Hi Marcel: Do you using Mac? If so, please unlock your "root" account, then change to the root account (re-login as root or using 'su' command in terminal window). We also have this problem one month ago. It is because that the default setting for root account in OS X 10.7.x is hidden in the beginning, and FS need root account to operate. So if your OS X is "upgraded" to 10.7.x, then you will have problem. The FS ran smoothly under our "old" version OS X (10.6.x).
Hope this help. 2012/3/6 Marcel Zwiers <m.zwi...@fcdonders.ru.nl>: > Hi Michael, > > Thanks for your help and suggestions! > > I'd have to try to recreate the error, but I have an idea of what it could > be (assuming > /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness/BIG1026_1 is > a directory). > > Actually not yet, > /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness is a > directory but BIG1026_1 is supposed to be created by recon-all (but wasn't > as a consequence of the error). > > While you may have read, write, and execute permissions to your colleague's > directory, you must make sure that these permissions have been recursively > added to the contents of that directory (child directories, child directory > files, and directory files). > > There are only *.nii.gz files in that directory plus a few extra files and > (symbolic links to) folders that I assume should have nothing to do with the > error? The content looks like this (ls -al): > > drwxrwxr-x 2 marhoo big 352256 Mar 6 09:51 ./ > drwxrwx--x 15 marhoo big 4096 Feb 29 15:49 ../ > -rw------- 1 marzwi big 12219623 Mar 2 16:06 BIG1026_1.nii.gz > [..] > -rw------- 1 marzwi big 12219623 Mar 2 16:06 BIG4025_1.nii.gz > -rw-rwxr-- 1 marhoo big 75806 Feb 27 10:54 BIG_aseg_stats.log* > lrwxrwxrwx 1 marhoo big 34 Feb 19 09:12 fsaverage -> > /opt/freesurfer/subjects/fsaverage/ > lrwxrwxrwx 1 marhoo big 38 Feb 19 09:12 lh.EC_average -> > /opt/freesurfer/subjects/lh.EC_average/ > lrwxrwxrwx 1 marhoo big 38 Feb 19 09:12 rh.EC_average -> > /opt/freesurfer/subjects/rh.EC_average/ > -rw-rwxr-- 1 marhoo big 18200 Sep 27 10:39 v5.0.txt* > -rw-rwxr-- 1 marhoo big 3220 Sep 27 10:39 v5.1.txt* > -rw-rwxrw- 1 marhoo big 523 Feb 24 10:07 .xdebug_tkmedit* > > I believe that your problem is that the file BIG1026_1.nii.gz (however, from > my experience this file should not simply be in the BIG1026_1 folder but in > the orig directory of the mri folder) has not inherited the specified > permissions from its parent directory. > > My username is marzwi, I am member of the big group and I have rw > permissions of all the files and directories (see listing above). > > If this does not correct the error, set the environmental SUBJECTS_DIR > variable to the directory housing the subject directories (making sure that > your colleague gives you sufficient access to this directory), lose the -sd > path in the command, and make sure that you have read, write, execute > permissions recursively added to the directories and files that you will be > working with. > > I did that but the error message remains. Here's the full message, started > from a newly opened bash terminal: > > -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /opt/freesurfer > FSFAST_HOME /opt/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /opt/freesurfer/subjects > MNI_DIR /opt/freesurfer/mni > FSL_DIR /opt/fsl > mentat002:$ export > SUBJECTS_DIR=/home/mrphys/marzwi/BIG/Freesurfer_CorticalThickness > mentat002:$ recon-all -subject BIG1026_1 -i BIG1026_1.nii.gz -autorecon1 > > /bin/pwd: cannot open directory `../..': Permission denied > mkdir: cannot create directory `/BIG1026_1': Permission denied > mkdir: cannot create directory `/BIG1026_1': Permission denied > cp: cannot create regular file `/BIG1026_1/scripts/build-stamp.txt': No such > file or directory > cat: /BIG1026_1/scripts/build-stamp.txt: No such file or directory > INFO: FreeSurfer build stamps do not match > Subject Stamp: > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > INFO: SUBJECTS_DIR is > Actual FREESURFER_HOME /opt/freesurfer-v5.1 > /BIG1026_1: No such file or directory. > > Another option would be if your colleague set up a "subjects directory" > within his parent directory and add each subject's folder to this directory > and then setting this as your SUBJECTS_DIR variable (ensuring you have read, > write, execute permissions). > > I created a subfolder, copied the BIG1026_1.nii.gz file into it and ran > recon-all using this subfolder as SUBJECTS_DIR but I kept getting permission > denied errors. > > I hope this helps; however, not knowing the version of free surfer that you > are running nor the operating system makes it difficult to troubleshoot your > problem. Let me know if you arrive at a solution or require further > assistance. > > Thanks, > > Michael Nowak > > > I hope the info above can help troubleshooting my problem. Thanks a lot > Michael! > > Cheers, > Marcel > > > > On Mon, Mar 5, 2012 at 9:55 PM, Marcel Zwiers <m.zwi...@fcdonders.ru.nl> > wrote: >> Hi, >> >> I am new to FS and have encountered a weird problem that I do not know how >> to solve and did not find any earlier >> postings on. When I run recon-all on a file in my own home directory >> everything works normally: >> >> recon-all -subject BIG1026_1 -sd /home/mrphys/marzwi/test -i >> BIG1026_1.nii.gz >> -autorecon1 >> [..] >> >> However, if I run the same command on the same file, except that this file >> is now located in a directory of a >> colleague of mine that I certainly have full access to (+r+w+x), I >> immediately get a 'permission denied' error: > >> recon-all -subject BIG1026_1 -sd /home/control/marhoo/Projects >> /BIG/Freesurfer_CorticalThickness -i BIG1026_1.nii.gz -autorecon1 >> pwd: cannot open directory `../..': Permission denied >> /bin/pwd: cannot open directory `../..': Permission denied >> mkdir: cannot create directory `/BIG1026_1': Permission denied >> [..] >> >> From the error message it seems to me as if FS is trying to access the >> parent directory (of which I do not have >> full rights but only -r-w+x)? As this does not make a lot of sense to me I >> suspect there must be another cause >> and hope you have any ideas here. >> >> Cheers, >> Marcel > > > -- > ________________________________ > Marcel Zwiers www.ru.nl/donders > MR techniques +31-(0)24-3668495 > > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen, The Netherlands > ________________________________ > > > _______________________________________________ > 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. > -- Best regards -- 杜政昊 Cheng-Hao Tu, PhD Post Doctoral Research Fellow Integrated Brain Research Unit Department of Medical Research and Education Taipei Veterans General Hospital No.201, Sect.2, Shih-Pai Rd. Taipei Taiwan Email: lordo...@ms10.hinet.net or lordowe...@gmail.com Tel: +886-2-28712121 ext 3474 Fax: +886-2-28745182 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
