Try something like:

cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage .

Confirm the linked directory is now in your $SUBJECTS_DIR, then try running your script.

On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud zeydabadi@gmail.com wrote:

Paul,

The fsaverages are in $FREESURFER_HOME/subjects. So does it mean that the program couldn't make a link between my actual image places and $FREESURFER_HOME/subjects/fsaverage ? what can I do to fix it ?

Thank you, Mahmoud

On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach pabeach1@gmail.com wrote:

...

The general fsaverage (as well as it's other iterations, fsaverages 3-6) should be located in your $FREESURFER_HOME/subjects directory. You could symbolically link it over to your $SUBJECTS_DIR.

On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud zeydabadi@gmail.com wrote:

...

Dear All,

I ran the following script:

#!/bin/bash SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm -subject case022_tp2 -all

and got the error below at the end. Could anybody please let me know how to fix it.

Thank you, Mahmoud

Reporting on 70 segmentations mri_segstats done /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label #-------------------------------------------- #@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014 INFO: *fsaverage subject does not exist in SUBJECTS_DIR* INFO: Creating symlink to fsaverage subject...

cd /mnt/hgfs/DBSI/volumetric/MGZ; ln -s /usr/local/freesurfer/subjects/fsaverage; cd -

ln: *failed to create symbolic link './fsaverage': Operation not supported*

mri_label2label --srcsubject fsaverage --srclabel /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label --trgsubject case022_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface

No such file or directory mri_label2label: could not open label file /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label

srclabel = /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = case022_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 /mnt/hgfs/DBSI/volumetric/MGZ FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /mnt/hgfs/DBSI/volumetric/MGZ/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 case022_tp2 exited with ERRORS at Tue Sep 16 19:26:47 PDT 2014

For more details, see the log file /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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-- Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program
• MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

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you have to tell the symbolic link where to put the directory

copy this exactly into your terminal, including the period at the end

SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage .

On Wed, Sep 17, 2014 at 9:46 AM, Mahmoud zeydabadi@gmail.com wrote:

Paul,

I tried this: SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage

and got this: ln: failed to create symbolic link ‘./fsaverage’: Operation not supported

any idea ?

Mahmoud

On Wed, Sep 17, 2014 at 6:27 AM, Paul Beach pabeach1@gmail.com wrote:

...

Try something like:

cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage .

Confirm the linked directory is now in your $SUBJECTS_DIR, then try running your script.

On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud zeydabadi@gmail.com wrote:

...

Paul,

The fsaverages are in $FREESURFER_HOME/subjects. So does it mean that the program couldn't make a link between my actual image places and $FREESURFER_HOME/subjects/fsaverage ? what can I do to fix it ?

Thank you, Mahmoud

On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach pabeach1@gmail.com wrote:

...

The general fsaverage (as well as it's other iterations, fsaverages 3-6) should be located in your $FREESURFER_HOME/subjects directory. You could symbolically link it over to your $SUBJECTS_DIR.

On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud zeydabadi@gmail.com wrote:

...

Dear All,

I ran the following script:

#!/bin/bash SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm -subject case022_tp2 -all

and got the error below at the end. Could anybody please let me know how to fix it.

Thank you, Mahmoud

Reporting on 70 segmentations mri_segstats done /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label #-------------------------------------------- #@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014 INFO: *fsaverage subject does not exist in SUBJECTS_DIR* INFO: Creating symlink to fsaverage subject...

cd /mnt/hgfs/DBSI/volumetric/MGZ; ln -s /usr/local/freesurfer/subjects/fsaverage; cd -

ln: *failed to create symbolic link './fsaverage': Operation not supported*

mri_label2label --srcsubject fsaverage --srclabel /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label --trgsubject case022_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface

No such file or directory mri_label2label: could not open label file /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label

srclabel = /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = case022_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 /mnt/hgfs/DBSI/volumetric/MGZ FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /mnt/hgfs/DBSI/volumetric/MGZ/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 case022_tp2 exited with ERRORS at Tue Sep 16 19:26:47 PDT 2014

For more details, see the log file /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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-- Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program
• MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

---

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-- Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program
• MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

---

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Hmm. Well I'm stumped. Sorry. :-/

Any Freesurfer gurus have some ideas here?

