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 Sep 2014, Mahmoud wrote:

Hi Bruce,

Actually 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 !

Thank you, Mahmoud

On Fri, Sep 19, 2014 at 8:21 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Mahmoud

  were you able to create a symlink to fsaverage in your
  SUBJECTS_DIR? If not, that is the reason for this error
  Bruce

  On Thu, 18 Sep 2014, Mahmoud wrote:

        Dear all,

        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. 

        Could anybody please help me. The recon-all.log file
        is attached.

        Thank you,
        Mahmoud

        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...

         cd /usr/local/freesurfer/subjects; ln -s
        /usr/local/freesurfer/subjects/fsaverage; cd - 


         mri_label2label --srcsubject fsaverage --srclabel
        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
        --trgsubject
        case018_tp2 --trglabel ./lh.BA1.label --hemi lh
        --regmethod surface 

        Too many levels of symbolic links
        mri_label2label: could not open label file
        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

        srclabel =
        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
        srcsubject = fsaverage
        trgsubject = case018_tp2
        trglabel = ./lh.BA1.label
        regmethod = surface

        srchemi = lh
        trghemi = lh
        trgsurface = white
        srcsurfreg = sphere.reg
        trgsurfreg = sphere.reg
        usehash = 1
        Use ProjAbs  = 0, 0
        Use ProjFrac = 0, 0
        DoPaint 0

        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

        recon-all -s case018_tp2 exited with ERRORS at Thu
        Sep 18 20:23:27 EDT 2014

        For more details, see the log file
        /usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log

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And here is a screen shot of subjects directory ...

On Fri, Sep 19, 2014 at 9:07 AM, Mahmoud zeydabadi@gmail.com wrote:

Bruce,

Here is the info when I open a new 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:~>

On Fri, Sep 19, 2014 at 8:56 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 Sep 2014, Mahmoud wrote:

Hi Bruce,

...

Actually 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 !

Thank you, Mahmoud

On Fri, Sep 19, 2014 at 8:21 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Mahmoud

  were you able to create a symlink to fsaverage in your
  SUBJECTS_DIR? If not, that is the reason for this error
  Bruce

  On Thu, 18 Sep 2014, Mahmoud wrote:

        Dear all,

        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.

        Could anybody please help me. The recon-all.log file
        is attached.

        Thank you,
        Mahmoud

        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...

         cd /usr/local/freesurfer/subjects; ln -s
        /usr/local/freesurfer/subjects/fsaverage; cd -


         mri_label2label --srcsubject fsaverage --srclabel
        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
        --trgsubject
        case018_tp2 --trglabel ./lh.BA1.label --hemi lh
        --regmethod surface

        Too many levels of symbolic links
        mri_label2label: could not open label file
        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

        srclabel =
        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
        srcsubject = fsaverage
        trgsubject = case018_tp2
        trglabel = ./lh.BA1.label
        regmethod = surface

        srchemi = lh
        trghemi = lh
        trgsurface = white
        srcsurfreg = sphere.reg
        trgsurfreg = sphere.reg
        usehash = 1
        Use ProjAbs  = 0, 0
        Use ProjFrac = 0, 0
        DoPaint 0

        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

        recon-all -s case018_tp2 exited with ERRORS at Thu
        Sep 18 20:23:27 EDT 2014

        For more details, see the log file
        /usr/local/freesurfer/subjects/case018_tp2/scripts/

recon-all.log

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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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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.

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 you are 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 I open a new 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:~>

On Fri, Sep 19, 2014 at 8:56 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 Sep 2014, Mahmoud wrote:

        Hi Bruce,

        Actually 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 !

        Thank you,
        Mahmoud


        On Fri, Sep 19, 2014 at 8:21 AM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Mahmoud

              were you able to create a symlink to fsaverage
        in your
              SUBJECTS_DIR? If not, that is the reason for
        this error
              Bruce

              On Thu, 18 Sep 2014, Mahmoud wrote:

                    Dear all,

                    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.

                    Could anybody please help me. The
        recon-all.log file
                    is attached.

