Hi Bruce,

thanks for the reply. Here comes the output (see attached).

I just downloaded the VM with freesurfer from your website, fyi.

Yours Frank ---------------- PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim

Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner@MedMa.Uni-Heidelberg.de Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 9. Februar 2016 14:12 An: Freesurfer support list Betreff: Re: [Freesurfer] Processing of young children using Freesurfer

hmmm, this doesn't seem to have to do with your data but maybe is an installation problem? It says it failed but doesn't give an error message, which is unusual. Can you try just typing in directly:

cd /media/sf_cdh_ventrikel/test_002/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

and send us the output?

cheers Bruce

On Tue, 9 Feb 2016, Zoellner, Frank wrote:

Hi,   I am currently working on a project involving brain morphometry of 2 year old children. We are interested in segmenting the ventricle and I tried to run freesurfer using the standard recon-all  -all for a first test.   Unfortunately, freesurfer reports an error (see attached log file).   I also read about that it is advised to run freesurfer with patient age >5 but maybe someone has an idea how to solve this. As far as I get from the step it crashes at the intensity correction step? Do I need to calculate some sort of template maybe ?   Any comments welcome   Yours Frank

---

PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim   Phone: +49 (0)621 3835117 Fax:   +49 (0)621 3835123 Email: Frank.Zoellner@MedMa.Uni-Heidelberg.de Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

yes, something wrong with the installation but it's outside of my expertise. Zeke: can you take a look?

thanks Bruce On Thu, 11 Feb 2016, Zoellner, Frank wrote:

Hi,

did you find a hint why my installation of freesurfer is not processing the data at that stage ? It seems to be a general problem, we tried also with other data sets of elder people etc ..

Any help appreciated.

Yours Frank

---

PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim

Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner@MedMa.Uni-Heidelberg.de Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Zoellner, Frank Gesendet: Dienstag, 9. Februar 2016 15:49 An: Freesurfer support list Betreff: Re: [Freesurfer] Processing of young children using Freesurfer

Hi Bruce,

thanks for the reply. Here comes the output (see attached).

I just downloaded the VM with freesurfer from your website, fyi.

Yours Frank

---

PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim

Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner@MedMa.Uni-Heidelberg.de Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 9. Februar 2016 14:12 An: Freesurfer support list Betreff: Re: [Freesurfer] Processing of young children using Freesurfer

hmmm, this doesn't seem to have to do with your data but maybe is an installation problem? It says it failed but doesn't give an error message, which is unusual. Can you try just typing in directly:

cd /media/sf_cdh_ventrikel/test_002/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

and send us the output?

cheers Bruce

On Tue, 9 Feb 2016, Zoellner, Frank wrote:

...

Hi,   I am currently working on a project involving brain morphometry of 2 year old children. We are interested in segmenting the ventricle and I tried to run freesurfer using the standard recon-all  -all for a first test.   Unfortunately, freesurfer reports an error (see attached log file).   I also read about that it is advised to run freesurfer with patient age >5 but maybe someone has an idea how to solve this. As far as I get from the step it crashes at the intensity correction step? Do I need to calculate some sort of template maybe ?   Any comments welcome   Yours Frank

---

PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim   Phone: +49 (0)621 3835117 Fax:   +49 (0)621 3835123 Email: Frank.Zoellner@MedMa.Uni-Heidelberg.de Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

---

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

Ok thx for the info.

Yours Frank

Am 11.02.2016 um 17:29 schrieb Z K zkaufman@nmr.mgh.harvard.edu:

This is a known issue with the VirtualBox installation of freesurfer and is related to the mni tools. The mri_nu_correct stage will fail when subjects directory is in a shared folder between the host machine and the VirtualBox environment. Only known solution is to import the entire subject data into the virtual machine.

-Zeke

On 02/11/2016 08:48 AM, Bruce Fischl wrote:

...

yes, something wrong with the installation but it's outside of my expertise. Zeke: can you take a look?

thanks Bruce On Thu, 11 Feb 2016, Zoellner, Frank wrote:

...

Hi,

did you find a hint why my installation of freesurfer is not processing the data at that stage ? It seems to be a general problem, we tried also with other data sets of elder people etc ..

Any help appreciated.

Yours Frank

---

PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim

Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner@MedMa.Uni-Heidelberg.de Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Zoellner, Frank Gesendet: Dienstag, 9. Februar 2016 15:49 An: Freesurfer support list Betreff: Re: [Freesurfer] Processing of young children using Freesurfer

Hi Bruce,

thanks for the reply. Here comes the output (see attached).

I just downloaded the VM with freesurfer from your website, fyi.

Yours Frank

---

PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim

Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner@MedMa.Uni-Heidelberg.de Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

-----Ursprüngliche Nachricht----- Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl Gesendet: Dienstag, 9. Februar 2016 14:12 An: Freesurfer support list Betreff: Re: [Freesurfer] Processing of young children using Freesurfer

hmmm, this doesn't seem to have to do with your data but maybe is an installation problem? It says it failed but doesn't give an error message, which is unusual. Can you try just typing in directly:

cd /media/sf_cdh_ventrikel/test_002/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz

and send us the output?

cheers Bruce

On Tue, 9 Feb 2016, Zoellner, Frank wrote:

...

Hi,

I am currently working on a project involving brain morphometry of 2 year old children. We are interested in segmenting the ventricle and I tried to run freesurfer using the standard recon-all -all for a first test.

Unfortunately, freesurfer reports an error (see attached log file).

I also read about that it is advised to run freesurfer with patient age >5 but maybe someone has an idea how to solve this. As far as I get from the step it crashes at the intensity correction step? Do I need to calculate some sort of template maybe ?

Any comments welcome

Yours Frank

---

PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim

Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner@MedMa.Uni-Heidelberg.de Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

---

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.

---------------- PD Dr. Frank Zoellner Group Leader "MRI and Medical Image Analysis" Computer Assisted Clinical Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim

Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner@MedMa.Uni-Heidelberg.de Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/