Re: [Freesurfer] bvals and bvecs for dt_recon
How is the format different? Is it in 3 rows instead of 3 columns? If so, it should be straightforward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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] bvals and bvecs for dt_recon
Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in the wiki or in the distribution. And I am downing tutorial data now. Hope it is there. BTW, do you have an example? I know how to get those from private dicom tags. Gen -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Thursday, March 13, 2014 1:37 PM To: Gennan Chen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bvals and bvecs for dt_recon How is the format different? Is it in 3 rows instead of 3 columns? If so, it should be straightforward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen __ __ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator 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. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] bvals and bvecs for dt_recon
dcm2nii should give you bvecs and bvals If you just want to transpose the file, I wrote a script to do it (attached). On 03/13/2014 04:50 PM, Gennan Chen wrote: Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in the wiki or in the distribution. And I am downing tutorial data now. Hope it is there. BTW, do you have an example? I know how to get those from private dicom tags. Gen -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Thursday, March 13, 2014 1:37 PM To: Gennan Chen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bvals and bvecs for dt_recon How is the format different? Is it in 3 rows instead of 3 columns? If so, it should be straightforward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen __ __ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator 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. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer transpose.sh Description: application/shellscript ___ 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] bvals and bvecs for dt_recon
Attached are examples of the bvals.dat and bvecs.dat files extracted from siemens dicoms by dt_recon. This was for a 60 dir DTI scan w/ 10 b0s. On Thu, 13 Mar 2014, Chris Watson wrote: dcm2nii should give you bvecs and bvals If you just want to transpose the file, I wrote a script to do it (attached). On 03/13/2014 04:50 PM, Gennan Chen wrote: Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in t he wiki or in the distribution. And I am downing tutorial data now. Hope it is there. BTW, do yo u have an example? I know how to get those from private dicom tags. Gen -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Thursday, March 13, 2014 1:37 PM To: Gennan Chen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bvals and bvecs for dt_recon How is the format different? Is it in 3 rows instead of 3 columns? If so, it should be straightfo rward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen __ __ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator The information in this e-mail is intended only for the person to whom it is addressed. If you be lieve this e-mail was sent to you in error and the e-mail contains patient information, please co ntact 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. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibite d. If you are not the intended recipient, please contact the sender by reply email and destroy al l copies of the original message. If you are the intended recipient, please be advised that the c ontent of this message is subject to access, review and disclosure by the sender's Email System A dministrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.586792 -0.376583 -0.716841 0.894195 0.022917 0.447091 0.729281 -0.410970 0.547041 -0.154251 0.964369 -0.214941 0.117136 0.773539 -0.622830 -0.407575 -0.414994 -0.813427 0.211330 0.753738 0.622269 0.095375 -0.969517 0.225700 -0.135450 -0.033490 -0.990218 -0.142125 -0.750521 -0.645383 -0.637009 0.746109 -0.193757 0.080563 0.971669 0.222192 0.106871 -0.021213 0.994047 0.298747 0.387214 0.872247 -0.207492 -0.803432 0.558072 0.331125 -0.040337 -0.942724 -0.805294 -0.589494 -0.063231 0.337278 -0.749774 -0.569282 0.592396 -0.761390 0.263348 -0.088979 -0.465650 0.880485 -0.527982 -0.430927 0.731803 -0.369111 -0.927082 0.065397 0.311914 0.926381 -0.211018 -0.684511 0.439336 -0.581746 -0.030114 -0.966623 -0.254425 -0.337568 0.744654 -0.575794 -0.574804 0.024806 -0.817915 0.271135 -0.747834 0.605996 -0.935185 0.185421 0.301743 0.889083 0.309665 -0.337104 -0.884343 0.033574 -0.465629 0.545045 0.586317 -0.599298 -0.350774 -0.016274 0.936319 0.416158 -0.900528 -0.125943
Re: [Freesurfer] bvals and bvecs for dt_recon
Thxs for all the help. On March 13, 2014 at 2:19:16 PM, Louis Nicholas Vinke (vi...@nmr.mgh.harvard.edumailto:vi...@nmr.mgh.harvard.edu) wrote: Attached are examples of the bvals.dat and bvecs.dat files extracted from siemens dicoms by dt_recon. This was for a 60 dir DTI scan w/ 10 b0s. On Thu, 13 Mar 2014, Chris Watson wrote: dcm2nii should give you bvecs and bvals If you just want to transpose the file, I wrote a script to do it (attached). On 03/13/2014 04:50 PM, Gennan Chen wrote: Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in t he wiki or in the distribution. And I am downing tutorial data now. Hope it is there. BTW, do yo u have an example? I know how to get those from private dicom tags. Gen -Original Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Thursday, March 13, 2014 1:37 PM To: Gennan Chen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bvals and bvecs for dt_recon How is the format different? Is it in 3 rows instead of 3 columns? If so, it should be straightfo rward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen __ __ This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator The information in this e-mail is intended only for the person to whom it is addressed. If you be lieve this e-mail was sent to you in error and the e-mail contains patient information, please co ntact 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. This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibite d. If you are not the intended recipient, please contact the sender by reply email and destroy al l copies of the original message. If you are the intended recipient, please be advised that the c ontent of this message is subject to access, review and disclosure by the sender's Email System A dministrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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.