On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud zeydabadi@gmail.com wrote:

Paul

it shows again: ln: failed to create symbolic link ‘./fsaverage’: Operation not supported

!!!

On Wed, Sep 17, 2014 at 6:50 AM, Paul Beach pabeach1@gmail.com wrote:

...

you have to tell the symbolic link where to put the directory

copy this exactly into your terminal, including the period at the end

SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage .

On Wed, Sep 17, 2014 at 9:46 AM, Mahmoud zeydabadi@gmail.com wrote:

...

Paul,

I tried this: SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage

and got this: ln: failed to create symbolic link ‘./fsaverage’: Operation not supported

any idea ?

Mahmoud

On Wed, Sep 17, 2014 at 6:27 AM, Paul Beach pabeach1@gmail.com wrote:

...

Try something like:

cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage .

Confirm the linked directory is now in your $SUBJECTS_DIR, then try running your script.

On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud zeydabadi@gmail.com wrote:

...

Paul,

The fsaverages are in $FREESURFER_HOME/subjects. So does it mean that the program couldn't make a link between my actual image places and $FREESURFER_HOME/subjects/fsaverage ? what can I do to fix it ?

Thank you, Mahmoud

On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach pabeach1@gmail.com wrote:

...

The general fsaverage (as well as it's other iterations, fsaverages 3-6) should be located in your $FREESURFER_HOME/subjects directory. You could symbolically link it over to your $SUBJECTS_DIR.

On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud zeydabadi@gmail.com wrote:

> Dear All, > > I ran the following script: > > #!/bin/bash > SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ > recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm > -subject case022_tp2 -all > > and got the error below at the end. Could anybody please let me know > how to fix it. > > Thank you, > Mahmoud > > > Reporting on 70 segmentations > mri_segstats done > /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label > #-------------------------------------------- > #@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014 > INFO: *fsaverage subject does not exist in SUBJECTS_DIR* > INFO: Creating symlink to fsaverage subject... > > cd /mnt/hgfs/DBSI/volumetric/MGZ; ln -s > /usr/local/freesurfer/subjects/fsaverage; cd - > > ln: *failed to create symbolic link './fsaverage': Operation not > supported* > > mri_label2label --srcsubject fsaverage --srclabel > /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label --trgsubject > case022_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface > > No such file or directory > mri_label2label: could not open label file > /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label > > srclabel = /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label > srcsubject = fsaverage > trgsubject = case022_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 /mnt/hgfs/DBSI/volumetric/MGZ > FREESURFER_HOME /usr/local/freesurfer > Loading source label. > Invalid argument > ERROR reading > /mnt/hgfs/DBSI/volumetric/MGZ/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 case022_tp2 exited with ERRORS at Tue Sep 16 19:26:47 > PDT 2014 > > For more details, see the log file > /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > _______________________________________________ > 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. > >

-- Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program
• MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

---

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-- Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program
• MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

---

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-- Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program
• MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

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No it doesnt make a difference.

Are you using a the virtual machine version of freesurfer with a shared folder? Or some other system where you are mounting a readonly file system? That is most likely your issue.

You will have to place your subjects directory onto a location in which you have write permissions.

-Zeke

On 09/17/2014 10:16 AM, Mahmoud wrote:

Paul,

I am using bash instead of tcsh. Does it make any difference ?

Mahmoud

On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach <pabeach1@gmail.com mailto:pabeach1@gmail.com> wrote:

Hmm. Well I'm stumped. Sorry.  :-/

Any Freesurfer gurus have some ideas here?

On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud <zeydabadi@gmail.com
<mailto:zeydabadi@gmail.com>> wrote:

    Paul

    it shows again:
    ln: failed to create symbolic link ‘./fsaverage’: Operation not
    supported

    !!!

