Dear FS developers, I have problem as follow when I tried file input/output (original images can not be identified)
Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i im_0001.dcm ERROR: must specify a subject id Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i IM_0001.dcm -s anon mkdir: /Applications/freesurfer/subjects/anon: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c /Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or directory. Xues-MacBook-Air:00000001 DannyDeng$ recon-all -i IM_0001.dcm -s anon mkdir: /Applications/freesurfer/subjects/anon: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied mkdir: /Applications/freesurfer/subjects/anon/scripts: Permission denied cp: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/subjects/anon/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c /Applications/freesurfer/subjects/anon/scripts/patchdir.txt: No such file or directory. Xues-MacBook-Air:00000001 DannyDeng$ Please help. Thanks. Best Regards, Danny Deng > On Nov 22, 2017, at 1:33 AM, Hwee Ling Lee <hweeling....@gmail.com> 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 > <mailto: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 > <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.
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