[Freesurfer] Tracula -qa flag
Dear Freesurfer experts, I'm trying to run Tracula -prep after sourcing Freesurfer 5.3. The file subjid/dmri/dwi_motion.txt is not included in the output. I then ran: trac-all -qa -c dmrirc and got the error message: flag -qa unrecognized Do you know what could have gone wrong? Do I have to download the updated Tracula version from here: http://ftp.nmr.mgh.harvard.edu/fswiki/Tracula ? Thank you, Trang ___ 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.
[Freesurfer] bbregister and fnirt
Hi all, We're conducting the registration using bbregister that gives us a registration matrix (a .dat file) BUT the original structural file remains intact, i.e. the registered output can be viewed but not stored. Can we store the co-registered structural image as a .nii file? And if so, how? We are using the Connectivity Toolbox that requires structural data to be coregistered with functional data, and there is no way we can feed in the .dat file. Also, what are your thoughts on first using bbregister for linear coregistration, and then use fnirt on the output to get nonlinear coregistration? We ask this because we are working on a younger population (ages 8-25) with autism spectrum disorder and the data is affected by motion. Should we also be using --init-fsl instead of --init-spm if we want to use fnirt? Thank you for your help, Trang ___ 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.
[Freesurfer] Checking raw dicom files
Dear Freesurfer experts, After I ran the functional to structural registration using the bbregister command, it looks like the dorsal part of the brain for this participant is cut off in the BOLD images. When we ran the scan, we made sure that the slice prescription covered the entire brain. We also looked at the functional scan in the control room right after the scan and it looked ok. We aren't sure what went wrong and why the bold data is cut off. Is there any way I can look at the raw dicom files to check if it includes the entire brain? Thank you, Trang ___ 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] Checking raw dicom files
Dear Bruce, Thank you for your response. I just looked at the f.nii file using fslview and it looks like the top is cut off. Trang what are you visualizing it in? If you just look at it without the registration does it look ok? On Thu, 4 Apr 2013, qtngu...@nmr.mgh.harvard.edu wrote: Dear Freesurfer experts, After I ran the functional to structural registration using the bbregister command, it looks like the dorsal part of the brain for this participant is cut off in the BOLD images. When we ran the scan, we made sure that the slice prescription covered the entire brain. We also looked at the functional scan in the control room right after the scan and it looked ok. We aren't sure what went wrong and why the bold data is cut off. Is there any way I can look at the raw dicom files to check if it includes the entire brain? Thank you, Trang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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.
[Freesurfer] error finding data on bourget
Dear Freesurfer experts, I'm trying to run structural reconstruction for two subjects DODASD016 and DODASD017. DODASD016 was scanned last Wed Oct 10 and last week I was able to findsession DODASD016, run dcmdir-info-mgh, and run recon-all using pbsubmit. However, after this was done I was unable to unpack the Bold DTI Data from Bourget. We believe that the recon-all didn't work and when we tried to re-run: (for DODASD016) dcmdir-info-mgh /cluster/archive/301/siemens/TrioTim-35006-20121010-153034-596000 (and for DODASD017) dcmdir-info-mgh /cluster/archive/301/siemens/TrioTim-35006-20121017-153207-445000 ...I got the error message ERROR: finding data Can you help me resolve this issue? Or can you direct me to someone who can help? Thank you! Trang ___ 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.
