Alright, I followed the directions online and believe I have sent my file "JeffSegFileExample" to your "transfer/incoming" folder in the ftp server.
-----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Tuesday, November 15, 2016 5:12 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [WARNING : A/V UNSCANNABLE]RE: Left Thalamus and Pallidum segmentation problem Hi Jeffrey the tarred and gzipped subject folder should be a lot bigger - way too big to email. YOu'll need to upload it to our ftp site cheers Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote: > Here is the tar zip of the subject folder. This is the first time I have ever > done this type of compression, so please let me know if anything seems awry. > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce > Fischl > Sent: Tuesday, November 15, 2016 3:05 PM > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Left Thalamus and Pallidum segmentation > problem > > Hi Jeffrey > > if you upload the entire subject dir (gzip and tar) we will take a look > cheers Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote: > >> Thank you for replying so promptly. >> I changed it to the norm.mgz, but it didn't alter how the segementation >> aligned with the brain. The norm.mgz shows the pallidum in more detail, but >> also that it is not contained with the segementation. >> >> So, I suppose my original question is still the same. >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce >> Fischl >> Sent: Tuesday, November 15, 2016 12:06 PM >> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] Left Thalamus and Pallidum segmentation >> problem >> >> Hi Jeffrey >> >> you can't tell the boundaries overlaying on the brainmask.mgz as it will >> erode thalamus and pallidum. Look at the norm.mgz to check whether the >> borders are accurate Bruce On Tue, 15 Nov 2016, Jeffrey Crawford wrote: >> >>> >>> Hello there! >>> >>> >>> >>> I was wondering if I could get some help on an issue I am noticing >>> in the segmentation of the left thalamus and left Pallidum on my scans. >>> I’ve included pictures of tkmedit so you can see what I mean. The >>> tkmedit uses this code: tkmedit SZ2014 brainmask.mgz lh.white -aux >>> norm.mgz -aux-surface rh.white -segmentation aparc+aseg.mgz >>> >>> >>> >>> All of my scans have been through the entire recon-all process and , >>> out of my sample of about 172 patients and controls, just about 29 >>> of them show this odd segmentation on, almost always, the left >>> hemisphere. The left thalamus seems to be over estimating the size and the >>> pallidum is underestimating its size. I was wondering why this would be and >>> if the community thought it would be okay to go back and manually edit the >>> segementation to fit the subcorticals structures better? >>> >>> >>> >>> Also, since I have never done such editing, is it advisable or even >>> possible to do so? >>> >>> >>> >> > _______________________________________________ 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.
