Yes, I still don't understand. That snippet of code that you point out is embedded in an if statement: if($DoCleanTal || ! -e $xfm) then Copy endif
! -e $xfm means that the file must not already exist. So, as long as that file exists, it will not copy over it ($DoCleanTal is a special flag that you are not using). So I think I understand what you are doing, but I just don't understand why the xfm is changing. One thing you can do is to just change the permissions on the file, eg, chmod a-w talairach.xfm This will remove write permissions so that the file cannot change. On 2/14/2022 11:18 AM, Goeckner, Bryna wrote: > External Email - Use Caution > > Hi Dr. Greve, > > Thanks again for your help on this. I will try to explain things a bit > better, but please let me know if you have additional questions. > > I used tkregister2 to fix a bad talairach and then tried to redo the > recon-all. Since we had used a few special flags in our recon-all, I tried > to repeat those by running this command: > recon-all -subject $1 \ > -T2 $2/rawT2.ORIG.nii.gz \ > -T2pial \ > -parallel -openmp 12 \ > -3T \ > -all > > When this was used, the fixed talairach was overwritten. I believe this is > shown by the following line in recon-all.log: cp > transforms/talairach.auto.xfm transforms/talairach.xfm > When I would check the talariach after the recon, the talairach.xfm file > would again be the original bad talairach. > > In order to avoid this overwrite, I tried running two separate processes > (same subject, same fixed talairach): one with -notal-check, and one with > -notalairach. These both preserved the fixed talairach but produced slightly > different results (different aparc & aseg values). > The exact code I used is here: > #1st process > recon-all -subject $1 \ > -T2 $2/rawT2.ORIG.nii.gz \ > -T2pial \ > -parallel -openmp 12 \ > -3T \ > -all \ > -notal-check > > #2nd process > recon-all -subject $1 \ > -T2 $2/rawT2.ORIG.nii.gz \ > -T2pial \ > -parallel -openmp 12 \ > -3T \ > -all \ > -notalairach > > I am not sure what happens within recon-all to make these two processes > generate different values. > > Ultimately, what I want to determine is after we fix a talairach, how should > we redo the recon to ensure the fixed talairach is being used for all > downstream recon-all steps. Do you have a recommendation about using either > -notal-check or -notalairach (or is there another preferred way to do this)? > > Thanks again for your help with this! > > Bryna Goeckner (she/her) > Graduate Student > Medical College of Wisconsin > Neuroscience Doctoral Program > > -----Original Message----- > From: Douglas N. Greve <dgr...@mgh.harvard.edu> > Sent: Sunday, February 13, 2022 4:30 PM > To: Goeckner, Bryna <bgoeck...@mcw.edu>; Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: FW: [Freesurfer] Problems with recon for manually fixed Talairach > > ATTENTION: This email originated from a sender outside of MCW. Use caution > when clicking on links or opening attachments. > ________________________________ > > 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
