Dear Bruce, Sorry about the screenshot of text.
You are right that it still uses the older version of recon-all. How do I fix this then? I can't delete the older version because I don't have access to it at all. Thanks for your patience. Cheers, Hweeling On 22 November 2017 at 15:52, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Hweeling > > please don't send us screenshots of text - either attach the file or > include text in the email. > > I'm pretty sure you are using an older recon-all script with a newer > FREESURFER_HOME. Try typing: > > which recon-all > > I bet it points to somewhere other than your V6 FREESURFER_HOME/bin dir > > cheers > Bruce > > > > On Wed, 22 Nov 2017, Hwee Ling Lee wrote: > > Dear Bruce, >> >> Thanks for your patience. Attached you will find the screenshot of my >> server. In my institute's >> server, there is an older version of freesurfer, which I then change to a >> newer version before >> starting the recon-all. >> >> I look forward to your reply. >> >> Thanks. >> >> Cheers, >> Hweeling >> >> >> >> On 22 November 2017 at 15:31, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> can you send us the recon-all.log? >> On Wed, 22 Nov 2017, Hwee Ling Lee wrote: >> >> Hi Bruce, >> >> I downloaded the latest version of freesurfer, "CentOS 6 >> x86_64 (64b)". >> >> Cheers, >> Hweeling >> >> >> On 21 November 2017 at 23:57, Bruce Fischl < >> fis...@nmr.mgh.harvard.edu> >> wrote: >> oh, this may be a version mismatch then. Which version >> of FS are you >> using? >> On Tue, 21 Nov 2017, Hwee Ling Lee wrote: >> >> Dear Bruce, >> Thanks for your reply. >> I checked the folder and did not find the file >> that was >> requested. >> >> What I have in the average folder that has >> 'RB*.gca' are >> 'RB_all_2016-05-10.vc700.gca' and >> 'RB_all_withskull_2016-05-10.vc700.gca'. >> The other file in that folder is >> 'RB_all_2008-03-26.mni152.2mm.lta'. >> >> Cheers, >> Hweeling >> >> On Nov 21, 2017 18:05, "Bruce Fischl" >> <fis...@nmr.mgh.harvard.edu> wrote: >> Hi Hweeling >> >> what is FREESURFER_HOME set to in the >> environment? Does >> that file >> exist? It is a >> standard part of our distribution >> >> cheers >> Bruce >> >> >> On Tue, 21 Nov 2017, Hwee Ling Lee wrote: >> >> Dear all, >> >> I have T1 images collected from the >> 7T MRI scanner. >> >> I downloaded the most recent >> freesurfer software, >> and followed >> all >> instructions to install the software >> before using >> it. >> >> I would like to segment the T1 data >> using its high >> resolution >> image, and >> also to segment the hippocampal >> subfields. >> >> For command, I use this: >> >> recon-all -all -s <subject name> >> -hires -i <subject >> dicom T1 >> image frame 1 >> location> >> >> However, I get an error message: >> >> cannot find >> $FREESURFER_HOME/average/RB_all_2008-03-26.gca >> >> I'm not sure what I did wrong. >> >> Also, how can I combine high >> resolution segmentation >> and >> hippocampal >> subfields segmentation? >> >> Could someone please help? >> >> Thanks. >> >> Best regards, >> Hweeling >> >> >> >> >> >> 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. >> >> >> >> >> >> >>
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