Hi Doug, Thanks for the quick reply! It seems the value of the writing is much higher than any value elsewhere in the image (over 4000). Instructions on how to replace this value with values of nearby voxels would be great -- hopefully that will allow us to run the autorecon1 command on it.
Thanks, Alex > Hi Alex, there's no way to "erase" it in a way that you can recover the > underlying signal. I'm surprised that such small things are causing the > talairach to crash. If the writing is always the same value and that > value does not appear in other parts of the image, you might be able > to replace the value with values of nearby voxels. Let me know if you > need some instructions on this. > doug > > On 08/22/2012 02:08 PM, Alexandra Tanner wrote: >> Hi Doug, >> >> I'm currently working with 4-6 year old clinical pediatric non-Siemens >> DICOM files that I'm unpacking and preprocessing in freesurfer. So far >> we've been able to unpack the DICOMS to .nii format and successfully >> begin >> the autorecon process for our first few subjects. We've noticed, when >> looking at the raw scans for some of our subjects, however, there is >> writing (probably information from the scan console) included in the >> images, and in some slices, slightly overlapping with the outer edge of >> the skull/brain. When attempting to run the autorecon1 on these scans, >> the >> command terminates during the talairach transform. We're thinking, since >> we don't have this issue with all of our subjects, the writing may be >> what >> is causing the problem. >> >> I'm wondering if you know of any way to remove the writing from the >> images >> (I tried seeing if I could erase the lettering in tkmedit but it seems >> it >> can't be erased manually). Attached is a screenshot of a coronal slice >> with the writing. Any suggestions would be greatly appreciated! >> >> Thanks, >> Alex >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > _______________________________________________ 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.
