Hi Bruce, Thanks for the reply, I attempted to direct Subjects_dir to the folder with my data but I received the following error.
Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ export SUBJECTS_DIR=/Desktop/Brain_Child_subs Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ recon-all -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all & [1] 13867 Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ ERROR: Flag all unrecognized. -sd /Desktop/Brain_Child_subs -i T1_original_joya.nii -subject joya all Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 recon-all -s joya exited with ERRORS at Mon Jan 25 21:12:58 PST 2016 Thanks so much, Jasmin On Mon, Jan 25, 2016 at 6:33 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Jasmin > > you need to create a directory where you have write permission and room > for the subject reconstruction to be written to, then set the SUBJECTS_DIR > environment variable to point to it. At the moment you are trying to use > the subject directory we distribute, which is in some system (and > read-only) location. You can do this on the command line of recon-all via: > > recon-all -sd <path to directory> ... > > cheers > Bruce > > > > On Sun, 24 Jan 2016, Jasmin Alves wrote: > > Hello Freesurfer, >> >> I am trying to learn freesurfer and ran into the following issues below >> running the recon -all command. >> >> FREESURFER_HOME: /Applications/freesurfer >> >> Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 >> >> Kernel info: Darwin 14.5.0 x86_64 >> >> 1) >> >> joya >> >> 2) >> >> Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i >> T1_original_joya.nii >> -subject joya -all & >> >> >> 3) >> >> [1] 12300 >> >> Jasmins-MacBook-Pro:subjects jasminalves$ mkdir: >> /Applications/freesurfer/subjects/joya: Permission denied >> >> mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied >> >> mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied >> >> cp: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No >> such >> file or directory >> >> cat: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No >> such >> file or directory >> >> INFO: FreeSurfer build stamps do not match >> >> Subject Stamp: >> >> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 >> >> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects >> >> Actual FREESURFER_HOME /Applications/freesurfer >> >> /Applications/freesurfer/subjects/joya: No such file or directory. >> >> >> [1]+ Exit 1 recon-all -i T1_original_joya.nii -subject >> joya -a >> >> Thank you,Jasmin >> >> Jasmin AlvesPredoctoral Student >> Medical Biology Graduate Program >> University of Southern California >> jal...@usc.edu >> >> >> > _______________________________________________ > 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. > > -- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jal...@usc.edu
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