                    Thank you,
                    Mahmoud

                    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...

                     cd /usr/local/freesurfer/subjects; ln
        -s

        /usr/local/freesurfer/subjects/fsaverage; cd -


                     mri_label2label --srcsubject fsaverage
        --srclabel

        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
                    --trgsubject
                    case018_tp2 --trglabel ./lh.BA1.label
        --hemi lh
                    --regmethod surface

                    Too many levels of symbolic links
                    mri_label2label: could not open label
        file

        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

                    srclabel =

        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
                    srcsubject = fsaverage
                    trgsubject = case018_tp2
                    trglabel = ./lh.BA1.label
                    regmethod = surface

                    srchemi = lh
                    trghemi = lh
                    trgsurface = white
                    srcsurfreg = sphere.reg
                    trgsurfreg = sphere.reg
                    usehash = 1
                    Use ProjAbs  = 0, 0
                    Use ProjFrac = 0, 0
                    DoPaint 0

                    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

                    recon-all -s case018_tp2 exited with
        ERRORS at Thu
                    Sep 18 20:23:27 EDT 2014

                    For more details, see the log file

        /usr/local/freesurfer/subjects/case018_tp2/scripts/

recon-all.log

        _______________________________________________
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        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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---

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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 you are 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 I open a new 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:~>

        On Fri, Sep 19, 2014 at 8:56 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 Sep 2014, Mahmoud wrote:

                    Hi Bruce,

                    Actually 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 !

                    Thank you,
                    Mahmoud


                    On Fri, Sep 19, 2014 at 8:21 AM, Bruce
        Fischl
                    <fischl@nmr.mgh.harvard.edu>
                    wrote:
                          Hi Mahmoud

                          were you able to create a symlink
        to fsaverage
                    in your
                          SUBJECTS_DIR? If not, that is the
        reason for
                    this error
                          Bruce

                          On Thu, 18 Sep 2014, Mahmoud
        wrote:

                                Dear all,

                                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.

                                Could anybody please help
        me. The
                    recon-all.log file
                                is attached.

                                Thank you,
                                Mahmoud

                                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...

                                 cd
        /usr/local/freesurfer/subjects; ln
                    -s


        /usr/local/freesurfer/subjects/fsaverage; cd -


                                 mri_label2label
        --srcsubject fsaverage
                    --srclabel


        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
                                --trgsubject
                                case018_tp2 --trglabel
        ./lh.BA1.label
                    --hemi lh
                                --regmethod surface

                                Too many levels of symbolic
        links
                                mri_label2label: could not
        open label
                    file


        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

                                srclabel =


        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
                                srcsubject = fsaverage
                                trgsubject = case018_tp2
                                trglabel = ./lh.BA1.label
                                regmethod = surface

                                srchemi = lh
                                trghemi = lh
                                trgsurface = white
                                srcsurfreg = sphere.reg
                                trgsurfreg = sphere.reg
                                usehash = 1
                                Use ProjAbs  = 0, 0
                                Use ProjFrac = 0, 0
                                DoPaint 0

                                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

                                recon-all -s case018_tp2
        exited with
                    ERRORS at Thu
                                Sep 18 20:23:27 EDT 2014

                                For more details, see the
        log file


        /usr/local/freesurfer/subjects/case018_tp2/scripts/

recon-all.log

        _______________________________________________
                    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.




        _______________________________________________
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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 you are
        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 I open a new
        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:~>

                    On Fri, Sep 19, 2014 at 8:56 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 Sep 2014, Mahmoud
        wrote:

                                Hi Bruce,

                                Actually 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 !

                                Thank you,
                                Mahmoud


                                On Fri, Sep 19, 2014
        at 8:21 AM, Bruce
                    Fischl
                               
        <fischl@nmr.mgh.harvard.edu>
                                wrote:
                                      Hi Mahmoud

                                      were you able to
        create a symlink
                    to fsaverage
                                in your
                                      SUBJECTS_DIR? If
        not, that is the
                    reason for
                                this error
                                      Bruce

                                      On Thu, 18 Sep
        2014, Mahmoud
                    wrote:

                                            Dear all,

                                            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. 

                                            Could
        anybody please help
                    me. The
                                recon-all.log file
                                            is
        attached.

                                            Thank you,
                                            Mahmoud

                                            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...

