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 Caution > > OK, so I only need to run a single command to incorporate the all edits: > recon-all -s subj -hires -qcache > > Jim > > "The materials in this email are private and may contain Protected Health > Information. If you are not the intended recipient, be advised that any > unauthorized use, disclosure, copying, distribution or the taking of any > action in reliance on the contents of this information is strictly > prohibited. If you have received this email in error, please immediately > notify the sender via telephone or return email." > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@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 Caution >> >> Just 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 >> >> "The materials in this email are private and may contain Protected Health >> Information. If you are not the intended recipient, be advised that any >> unauthorized use, disclosure, copying, distribution or the taking of any >> action in reliance on the contents of this information is strictly >> prohibited. If you have received this email in error, please immediately >> notify the sender via telephone or return email." >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@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 Caution >>> >>> I 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 >>> >>> >>> "The materials in this email are private and may contain Protected Health >>> Information. If you are not the intended recipient, be advised that any >>> unauthorized use, disclosure, copying, distribution or the taking of any >>> action in reliance on the contents of this information is strictly >>> prohibited. If you have received this email in error, please immediately >>> notify the sender via telephone or return email." >>> >>> -----Original Message----- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@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 >>>> >>>> "The materials in this email are private and may contain Protected >>>> Health Information. If you are not the intended recipient, be >>>> advised that any unauthorized use, disclosure, copying, distribution >>>> or the taking of any action in reliance on the contents of this >>>> information is strictly prohibited. If you have received this email >>>> in error, please immediately notify the sender via telephone or return >>>> email." >>>> >>>> *From:*freesurfer-boun...@nmr.mgh.harvard.edu >>>> [mailto:freesurfer-boun...@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 >>>> >>>> >>>> -------------------------------------------------------------------- >>>> - >>>> - >>>> -- >>>> >>>> The materials in this message are private and may contain >>>> Protected Healthcare Information or other information of a >>>> sensitive nature. If you are not the intended recipient, be >>>> advised that any unauthorized use, disclosure, copying or the >>>> taking of any action in reliance on the contents of this >>>> information is strictly prohibited. If you have received this >>>> email in error, please immediately notify the sender via telephone >>>> or return mail. >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> >>>> Freesurfer mailing list >>>> >>>> Freesurfer@nmr.mgh.harvard.edu >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> -------------------------------------------------------------------- >>>> - >>>> - >>>> -- >>>> >>>> The materials in this message are private and may contain Protected >>>> Healthcare Information or other information of a sensitive nature. >>>> If you are not the intended recipient, be advised that any >>>> unauthorized use, disclosure, copying or the taking of any action in >>>> reliance on the contents of this information is strictly prohibited. >>>> If you have received this email in error, please immediately notify >>>> the sender via telephone or return mail. >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to whom it >>> is addressed. If you believe this e-mail was sent to you in error and the >>> e-mail contains patient information, please contact the Partners Compliance >>> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent >>> to you in error but does not contain patient information, please contact >>> the sender and properly dispose of the e-mail. >>> >>> >>> ________________________________ >>> The materials in this message are private and may contain Protected >>> Healthcare Information or other information of a sensitive nature. If you >>> are not the intended recipient, be advised that any unauthorized use, >>> disclosure, copying or the taking of any action in reliance on the contents >>> of this information is strictly prohibited. If you have received this email >>> in error, please immediately notify the sender via telephone or return mail. >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> ________________________________ >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. If you >> are not the intended recipient, be advised that any unauthorized use, >> disclosure, copying or the taking of any action in reliance on the contents >> of this information is strictly prohibited. If you have received this email >> in error, please immediately notify the sender via telephone or return mail. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ________________________________ > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. 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