Hi Bronwyn, I tried to replicate your issue using both v5.3 and the current dev environment, but I had no luck. I'm guessing the problem has to do with combining the development binary along with 5.3, so I suggest using the 5.3 version of mris_make_surfaces to fix this.
best, Andrew ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bronwyn Overs <b.ov...@neura.edu.au> Sent: Sunday, July 09, 2017 7:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] Medial Surface Problem Hi Bruce, I have now re-uploaded all the requested files and info via the ftp site (see below). The zipped file name is fsMedialSurfaceProblem.zip Name (surfer.nmr.mgh.harvard.edu:Bronwyn): anonymous 331 Please specify the password. Password: 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. ftp> cd transfer/incoming 250 Directory successfully changed. ftp> put fsMedialSurfaceProblem.zip local: fsMedialSurfaceProblem.zip remote: fsMedialSurfaceProblem.zip 229 Entering Extended Passive Mode (|||37889|). 150 Ok to send data. 100% |***********************************| 2017 MiB 51.01 KiB/s 00:00 ETA 226 Transfer complete. 2116019235 bytes sent in 11:15:08 (51.01 KiB/s) Kind regards, Bronwyn Overs Research Assistant [Neuroscience Research Australia] Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au> [Follow @neuraustralia on twitter]<https://twitter.com/neuraustralia>[Follow NeuRA on facebook]<https://www.facebook.com/NeuroscienceResearchAustralia>[Subscribe to the NeuRA Magazine]<http://www.neura.edu.au/help-research/subscribe> On 5 Jul 2017, at 3:40 am, Bruce Fischl <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> wrote: sure. Can you upload the data again to our ftp site? Don't use the filedrop - use ftp and make sure you include the cross and the long of all the timepoints for this subject, and also the coordinates of the location you are seeing the problem cheers Bruce On Tue, 4 Jul 2017, Bronwyn Overs wrote: Thanks Bruce. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au<http://neura.edu.au> Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the NeuRA Magazine On 3 Jul 2017, at 11:55 pm, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: Hi Bronwyn not yet, but we'll get to it soon cheers Bruce On Mon, 3 Jul 2017, Bronwyn Overs wrote: Hi Bruce, Just wanted to check in on the status of reviewing our medial surface problem. Any luck so far? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the NeuRA Magazine On 14 Jun 2017, at 9:52 am, Bronwyn Overs <b.ov...@neura.edu.au> wrote: Hi Bruce, That's fine, thanks very much. Bronwyn Overs Research Assistant <neura-logo-email.png> Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 neura.edu.au Twitter | Facebook | Subscribe ___________________________________________________________________________ _ From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Wednesday, 14 June, 2017 00:02:04 Subject: Re: [Freesurfer] Medial Surface Problem thanks Bronwyn I got them. It will take a bit for us to get to as this is in the long stream and we have a new postdoc who will be taking it over. cheers Bruce On Tue, 13 Jun 2017, Bronwyn Overs wrote: > Hi Bruce, > Sure, files have been dropped again. > > Kind regards, > > Bronwyn Overs > Research Assistant > > Neuroscience Research Australia > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 > > neura.edu.au > > Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the > NeuRA Magazine > > > On 13 Jun 2017, at 11:44 am, Bruce Fischl > <fis...@nmr.mgh.harvard.edu> wrote: > > Hi Bronwyn > Can you filedrop it again? I don't think I have it > Thanks > Bruce > > On May 15, 2017, at 8:27 PM, Bronwyn Overs <b.ov...@neura.edu.au> > wrote: > > Hi Bruce, > Thank you for offering to take a look at this medial surface > problem. > > I have uploaded all of the relevant files to through the > Martinos Centre FileDrop v2.0 to your email address > (fis...@nmr.mgh.harvard.edu). Please let me know if you require > any additional information. > > Kind regards, > > Bronwyn Overs > Research Assistant > > Neuroscience Research Australia > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 > > neura.edu.au > > Follow @neuraustralia on twitter Follow NeuRA on facebook > Subscribe to the NeuRA Magazine > > > On 5 May 2017, at 8:25 am, Bruce Fischl > <fis...@nmr.mgh.harvard.edu> wrote: > > if someone can upload a dataset as well as the exact > coordinates of the problem I'll take a look > > cheers > Bruce > > On Fri, 5 May 2017, Yann Quidé wrote: > > Hi all, > We also have the same issue, any > idea/suggestion? > Thanks. > Yann > > On 27 Apr 2017, at 9:43 am, Bronwyn Overs > <b.ov...@neura.edu.au> > wrote: > Hi Mailing List, > Still trying to solve the below medial surface > problem. Does anyone > have any ideas? > Kind regards, > Bronwyn Overs > Research Assistant > Neuroscience Research Australia > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 > Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 > 1265 > neura.edu.au > Follow @neuraustralia on twitter Follow NeuRA > on facebook Subscribe to > the NeuRA Magazine > > On 28 Mar 2017, at 10:51 pm, Yann Quidé > <yannqu...@gmail.com> wrote: > Dear all, > I have an equivalent issue with my data. Any > idea on how to fix > this? > Thanks. > Yann > > Begin forwarded message: > From: Bronwyn Overs <b.ov...@neura.edu.au> > Subject: Re: [Freesurfer] Medial Surface > Problem > Date: 20 March 2017 10:28:37 am AEDT > To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu> > Reply-To: Freesurfer support list > <freesurfer@nmr.mgh.harvard.edu> > Hello again mailing list, > Can anyone address the possible cause of the > medial > surface problem shown below (overestimating of > rh medial > surface, shows up in the long image and not > the tp or base > images). Forgot to mention that I am using > freesurfer v5.3 > with an updated mris_make_surfaces binary > (sourced from > thedevelopmentversionat ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurf er/ dev_binarie > s/cento > s6_x86_64/ ). > Here is the image again: > <unknown.png> > Kind regards, > Bronwyn Overs > Research Assistant > Neuroscience Research Australia > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 > Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 > 1265 > neura.edu.au > Follow @neuraustralia on twitter Follow NeuRA > on facebook > Subscribe to the NeuRA Magazine > > On 6 Mar 2017, at 1:17 pm, Bronwyn Overs > <b.ov...@neura.edu.au> wrote: > Hi mailing list, > I am currently processing a longitudinal image > and > have come across a problem at the medial > surface in > the long image (step 3). As you can see in the > attached image, the rh medial surface has been > significantly overestimated and extends into > the lh > surface. This error showed up only in only 1 > of the > 2 long images for this subject, and both the > time-point images and the base are perfectly > fine. > Do you know why this is happening? > <Screen Shot 2017-03-06 at 1.09.53 pm.png> > Kind regards, > Bronwyn Overs > Research Assistant > Neuroscience Research Australia > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 > Australia > M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 > 1265 > neura.edu.au > Follow @neuraustralia on twitter Follow NeuRA > on > facebook Subscribe to the NeuRA Magazine > _______________________________________________ > 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. > _______________________________________________ > 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. > _______________________________________________ > 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. > _______________________________________________ > 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. > > _______________________________________________ > 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. > > > _______________________________________________ > 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. > > > > _______________________________________________ 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. _______________________________________________ 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. _______________________________________________ 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