                                             cd
                    /usr/local/freesurfer/subjects; ln
                                -s
                                           
                               
                   
        /usr/local/freesurfer/subjects/fsaverage; cd
        - 


                                           
         mri_label2label
                    --srcsubject fsaverage
                                --srclabel
                                           
                               
                   
        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
                                           
        --trgsubject
                                           
        case018_tp2 --trglabel
                    ./lh.BA1.label
                                --hemi lh
                                           
        --regmethod surface 

                                            Too many
        levels of symbolic
                    links
                                           
        mri_label2label: could not
                    open label
                                file
                                           
                               
                   
        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

                                            srclabel =
                                           
                               
                   
        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
                                            srcsubject
        = fsaverage
                                            trgsubject
        = case018_tp2
                                            trglabel =
        ./lh.BA1.label
                                            regmethod
        = surface

                                            srchemi =
        lh
                                            trghemi =
        lh
                                            trgsurface
        = white
                                            srcsurfreg
        = sphere.reg
                                            trgsurfreg
        = sphere.reg
                                            usehash =
        1
                                            Use
        ProjAbs  = 0, 0
                                            Use
        ProjFrac = 0, 0
                                            DoPaint 0

                                           
        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

                                            recon-all
        -s case018_tp2
                    exited with
                                ERRORS at Thu
                                            Sep 18
        20:23:27 EDT 2014

                                            For more
        details, see the
                    log file
                                           
                               
                   
        /usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log


                               
                   
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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 you are
                    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 I open
        a new
                    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:~>

                                On Fri, Sep 19, 2014 at 8:56
        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 Sep 2014,
        Mahmoud
                    wrote:

                                            Hi Bruce,

                                            Actually 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 !

                                            Thank you,
                                            Mahmoud


                                            On Fri, Sep 19,
        2014
                    at 8:21 AM, Bruce
                                Fischl
                                           
                    <fischl@nmr.mgh.harvard.edu>
                                            wrote:
                                                  Hi Mahmoud

                                                  were you
        able to
                    create a symlink
                                to fsaverage
                                            in your
                                                 
        SUBJECTS_DIR? If
                    not, that is the
                                reason for
                                            this error
                                                  Bruce

                                                  On Thu, 18
        Sep
                    2014, Mahmoud
                                wrote:

                                                        Dear
        all,

                                                       
        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. 

                                                       
        Could
                    anybody please help
                                me. The
                                            recon-all.log
        file
                                                        is
                    attached.

                                                       
        Thank you,
                                                       
        Mahmoud

                                                       
        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...

                                                         cd
                               
        /usr/local/freesurfer/subjects; ln
                                            -s
                                                       
                                           
                               
                   
        /usr/local/freesurfer/subjects/fsaverage; cd
                    - 


                                                       
                     mri_label2label
                                --srcsubject fsaverage
                                            --srclabel
                                                       
                                           
                               
                   
        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
                                                       
                    --trgsubject
                                                       
                    case018_tp2 --trglabel
                                ./lh.BA1.label
                                            --hemi lh
                                                       
                    --regmethod surface 

                                                        Too
        many
                    levels of symbolic
                                links
                                                       
                    mri_label2label: could not
                                open label
                                            file
                                                       
                                           
                               
                   
        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

                                                       
        srclabel =
                                                       
                                           
                               
                   
        /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label
                                                       
        srcsubject
                    = fsaverage
                                                       
        trgsubject
                    = case018_tp2
                                                       
        trglabel =
                    ./lh.BA1.label
                                                       
        regmethod
                    = surface

                                                       
        srchemi =
                    lh
                                                       
        trghemi =
                    lh
                                                       
        trgsurface
                    = white
                                                       
        srcsurfreg
                    = sphere.reg
                                                       
        trgsurfreg
                    = sphere.reg
                                                       
        usehash =
                    1
                                                        Use
                    ProjAbs  = 0, 0
                                                        Use
                    ProjFrac = 0, 0
                                                       
        DoPaint 0

                                                       
                    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

                                                       
        recon-all
                    -s case018_tp2
                                exited with
                                            ERRORS at Thu
                                                        Sep
        18
                    20:23:27 EDT 2014

                                                        For
        more
                    details, see the
                                log file
                                                       
                                           
                               
                   
        /usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log


                                           
                               