    On Wed, Sep 17, 2014 at 6:50 AM, Paul Beach <pabeach1@gmail.com
    <mailto:pabeach1@gmail.com>> wrote:

        you have to tell the symbolic link where to put the directory

        copy this exactly into your terminal, including the period
        at the end

        SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
        cd $SUBJECTS_DIR
        ln -s $FREESURFER_HOME/subjects/fsaverage .



        On Wed, Sep 17, 2014 at 9:46 AM, Mahmoud
        <zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>> wrote:

            Paul,

            I tried this:
            SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
            cd $SUBJECTS_DIR
            ln -s $FREESURFER_HOME/subjects/fsaverage

            and got this:
            ln: failed to create symbolic link ‘./fsaverage’:
            Operation not supported

            any idea ?

            Mahmoud

            On Wed, Sep 17, 2014 at 6:27 AM, Paul Beach
            <pabeach1@gmail.com <mailto:pabeach1@gmail.com>> wrote:

                Try something like:

                cd $SUBJECTS_DIR
                ln -s $FREESURFER_HOME/subjects/fsaverage .

                Confirm the linked directory is now in your
                $SUBJECTS_DIR, then try running your script.

                On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud
                <zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>>
                wrote:

                    Paul,

                    The fsaverages are in $FREESURFER_HOME/subjects.
                    So does it mean that the program couldn't make a
                    link between my actual image places and
                    $FREESURFER_HOME/subjects/fsaverage ?
                    what can I do to fix it ?

                    Thank you,
                    Mahmoud

                    On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach
                    <pabeach1@gmail.com <mailto:pabeach1@gmail.com>>
                    wrote:

                        The general fsaverage (as well as it's other
                        iterations, fsaverages 3-6) should be
                        located in your $FREESURFER_HOME/subjects
                        directory. You could symbolically link it
                        over to your $SUBJECTS_DIR.

                        On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud
                        <zeydabadi@gmail.com
                        <mailto:zeydabadi@gmail.com>> wrote:

                            Dear All,

                            I ran the following script:

                            #!/bin/bash
                            SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
                            recon-all -i
                            /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm
                            -subject case022_tp2 -all

                            and got the error below at the end.
                            Could anybody please let me know how to
                            fix it.

                            Thank you,
                            Mahmoud


                            Reporting on  70 segmentations
                            mri_segstats done
                            /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label
                            #--------------------------------------------
                            #@# BA Labels lh Tue Sep 16 19:26:47 PDT
                            2014
                            INFO: *fsaverage subject does not exist
                            in SUBJECTS_DIR*
                            INFO: Creating symlink to fsaverage
                            subject...

                              cd /mnt/hgfs/DBSI/volumetric/MGZ; ln
                            -s
                            /usr/local/freesurfer/subjects/fsaverage; cd
                            -

                            ln: *failed to create symbolic link
                            './fsaverage': Operation not supported*

                              mri_label2label --srcsubject fsaverage
                            --srclabel
                            /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
                            --trgsubject case022_tp2 --trglabel
                            ./lh.BA1.label --hemi lh --regmethod
                            surface

                            No such file or directory
                            mri_label2label: could not open label
                            file
                            /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label

                            srclabel =
                            /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
                            srcsubject = fsaverage
                            trgsubject = case022_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
                            /mnt/hgfs/DBSI/volumetric/MGZ
                            FREESURFER_HOME /usr/local/freesurfer
                            Loading source label.
                            Invalid argument
                            ERROR reading
                            /mnt/hgfs/DBSI/volumetric/MGZ/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 case022_tp2 exited with
                            ERRORS at Tue Sep 16 19:26:47 PDT 2014

                            For more details, see the log file
                            /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log
                            To report a problem, see
                            http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


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                Michigan State University
                - College of Osteopathic Medicine
                - Neuroscience Program
                  - MSU *Co*gnitive and *Ge*riatric *N*eurology
                *T*eam (*CoGeNT*)

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- College of Osteopathic Medicine
- Neuroscience Program
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I dont know all the details regarding shared directories between the host and guest, but the bottom line is that if you can not manually create a symbolic link in the subjects dir than you will not be able to run recon-all.

Another option is to use the shared directory to copy the subjects dir into the file system in virtual machine space.

