Hi again,

Yes, assuming you are using the same version of FreeSurfer and since the WM volume is the same, the new surfaces you created should be similar to the September ones.

okay!

On Thu, 27 Oct 2005, Dahlia Sharon wrote:

Hi Ev,

recon-all.log says I ran recon-all stage 2 on Saturday, overwriting the good files from September. The subject I had really WANTED to edit at the time is already edited and fixed etc. My problem is with the overwritten files of the older subject. For this older subject, if I simply rerun stage2 and then stages 3&4, will that recalculate the correct surfaces from the (currently correct) mri/wm?

Thanks! Dahlia.

On Thu, 27 Oct 2005, Evelina Busa wrote:

...

Hi Dahlia

Since it seems unclear whether or not you edited the WM volume of this second subject whose surface files were overwritten, it might be helpful for you to first look at the recon-all.log text files in that subject's scripts/ directory, to see what commands you ran.

Probably what happened is that you recreated the surfaces unnecessarily, if the WM volume is correct. The files in mri/wm are from Sep12th, but the mri/filled volume files are new.

So back to the subject you *want* to edit/create surfaces for -- just make sure you likes its WM volume, and proceed with stages 3 & 4, if you haven't already.

I guess the main caveat here is that you're using the same version to recon all these subjects.

okay!

On Thu, 27 Oct 2005, Dahlia Sharon wrote:

...

Hi,

I overwrote several surface files (.inflated, .sulc, .curv, .smoothwm, .orig) by mistake while editing another subject. The volume in mri/wm/ is still the correct one. I should be able to run some of the recon steps again to get the correct surfaces back, but I don't want to do this without guidance so as not to make mistakes and start stepping over other files.

Can you tell me which commands to run to regenerate these surfaces correctly?

Thanks!!! Dahlia.

PS - the subject is ~dahlia/structurals/subj21_bay2

---

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Hi

ARe you talking about the inflated surfaces as viewed in tksurfer? I don't see why they wouldn't be identical for the old subject, since your subject's mri/wm/* are still dated Sep11th:

[evelina@fiat structurals]$ ls -l subj21_bay2/mri/wm total 17412 -rwxrwxrwx 1 dahlia meganal 65536 Sep 11 14:13 COR-001 -rwxrwxrwx 1 dahlia meganal 65536 Sep 11 14:13 COR-002 ...etc

...and all you ran was:

Sat Oct 22 14:26:20 EDT 2005 /autofs/space/mirabai_003/users/dahlia/structurals/subj21_bay2 /usr/local/freesurfer/dev/bin//recon-all -subjid subj21_bay2 -stage2 -hemi rh

....which should not have affected the wm volume anyway.

But looking at this subject's scripts/recon-all.log, it seems you used different versions:

Fri Sep 9 20:10:10 EDT 2005 /usr/local/freesurfer/beta/bin//recon-all

vs.

Sat Oct 22 14:26:20 EDT 2005 /autofs/space/mirabai_003/users/dahlia/structurals/subj21_bay2 /usr/local/freesurfer/dev/bin//recon-all -subjid subj21_bay2 -stage2 -

So probably you could just try rerunning stages 3 onward using your beta version that you used in September for this subject.

okay!

On Thu, 27 Oct 2005, Dahlia Sharon wrote:

Hey Ev, The problem is that the new surfaces don't currently look like the September ones - they look precisely like the new subject's surfaces before I did the final manual edits on Saturday. So I'm trying to find the way to get back the old surfaces. If I now rerun stages2-4, assuming the mri/wm/ volume is still correct, will I now get the correct old surfaces? Thanks! Dahlia.

On Thu, 27 Oct 2005, Evelina Busa wrote:

...

Hi again,

Yes, assuming you are using the same version of FreeSurfer and since the WM volume is the same, the new surfaces you created should be similar to the September ones.

okay!

On Thu, 27 Oct 2005, Dahlia Sharon wrote:

...

Hi Ev,

recon-all.log says I ran recon-all stage 2 on Saturday, overwriting the good files from September. The subject I had really WANTED to edit at the time is already edited and fixed etc. My problem is with the overwritten files of the older subject. For this older subject, if I simply rerun stage2 and then stages 3&4, will that recalculate the correct surfaces from the (currently correct) mri/wm?

Thanks! Dahlia.

On Thu, 27 Oct 2005, Evelina Busa wrote:

...

Hi Dahlia

Since it seems unclear whether or not you edited the WM volume of this second subject whose surface files were overwritten, it might be helpful for you to first look at the recon-all.log text files in that subject's scripts/ directory, to see what commands you ran.

Probably what happened is that you recreated the surfaces unnecessarily, if the WM volume is correct. The files in mri/wm are from Sep12th, but the mri/filled volume files are new.

So back to the subject you *want* to edit/create surfaces for -- just make sure you likes its WM volume, and proceed with stages 3 & 4, if you haven't already.

I guess the main caveat here is that you're using the same version to recon all these subjects.

okay!

On Thu, 27 Oct 2005, Dahlia Sharon wrote:

...

Hi,

I overwrote several surface files (.inflated, .sulc, .curv, .smoothwm, .orig) by mistake while editing another subject. The volume in mri/wm/ is still the correct one. I should be able to run some of the recon steps again to get the correct surfaces back, but I don't want to do this without guidance so as not to make mistakes and start stepping over other files.

Can you tell me which commands to run to regenerate these surfaces correctly?

Thanks!!! Dahlia.

PS - the subject is ~dahlia/structurals/subj21_bay2

---

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