                   
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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/fsaverageÂ
        /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:
        Â  Â  Â  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:
        Â  Â  Â  yes, you symlinked it to itself which is why
        you are
        Â  Â  Â  getting the infinite recursion error. You need
        to delete
        Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage

        Â  Â  Â  and download the fsaverage dir again, put it
        in that
        Â  Â  Â  directory, then symlink from your
        Â  Â  Â  /mnt/hgfs/mydata/fsaverage to
        Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage

        Â  Â  Â  cheers
        Â  Â  Â  Bruce
        Â  Â  Â  On Fri, 19 Sep 2014, Mahmoud wrote:

        Â  Â  Â  Â  Â  Â  Bruce,

        Â  Â  Â  Â  Â  Â  I already had my data in a shared folder
        Â  Â  Â  Â  Â  Â  (/mnt/hgfs/mydata) but I got the
        Â  Â  Â  Â  Â  Â  permission error the same point that I
        got the
        Â  Â  Â  Â  Â  Â  symlink error lastly. So, I
        Â  Â  Â  Â  Â  Â  tought that might be due to something
        related
        Â  Â  Â  Â  Â  Â  to shared directory.
        Â  Â  Â  Â  Â  Â  Then I copied my subjects under the
        Â  Â  Â  Â  Â  Â  $SUBJECTS_DIR but got the symlink error.

        Â  Â  Â  Â  Â  Â  running ls -l
        /usr/local/freesurfer/subjects
                    /fsaverage  shows me this:

        Â  Â  Â  Â  Â  Â  lrwxrwxrwx 1 mahmoud mahmoud 40 Sep 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

        Â  Â  Â  Â  Â  Â  Thank you,
        Â  Â  Â  Â  Â  Â  Mahmoud


        Â  Â  Â  Â  Â  Â  On Fri, Sep 19, 2014 at 9:23 AM, Bruce
        Fischl
        Â  Â  Â  Â  Â  Â  <fischl@nmr.mgh.harvard.edu>
        Â  Â  Â  Â  Â  Â  wrote:
                          the  directory
        Â  Â  Â  Â  Â  Â  /usr/local/freesurfer/subjects is for
        subjects
        Â  Â  Â  Â  Â  Â  Â  Â  Â  that we distribute and NOT where
        you
        Â  Â  Â  Â  Â  Â  should be putting your
        Â  Â  Â  Â  Â  Â  Â  Â  Â  subject data. Is that what you

are       doing? You may have          overwritten the fsaverage dir there. Can       you run:

        Â  Â  Â  Â  Â  Â  Â  Â  Â  ls -l
        Â  Â  Â  Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage

        Â  Â  Â  Â  Â  Â  Â  Â  Â  and send us the results?

        Â  Â  Â  Â  Â  Â  Â  Â  Â  you should create a directory
        elsewhere
        Â  Â  Â  Â  Â  Â  with your subject data
        Â  Â  Â  Â  Â  Â  Â  Â  Â  and point SUBJECTS_DIR at it

        Â  Â  Â  Â  Â  Â  Â  Â  Â  cheers
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Bruce

        Â  Â  Â  Â  Â  Â  Â  Â  Â  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 is the info when I

open a new       terminal:

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  --------
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â
        freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  --------
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  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:~>

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  On Fri, Sep 19, 2014 at

8:56 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

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  On Fri, 19 Sep

2014, Mahmoud       wrote:

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Hi

Bruce,

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

Actually 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 !

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Thank

you, Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Mahmoud

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  On

Fri, Sep 19, 2014       at 8:21 AM, Bruce             Fischl                         fischl@nmr.mgh.harvard.edu                   wrote:                      Hi Mahmoud

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  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  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

 On Thu, 18 Sep       2014, Mahmoud             wrote:

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    Dear all,

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  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  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    Could       anybody please help             me. The                   recon-all.log file                         is       attached.