-Zeke

On 09/17/2014 10:33 AM, Mahmoud wrote:

Zeke,

I'm running Ubuntu 14.04 as guest on a VMware® Workstation 10 and Windows 7-64 as host. I made a shared directory between windows and Ubuntu named DBSI where then I put the /volumetric/MGZ under it. So, how can I give permission for that ?

Mahmoud

On Wed, Sep 17, 2014 at 10:21 AM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:

No it doesnt make a difference.

Are you using a the virtual machine version of freesurfer with a shared
folder? Or some other system where you are mounting a readonly file
system? That is most likely your issue.

You will have to place your subjects directory onto a location in which
you have write permissions.

-Zeke

On 09/17/2014 10:16 AM, Mahmoud wrote:
> Paul,
>
> I am using bash instead of tcsh. Does it make any difference ?
>
> Mahmoud
>
> On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>
> <mailto:pabeach1@gmail.com <mailto:pabeach1@gmail.com>>> wrote:
>
>     Hmm. Well I'm stumped. Sorry.  :-/
>
>     Any Freesurfer gurus have some ideas here?
>
>     On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud <zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>
>     <mailto:zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>>> wrote:
>
>         Paul
>
>         it shows again:
>         ln: failed to create symbolic link ‘./fsaverage’: Operation not
>         supported
>
>         !!!
>
>         On Wed, Sep 17, 2014 at 6:50 AM, Paul Beach <pabeach1@gmail.com <mailto:pabeach1@gmail.com>
>         <mailto:pabeach1@gmail.com <mailto:pabeach1@gmail.com>>> wrote:
>
>             you have to tell the symbolic link where to put the directory
>
>             copy this exactly into your terminal, including the period
>             at the end
>
>             SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
>             cd $SUBJECTS_DIR
>             ln -s $FREESURFER_HOME/subjects/fsaverage .
>
>
>
>             On Wed, Sep 17, 2014 at 9:46 AM, Mahmoud
>             <zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>
<mailto:zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>>> wrote:
>
>                 Paul,
>
>                 I tried this:
>                 SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
>                 cd $SUBJECTS_DIR
>                 ln -s $FREESURFER_HOME/subjects/fsaverage
>
>                 and got this:
>                 ln: failed to create symbolic link ‘./fsaverage’:
>                 Operation not supported
>
>                 any idea ?
>
>                 Mahmoud
>
>                 On Wed, Sep 17, 2014 at 6:27 AM, Paul Beach
>                 <pabeach1@gmail.com <mailto:pabeach1@gmail.com>
<mailto:pabeach1@gmail.com <mailto:pabeach1@gmail.com>>> wrote:
>
>                     Try something like:
>
>                     cd $SUBJECTS_DIR
>                     ln -s $FREESURFER_HOME/subjects/fsaverage .
>
>                     Confirm the linked directory is now in your
>                     $SUBJECTS_DIR, then try running your script.
>
>                     On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud
 >                     <zeydabadi@gmail.com
<mailto:zeydabadi@gmail.com> <mailto:zeydabadi@gmail.com
<mailto:zeydabadi@gmail.com>>>
>                     wrote:
>
>                         Paul,
>
>                         The fsaverages are in $FREESURFER_HOME/subjects.
>                         So does it mean that the program couldn't make a
>                         link between my actual image places and
>                         $FREESURFER_HOME/subjects/fsaverage ?
>                         what can I do to fix it ?
>
>                         Thank you,
>                         Mahmoud
>
>                         On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach
 >                         <pabeach1@gmail.com
<mailto:pabeach1@gmail.com> <mailto:pabeach1@gmail.com
<mailto:pabeach1@gmail.com>>>
>                         wrote:
>
>                             The general fsaverage (as well as it's other
>                             iterations, fsaverages 3-6) should be
>                             located in your $FREESURFER_HOME/subjects
>                             directory. You could symbolically link it
>                             over to your $SUBJECTS_DIR.
>
>                             On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud
>                             <zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>
>                             <mailto:zeydabadi@gmail.com <mailto:zeydabadi@gmail.com>>> wrote:
>
>                                 Dear All,
>
>                                 I ran the following script:
>
>                                 #!/bin/bash
>                                 SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ
>                                 recon-all -i
>                                 /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm
>                                 -subject case022_tp2 -all
>
>                                 and got the error below at the end.
>                                 Could anybody please let me know how to
>                                 fix it.
>
>                                 Thank you,
>                                 Mahmoud
>
>
>                                 Reporting on  70 segmentations
