External Email - Use Caution Hi Bruce,
This is my full command line! I just started using this and I am not really sure what you mean by recon-all.log. Skolarikis-MacBook-Pro:~ kskol$ export FREESURFER_HOME=/Applications/freesurfer Skolarikis-MacBook-Pro:~ kskol$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Skolarikis-MacBook-Pro:~ kskol$ export SUBJECTS_DIR 'pwd' Skolarikis-MacBook-Pro:~ kskol$ echo $SUBJECTS_DIR/ /Applications/freesurfer/subjects/ Skolarikis-MacBook-Pro:~ kskol$ cp $FREESURFER_HOME/subjects/sample-001.mgz . Skolarikis-MacBook-Pro:~ kskol$ mri_convert sample-001.mgz sample-001.nii.gz mri_convert.bin sample-001.mgz sample-001.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to sample-001.nii.gz... Skolarikis-MacBook-Pro:~ kskol$ export SUBJECTS_DIR=/Applications/freesurfer Skolarikis-MacBook-Pro:~ kskol$ recon-all -i sample-001.nii.gz -s bert -all mkdir: /Applications/freesurfer/bert: Permission denied mkdir: /Applications/freesurfer/bert/scripts: Permission denied mkdir: /Applications/freesurfer/bert/scripts: Permission denied cp: /Applications/freesurfer/bert/scripts/build-stamp.txt: No such file or directory cat: /Applications/freesurfer/bert/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/bert/scripts/patchdir.txt: No such file or directory. Skolarikis-MacBook-Pro:~ kskol$ Thanks, Konstantina On 9 Jul 2018, at 15:33, Bruce Fischl <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> wrote: Hi Konstantina can you include the full command line, screen output and recon-all.log in the type of email? Otherwise it will be difficult for us to help thanks Bruce On Mon, 9 Jul 2018, Konstantina Skolariki wrote: External Email - Use Caution Hi Bruce, I managed to overcome said error but now during example 2 another error pops up. Skol-MacBook-Pro:~ kskol$ export SUBJECTS_DIR=<path to subject directory> -bash: syntax error near unexpected token `newline' Thanks, Konstantina ____________________________________________________________________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> Sent: 09 July 2018 17:17 To: Freesurfer support list Subject: Re: [Freesurfer] niiWrite(): error opening file tmp.nii Hi Konstantina do you have write access to the partition you are putting the subjects_dir on? And can you please send us the full command line, screen output and recon-all.log? cheers Bruce On Mon, 9 Jul 2018, Konstantina Skolariki wrote: > > External Email - Use Caution > > Hi FreeSurfer Developers, > I have downloaded freesurfer on my mac and after "setup & configuration” I > tried to perform example > 1 from "test your FreeSurfer Installation”. However when I type the command, > this error message > shows up: > > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > reading from sample-001.mgz... > TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 > i_ras = (-0, -1, -0) > j_ras = (-0, 0, -1) > k_ras = (-1, 0, 0) > writing to tmp.nii... > niiWrite(): error opening file tmp.nii > ERROR: failure writing tmp.nii > > Thanks, > Konstantina > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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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