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    Thank you,                         Mahmoud

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  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  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     cd             /usr/local/freesurfer/subjects; ln                   -s                                                             /usr/local/freesurfer/subjects/fsaverage; cd       -Â

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  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  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    Too many       levels of symbolic             links                               mri_label2label: could not             open label                   file                                                             /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    srclabel =                                                             /usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label                         srcsubject       = fsaverage                         trgsubject       = case018_tp2                         trglabel =       ./lh.BA1.label                         regmethod       = surface

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  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  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  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  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    recon-all       -s case018_tp2             exited with                   ERRORS at Thu                         Sep 18       20:23:27 EDT 2014

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    For more       details, see the             log file                                                            Â

/usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
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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/fsaverageÂ
        /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:
        Â  Â  Â  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:
        Â  Â  Â  yes, you symlinked it to itself which is why
        you are
        Â  Â  Â  getting the infinite recursion error. You

need

...

...

        to delete
        Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage

        Â  Â  Â  and download the fsaverage dir again, put it
        in that
        Â  Â  Â  directory, then symlink from your
        Â  Â  Â  /mnt/hgfs/mydata/fsaverage to
        Â  Â  Â  /usr/local/freesurfer/subjects/fsaverage

        Â  Â  Â  cheers
        Â  Â  Â  Bruce
        Â  Â  Â  On Fri, 19 Sep 2014, Mahmoud wrote:

        Â  Â  Â  Â  Â  Â  Bruce,

        Â  Â  Â  Â  Â  Â  I already had my data in a shared

folder

...

...

        Â  Â  Â  Â  Â  Â  (/mnt/hgfs/mydata) but I got the
        Â  Â  Â  Â  Â  Â  permission error the same point

that I

...

...

        got the
        Â  Â  Â  Â  Â  Â  symlink error lastly. So, I
        Â  Â  Â  Â  Â  Â  tought that might be due to

something

...

...

        related
        Â  Â  Â  Â  Â  Â  to shared directory.
        Â  Â  Â  Â  Â  Â  Then I copied my subjects under

the

...

...

        Â  Â  Â  Â  Â  Â  $SUBJECTS_DIR but got the symlink

error.

...

...

        Â  Â  Â  Â  Â  Â  running ls -l
        /usr/local/freesurfer/subjects
                    /fsaverage  shows me this:

        Â  Â  Â  Â  Â  Â  lrwxrwxrwx 1 mahmoud mahmoud 40

Sep 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

...

...

        Â  Â  Â  Â  Â  Â  Thank you,
        Â  Â  Â  Â  Â  Â  Mahmoud


        Â  Â  Â  Â  Â  Â  On Fri, Sep 19, 2014 at 9:23 AM,

Bruce

...

...

        Fischl
        Â  Â  Â  Â  Â  Â  <fischl@nmr.mgh.harvard.edu>
        Â  Â  Â  Â  Â  Â  wrote:
                          the  directory
        Â  Â  Â  Â  Â  Â  /usr/local/freesurfer/subjects is

for

...

...

        subjects
        Â  Â  Â  Â  Â  Â  Â  Â  Â  that we distribute

and NOT where

...

...

        you
        Â  Â  Â  Â  Â  Â  should be putting your
        Â  Â  Â  Â  Â  Â  Â  Â  Â  subject data. Is that

what you

...

...

are       doing? You may have          overwritten the

fsaverage dir

...

...

        there. Can
        Â  Â  Â  Â  Â  Â  you run:

        Â  Â  Â  Â  Â  Â  Â  Â  Â  ls -l
        Â  Â  Â  Â  Â  Â

/usr/local/freesurfer/subjects/fsaverage

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  and send us the

results?

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  you should create a

directory

...

...

        elsewhere
        Â  Â  Â  Â  Â  Â  with your subject data
        Â  Â  Â  Â  Â  Â  Â  Â  Â  and point

SUBJECTS_DIR at it

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  cheers
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Bruce

        Â  Â  Â  Â  Â  Â  Â  Â  Â  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 is

the info when I

...

...

open a new       terminal:

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  --------
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â
        freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  --------
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Setting

up environment

...

...

for       FreeSurfer/FS-FAST (and             FSL)            Â

FREESURFER_HOMEÂ Â

...

...

        Â  Â  Â  Â  Â  Â  /usr/local/freesurfer
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

FSFAST_HOMEÂ Â Â Â Â Â

...

...

        Â  Â  Â  Â  Â  Â  /usr/local/freesurfer/fsfast
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

FSF_OUTPUT_FORMAT nii.gz

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

SUBJECTS_DIRÂ Â Â Â Â

...

...