>                                 mri_segstats done
>                                 /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label
>                                 #--------------------------------------------
>                                 #@# BA Labels lh Tue Sep 16 19:26:47 PDT
>                                 2014
 >                                 INFO: *fsaverage subject does not
exist
 >                                 in SUBJECTS_DIR*
>                                 INFO: Creating symlink to fsaverage
>                                 subject...
>
>                                   cd /mnt/hgfs/DBSI/volumetric/MGZ; ln
>                                 -s
>                                 /usr/local/freesurfer/subjects/fsaverage; cd
>                                 -
>
 >                                 ln: *failed to create symbolic link
 >                                 './fsaverage': Operation not
supported*
 >
 >                                   mri_label2label --srcsubject
fsaverage
 >                                 --srclabel
 >
  /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
 >                                 --trgsubject case022_tp2 --trglabel
 >                                 ./lh.BA1.label --hemi lh --regmethod
 >                                 surface
 >
 >                                 No such file or directory
 >                                 mri_label2label: could not open label
 >                                 file
 >
  /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
 >
 >                                 srclabel =
 >
  /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label
 >                                 srcsubject = fsaverage
 >                                 trgsubject = case022_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
 >                                 /mnt/hgfs/DBSI/volumetric/MGZ
 >                                 FREESURFER_HOME /usr/local/freesurfer
 >                                 Loading source label.
 >                                 Invalid argument
 >                                 ERROR reading
 >
  /mnt/hgfs/DBSI/volumetric/MGZ/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 case022_tp2 exited with
 >                                 ERRORS at Tue Sep 16 19:26:47 PDT
2014
 >
 >                                 For more details, see the log file
 >
  /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log
 >                                 To report a problem, see
 > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 >
 >
 >
  _______________________________________________
 >                                 Freesurfer mailing list
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 >
  <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>                                 The information in this e-mail is
>                                 intended only for the person to whom it is
>                                 addressed. If you believe this e-mail
>                                 was sent to you in error and the e-mail
>                                 contains patient information, please
>                                 contact the Partners Compliance HelpLine at
>http://www.partners.org/complianceline .
>                                 If the e-mail was sent to you in error
>                                 but does not contain patient
>                                 information, please contact the sender
>                                 and properly
>                                 dispose of the e-mail.
>
>
>
>
>                             --
>                             Paul Beach
>                             DO/PhD candidate - Year VI
>                             Michigan State University
>                             - College of Osteopathic Medicine
>                             - Neuroscience Program
 >                               - MSU *Co*gnitive and *Ge*riatric
 >                             *N*eurology *T*eam (*CoGeNT*)
>
>                             _______________________________________________
>                             Freesurfer mailing list
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 >
  <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>                             The information in this e-mail is intended
>                             only for the person to whom it is
>                             addressed. If you believe this e-mail was
>                             sent to you in error and the e-mail
>                             contains patient information, please contact
>                             the Partners Compliance HelpLine at
>http://www.partners.org/complianceline . If
>                             the e-mail was sent to you in error
>                             but does not contain patient information,
>                             please contact the sender and properly
>                             dispose of the e-mail.
>
>
>
>                         _______________________________________________
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 >                         <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>                         The information in this e-mail is intended only
>                         for the person to whom it is
