I'm a bit puzzled by this. Are you saving the xfm file to talairach.xfm? In the log file, it clearly says:
INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm and there is no command in the log that indicates that it was overwritten, and I cannot replicate this behavior here On 1/31/2022 10:33 AM, Goeckner, Bryna wrote: > External Email - Use Caution > > Sorry - Sending these directly since I tried to send these earlier, but they > were blocked by the list-serve. > > Bryna Goeckner (she/her) > Graduate Student > Medical College of Wisconsin > Neuroscience Doctoral Program > > -----Original Message----- > From: Goeckner, Bryna > Sent: Friday, January 28, 2022 11:36 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Problems with recon for manually fixed Talairach > > I'm attaching the two recon-all.logs. Both were generated for same subject > using the same corrected talairach.xfm file, one with -notal-check and the > other with -notalairach. Please let me know if you have any other questions. > Thanks! > > Bryna Goeckner (she/her) > Graduate Student > Medical College of Wisconsin > Neuroscience Doctoral Program > > Subject: Re: [Freesurfer] Problems with recon for manually fixed > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <95652ab6-b36a-c708-edd7-b8734c1c7...@mgh.harvard.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Can you send the recon-all.log? > > On 1/27/2022 9:34 AM, Goeckner, Bryna wrote: >> External Email - Use Caution >> >> We are using FS 7.2 >> >> Bryna Goeckner (she/her) >> Graduate Student >> Medical College of Wisconsin >> Neuroscience Doctoral Program >> >> Date: Wed, 26 Jan 2022 16:43:44 -0500 >> From: "Douglas N. Greve" <dgr...@mgh.harvard.edu> >> Subject: Re: [Freesurfer] Problems with recon for manually fixed >> Talairach >> To: freesurfer@nmr.mgh.harvard.edu >> Message-ID: <8e0752c5-13fa-755e-c416-4253ce504...@mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> what version of FS are you using? >> >> On 1/21/2022 2:21 PM, Goeckner, Bryna wrote: >>> ????????External Email - Use Caution >>> >>> Hi, >>> >>> I am trying to decide how to proceed after manually updating a >>> talairach since various ways I?ve tried the recon process give me >>> different results. >>> >>> Our group used Freesurfer 7.2 for processing data with the T2 and 3T >>> flags as follows: >>> >>> recon-all -subject $1 -i $2/rawT1.ORIG.nii.gz -T2 >>> $2/rawT2.ORIG.nii.gz -T2pial -parallel -openmp 12 -3T -all >>> >>> After visual inspection, I made adjustments to the talairach using >>> tkregister2 and then used the code below to rerun the recon: >>> >>> recon-all -subject $1 -T2 $2/rawT2.ORIG.nii.gz -T2pial -parallel >>> -openmp 12 -3T? -all >>> >>> When this was done, the talairach.xfm file was restored to the >>> talairach from the original recon, while the talairach.xfm~ was still >>> the fixed version. At no point in this entire process did the >>> talairach (fixed or original) generate an error. >>> >>> To avoid the overwriting of the talairach.xfm file, I tried using >>> (separately) the -notalairach and -notal-check flags. For both, the >>> talairach.xfm file stayed as the fixed talairach, but I got different >>> aseg and aparc results. >>> >>> I?d like to know more about how these to flags differ and if you have >>> a recommendation on which process is best.? The plan is to eventually >>> use this data in TRACULA. >>> >>> Thanks for your help, >>> >>> *Bryna Goeckner*?(she/her) >>> >>> Graduate Student >>> >>> Medical College of Wisconsin >>> >>> Neuroscience Doctoral Program _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
