Hi all Now I am learning the trac-all using with DICOM data, but came across a problem. +++ mv -f /xxx/dmri/dwi_orig_flip.mghdti.bvecs /xxxx/dmri/bvecs mv: cannot stat `/xxx/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory +++ I check the dir /xxx/dmri/ and there are only two files 'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz' and a dir 'xfms'. Does trac-all extract bvals/bvecs automatically when start with DICOM data? My data is from a siemens scanner.
Thanks!
Xiangzhen
2012-02-03
Xiangzhen Kong
Unless your dicoms came from the same acquisition as the default MGH/Siemens one, you'll have to set bvecfile and bvalfile and provide those files yourself.
On Fri, 3 Feb 2012, Xiangzhen Kong wrote:
Hi all Now I am learning the trac-all using with DICOM data, but came across a problem. +++ mv -f /xxx/dmri/dwi_orig_flip.mghdti.bvecs /xxxx/dmri/bvecs mv: cannot stat `/xxx/dmri/dwi_orig_flip.mghdti.bvecs': No such file or dir ectory +++ I check the dir /xxx/dmri/ and there are only two files 'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz' and a dir 'xfms'. Does trac-all extract bvals/bvecs automatically when start with DICOM data? My data is from a siemens scanner. Thanks! Xiangzhen 2012-02-03
Xiangzhen Kong
Thank you very much, Anastasia. I have checked the related mails in the list and found not me came across this problem. As you said, I know how I can run my data. But I have a question. Why would we make trac-all compatible to other scanner or acquisitions, since we can get bvecs and bval from the DICOM header?
thank in advance.
Xiangzhen Kong
From: Anastasia Yendiki Date: 2012-02-04 00:52 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory
Unless your dicoms came from the same acquisition as the default MGH/Siemens one, you'll have to set bvecfile and bvalfile and provide those files yourself.
On Fri, 3 Feb 2012, Xiangzhen Kong wrote:
Hi all Now I am learning the trac-all using with DICOM data, but came across a problem. +++ mv?f?xxx/dmri/dwi_orig_flip.mghdti.bvecs?xxxx/dmri/bvecs mv:�cannot�stat�`/xxx/dmri/dwi_orig_flip.mghdti.bvecs':�No�such�file�or�dir ectory +++ I check the dir /xxx/dmri/ and there are only two files 'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz'?and a dir 'xfms'. Does trac-all extract bvals/bvecs automatically when start with DICOM data? My data is from a siemens scanner. ? Thanks! ? Xiangzhen ? 2012-02-03
Xiangzhen Kong
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.
Hi Xiangzhen - Currently mri_convert does not support extracting gradients and b-values from dicom files. If you can get the gradients and b-values from the dicom header yourself, that's great. Save them in text files and enter the path in your dmrirc file.
a.y
On Thu, 7 Jun 2012, Xiangzhen Kong wrote:
Thank you very much, Anastasia. I have checked the related mails in the list and found not me came across this problem. As you said, I know how I can run my data. But I have a question. Why would we make trac-all compatible to other scanner or acquisitions, since we can get bvecs and bval from the DICOM header? thank in advance.
Xiangzhen Kong From: Anastasia Yendiki Date: 2012-02-04 00:52 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Unless your dicoms came from the same acquisition as the default MGH/Siemens one, you'll have to set bvecfile and bvalfile and provide those files yourself. On Fri, 3 Feb 2012, Xiangzhen Kong wrote:
Hi all Now I am learning the trac-all using with DICOM data, but came across a problem. +++ mv?f?xxx/dmri/dwi_orig_flip.mghdti.bvecs?xxxx/dmri/bvecs mv:燾annot爏tat燻/xxx/dmri/dwi_orig_flip.mghdti.bvecs':燦o爏uch爁ile爋r
?? ??ir
ectory +++ I check the dir /xxx/dmri/ and there are only two files 'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz'?and a dir 'xfms'. Does trac-all extract bvals/bvecs automatically when start with DICOM dat
a?
My data is from a siemens scanner. ? Thanks! ? Xiangzhen ? 2012-02-03 _________________________________________________________________________
Xiangzhen Kong
The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C... rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
Thanks for your rapid reply .
best!
Xiangzhen Kong
发件人： Anastasia Yendiki 发送时间： 2012-06-07 23:19 收件人： Xiangzhen Kong 抄送： freesurfer 主题： Re: [Freesurfer] 回复: Re: /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory
Hi Xiangzhen - Currently mri_convert does not support extracting gradients and b-values from dicom files. If you can get the gradients and b-values from the dicom header yourself, that's great. Save them in text files and enter the path in your dmrirc file.
a.y
On Thu, 7 Jun 2012, Xiangzhen Kong wrote:
Thank you very much, Anastasia. I have checked the related mails in the list and found not me came across this problem. As you said, I know how I can run my data. But I have a question. Why would we make trac-all compatible to other scanner or acquisitions, since we can get bvecs and bval from the DICOM header?
thank in advance.
Xiangzhen Kong
From: Anastasia Yendiki Date: 2012-02-04 00:52 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory
Unless your dicoms came from the same acquisition as the default MGH/Siemens one, you'll have to set bvecfile and bvalfile and provide those files yourself.
On Fri, 3 Feb 2012, Xiangzhen Kong wrote:
Hi all Now I am learning the trac-all using with DICOM data, but came across a problem. +++ mv?f?xxx/dmri/dwi_orig_flip.mghdti.bvecs?xxxx/dmri/bvecs mv:燾annot爏tat燻/xxx/dmri/dwi_orig_flip.mghdti.bvecs':燦o爏uch爁ile爋r
?? ??ir
ectory +++ I check the dir /xxx/dmri/ and there are only two files 'dwi_orig_flip.nii.gz' , 'dwi_orig.nii.gz'?and a dir 'xfms'. Does trac-all extract bvals/bvecs automatically when start with DICOM dat
a?
My data is from a siemens scanner. ? Thanks! ? Xiangzhen ? 2012-02-03
Xiangzhen Kong
The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Xiangzhen Kong