>                         addressed. If you believe this e-mail was sent
>                         to you in error and the e-mail
>                         contains patient information, please contact the
>                         Partners Compliance HelpLine at
>http://www.partners.org/complianceline . If the
>                         e-mail was sent to you in error
>                         but does not contain patient information, please
>                         contact the sender and properly
>                         dispose of the e-mail.
>
>
>
>
>                     --
>                     Paul Beach
>                     DO/PhD candidate - Year VI
>                     Michigan State University
>                     - College of Osteopathic Medicine
>                     - Neuroscience Program
 >                       - MSU *Co*gnitive and *Ge*riatric *N*eurology
 >                     *T*eam (*CoGeNT*)
>
>                     _______________________________________________
>                     Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
 >                     <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>                     The information in this e-mail is intended only for
>                     the person to whom it is
>                     addressed. If you believe this e-mail was sent to
>                     you in error and the e-mail
>                     contains patient information, please contact the
>                     Partners Compliance HelpLine at
>http://www.partners.org/complianceline . If the
>                     e-mail was sent to you in error
>                     but does not contain patient information, please
>                     contact the sender and properly
>                     dispose of the e-mail.
>
>
>
>                 _______________________________________________
>                 Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
 >                 <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>                 The information in this e-mail is intended only for the
>                 person to whom it is
>                 addressed. If you believe this e-mail was sent to you in
>                 error and the e-mail
>                 contains patient information, please contact the
>                 Partners Compliance HelpLine at
>http://www.partners.org/complianceline . If the e-mail
>                 was sent to you in error
>                 but does not contain patient information, please contact
>                 the sender and properly
>                 dispose of the e-mail.
>
>
>
>
>             --
>             Paul Beach
>             DO/PhD candidate - Year VI
>             Michigan State University
>             - College of Osteopathic Medicine
>             - Neuroscience Program
 >               - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam
 >             (*CoGeNT*)
>
>             _______________________________________________
>             Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
 >             <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>             The information in this e-mail is intended only for the
>             person to whom it is
>             addressed. If you believe this e-mail was sent to you in
>             error and the e-mail
>             contains patient information, please contact the Partners
>             Compliance HelpLine at
>http://www.partners.org/complianceline . If the e-mail was
>             sent to you in error
>             but does not contain patient information, please contact the
>             sender and properly
>             dispose of the e-mail.
>
>
>
>         _______________________________________________
>         Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
 >         <mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>         The information in this e-mail is intended only for the person
>         to whom it is
>         addressed. If you believe this e-mail was sent to you in error
>         and the e-mail
>         contains patient information, please contact the Partners
>         Compliance HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent
>         to you in error
>         but does not contain patient information, please contact the
>         sender and properly
>         dispose of the e-mail.
>
>
>
>
>     --
>     Paul Beach
>     DO/PhD candidate - Year VI
>     Michigan State University
>     - College of Osteopathic Medicine
>     - Neuroscience Program
 >       - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)
 >
 >     _______________________________________________
 >     Freesurfer mailing list
 > Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>>
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>     The information in this e-mail is intended only for the person to
>     whom it is
>     addressed. If you believe this e-mail was sent to you in error and
>     the e-mail
>     contains patient information, please contact the Partners Compliance
>     HelpLine at
>http://www.partners.org/complianceline . If the e-mail was sent to
>     you in error
>     but does not contain patient information, please contact the sender
>     and properly
>     dispose of the e-mail.
>
>
>
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---

