External Email - Use Caution Hi Douglas,
I wonder why anybody has answered to my question about the outputs of cortical thickness with FreeSurfer. I am not familiarized with them and I would just to do statistical comparisons. Could you help me with this, please? Best regards, Rosie El mar., 22 may. 2018 12:36, Douglas N. Greve <dgr...@mgh.harvard.edu> escribió: > 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 >
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