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
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