There was no snapshot. Can you resend? On 10/24/2019 7:06 PM, Alexopoulos, Dimitrios wrote: > External Email - Use Caution > > I apologize for the confusion. Whether I use the -hires or -conf2hires flag > the subcortical segmentations look good. > > The cortical segmentations have some issues in the ventral medial area (see > snapshot below), which is likely caused by difficulty in FS delineating WM > superior to the gyrus rectus. I'm not sure how to correct this so I was > thinking the higher resolution data may lead to a better WM segmentation? > > Is my thinking correct? If so, which flag is best? > > Jim > > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Greve, Douglas N.,Ph.D. > Sent: Thursday, October 24, 2019 5:37 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon-all at native resolution > > You mean the surfaces using -hires look fine? If so, then continue to use > -hires > > On 10/24/19 6:32 PM, Alexopoulos, Dimitrios wrote: >> External Email - Use Caution >> >> The cortical parcellations in the aseg and aparc+seg have some issues in the >> orbital prefrontal regions and we're were hoping that the higher resolution >> images would help. The surfaces look fine. >> >> We should use the -hires flag instead in this scenario? >> >> Thx. >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Greve, Douglas N.,Ph.D. >> Sent: Thursday, October 24, 2019 5:06 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] recon-all at native resolution >> >> oh, sorry, yes it is. The surfaces are placed on the high res volumes, >> but the aseg will be at 1mm. If you need the aseg at highres, then you >> will need to use the -hires flag (but the surfaces will suffer) >> >> On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote: >>> External Email - Use Caution >>> >>> Doug, >>> >>> I copied over files and ran using the -conf2hires flag, however, the >>> orig.mgz/brainmask.mgz are resampled to 1mm isotropic not the native 0.8mm. >>> >>> Using the -hires flag maintains the orig.mgz/brainmask.mgz at native 0.8mm >>> resolution. >>> >>> Is this expected when running -conf2hires? >>> >>> Jim >>> >>> -----Original Message----- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Greve, Douglas >>> N.,Ph.D. >>> Sent: Tuesday, October 15, 2019 11:54 AM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] recon-all at native resolution >>> >>> better to use a patch I created for the HCP, see >>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hc >>> p >>> /readme >>> >>> >>> On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote: >>>> External Email - Use Caution >>>> >>>> We have data acquired at 0.8mm isotropic and would like to maintain >>>> this resolution in the processing stream rather than FS resampling to 1mm. >>>> >>>> Is the command to do this 'recon-all -hires -all'? >>>> >>>> Are there any drawback to doing this? >>>> >>>> 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 >>>> 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
