[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
Did you compare the number of slices to that of your sequence? I have had issues when overzealously pulling data off of bourget (that is before the files have completed being sent). A simple re-conversion to mgz (or whatever format you prefer) has fixed this when waiting a bit longer till bourget has finished (depending on the sequence you can check this by just counting the number of dicom files (usually should correspond to # of slices). HTH, D On Thu, Apr 4, 2013 at 2:46 PM, 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 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 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.
