Zeke,
I ran it as you say. we'll see what happens maybe in 18 hours or so ! BTW, if I get the same error or something else again, how can I continue from the point or error for the next time ?
On Fri, Sep 19, 2014 at 2:10 PM, zkaufman@nmr.mgh.harvard.edu wrote:
I believe if you simply run:
$> recon-all -i /volumetric/Case018/case018_tp2/22-1.dcm -subject case018_tp2 -all
You should be all set. You do not need to type any of the following commands:
clear cd /volumetric ln -s /usr/local/freesurfer/subjects/fsaverage
-Zeke
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. Youneed
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 sharedfolder
      (/mnt/hgfs/mydata) but I got the       permission error the same pointthat I
got the       symlink error lastly. So, I       tought that might be due tosomething
related       to shared directory.       Then I copied my subjects underthe
      $SUBJECTS_DIR but got the symlinkerror.
      running ls -l /usr/local/freesurfer/subjects       /fsaverage shows me this:       lrwxrwxrwx 1 mahmoud mahmoud 40Sep 18
20:23 Â Â Â Â Â Â/usr/local/freesurfer/subjects/fsaverage
-> Â Â Â Â Â Â/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 isfor
subjects          that we distributeand NOT where
you       should be putting your          subject data. Is thatwhat you
are       doing? You may have          overwritten the
fsaverage dir
there. Can       you run:          ls -l      Â/usr/local/freesurfer/subjects/fsaverage
         and send us theresults?
         you should create adirectory
elsewhere       with your subject data          and pointSUBJECTS_DIR at it
         cheers          Bruce          On Fri, 19 Sep 2014,Mahmoud
wrote: Â Â Â Â Â Â Â Â Â Â Â Â Bruce, Â Â Â Â Â Â Â Â Â Â Â Â Here isthe info when I
open a new       terminal:
            --------                   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0             --------             Settingup environment
for       FreeSurfer/FS-FAST (and             FSL)            Â
FREESURFER_HOMEÂ Â
      /usr/local/freesurfer            ÂFSFAST_HOME     Â
      /usr/local/freesurfer/fsfast            ÂFSF_OUTPUT_FORMAT nii.gz
           ÂSUBJECTS_DIR    Â
      /usr/local/freesurfer/subjects            ÂMNI_DIR                /usr/local/freesurfer/mni            Â
ubuntu:~>
            On Fri,Sep 19, 2014 at
8:56 AM,       Bruce Fischl             fischl@nmr.mgh.harvard.edu             wrote:              Â
 can you tell us
what your       FREESURFER_HOME is             and what
your
             Â SUBJECTS_DIR
is? You will       need to remove the             broken
link
             Â probably
             Â On Fri, 19 Sep
2014, Mahmoud       wrote:
             Â    Hi
Bruce,
             Â   Â
Actually I couldn't.       It says: ls: cannot             access              Â
   Â
                  /usr/local/freesurfer/subjects/fsaverage: Too       many              Â    levels
of symbolic       links              Â
    And
even I couldn't cd       to fsaverage !              Â
    In
fact there is no       directory under            Â
SUBJETCS_DIR
             Â    named
fsaverage, it       seems              Â
    the
fsaverage under       SUBJETCS_DIR is just             a broken              Â
    link,
and I have no       idea              Â
    why
the the link is       broken and how to             fix it.              Â
    Any
help would be       highly appreciated !
             Â    Thank
you, Â Â Â Â Â Â Â Â Â Â Â Â Â Â
   Â
Mahmoud
             Â    On
Fri, Sep 19, 2014       at 8:21 AM, Bruce             Fischl              Â
   Â
      <fischl@nmr.mgh.harvard.edu>              Â    wrote:
             Â     Â
 Hi Mahmoud
             Â     Â
 were you able to       create a symlink             to
fsaverage
             Â    in
your              Â
     Â
 SUBJECTS_DIR? If       not, that is the             reason
for
             Â    this
error              Â
     Â
 Bruce
             Â     Â
 On Thu, 18 Sep       2014, Mahmoud             wrote:
             Â     Â
    Dear all,
             Â     Â
    After       running "recon-all -i              Â
     Â
                 Â
   Â
                  $SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm              Â     Â
    -subject       case018_tp2 -all"             I'm
always
             Â   Â
getting the              Â
     Â
    following       error and really              Â
     Â
    don't know       how to fix.Â
             Â     Â
    Could       anybody please help             me. The              Â
   Â
recon-all.log file              Â
     Â
    is       attached.
             Â     Â
    Thank you,              Â
     Â
    Mahmoud
             Â     Â
    Reporting       on  70            Â
segmentations
             Â     Â
          mri_segstats done              Â
     Â
                 Â
   Â
                  /usr/local/freesurfer/subjects/case018_tp2/label              Â     Â
                 Â
   Â
                  #--------------------------------------------              Â     Â
    #@# BA       Labels lh Thu Sep 18             20:23:27
EDT
             Â    2014
             Â     Â
    INFO:       fsaverage subject does             not
exist
             Â    in
             Â     Â
          SUBJECTS_DIR              Â
     Â
    INFO:       Creating symlink to            Â
fsaverage
             Â   Â
subject...
             Â     Â
     cd             /usr/local/freesurfer/subjects; ln              Â
    -s
             Â     Â
                 Â
   Â
                  /usr/local/freesurfer/subjects/fsaverage; cd       -              Â     Â
           mri_label2label            Â
--srcsubject fsaverage
             Â   Â
--srclabel              Â
     Â
                 Â
   Â
                 Â/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
             Â     Â
          --trgsubject              Â
     Â
          case018_tp2 --trglabel            Â
./lh.BA1.label
             Â    --hemi
lh              Â
     Â
          --regmethod surfaceÂ
             Â     Â
    Too many       levels of symbolic             links              Â
     Â
          mri_label2label: could not             open
label
             Â    file
             Â     Â
                 Â
   Â
                 Â/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
             Â     Â
    srclabel =              Â
     Â
                 Â
   Â
                 Â/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
             Â     Â
    srcsubject       = fsaverage              Â
     Â
    trgsubject       = case018_tp2              Â
     Â
    trglabel =       ./lh.BA1.label              Â
     Â
    regmethod       = surface
             Â     Â
    srchemi =       lh              Â
     Â
    trghemi =       lh              Â
     Â
    trgsurface       = white              Â
     Â
    srcsurfreg       = sphere.reg              Â
     Â
    trgsurfreg       = sphere.reg              Â
     Â
    usehash =       1              Â
     Â
    Use       ProjAbs  = 0, 0              Â
     Â
    Use       ProjFrac = 0, 0              Â
     Â
    DoPaint 0
             Â     Â
          SUBJECTS_DIR               Â
   Â
      Â/usr/local/freesurfer/subjects
             Â     Â
          FREESURFER_HOME            Â
/usr/local/freesurfer
             Â     Â
    Loading       source label.              Â
     Â
    Invalid       argument              Â
     Â
    ERROR       reading              Â
     Â
                 Â
   Â
                 Â/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
             Â     Â
    Linux       ubuntu            Â
3.13.0-35-generic
             Â   Â
#62-Ubuntu SMP Fri              Â
     Â
    Aug 15       01:58:42 UTC 2014              Â
     Â
    x86_64       x86_64 x86_64            Â
GNU/Linux
             Â     Â
    recon-all       -s case018_tp2             exited
with
             Â    ERRORS
at Thu              Â
     Â
    Sep 18       20:23:27 EDT 2014
             Â     Â
    For more       details, see the             log file              Â
     Â
                 Â
   Â
                 Â/usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log
             Â   Â
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