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Hello, We are finishing up manual inspection and editing of our dataset. As part of this process, we used QATools to generate QA reports. While we were running our reports the tmp/control.dat file was deleted from many of our subject directories (the brains had already been recon'd, so the corrected surfaces were not affected). The timing certainly suggests these were related, but we have no way of knowing if something else unrelated to QAtools happened that caused these files to be deleted. So two questions:
1) Has anyone else had an experience with QAtools where the control.dat file was deleted, or have any insight about why this could have happened? 2) Is the data in control.dat stored anywhere else? For example, can it be recovered from mri/ctrl_pts.mgz? We are mostly fine, but a few brains will need to have control points re-applied.
Something of a shot in the dark, but we would love any suggestions. Thanks, -Matt
Version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 uname -a: Linux vmpfc 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1+deb8u2 (2017-03-07) x86_64 GNU/Linux
External Email - Use Caution
Hi all, Sorry for the bump but I wanted to take one more shot at this. We're making it back but we've lost many, many hours of editing work. Has anyone else had experiences with QAtools, or other FreeSurfer utilities, removing control point data, or discovered any way to recover control.dat from other files? Thank you, -Matt
On Mon, May 21, 2018 at 11:35 AM Matthew Peverill mrpeverill@gmail.com wrote:
Hello, We are finishing up manual inspection and editing of our dataset. As part of this process, we used QATools to generate QA reports. While we were running our reports the tmp/control.dat file was deleted from many of our subject directories (the brains had already been recon'd, so the corrected surfaces were not affected). The timing certainly suggests these were related, but we have no way of knowing if something else unrelated to QAtools happened that caused these files to be deleted. So two questions:
- Has anyone else had an experience with QAtools where the control.dat
file was deleted, or have any insight about why this could have happened? 2) Is the data in control.dat stored anywhere else? For example, can it be recovered from mri/ctrl_pts.mgz? We are mostly fine, but a few brains will need to have control points re-applied.
Something of a shot in the dark, but we would love any suggestions. Thanks, -Matt
Version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 uname -a: Linux vmpfc 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1+deb8u2 (2017-03-07) x86_64 GNU/Linux
-- Matthew Peverill mrpeverill@gmail.com (preferred)
Hi Matt
I'm sorry to hear it. I've never heard of anything of ours deleting the control.dat unless you run recon-all with the appropriate -clean switch.
I don't know an easy way to recover them. Do you need them back? You could do something like copy the subject, run the intensity normalization on the copy, then look for points that are exactly 110 in the old (control-point-normalized) brain.mgz and the new one without control points, that are also wm in the aseg.mgz. This won't be exactly the control points, but would let you rerun without losing too much if that is what you are worried about
cheers Bruce
On Tue, 12 Jun 2018, Matthew Peverill wrote:
External Email - Use Caution
Hi all,Sorry for the bump but I wanted to take one more shot at this. We're making it back but we've lost many, many hours of editing work. Has anyone else had experiences with QAtools, or other FreeSurfer utilities, removing control point data, or discovered any way to recover control.dat from other files? Thank you, -Matt
On Mon, May 21, 2018 at 11:35 AM Matthew Peverill mrpeverill@gmail.com wrote: Hello, We are finishing up manual inspection and editing of our dataset. As part of this process, we used QATools to generate QA reports. While we were running our reports the tmp/control.dat file was deleted from many of our subject directories (the brains had already been recon'd, so the corrected surfaces were not affected). The timing certainly suggests these were related, but we have no way of knowing if something else unrelated to QAtools happened that caused these files to be deleted. So two questions:
- Has anyone else had an experience with QAtools where the control.dat file was deleted, or
have any insight about why this could have happened? 2) Is the data in control.dat stored anywhere else? For example, can it be recovered from mri/ctrl_pts.mgz? We are mostly fine, but a few brains will need to have control points re-applied.
Something of a shot in the dark, but we would love any suggestions. Thanks, -Matt
Version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 uname -a: Linux vmpfc 3.16.0-4-amd64 #1 SMP Debian 3.16.39-1+deb8u2 (2017-03-07) x86_64 GNU/Linux
-- Matthew Peverill mrpeverill@gmail.com (preferred)
-- Matthew Peverill 857-277-9083 mrpeverill@gmail.com (preferred)
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Matthew Peverill