel2image to get the output of dteig as a series of NIFTI images (see <a href="http://camino.cs.ucl.ac.uk/index.php?n=Main.Fileformats" rel="noreferrer" target="_blank">http://camino.cs.ucl.ac.uk/<wbr>index.php?n=Main.Fileformats</a>). It would be nice to have a dteig2nii to automate this, but we don't currently have that.<br>
<br>
If you are using DTI-TK, then you can take the NIFTI DT and use it's TVTool to get the eigen system, as well as AD, RD, MD, FA, etc.<br>
<div><div class="h5"><br>
<br>
<br>
<br>
> On Aug 5, 2016, at 5:33 PM, xiaoping qu <<a href="mailto:quxiaoping1@gmail.com">quxiaoping1@gmail.com</a>> wrote:<br>
><br>
> Hi Camino experts,<br>
><br>
> I am Xiaoping, a new user to Camino.<br>
><br>
> Since I want the diffusion tensor components to do registration with DTITK, I am very interested in tensor type and how to abstract tensor components from a tensor file.<br>
><br>
> 1. I tried to use dtfit to fit a tensor with Bdouble format and can use dt2nii to convert Bdouble format file to nifti format.<br>
> According your on line documents, I find that the tensor.Bdouble from dtfit is upper triangle but no idea about the nifti tensor format?<br>
> Can you tell me that after dt2nii, what type the nifty format tensor is ? upper triangle or lower triangular?<br>
><br>
><br>
> 2. If I want to extract tensor components like dxx, dxy, dxz, dyy, dzz from tensor.nii.gz, what kind of function I can use?<br>
><br>
><br>
><br>
> 3. Aso, according to the online documents about camino, I just find analyzedti is a command to get individual analyze format components. If I have the DWI nifti.gz format image and its binary mask(nii,gz) and scheme file. How can I use analyzedti to get individual tensor components?<br>
><br>
> Do I need to fist img2voxel to convert dwi to voxel order as Bfloat file,<br>
> and then use voxel2scanner to convert dwi.Bfloat to scanner order as Bdouble file, and then use AnalyzeHeader to convert Bdouble to analyze format, and finally use Analyzedti to get analyze format tensor components?<br>
><br>
><br>
><br>
> Thanks,<br>
> Xiaoping<br>
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</blockquote></div><br></div>