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

Yeah, I was starting to wonder if he was having permissions issues as well.

On Wed, Sep 17, 2014 at 10:16 AM, Mahmoud zeydabadi@gmail.com wrote:

Paul,

I am using bash instead of tcsh. Does it make any difference ?

Mahmoud

On Wed, Sep 17, 2014 at 7:09 AM, Paul Beach pabeach1@gmail.com wrote:

...

Hmm. Well I'm stumped. Sorry. :-/

Any Freesurfer gurus have some ideas here?

On Wed, Sep 17, 2014 at 9:59 AM, Mahmoud zeydabadi@gmail.com wrote:

...

Paul

it shows again: ln: failed to create symbolic link ‘./fsaverage’: Operation not supported

!!!

On Wed, Sep 17, 2014 at 6:50 AM, Paul Beach pabeach1@gmail.com wrote:

...

you have to tell the symbolic link where to put the directory

copy this exactly into your terminal, including the period at the end

SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage .

On Wed, Sep 17, 2014 at 9:46 AM, Mahmoud zeydabadi@gmail.com wrote:

...

Paul,

I tried this: SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage

and got this: ln: failed to create symbolic link ‘./fsaverage’: Operation not supported

any idea ?

Mahmoud

On Wed, Sep 17, 2014 at 6:27 AM, Paul Beach pabeach1@gmail.com wrote:

...

Try something like:

cd $SUBJECTS_DIR ln -s $FREESURFER_HOME/subjects/fsaverage .

Confirm the linked directory is now in your $SUBJECTS_DIR, then try running your script.

On Wed, Sep 17, 2014 at 9:20 AM, Mahmoud zeydabadi@gmail.com wrote:

> Paul, > > The fsaverages are in $FREESURFER_HOME/subjects. So does it mean > that the program couldn't make a link between my actual image places and $FREESURFER_HOME/subjects/fsaverage > ? > what can I do to fix it ? > > Thank you, > Mahmoud > > On Wed, Sep 17, 2014 at 9:16 AM, Paul Beach pabeach1@gmail.com > wrote: > >> The general fsaverage (as well as it's other iterations, fsaverages >> 3-6) should be located in your $FREESURFER_HOME/subjects directory. You >> could symbolically link it over to your $SUBJECTS_DIR. >> >> On Wed, Sep 17, 2014 at 9:09 AM, Mahmoud zeydabadi@gmail.com >> wrote: >> >>> Dear All, >>> >>> I ran the following script: >>> >>> #!/bin/bash >>> SUBJECTS_DIR=/mnt/hgfs/DBSI/volumetric/MGZ >>> recon-all -i /mnt/hgfs/DBSI/volumetric/Case022/Case022_tp2/3-1.dcm >>> -subject case022_tp2 -all >>> >>> and got the error below at the end. Could anybody please let me >>> know how to fix it. >>> >>> Thank you, >>> Mahmoud >>> >>> >>> Reporting on 70 segmentations >>> mri_segstats done >>> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/label >>> #-------------------------------------------- >>> #@# BA Labels lh Tue Sep 16 19:26:47 PDT 2014 >>> INFO: *fsaverage subject does not exist in SUBJECTS_DIR* >>> INFO: Creating symlink to fsaverage subject... >>> >>> cd /mnt/hgfs/DBSI/volumetric/MGZ; ln -s >>> /usr/local/freesurfer/subjects/fsaverage; cd - >>> >>> ln: *failed to create symbolic link './fsaverage': Operation not >>> supported* >>> >>> mri_label2label --srcsubject fsaverage --srclabel >>> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label --trgsubject >>> case022_tp2 --trglabel ./lh.BA1.label --hemi lh --regmethod surface >>> >>> No such file or directory >>> mri_label2label: could not open label file >>> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label >>> >>> srclabel = >>> /mnt/hgfs/DBSI/volumetric/MGZ/fsaverage/label/lh.BA1.label >>> srcsubject = fsaverage >>> trgsubject = case022_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 /mnt/hgfs/DBSI/volumetric/MGZ >>> FREESURFER_HOME /usr/local/freesurfer >>> Loading source label. >>> Invalid argument >>> ERROR reading >>> /mnt/hgfs/DBSI/volumetric/MGZ/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 case022_tp2 exited with ERRORS at Tue Sep 16 19:26:47 >>> PDT 2014 >>> >>> For more details, see the log file >>> /mnt/hgfs/DBSI/volumetric/MGZ/case022_tp2/scripts/recon-all.log >>> To report a problem, see >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> >>> >>> _______________________________________________ >>> 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. >>> >>> >> >> >> -- >> Paul Beach >> DO/PhD candidate - Year VI >> Michigan State University >> - College of Osteopathic Medicine >> - Neuroscience Program >> - MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*) >> >> _______________________________________________ >> 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. > >

-- Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program
• MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

---

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.

-- Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program
• MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

---

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.

-- Paul Beach DO/PhD candidate - Year VI Michigan State University

• College of Osteopathic Medicine
• Neuroscience Program
• MSU *Co*gnitive and *Ge*riatric *N*eurology *T*eam (*CoGeNT*)

---

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.