You can run it from the same command line. doug On 8/22/12 8:45 AM, Sarosh, Cyrus wrote: > Doug, > > Sorry for so many questions, but can I run the autorecon3 command with my > previous recon-all -subjid (subject ID) -autorecon-pial or will the > autorecon3 have to follow the previous command? > > 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 21, 2012 3:52 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz > > Run it with -autorecon3 > doug > > On 08/21/2012 10:44 AM, Sarosh, Cyrus wrote: >> 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 >> >> > -- > 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 > >
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