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Ok. So no my '-all' flag? I just want to make sure as we're re-running a 100+ edited subjects and I had read elsewhere that the '-all' flag is required.
Jim
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-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Monday, May 21, 2018 3:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -qcache in recon-all commnd
You don't even need to include -hires (though I don't think it hurts anything)
On 05/21/2018 04:25 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionOK, so I only need to run a single command to incorporate the all edits: recon-all -s subj -hires -qcache
Jim
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-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Monday, May 21, 2018 3:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -qcache in recon-all commnd
Yes, run the same optional flag. When you run -qcache, do not include -all
On 05/21/2018 04:02 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionJust want to confirm which command to issue to rerun 6.0 incorporating manual edits to the wm.mgz, brainmask.mgz andadding control points that were made in no specific order. The data was originally processed using the following: recon-all -s subj -hires and -qcache -all
In order to capture all the edits is it best to use the same optional flags when the stream is rerun? That is, is it best just to use the same command to rerun: recon-all -s subj -hires and -qcache -all
Jim
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-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Tuesday, May 08, 2018 11:19 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -qcache in recon-all commnd
Yes, I think so
On 05/07/2018 10:35 PM, Alexopoulos, Dimitrios wrote:
External Email - Use CautionI ran 'recon-all -all -hires -qcache' on several datasets. I made numerous edits of the brainmansk.mgz (for dura removal) and added control points and want to rerun with the changes.
I thought I could rerun with changes using; 'recon-all -make all' Do I need to include the -hires and -qcache flags again when invoking the above command with -make?
Jim
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-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Thursday, April 12, 2018 1:01 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -qcache in recon-all commnd
Right. And you'd need to redo it after all manual edits
On 04/12/2018 11:06 AM, Alexopoulos, Dimitrios wrote:
Thanks. We are starting an analysis of a pediatric cohort using FS 6.0 and may/may not use QDEC downstream for surface-based group analysis.
That said, it sounds like it is not a bad idea use -qcache other than more preprocessing time.
Basically, same output as without -qcahe but more files created that may be used later for QDEC?
Jim
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*From:*freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* Wednesday, April 11, 2018 10:29 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] -qcache in recon-all commnd
It is not. -qcache is a preprocessing step prior to doing group analysis with QDEC. If you use it, you should only do so after you have finished all the individual analysis (eg, manual edits)
On 4/11/18 10:02 PM, Alexopoulos, Dimitrios wrote:
Is it recommended to use the -qcache flag in the basic recon-all -all command? What does it do and what are the advantage of using it? Jim
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