DWIConvert

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DWIConvert

Emily Louise Belleau



From: Emily Louise Belleau
Sent: Tuesday, February 17, 2015 1:09 PM
To: [hidden email]
Subject: Re: DWIConvert
 



From: Emily Louise Belleau
Sent: Tuesday, February 17, 2015 12:44 PM
To: [hidden email]
Subject: DWIConvert
 

Hello,


 I had a question regarding DWIConvert through  3d Slicer 4.4.0. gui.


I have been trying to convert my dicom files to .nrrd files but am having trouble.  However, I don't believe the scanner that I collected my data with is supported (GE Medical Systems Discovery MR750 HFS).


So, my second thought was to go from FSL nifti to .nrrd.  I do have my data converted to the FSL format. However I am still having some issues going this route.


I tried simply using DWI Convert through the Slicer gui by inputting my .nii file along with my bvec and bvals files.


Do you have any thoughts on what could be going on or alternative ideas?



Perhaps I am not using the correct formatted files? The initial program I had used outputs a number of files ( I have attached):


1.) dwi_orig.nii.gz -- Original DWI file converted to NIfTI format (didn't attach to big)

2.) dwi_orig.mghdti.bvals -- Original list of b-values

3.)dwi_orig.mghdti.bvecs -- Original list of gradient vectors

4.)dwi_orig_flip.nii.gz -- DWI converted to the orientation preferred by FSL (didn't attach too big)

5.)bvals -- List of b-values in FSL format

6.)bvecs.norot -- List of gradient vectors in FSL format


Sorry to bombard you with this, I would appreciate any guidance you are willing to give! I assume that inputting the dwi_orig_flip, the bvecs.norot, and the bvals file?


Emily



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Re: DWIConvert

Chiara Maffei
Dear Emily,

Can I ask what you mean by some issues? Can you specify what goes wrong in the conversion?
I am asking because I also have troubles in using nifti to nrrd in dwi convert. However the dicom to nrrd works fine for me. Maybe we can help each other. 

Best

Chiara 

On 17/feb/2015, at 20:22, Emily Louise Belleau <[hidden email]> wrote:



From: Emily Louise Belleau
Sent: Tuesday, February 17, 2015 1:09 PM
To: [hidden email]
Subject: Re: DWIConvert
 



From: Emily Louise Belleau
Sent: Tuesday, February 17, 2015 12:44 PM
To: [hidden email]
Subject: DWIConvert
 

Hello,


 I had a question regarding DWIConvert through  3d Slicer 4.4.0. gui.


I have been trying to convert my dicom files to .nrrd files but am having trouble.  However, I don't believe the scanner that I collected my data with is supported (GE Medical Systems Discovery MR750 HFS).


So, my second thought was to go from FSL nifti to .nrrd.  I do have my data converted to the FSL format. However I am still having some issues going this route.


I tried simply using DWI Convert through the Slicer gui by inputting my .nii file along with my bvec and bvals files.


Do you have any thoughts on what could be going on or alternative ideas?



Perhaps I am not using the correct formatted files? The initial program I had used outputs a number of files ( I have attached):


1.) dwi_orig.nii.gz -- Original DWI file converted to NIfTI format (didn't attach to big)

2.) dwi_orig.mghdti.bvals -- Original list of b-values

3.)dwi_orig.mghdti.bvec  -- Original list of gradient vectors

4.)dwi_orig_flip.nii.gz -- DWI converted to the orientation preferred by FSL (didn't attach too big)

5.)bvals -- List of b-values in FSL format

6.)bvecs.norot -- List of gradient vectors in FSL format


Sorry to bombard you with this, I would appreciate any guidance you are willing to give! I assume that inputting the dwi_orig_flip, the bvecs.norot, and the bvals file?


Emily


_______________________________________________
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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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Re: DWIConvert

Emily Louise Belleau

Hi Chiara,



I was actually able to get my dicoms to convert to .nrrd yeah! However,  similar to you, I will now need to convert the .nrrd file to FSL so that I can run other processes using another program.


When looking at the DWI Convert Gui, I see that there is an nrrd to fsl and an fsl to nrrd option. However, I don't see where you can input your nrrd file? And,  I see there is a place to specifiy an output directory for the bvec and bval files to be placed. However, when I click on those, it looks like it wants me to open a file and choose a directory. Very confusing? What types of issues are you having?


Emily


From: Chiara Maffei <[hidden email]>
Sent: Tuesday, February 17, 2015 3:11 PM
To: Emily Louise Belleau
Cc: [hidden email]
Subject: Re: [slicer-users] DWIConvert
 
Dear Emily,

Can I ask what you mean by some issues? Can you specify what goes wrong in the conversion?
I am asking because I also have troubles in using nifti to nrrd in dwi convert. However the dicom to nrrd works fine for me. Maybe we can help each other. 

Best

Chiara 

On 17/feb/2015, at 20:22, Emily Louise Belleau <[hidden email]> wrote:



From: Emily Louise Belleau
Sent: Tuesday, February 17, 2015 1:09 PM
To: [hidden email]
Subject: Re: DWIConvert
 



From: Emily Louise Belleau
Sent: Tuesday, February 17, 2015 12:44 PM
To: [hidden email]
Subject: DWIConvert
 

Hello,


 I had a question regarding DWIConvert through  3d Slicer 4.4.0. gui.


I have been trying to convert my dicom files to .nrrd files but am having trouble.  However, I don't believe the scanner that I collected my data with is supported (GE Medical Systems Discovery MR750 HFS).


So, my second thought was to go from FSL nifti to .nrrd.  I do have my data converted to the FSL format. However I am still having some issues going this route.


I tried simply using DWI Convert through the Slicer gui by inputting my .nii file along with my bvec and bvals files.


Do you have any thoughts on what could be going on or alternative ideas?



Perhaps I am not using the correct formatted files? The initial program I had used outputs a number of files ( I have attached):


1.) dwi_orig.nii.gz -- Original DWI file converted to NIfTI format (didn't attach to big)

2.) dwi_orig.mghdti.bvals -- Original list of b-values

3.)dwi_orig.mghdti.bvec  -- Original list of gradient vectors

4.)dwi_orig_flip.nii.gz -- DWI converted to the orientation preferred by FSL (didn't attach too big)

5.)bvals -- List of b-values in FSL format

6.)bvecs.norot -- List of gradient vectors in FSL format


Sorry to bombard you with this, I would appreciate any guidance you are willing to give! I assume that inputting the dwi_orig_flip, the bvecs.norot, and the bvals file?


Emily


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/4.3/FAQ


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

_______________________________________________
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[hidden email]
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To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
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dispose of the e-mail.