[Freesurfer] preferred method for generating appropriate bvecs for tracula
Hi, I have dicoms that I turn to nifti using dcm2nii (with the default settings plus anonymization option turned on [-a y]). The bvec files it generates by default are 3 rows by n columns (where n is b0 number + directions). I am under the impression tracula requires this to be converted to a n row by 3 column file. 1) is this correct, 2) is there a preferred way to perform this transformation on linux systems? Thanks you, -Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
set x = `cat bvecs | awk '{if (NR==1) print}'`
set y = `cat bvecs | awk '{if (NR==2) print}'`
set z = `cat bvecs | awk '{if (NR==3) print}'`
@ k = 1
while ( $k <= `head -1 bvecs|wc -w` )
echo $x[$k] $y[$k] $z[$k]
@ k = $k + 1
end
I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I
think there was a thread recently that suggested it might.
On Wed, 7 Aug 2013, Salil Soman wrote:
> Hi,
> I have dicoms that I turn to nifti using dcm2nii (with the default settings
> plus anonymization option turned on [-a
> y]). The bvec files it generates by default are 3 rows by n columns (where n
> is b0 number + directions). I am under
> the impression tracula requires this to be converted to a n row by 3 column
> file. 1) is this correct, 2) is there a
> preferred way to perform this transformation on linux systems?
>
> Thanks you,
>
> -Sal
>
>
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Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
Thank you for the email.
I saw a warning to check for flipping L-R from the dcm2nii site:
http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html
Is the problem you mentioned vendor specific (I have all GE data). Is there
a different tool you would recommend for generating the bvec files? I would
prefer to run tracula right off the original dicom images but transferring
them to the cluster and anonymizing them would be prohibitively difficult.
I could not find the freesurfer archive message you referred to. Any
pointers would be greatly appreciated.
Best wishes,
Sal
On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> set x = `cat bvecs | awk '{if (NR==1) print}'`
> set y = `cat bvecs | awk '{if (NR==2) print}'`
> set z = `cat bvecs | awk '{if (NR==3) print}'`
>
> @ k = 1
> while ( $k <= `head -1 bvecs|wc -w` )
> echo $x[$k] $y[$k] $z[$k]
> @ k = $k + 1
> end
>
> I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I
> think there was a thread recently that suggested it might.
>
>
> On Wed, 7 Aug 2013, Salil Soman wrote:
>
> Hi,
>> I have dicoms that I turn to nifti using dcm2nii (with the default
>> settings plus anonymization option turned on [-a
>> y]). The bvec files it generates by default are 3 rows by n columns
>> (where n is b0 number + directions). I am under
>> the impression tracula requires this to be converted to a n row by 3
>> column file. 1) is this correct, 2) is there a
>> preferred way to perform this transformation on linux systems?
>>
>> Thanks you,
>>
>> -Sal
>>
>>
>>
>
> 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.
>
>
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
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Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
Hi Sal - Right now you'd just have to try it on one data set and look at
the eigenvectors of the tensor (display dmri/dtifit_V1.nii.gz as lines) to
make sure they're pointing in the right way.
I'm hoping for the next freesurfer release to finally get mri_convert to
read gradient vectors off the dicom header in a way that ends this
gradient flipping madness once and for all. But for now you just have to
check before you proceed, sorry!
a.y
On Wed, 7 Aug 2013, Salil Soman wrote:
Thank you for the email.
I saw a warning to check for flipping L-R from the dcm2nii site:
http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html
Is the problem you mentioned vendor specific (I have all GE data). Is there a
different tool you would recommend for
generating the bvec files? I would prefer to run tracula right off the original
dicom images but transferring them to
the cluster and anonymizing them would be prohibitively difficult.
I could not find the freesurfer archive message you referred to. Any pointers
would be greatly appreciated.
