Hi Anastasia, I am setting up the dmrirc file to run Tracula. I am using Siemens Dicoms, so I did not specify any setting for bval and bvec, but when trac-all -prep starts running it gives the following error: mv: cannot stat 'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory
Ok, so I understand that our problem is that we don't have MGH Siemens Dicom.
So I used dcm2nii to convert it to .nii files and each conversion gives me a SubjectID.bval and SubjectID.bvec. Every .bval is the same file, but every .bvec file is a different one.
I can edit "set dcm_list = " to include all the newly created .nii files, but
My question is: - How can I specify every .bvec value for every subject? In the dmrirc file everything I see is a "set bvecfile = " option.
Thank you very much, Gari
Hi Gari - Sorry, right now the assumption is that the gradient vectors are the same for all subjects. How different are they?
a.y
On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Anastasia,I am setting up the dmrirc file to run Tracula. I am using Siemens Dicoms, so I did not specify any setting for bval and bvec, but when trac-all -prep starts running it gives the following error: mv: cannot stat 'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory
Ok, so I understand that our problem is that we don't have MGH Siemens Dicom.
So I used dcm2nii to convert it to .nii files and each conversion gives me a SubjectID.bval and SubjectID.bvec. Every .bval is the same file, but every .bvec file is a different one.
I can edit "set dcm_list = " to include all the newly created .nii files, but
My question is:
- How can I specify every .bvec value for every subject? In the dmrirc file
everything I see is a "set bvecfile = " option.
Thank you very much, Gari
Hi! Thanks for the fast answer. If I do: diff id1.bvec id2.bvec I can see some clear differences.
I was told that in FSL I should use the bvecs and bvals created in dcm2nii per subject, so I understand I should do the same now? Do you think an option would be to script the creation of a dmrirc file per each subject and then launch as many trac-alls as subjects?
Thanks again, Gari
On Thursday, September 26, 2013, Anastasia Yendiki wrote:
Hi Gari - Sorry, right now the assumption is that the gradient vectors are the same for all subjects. How different are they?
a.y
On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Hi Anastasia,I am setting up the dmrirc file to run Tracula. I am using
Siemens Dicoms, so I did not specify any setting for bval and bvec, but when trac-all -prep starts running it gives the following error: mv: cannot stat 'paths.../SubjectID/dmri/dwi_**orig_flip.mghdti.bvecs': No such file or directory
Ok, so I understand that our problem is that we don't have MGH Siemens Dicom.
So I used dcm2nii to convert it to .nii files and each conversion gives me a SubjectID.bval and SubjectID.bvec. Every .bval is the same file, but every .bvec file is a different one.
I can edit "set dcm_list = " to include all the newly created .nii files, but
My question is:
- How can I specify every .bvec value for every subject? In the dmrirc
file everything I see is a "set bvecfile = " option.
Thank you very much, Gari
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/**compliancelinehttp://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 Gari - Yes, that's your best option right now. Sorry for the inconvenience. I'll make sure to add the option to have one gradient file per subject in the next version.
a.y
On Thu, 26 Sep 2013, Garikoitz Lerma-Usabiaga wrote:
Hi! Thanks for the fast answer. If I do: diff id1.bvec id2.bvec I can see some clear differences.
I was told that in FSL I should use the bvecs and bvals created in dcm2nii per subject, so I understand I should do the same now? Do you think an option would be to script the creation of a dmrirc file per each subject and then launch as many trac-alls as subjects?
Thanks again, Gari
On Thursday, September 26, 2013, Anastasia Yendiki wrote:
Hi Gari - Sorry, right now the assumption is that the gradient vectors are the same for all subjects. How different are they? a.y On Wed, 25 Sep 2013, Garikoitz Lerma-Usabiaga wrote: Hi Anastasia,I am setting up the dmrirc file to run Tracula. I am using Siemens Dicoms, so I did not specify any setting for bval and bvec, but when trac-all -prep starts running it gives the following error: mv: cannot stat 'paths.../SubjectID/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Ok, so I understand that our problem is that we don't have MGH Siemens Dicom. So I used dcm2nii to convert it to .nii files and each conversion gives me a SubjectID.bval and SubjectID.bvec. Every .bval is the same file, but every .bvec file is a different one. I can edit "set dcm_list = " to include all the newly created .nii files, but My question is: - How can I specify every .bvec value for every subject? In the dmrirc file everything I see is a "set bvecfile = " option. Thank you very much, Gari 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.
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Garikoitz Lerma-Usabiaga