Zeke,
I created another directory named "volumetric" and put my data under it. To final check before running the recon-all, here is the info from terminal: -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni ubuntu:~> cd /volumetric ubuntu:/volumetric> ls Case018 Case022
and I'm going to run this:
#!/bin/tcsh
clear cd /volumetric ln -s /usr/local/freesurfer/subjects/fsaverage
recon-all -i /volumetric/Case018/case018_tp2/22-1.dcm -subject case018_tp2 -all
On Fri, Sep 19, 2014 at 1:24 PM, zkaufman@nmr.mgh.harvard.edu wrote:
Mahmoud,
If I recall correctly, your on a virtual machine with the /mnt/hgfs/mydata directory being a shared directory, and you werent able to write to it when running recon-all.
So, what you want to do is create another directory within your virtual machine that holds your subjects data. You will still need the $FREESURFER_HOME/subjects directory because that directory contains files required by recon-all, so you will have a separate directory which contains your subjects.
You should not be creating symlinks or anything like that.
Just restore the fsaverage directory from the link I sent you back into $FREESURFER_HOME/subjects, put your subject data somewhere else in the VM, and run recon-all with the correct arguments.
-Zeke
yes, that is true. If it's already there the symlink will fail. You should be able to rm it if it is there an incorrect (or leave it if it is there and correct) On Fri, 19 Sep 2014, Mahmoud wrote:
Bruce and Zeke, Thank you so much for your advice. The last question before running the recon again. if I say: cd /mnt/hgfs/mydata ln -s /usr/local/freesurfer/subjects/fsaverage
It means that I shouldn't already have the fsaverage under /mydata directory, right ?
Mahmoud
On Fri, Sep 19, 2014 at 12:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: the easiest thing to do is:
cd /mnt/hgfs/mydata ln -s /usr/local/freesurfer/subjects/fsaverage then you don't have to worry about source and target. It will implicitly create the symlink in $PWD cheers Bruce On Fri, 19 Sep 2014, Mahmoud wrote: Bruce, By "symlink from your /mnt/hgfs/mydata/fsaverage to /usr/local/freesurfer/subjects/fsaverage" you mean "ln -s /mnt/hgfs/mydata/fsaverage /usr/local/freesurfer/subjects/fsaverage" ? which fsaverage is the target ? Thanks, Mahmoud On Fri, Sep 19, 2014 at 9:50 AM, Mahmoud <zeydabadi@gmail.com> wrote:    Bruce, Thank you for your follow up and advice. Please let me know: 1- How to download the fsaverage again? 2- should I do the symlink manually or it will be done by recon-all later ? 3- What steps should I take before running the recon-all -all ? should I create any specific directory? set any permission ? Best, Mahmoud On Fri, Sep 19, 2014 at 9:41 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:    yes, you symlinked it to itself which is why you are    getting the infinite recursion error. You need to delete    /usr/local/freesurfer/subjects/fsaverage    and download the fsaverage dir again, put it in that    directory, then symlink from your    /mnt/hgfs/mydata/fsaverage to    /usr/local/freesurfer/subjects/fsaverage    cheers    Bruce    On Fri, 19 Sep 2014, Mahmoud wrote:       Bruce,       I already had my data in a shared folder       (/mnt/hgfs/mydata) but I got the       permission error the same point that I got the       symlink error lastly. So, I       tought that might be due to something related       to shared directory.       Then I copied my subjects under the       $SUBJECTS_DIR but got the symlink error.       running ls -l /usr/local/freesurfer/subjects       /fsaverage shows me this:       lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 18 20:23       /usr/local/freesurfer/subjects/fsaverage ->       /usr/local/freesurfer/subjects/fsaverage       Thank you,       Mahmoud       On Fri, Sep 19, 2014 at 9:23 AM, Bruce Fischl       <fischl@nmr.mgh.harvard.edu>       wrote:          the directory       /usr/local/freesurfer/subjects is for subjects          that we distribute and NOT where you       should be putting your          subject data. Is that what youare       doing? You may have          overwritten the fsaverage dir there. Can       you run:
         ls -l       /usr/local/freesurfer/subjects/fsaverage          and send us the results?          you should create a directory elsewhere       with your subject data          and point SUBJECTS_DIR at it          cheers          Bruce          On Fri, 19 Sep 2014, Mahmoud wrote:             Bruce,             Here is the info when Iopen a new       terminal:
            --------                   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0             --------             Setting up environmentfor       FreeSurfer/FS-FAST (and             FSL)             FREESURFER_HOME        /usr/local/freesurfer             FSFAST_HOME            /usr/local/freesurfer/fsfast             FSF_OUTPUT_FORMAT nii.gz             SUBJECTS_DIR           /usr/local/freesurfer/subjects             MNI_DIR                /usr/local/freesurfer/mni             ubuntu:~>
            On Fri, Sep 19, 2014 at8:56 AM,       Bruce Fischl             fischl@nmr.mgh.harvard.edu             wrote:                can you tell us what your       FREESURFER_HOME is             and what your                SUBJECTS_DIR is? You will       need to remove the             broken link                probably
               On Fri, 19 Sep2014, Mahmoud       wrote:
                  HiBruce,
                 ÂActually I couldn't.       It says: ls: cannot             access                                     /usr/local/freesurfer/subjects/fsaverage: Too       many                   levels of symbolic       links                   And even I couldn't cd       to fsaverage !                   In fact there is no       directory under             SUBJETCS_DIR                   named fsaverage, it       seems                   the fsaverage under       SUBJETCS_DIR is just             a broken                   link, and I have no       idea                   why the the link is       broken and how to             fix it.                   Any help would be       highly appreciated !
                  Thankyou,                   Mahmoud
                  OnFri, Sep 19, 2014       at 8:21 AM, Bruce             Fischl                         fischl@nmr.mgh.harvard.edu                   wrote:                      Hi Mahmoud
                   Â were you able to       create a symlink             to fsaverage                   in your                      SUBJECTS_DIR? If       not, that is the             reason for                   this error                      Bruce
                   Â On Thu, 18 Sep       2014, Mahmoud             wrote:
                   Â    Dear all,
                   Â    After       running "recon-all -i                                                             $SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm                         -subject       case018_tp2 -all"             I'm always                   getting the                         following       error and really                         don't know       how to fix.Â
                   Â    Could       anybody please help             me. The                   recon-all.log file                         is       attached.
                   Â    Thank you,                         Mahmoud
                   Â    Reporting       on  70             segmentations                               mri_segstats done                                                             /usr/local/freesurfer/subjects/case018_tp2/label                                                             #--------------------------------------------                         #@# BA       Labels lh Thu Sep 18             20:23:27 EDT                   2014                         INFO:       fsaverage subject does             not exist                   in                               SUBJECTS_DIR                         INFO:       Creating symlink to             fsaverage                   subject...
                   Â     cd             /usr/local/freesurfer/subjects; ln                   -s                                                             /usr/local/freesurfer/subjects/fsaverage; cd       -Â
                   Â           mri_label2label             --srcsubject fsaverage                   --srclabel                                                             /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label                               --trgsubject                               case018_tp2 --trglabel             ./lh.BA1.label                   --hemi lh                               --regmethod surfaceÂ
                   Â    Too many       levels of symbolic             links                               mri_label2label: could not             open label                   file                                                             /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
                   Â    srclabel =                                                             /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label                         srcsubject       = fsaverage                         trgsubject       = case018_tp2                         trglabel =       ./lh.BA1.label                         regmethod       = surface
                   Â    srchemi =       lh                         trghemi =       lh                         trgsurface       = white                         srcsurfreg       = sphere.reg                         trgsurfreg       = sphere.reg                         usehash =       1                         Use       ProjAbs  = 0, 0                         Use       ProjFrac = 0, 0                         DoPaint 0
                   Â          SUBJECTS_DIR                           /usr/local/freesurfer/subjects                               FREESURFER_HOME             /usr/local/freesurfer                         Loading       source label.                         Invalid       argument                         ERROR       reading                                                             /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label                         Linux       ubuntu             3.13.0-35-generic                   #62-Ubuntu SMP Fri                         Aug 15       01:58:42 UTC 2014                         x86_64       x86_64 x86_64             GNU/Linux
                   Â    recon-all       -s case018_tp2             exited with                   ERRORS at Thu                         Sep 18       20:23:27 EDT 2014
                   Â    For more       details, see the             log file                                                            Â
/usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log
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