Best wishes,
Sal
On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki
wrote:
set x = `cat bvecs | awk '{if (NR==1) print}'`
set y = `cat bvecs | awk '{if (NR==2) print}'`
set z = `cat bvecs | awk '{if (NR==3) print}'`
@ k = 1
while ( $k <= `head -1 bvecs|wc -w` )
echo $x[$k] $y[$k] $z[$k]
@ k = $k + 1
end
I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I
think there was a thread recently
that suggested it might.
On Wed, 7 Aug 2013, Salil Soman wrote:
Hi,
I have dicoms that I turn to nifti using dcm2nii (with the default
settings plus anonymization
option turned on [-a
y]). The bvec files it generates by default are 3 rows by n columns
(where n is b0 number +
directions). I am under
the impression tracula requires this to be converted to a n row by
3 column file. 1) is this
correct, 2) is there a
preferred way to perform this transformation on linux systems?
Thanks you,
-Sal
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.
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
___
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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
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Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
Thank you for your response. Is there a best way to review the eigenvectors (tkmedit, freeview, other program?). Thank you. -S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
Freeview can do this in principle, but the current version of freeview has a known bug with displaying eigenvectors as lines (see known issues in http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes), so for now you can use fslview. On Wed, 7 Aug 2013, Salil Soman wrote: Thank you for your response. Is there a best way to review the eigenvectors (tkmedit, freeview, other program?). Thank you. -S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
Hi Anastasia,
Thank you for this code piece. Is there a way to modify it so that set y's
sign gets flipped? (I have a dataset where its is acquired on GE (so the Y
row gets flipped)?
Thank you!
-Sal
On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> set x = `cat bvecs | awk '{if (NR==1) print}'`
> set y = `cat bvecs | awk '{if (NR==2) print}'`
> set z = `cat bvecs | awk '{if (NR==3) print}'`
>
> @ k = 1
> while ( $k <= `head -1 bvecs|wc -w` )
> echo $x[$k] $y[$k] $z[$k]
> @ k = $k + 1
> end
>
> I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I
> think there was a thread recently that suggested it might.
>
>
> On Wed, 7 Aug 2013, Salil Soman wrote:
>
> Hi,
>> I have dicoms that I turn to nifti using dcm2nii (with the default
>> settings plus anonymization option turned on [-a
>> y]). The bvec files it generates by default are 3 rows by n columns
>> (where n is b0 number + directions). I am under
>> the impression tracula requires this to be converted to a n row by 3
>> column file. 1) is this correct, 2) is there a
>> preferred way to perform this transformation on linux systems?
>>
>> Thanks you,
>>
>> -Sal
>>
>>
>>
>
> 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.
>
>
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
___
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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
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Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
Once the file is in 3-column format:
cat yourfilename | awk '{print $1 -$2 $3}'
On Thu, 31 Oct 2013, Salil Soman wrote:
Hi Anastasia,
Thank you for this code piece. Is there a way to modify it so that set y's
sign gets flipped? (I have a dataset where its is acquired on GE (so the Y
row gets flipped)?
Thank you!
-Sal
On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki
wrote:
set x = `cat bvecs | awk '{if (NR==1) print}'`
set y = `cat bvecs | awk '{if (NR==2) print}'`
set z = `cat bvecs | awk '{if (NR==3) print}'`
@ k = 1
while ( $k <= `head -1 bvecs|wc -w` )
echo $x[$k] $y[$k] $z[$k]
@ k = $k + 1
end
I'd make sure though dcm2nii doesn't L-R flip the gradient
vectors, I think there was a thread recently that suggested it
might.
On Wed, 7 Aug 2013, Salil Soman wrote:
Hi,
I have dicoms that I turn to nifti using dcm2nii
(with the default settings plus anonymization option
turned on [-a
y]). The bvec files it generates by default are 3
rows by n columns (where n is b0 number +
directions). I am under
the impression tracula requires this to be converted
to a n row by 3 column file. 1) is this correct, 2)
is there a
preferred way to perform this transformation on
linux systems?
Thanks you,
-Sal
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.
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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