[Camino-users] problems creating .Bfloat file

[Christina Hugenschmidt]

Thanks Philip - I ran the command you put below (image2voxel -4dimage dwi.nii.gz -outputfile data.Bfloat) and it successfully created the file. However, the Bfloat file is populated with 0s (if I run the command cat file.Bfloat | float2txt | head -50. When I looked at the first Bfloat file I made more laboriously, the same was true (the Bfloat file is 0s). Do you have any idea why this might be? 

Christina E. Hugenschmidt, PhD
Instructor

Section on Gerontology & Geriatric Medicine
Medical Center Boulevard \ Winston-Salem, NC 27157
P 336.713.4190 \ f 336.713.8588
chugensc at wakehealth.edu



-----Original Message-----
From: Philip A Cook [mailto:cookpa at mail.med.upenn.edu] 
Sent: Friday, March 22, 2013 3:18 PM
To: Christina Hugenschmidt
Cc: camino-users at www.nitrc.org
Subject: Re: [Camino-users] problems creating .Bfloat file

Hi Christina,

If you are using dcm2nii it should be possible to convert your data and scheme file in one step apiece.

For the data:

  image2voxel -4dimage dwi.nii.gz -outputfile data.Bfloat

For the scheme file:

  fsl2scheme -bvecfile image.bvec -bvalfile image.bval -bscale 1 > scheme

Here I've used -bscale 1 so that b-values will stay in units of s / mm^2. This is OK for most DTI uses but it will be an issue if you run dtlutgen or datasynth - in which case you will need extra options to let those programs know that you are using s / mm^2

Then you should be able to do

  modelfit -inputfile data.Bfloat -schemefile scheme -model ldt -bgmask mask.nii -outputfile dt.Bdouble


If you have a recent version of Camino you can also import NIfTI data directly

  modelfit -inputfile dwi.nii.gz -schemefile scheme -model ldt -bgmask mask.nii -outputfile dt.Bdouble

This will use a bit more RAM though


On Mar 22, 2013, at 2:29 PM, Christina Hugenschmidt wrote:

> Hi,
> 
>  
> 
> I am new to camino and quite a novice w/r/t programming. I was able to successfully run the tutorial on the human tutorial data. With those disclosures, here is my question. The first time I tried to create an FA image on my own data, it was empty. After emailing with Uran and reading the data import page, I decided the problem is likely that my data are in the wrong format. I have data acquired on a 3T Siemens scanner (30 directions + 1 B0) that are 16 bit signed integer and little endian.
> 
>  
> 
> I followed the instructions on the data import page (specified the size of the data set, stripped the nifti header to make a raw data file, and used the scanner2voxel and shredder command at the bottom of the page). I had already made a scheme file from the bval and bvec files created by dcm2nii. The scheme file seems to be correct when I look at it, so I tried again to run the tutorial. When I ran the command modelfit -inputdatafile file.Bfloat -schemefile file.scheme - model ldt -bgmask file_mask.nii -outputfile dt.Bdouble, I got the warning "couldn't parse arg 0: '-inputdatafile'" then "couldn't parse arg 1: 'file.Bfloat'".
> 
>  
> 
> I'm not sure what I'm doing wrong, and I would appreciate any insights.
> 
>  
> 
> Thanks,
> 
> Christina
> 
>  
> 
> Christina E. Hugenschmidt, PhD
> Instructor
> <image001.gif>
> Section on Gerontology & Geriatric Medicine Medical Center Boulevard \ 
> Winston-Salem, NC 27157 P 336.713.4190 \ f 336.713.8588 
> chugensc at wakehealth.edu
>  
>  
> 
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