from:"Zoellner, Frank"

Re: [Freesurfer] Processing of young children using Freesurfer

2016-02-10 Thread Zoellner, Frank

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.zoell...@medma.uni-heidelberg.de 
Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@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.zoell...@medma.uni-heidelberg.de 
Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@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.zoell...@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.

[Freesurfer] Processing of young children using Freesurfer

2016-02-09 Thread Zoellner, Frank

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.zoell...@medma.uni-heidelberg.de
Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/





recon-all.log
Description: 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.

Re: [Freesurfer] Processing of young children using Freesurfer

2016-02-09 Thread Zoellner, Frank

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.zoell...@medma.uni-heidelberg.de 
Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/


-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@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.zoell...@medma.uni-heidelberg.de
> Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/
>  
>  
>  
> 
>
/media/sf_cdh_ventrikel/test_002/mri
/usr/local/freesurfer/bin/mri_nu_correct.mni
--n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
nIters 1
$Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 
UTC 2012 i686 i686 i386 GNU/Linux
Tue Feb  9 09:44:44 EST 2016
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 
2010-02-20 at 20:19:13
tmpdir is ./tmp.mri_nu_correct.mni.3493
/media/sf_cdh_ventrikel/test_002/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3493/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3493/nu0.mnc -odt float 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig.mgz...
TR=1620.00, TE=2.67, TI=900.00, flip angle=9.00
i_ras = (-1, -2.23517e-08, 1.86265e-08)
j_ras = (-7.45058e-08, 6.28643e-09, -1)
k_ras = (-2.98023e-08, 1, 2.09548e-09)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.3493/nu0.mnc...
 

Iteration 1 Tue Feb  9 09:44:47 EST 2016
nu_correct -clobber ./tmp.mri_nu_correct.mni.3493/nu0.mnc 
./tmp.mri_nu_correct.mni.3493/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3493/0/ 
-iterations 1000 -distance 50
[fsuser@xubuntu-VirtualBox:/media/sf_cdh_ventrikel/test_002/mri/] [2016-02-09 
09:44:47] running:
  /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 
0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 
1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir 
./tmp.mri_nu_correct.mni.3493/0/ ./tmp.mri_nu_correct.mni.3493/nu0.mnc 
./tmp.mri_nu_correct.mni.3493/nu1.imp

Assertion failed at line 827 in file templates/CachedArray.cc
nu_estimate_np_and_em: crashed while running volume_stats (termination 
status=256)
nu_correct: crashed while running nu_estimate_np_and_em (termination status=256)
 
 
 
ERROR: file ./tmp.mri_nu_correct.mni.3493/nu1.mnc does not exist!
___
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.

Re: [Freesurfer] Processing of young children using Freesurfer

2016-02-09 Thread Zoellner, Frank

Hi again,

just an update, I treid this all again with an older child (109 years) but same 
thing happens.
Logfile attached.

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.zoell...@medma.uni-heidelberg.de<mailto:frank.zoell...@medma.uni-heidelberg.de>
Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Zoellner, Frank
Gesendet: Dienstag, 9. Februar 2016 10:35
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Processing of young children using Freesurfer

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.zoell...@medma.uni-heidelberg.de<mailto:frank.zoell...@medma.uni-heidelberg.de>
Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/





recon-all.log
Description: 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.

Re: [Freesurfer] Processing of young children using Freesurfer

[Freesurfer] Processing of young children using Freesurfer

Re: [Freesurfer] Processing of young children using Freesurfer

Re: [Freesurfer] Processing of young children using Freesurfer

4 matches

Site Navigation

Mail list logo

Footer information