Dear Bruce, Thanks for your tip. Actually, it didn't work for me. I went to ask one of my colleagues, Martin Reuter, for help, and it turns out that the permission of my files in the $FREESURFER_HOME/bin folder have been changed to 'read only'. Martin helped me to change the files in the $FREESURFER_HOME/bin folder to all executable files by using this command: 'chmod u+w *'.
Hence, I'm replying to this thread so that I hope this will help others in the future with similar problems. Thanks again for your patience! Cheers, Hweeling On 23 November 2017 at 16:24, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > you need to change your path so that > > which recon-all > > gives you the v6 one. something like: > > set path = ($FREESURFER_HOME/bin $path) > rehash > > where FREESURFER_HOME points to the v6 version > > cheers > Bruce > > > On Wed, 22 Nov 2017, Hwee Ling Lee wrote: > > 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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