Doug, Thanks for the update and not much time was wasted so no worries. I edited the brainmask.mgz file and ran the new recon-all command with autorecon-pial, which created a new brain.finalsurfs.mgz with the dura edited out and correct surfs. New stat files were created, but no new aparc+aseg.mgz file. Loading this file still shows the segmentation including dura in the cortex and the modification date is the original recon-all date. Is there any way to create a new aparc+aseg.mgz file with this new surf data?
Thanks, Cyrus -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 20, 2012 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus, my apologies, I told you to edit the wrong file. You should edit brainmask.mgz, not brainmask.finalsurfs.mgz. Sorry about, I hope you did not waste too much time. doug On 08/20/2012 09:31 AM, Sarosh, Cyrus wrote: > Doug, > > I edited the dura from the brain.finalsurfs.mgz file using the command > tkmedit (subject ID) brain.finalsurfs.mgz -aux T1.mgz -surfs and going > through the necessary slices that need fixing and erase the dura. I then ran > this subject with the command recon-all -subjid (subject ID) -autorecon-pial. > Looking at the date modified information it appears that new stat files were > created, but no new aparc+aseg.mgz file was created. I loaded the > brain.finalsurfs.mgz file, which contained a modify date of when I ran the > new recon-all command and it looked identical to the original > brain.finalsurfs.mgz file, so all of my edits were gone and all of the surfs > were incorrect just like before. Also, loading the aparc+aseg.mgz file it > looks identical to the previous aparc+aseg.mgz, so no changes were made. > Looking at the log it appears my edits were useless because the first step > that runs is the -maskbfs step which appears to generate the > brain.finalsurfs.mgz file. So, do I need to edit a different file or was my > command line incorrect? > > Thanks, > > Cyrus > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N > Greve > Sent: Tuesday, August 14, 2012 1:43 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz > > > For GM volume and thickness, you will certainly want to fix it. Given how big > the PET voxels are, it might not be such a big deal for that. To fix it, you > would edit the dura from the brain.finalsurfs.mgz and run recon-all with > -autorecon-pial. This will fix aparc+aseg and re-generate the stats files. > doug > > > On 08/14/2012 01:40 PM, Sarosh, Cyrus wrote: >> Doug, >> >> Well we want to use the stats information for gray matter volume and >> thickness of certain vois and we want to use the aparc+aseg file to run PET >> image analysis to collect data from certain vois. Would performing the given >> actions correct any incorrect data in the stats files and create a new >> aparc+aseg.mgz file or will this require separate actions? >> >> Thanks, >> >> Cyrus >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >> N Greve >> Sent: Tuesday, August 14, 2012 11:28 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz >> >> >> Depending upon how bad it is and what you are going to do with it, it may be >> a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run >> recon-all -autorecon-pial ... >> doug >> >> >> On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote: >>> Doug, >>> >>> I looked at the surface files by using the command -tkmedit (subject ID) >>> brainmask.mgz -surfs -aseg. I also viewed the same surfs using the T1.mgz >>> file. The pial surface (red line) does identify the dura as part of the >>> cortex, but it doesn't look as bad as the aseg.mgz vois made it appear. >>> >>> Cyrus >>> >>> -----Original Message----- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >>> N Greve >>> Sent: Monday, August 13, 2012 4:13 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz >>> >>> Hi Cyrus, this may or may not be a problem. The cortical label in >>> aseg.mgz is not used for this reason. Usually, the surface-based >>> method will exclude the dura in these situations. Are the surfaces >>> accurate or are they including dura as well? BTW, you should not be >>> editing the >>> aparc+aseg.mgz. >>> doug >>> >>> On 08/13/2012 01:04 PM, Sarosh, Cyrus wrote: >>>> Hello FreeSurfer Users, >>>> >>>> I looked for a possible solution to my problem in the Mail Archive and >>>> found this article referring to almost the exact same problem I am having: >>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314. >>>> h t ml. Basically,pieces of the subarachnoid space/pia >>>> mater/arachnoid/dura mater/skull are being segmented as the cortex >>>> in certain slices and this occurs when it is physically adjacent to the >>>> gray matter. Besides this point everything else seems to be running smooth. >>>> In the related article I found that this may be caused by the MR >>>> parameters so I will give you the acquisition information that I know. >>>> Theacquisitions are SPGRs, taken on either a GE 3T or 1.5T and the >>>> resolution is 1mm isotropic. Any solutions besides going through >>>> each series slice by >>>> slice and making corrections would be greatly appreciated. >>>> >>>> Thanks, >>>> >>>> Cyrus >>>> >>>> ********************************************************** >>>> Electronic Mail is not secure, may not be read every day, and >>>> should not be used for urgent or sensitive issues >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> 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. >>> >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should >>> not be used for urgent or sensitive issues >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> 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 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > 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 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