        Â  Â  Â  Â  Â  Â  /usr/local/freesurfer/subjects
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

MNI_DIR                /usr/local/freesurfer/mni            Â

ubuntu:~>

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  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  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

 SUBJECTS_DIR

...

...

is? You will       need to remove the             broken

link

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

 probably

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

 On Fri, 19 Sep

...

...

2014, Mahmoud       wrote:

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    Hi

...

...

Bruce,

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

   Â

...

...

Actually I couldn't.       It says: ls: cannot             access              Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â
        /usr/local/freesurfer/subjects/fsaverage: Too
        Â  Â  Â  Â  Â  Â  many
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  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  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  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  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    Thank

...

...

you, Â Â Â Â Â Â Â Â Â Â Â Â Â Â

   Â

...

...

Mahmoud

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    On

...

...

Fri, Sep 19, 2014       at 8:21 AM, Bruce             Fischl              Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  <fischl@nmr.mgh.harvard.edu>
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    wrote:

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

 Hi Mahmoud

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

 were you able to       create a symlink             to

fsaverage

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    in

...

...

your              Â

     Â

...

...

 SUBJECTS_DIR? If       not, that is the             reason

for

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    this

...

...

error              Â

     Â

...

...

 Bruce

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

 On Thu, 18 Sep       2014, Mahmoud             wrote:

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    Dear all,

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    After       running "recon-all -i              Â

     Â

...

...

                 Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â
        $SUBJECTS_DIR/Case018/case018_tp2/22-1.dcm
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    -subject       case018_tp2 -all"             I'm

always

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

   Â

...

...

getting the              Â

     Â

...

...

    following       error and really              Â

     Â

...

...

    don't know       how to fix.Â

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    Could       anybody please help             me. The              Â

   Â

...

...

recon-all.log file              Â

     Â

...

...

    is       attached.

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    Thank you,              Â

     Â

...

...

    Mahmoud

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    Reporting       on  70            Â

segmentations

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

          mri_segstats done              Â

     Â

...

...

                 Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â
        /usr/local/freesurfer/subjects/case018_tp2/label
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

                 Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â
        #--------------------------------------------
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    #@# BA       Labels lh Thu Sep 18             20:23:27

EDT

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    2014

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    INFO:       fsaverage subject does             not

exist

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    in

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

          SUBJECTS_DIR              Â

     Â

...

...

    INFO:       Creating symlink to            Â

fsaverage

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

   Â

...

...

subject...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

     cd             /usr/local/freesurfer/subjects; ln              Â

    -s

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

                 Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â
        /usr/local/freesurfer/subjects/fsaverage; cd
        Â  Â  Â  Â  Â  Â  -Â


        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

           mri_label2label            Â

--srcsubject fsaverage

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

   Â

...

...

--srclabel              Â

     Â

...

...

                 Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â

/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

...

...

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

          --trgsubject              Â

     Â

...

...

          case018_tp2 --trglabel            Â

./lh.BA1.label

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    --hemi

...

...

lh              Â

     Â

...

...

          --regmethod surfaceÂ

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    Too many       levels of symbolic             links              Â

     Â

...

...

          mri_label2label: could not             open

label

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    file

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

                 Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â

/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

...

...

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    srclabel =              Â

     Â

...

...

                 Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â

/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

...

...

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    srcsubject       = fsaverage              Â

     Â

...

...

    trgsubject       = case018_tp2              Â

     Â

...

...

    trglabel =       ./lh.BA1.label              Â

     Â

...

...

    regmethod       = surface

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  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  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

          SUBJECTS_DIR               Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â

/usr/local/freesurfer/subjects

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

          FREESURFER_HOME            Â

/usr/local/freesurfer

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    Loading       source label.              Â

     Â

...

...

    Invalid       argument              Â

     Â

...

...

    ERROR       reading              Â

     Â

...

...

                 Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â

/usr/local/freesurfer/subjects/fsaverage/label/lh.BA1.label

...

...

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    Linux       ubuntu            Â

3.13.0-35-generic

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  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  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    recon-all       -s case018_tp2             exited

with

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    ERRORS

...

...

at Thu              Â

     Â

...

...

    Sep 18       20:23:27 EDT 2014

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

     Â

...

...

    For more       details, see the             log file              Â

     Â

...

