This directory already exists. I had already made it, which is why I am confused that it cannot be found.
On Wed, Jan 27, 2016 at 10:43 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Jasmin > > oh, I take it back. It looks like the SUBJECTS_DIR you pointed it at > didn't exist. Create it first with > > mkdir /Desktop/Brain_Child_subs > > then try rerunning. > Bruce > > > > On Wed, 27 Jan 2016, Jasmin Alves wrote: > > Hi Bruce, >> Could you elaborate on what you mean I need to specify the input volume? >> >> Thanks, >> Jasmin >> >> On Wed, Jan 27, 2016 at 5:48 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> > >> wrote: >> Hi Jasmin >> >> if this is the first time you have run this subject (that is, >> the subject dir doesn't exist within $SUBJECTS_DIR), you still >> need to specify the input volume with -i T1_original_joya.nii >> >> cheers >> Bruce >> >> On Tue, 26 Jan 2016, Jasmin Alves wrote: >> >> Bruce, >> Sorry to be a pain, but for some reason, I cannot >> still get recon-all to >> work. >> >> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ >> recon-all -sd >> /Desktop/Brain_Child_subs -i T1_original_joya.nii >> -subject joya -all & >> >> [1] 14655 >> >> Jasmins-MacBook-Pro:Brain_Child_subs jasminalves$ >> ERROR: SUBJECTS_DIR >> /Desktop/Brain_Child_subs does not exist. >> >> Thanks, >> >> Jasmin >> >> >> On Tue, Jan 26, 2016 at 6:19 AM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Jasmin >> >> you need a '-' sign first. It should be: >> >> recon-all -sd /Desktop/Brain_Child_subs -i >> T1_original_joya.nii >> -subject \ >> joya -all & >> >> cheers >> Bruce >> >> On Mon, 25 Jan 2016, Jasmin Alves wrote: >> >> 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 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 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 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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