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 CautionHi 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 dgreve@mgh.harvard.edu Sent: Sunday, February 13, 2022 4:30 PM To: Goeckner, Bryna bgoeckner@mcw.edu; Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: FW: [Freesurfer] Problems with recon for manually fixed Talairach
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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 CautionSorry - 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-b8734c1c7402@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 CautionWe 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" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Problems with recon for manually fixed Talairach To: freesurfer@nmr.mgh.harvard.edu Message-ID: 8e0752c5-13fa-755e-c416-4253ce5043b3@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