External Email - Use Caution Hoping to get some clarification. Any further comments on the correct command to run after making manual edits to wm, brainmask, and adding control control points? The studies were originally processed using the following: recon-all -s -i -hippocampal-subfields-T1 -hires -all -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 Alexopoulos, Dimitrios Sent: Friday, May 25, 2018 12:47 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] -qcache in recon-all commnd External Email - Use Caution Any further comments on the correct command to run after making manual edits. Specifically, should the '-hippocampal-subfields-T1' flag be used again in the rerun 'recon-all -all' command after manual edits? 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 Alexopoulos, Dimitrios Sent: Wednesday, May 23, 2018 10:38 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] -qcache in recon-all commnd External Email - Use Caution Any further advice on whether to include '-hippocampal-subfields-T1' flag in the rerun after manual edits? 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 22, 2018 11:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -qcache in recon-all commnd Sorry, I don't know. I doubt it. Maybe Eugenio can weigh in On 05/22/2018 12:11 PM, Alexopoulos, Dimitrios wrote: > External Email - Use Caution > > Thanks Doug. > > Sorry for the multiple posts. I forgot to mention that the original recon-all > run included the '-hippocampal-subfields-T1' flag. > > Does this flag need to be included in the rerun (after manual edits) > recon-all command? > > 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 4:52 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] -qcache in recon-all commnd > > You can run this: > recon-all -s -all -hires > but it might run more things than you need (no harm, just computer time). > Depending on what you have edited, you may be able to use one of the > -autorecon flags to speed things up. > > > On 05/21/2018 04:48 PM, Alexopoulos, Dimitrios wrote: >> External Email - Use Caution >> >> We have not re-run anything yet. The data was originally generated using' >> recon-all -s -all -hires -qcache'. >> >> We have since made manual edits to the wm, brainmask and added control >> points, and now want to rerun to incorporate these changes. >> What would be the correct command? >> >> 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 3:40 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] -qcache in recon-all commnd >> >> >> 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 >> >> ________________________________ >> 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 ________________________________ 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 ________________________________ 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
