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Jun 7, 2017  10:06 AM | afouto - ISR - IST
Convertion problems
Hi,

I did some preprocessing steps on my diffusion data using FSL. More specifically, eddy-current distortions were corrected using FSL's eddy and then tensor fitting was performed using FSL's dtifit. At this stage I would like to perform an outliers detection with DTIPrep before starting Glm's analysis. However, I'm having trouble with the first stage of the convertion to Nrrd. I'm using Slicer 4.4 (linux version) instead of the most recent version because the extension for DTIPrep is not avaliable on the latter one. I followed the steps indicated in this tutorial to convert Dicom to Nrrd but nothing happends and I didn't even receive any error message (http://dmri.slicer.org/docs/tutorials/DW...). I also tried the convertion FSL to Nrrd but I didn't get any results either. The folder that I created to save the outputs remained empty. I'm more interested in the convertion FSL to Nrrd, once I already have the images preprocessed in the Nifti format.

I would appreciate some help to get over this first step and perform the outliers analyses.

Thanks in advance for the help

Best regards,
Ana F.
Jun 8, 2017  06:06 AM | Martin Styner
RE: Convertion problems
Dear Ana
1. Yes, we know that DTIPrep does not load into the current Slicer's extension browser. One workaround is to use 4.4 like you did. We expect that DTIPrep will be available later this year in the current Slicer version. Having to keep up with Slicer versions is actually a clear downside of using Slicer as a dissemination infrastructure.

2. Not sure why you would use dicom to nrrd in your setting, if I understand correctly you want to convert your nifti (nii.gz) to nrrd . For that purpose use the same tool (DWIConvert) but you would need the newest Slicer version (the older DWIConvert had bugs in the nifti conversion)

3. Most importantly, I am not sure DTIPrep is the right tool for you. DTIPrep really designed for processing the DWI data (by getting rid of bad DWIs) not the fitted tensors. Btw, eddy current correction in DTIPrep is slightly better than FSL (though both are very similar) as it uses an iteratively averaged B0 for the correction. Now, if you would like to detect outliers in the fitted tensors there are other packages such as tortoise which provide an implementation of RESTORE for exactly this purpose.

Best regards
Martin
Originally posted by afouto:
Hi,

I did some preprocessing steps on my diffusion data using FSL. More specifically, eddy-current distortions were corrected using FSL's eddy and then tensor fitting was performed using FSL's dtifit. At this stage I would like to perform an outliers detection with DTIPrep before starting Glm's analysis. However, I'm having trouble with the first stage of the convertion to Nrrd. I'm using Slicer 4.4 (linux version) instead of the most recent version because the extension for DTIPrep is not avaliable on the latter one. I followed the steps indicated in this tutorial to convert Dicom to Nrrd but nothing happends and I didn't even receive any error message (http://dmri.slicer.org/docs/tutorials/DW...). I also tried the convertion FSL to Nrrd but I didn't get any results either. The folder that I created to save the outputs remained empty. I'm more interested in the convertion FSL to Nrrd, once I already have the images preprocessed in the Nifti format.

I would appreciate some help to get over this first step and perform the outliers analyses.

Thanks in advance for the help

Best regards,
Ana F.
Jun 9, 2017  02:06 AM | afouto - ISR - IST
RE: Convertion problems
Dear Martin,

Thank you very much for the quick response and all the tips. Once I'm already in an advanced stage of the processing I will try the outliers detection with RESTORE as you suggested. Later if I have enough time I will try to perform the entire pipeline of DTIPrep with the dicoms.

Keep up the good work with DTIPrep!

Best regards,
Ana F.
Jan 24, 2018  01:01 PM | XIAO YANG
RE: Convertion problems
Hi Martin,
I am current working on a project with DTI data. I want to convert my nifti (nii) to nrrd. I also met some problems when I tried to do NifitFSL To Nrrd in 3D Slicer 4.8.1 in Windows 10, 64-bit OS (I've already converted the DICOM data which collected from Philip to NIfTI nii by dcm2nii) . I set the panel as showing in the attachment.

I also checked that the .bval file contains the information as: o 1000 1000.....while the .bvec file contains rows correspond to x/y/z column compnents respectively. These may be the supported FSL-style by DWIConvert.

However, when I clicked the "Apply", the error came out as following: DWIConvert.exe has stopped working.  I tested this for several subjects. There was always the same error.

Diffusion-weighted DICOM Import (DWIConvert) standard error:

Error: ReadVolume: Unsupported source pixel type.
Input volume: float
Output volume: short
The only supported output type is . You may consider using allowLossyConversion option.
However, use this option with caution! Conversion from images of a different type may cause data loss due to rounding or truncation.

Could you help me with this problem?
Thanks in advance!
Xiao
Attachment: setting.png
Jan 24, 2018  02:01 PM | XIAO YANG
RE: Convertion problems
Hi Martin, when I checked the Allow lossy image conversion option. It worked and I got the nhdr format image in the output directory. It worked both in Windows and Mac OS. 
However, it further raised two problems because I want to do this in the loop. 

First, it seemed that I couldn't install the Slicer well in my own macbook. Each time I opened Slicer by clicking the icon, it came out the warning as follows: "Slicer" can't be opened because the identity of the developer cannot be confirmed. I don't know why this happens everytime.
 
Secondly, i tried to use the software in Linux OS. I did as the tutorial suggested, I opened the tar.gz archive and copy directory to the location of my current folder. But when i typed the "DWIConvert", I got an error message "command not found". So do the "DWIConverter" command. (I saw your suggestion to others' problems.)Just the same error. Is there any software I need to install? So far I just got only Slicer 4.8.1 for Linux.

Thank you,
Xiao
Jan 25, 2018  12:01 PM | Martin Styner
RE: Convertion problems
Hi Xiao

I will try to answer these, though they are probably more appropriate for the Slicer discussion/help boards as they do not affect DTIprep directly.

1) I think that warning disappears when you open it with a shift/right click (a menu opens up and select "Open" ).

2) In linux, you can access any Slicer module via "Slicer --launch ", e.g. Slicer --launch DWIConvert . I don't think that works in Mac OSX or Windows (not fully sure)

Best regards
Martin
Jan 26, 2018  07:01 AM | Martin Styner
RE: Convertion problems
Hi Xiao

I will try to answer these, though they are probably more appropriate for the Slicer discussion/help boards as they do not affect DTIprep directly.

1) I think that warning disappears when you open it with a shit/right click (a menu opens up and select "Open" ).

2) In linux, you can access any Slicer module via "Slicer --launch ", e.g. Slicer --launch DWIConvert . I don't think that works in Mac OSX or Windows (not fully sure)

Best regards
Martin