If you have editeid all your subjects and re-run (with -all or appropirate -auto-reconX flag), then you can run -qcache without those flags
On 05/21/2018 04:36 PM, Alexopoulos, Dimitrios wrote: > External Email - Use Caution > > 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 > > > "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 3:28 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 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. 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