...

                 Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â

/usr/local/freesurfer/subjects/case018_tp2/scripts/recon-all.log

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â
        _______________________________________________
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

   Â

...

...

Freesurfer mailing       list              Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Freesurfer@nmr.mgh.harvard.edu
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

   Â

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    The

...

...

information in       this e-mail is             intended

only for

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    the

...

...

person to whom              Â

    it is

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

   Â

...

...

addressed. If you       believe this e-mail             was sent

to

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    you in

...

...

error and the              Â

    e-mail

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

   Â

...

...

contains patient       information, please             contact

the

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

   Â

...

...

Partners Compliance              Â

   Â

...

...

HelpLine at              Â

   Â

...

...

        Â  Â  Â  Â  Â  Â

http://www.partners.org/complianceline .

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  If the
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

    e-mail

...

...

was sent to you              Â

    in

...

...

error              Â

    but

...

...

does not contain       patient            Â

information, please

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

   Â

...

...

contact the sender              Â

    and

...

...

properly              Â

   Â

...

...

dispose of the e-mail.

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â
        _______________________________________________
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

Freesurfer mailing list

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Freesurfer@nmr.mgh.harvard.edu
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  The

information in this

...

...

        e-mail is
        Â  Â  Â  Â  Â  Â  intended only for
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  the

person to whom

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  it is
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â

addressed. If you

...

...

believe this       e-mail was sent to             you in

error and the

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  e-mail
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  contains

patient

...

...

        information,
        Â  Â  Â  Â  Â  Â  please contact the
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Partners

Compliance

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  HelpLine

at

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â
        Â  Â  Â  Â  Â  Â

http://www.partners.org/complianceline .

...

...

        If
        Â  Â  Â  Â  Â  Â  the
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  e-mail

was sent to you

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  in error
        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  but does

not contain

...

...

patient       information, please             contact

the sender

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  and

properly

...

...

        Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  Â  dispose

of the e-mail.

...

...

        Â  Â  Â  Â  Â  Â
        _______________________________________________
        Â  Â  Â  Â  Â  Â  Freesurfer mailing list
        Â  Â  Â  Â  Â  Â  Freesurfer@nmr.mgh.harvard.edu
        Â  Â  Â  Â  Â  Â

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

...

...

        Â  Â  Â  Â  Â  Â  The information in this e-mail

is

...

...

        intended
        Â  Â  Â  Â  Â  Â  only for the person to whom
        Â  Â  Â  Â  Â  Â  it is
        Â  Â  Â  Â  Â  Â  addressed. If you believe this

e-mail

...

...

        was sent
        Â  Â  Â  Â  Â  Â  to you in error and the
        Â  Â  Â  Â  Â  Â  e-mail
        Â  Â  Â  Â  Â  Â  contains patient information,

please

...

...

        contact
        Â  Â  Â  Â  Â  Â  the Partners Compliance
        Â  Â  Â  Â  Â  Â  HelpLine at
        Â  Â  Â  Â  Â  Â

http://www.partners.org/complianceline .

...

...

        If
        Â  Â  Â  Â  Â  Â  the e-mail was sent to you
        Â  Â  Â  Â  Â  Â  in error
        Â  Â  Â  Â  Â  Â  but does not contain patient
        information,
        Â  Â  Â  Â  Â  Â  please contact the sender
        Â  Â  Â  Â  Â  Â  and properly
        Â  Â  Â  Â  Â  Â  dispose of the e-mail.




        _______________________________________________
        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.

---

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.

---

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Here is the proper link.

ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/fsaverage.tar.gz

...

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

The "target" fsaverage is the one that came with the installation. Which you no longer have so I have created a link for you to download it again and put it back in your $SUBJECTS_DIR (see next answer).

...

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?

Ive created a link for you to download it: ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/Linux_centos4_x86_64/fsaverage.tar.gz

...

...

2- should I do the symlink manually or it will be done by recon-all later ?

Just extract the file above into your $SUBJECTS_DIR so that you have a $SUBJECTS_DIR/fsaverage directory and recon-all will take care of the rest.

...

...

3- What steps should I take before running the recon-all -all ? should I create any specific directory? set any permission ?

None. Hopefully this will just work.

-Zeke _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer