[Freesurfer] 5.3.0, mri_segstats

2013-10-07 Thread EK Kim
Dear experts,
I updated FreeSurfer as a 5.3.0 version but have a problem about the
missing ribbon.mgz when running recon-all procedure.
I found the ftp address but couldn't find the mri_segstats.
(ftp:/surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats)

Could you let me know the right address of the file?

Best,

EK.
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Re: [Freesurfer] WM/GM boundary changes and control points

2012-10-14 Thread EK Kim
I've been struggling to upload the file to the ftp server, but failed in
several times.
Sorry for bothering you, but I will send an e-mail when the uploading is
done.


Best,

EK
2012/10/14 Bruce Fischl fis...@nmr.mgh.harvard.edu

 I found EK_test.zip, but neither tar nor unzip knows how to uncomress it.
 What format is it? Or maybe it's corrupted...


 On Sat, 13 Oct 2012, EK Kim wrote:

 Bruce, and other experts, thank you for your time :)

 I'm now uploading the data folder (before cp and after cp) to the
 freesurfer incoming directory.


 We obtained the 3D-SPGR axial images using 3T GE system which have
 8HRBRAIN receiving coil.
 Data acquisition matrix is 320-by192, FOV is 200-by-200.

 Other parameters;
 slice thickness =1.5
 TR=5.924
 TE=1.472
 Flip angle: 20
 Inversion Time=400
 Imaging Frequency 127.88
 Percent Phase FOV =80

 Sincerely,

 EK



 2012/10/11 Bruce Fischl fis...@nmr.mgh.harvard.edu
   Hi EK

   that is a really low-contrast image. Can you tell me about the
 acquisition parameters and resolution? Also, I can't
   diagnose your problem from just the volume I'll need the entire
 (tarred and gzipped) subject directory. Finally,
   please cc the list on these emails so that others can help you!

   Bruce
   On Thu, 11 Oct 2012, EK Kim wrote:

 I uploaded the files to transfer/incoming folder.


 Best,

 EK

 2012/10/11 Bruce Fischl fis...@nmr.mgh.harvard.edu
   If you upload the subject to our FTP site I will take a
 look
 Bruce



 On Oct 10, 2012, at 9:29 PM, EK Kim kse...@gmail.com wrote:

   Thank you for your answer.
 I'm not sure I understand your question right,
 but I just processed the file using following procedures.
 1. recon-all -autorecon1 -nuintensitycor-3T (because mine was
 3T)
 2. skullstripping brain mask using gcuts
 3. adding control points (only on the left hemisphere)
 4. recon-all -autorecon2-cp
 and this figure was made by a commnad line, [tkmedit wm.mgz
 -aux
 brain.mgz -surfs].
 Best,
 EK.

 2012/10/10 Bruce Fischl fis...@nmr.mgh.harvard.edu
   what was the name of the file that you transferred?
   On Wed, 10 Oct 2012, EK Kim wrote:

 I already uploaded this problem 2 days
 ago, reprocessing the subject to make
 sure about control points.
 However when I added the control points
 to the left hemisphere,
 the right hemisphere surface was changed
 severely.
 I used the command line, recon-all
 -autorecon2-cp -s subjectID.
 Could you tell me why does it occur and
 how to deal with it?


 Best,

 EK




 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
 
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  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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Re: [Freesurfer] WM/GM boundary changes and control points

2012-10-14 Thread EK Kim
I uploaded the EK_test_new.tar file to the ftp incoming folder.
I think it might work.
Thank you for you time and consideration.





2012/10/15 EK Kim kse...@gmail.com

 I've been struggling to upload the file to the ftp server, but failed in
 several times.
 Sorry for bothering you, but I will send an e-mail when the uploading is
 done.


 Best,

 EK
 2012/10/14 Bruce Fischl fis...@nmr.mgh.harvard.edu

 I found EK_test.zip, but neither tar nor unzip knows how to uncomress it.
 What format is it? Or maybe it's corrupted...


 On Sat, 13 Oct 2012, EK Kim wrote:

 Bruce, and other experts, thank you for your time :)

 I'm now uploading the data folder (before cp and after cp) to the
 freesurfer incoming directory.


 We obtained the 3D-SPGR axial images using 3T GE system which have
 8HRBRAIN receiving coil.
 Data acquisition matrix is 320-by192, FOV is 200-by-200.

 Other parameters;
 slice thickness =1.5
 TR=5.924
 TE=1.472
 Flip angle: 20
 Inversion Time=400
 Imaging Frequency 127.88
 Percent Phase FOV =80

 Sincerely,

 EK



 2012/10/11 Bruce Fischl fis...@nmr.mgh.harvard.edu
   Hi EK

   that is a really low-contrast image. Can you tell me about the
 acquisition parameters and resolution? Also, I can't
   diagnose your problem from just the volume I'll need the entire
 (tarred and gzipped) subject directory. Finally,
   please cc the list on these emails so that others can help you!

   Bruce
   On Thu, 11 Oct 2012, EK Kim wrote:

 I uploaded the files to transfer/incoming folder.


 Best,

 EK

 2012/10/11 Bruce Fischl fis...@nmr.mgh.harvard.edu
   If you upload the subject to our FTP site I will take
 a look
 Bruce



 On Oct 10, 2012, at 9:29 PM, EK Kim kse...@gmail.com
 wrote:

   Thank you for your answer.
 I'm not sure I understand your question right,
 but I just processed the file using following procedures.
 1. recon-all -autorecon1 -nuintensitycor-3T (because mine was
 3T)
 2. skullstripping brain mask using gcuts
 3. adding control points (only on the left hemisphere)
 4. recon-all -autorecon2-cp
 and this figure was made by a commnad line, [tkmedit wm.mgz
 -aux
 brain.mgz -surfs].
 Best,
 EK.

 2012/10/10 Bruce Fischl fis...@nmr.mgh.harvard.edu
   what was the name of the file that you transferred?
   On Wed, 10 Oct 2012, EK Kim wrote:

 I already uploaded this problem 2 days
 ago, reprocessing the subject to make
 sure about control points.
 However when I added the control points
 to the left hemisphere,
 the right hemisphere surface was changed
 severely.
 I used the command line, recon-all
 -autorecon2-cp -s subjectID.
 Could you tell me why does it occur and
 how to deal with it?


 Best,

 EK




 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/**compliancelinehttp://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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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


Re: [Freesurfer] WM/GM boundary changes and control points

2012-10-13 Thread EK Kim
Bruce, and other experts, thank you for your time :)

I'm now uploading the data folder (before cp and after cp) to the
freesurfer incoming directory.


We obtained the 3D-SPGR axial images using 3T GE system which have 8HRBRAIN
receiving coil.
Data acquisition matrix is 320-by192, FOV is 200-by-200.

Other parameters;
slice thickness =1.5
TR=5.924
TE=1.472
Flip angle: 20
Inversion Time=400
Imaging Frequency 127.88
Percent Phase FOV =80

Sincerely,

EK



2012/10/11 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Hi EK

 that is a really low-contrast image. Can you tell me about the acquisition
 parameters and resolution? Also, I can't diagnose your problem from just
 the volume I'll need the entire (tarred and gzipped) subject directory.
 Finally, please cc the list on these emails so that others can help you!

 Bruce

 On Thu, 11 Oct 2012, EK Kim wrote:

  I uploaded the files to transfer/incoming folder.


 Best,

 EK

 2012/10/11 Bruce Fischl fis...@nmr.mgh.harvard.edu
   If you upload the subject to our FTP site I will take a look
 Bruce



 On Oct 10, 2012, at 9:29 PM, EK Kim kse...@gmail.com wrote:

   Thank you for your answer.
 I'm not sure I understand your question right,
 but I just processed the file using following procedures.
 1. recon-all -autorecon1 -nuintensitycor-3T (because mine was
 3T)
 2. skullstripping brain mask using gcuts
 3. adding control points (only on the left hemisphere)
 4. recon-all -autorecon2-cp
 and this figure was made by a commnad line, [tkmedit wm.mgz -aux
 brain.mgz -surfs].
 Best,
 EK.

 2012/10/10 Bruce Fischl fis...@nmr.mgh.harvard.edu
   what was the name of the file that you transferred?
   On Wed, 10 Oct 2012, EK Kim wrote:

 I already uploaded this problem 2 days
 ago, reprocessing the subject to make
 sure about control points.
 However when I added the control points
 to the left hemisphere,
 the right hemisphere surface was changed
 severely.
 I used the command line, recon-all
 -autorecon2-cp -s subjectID.
 Could you tell me why does it occur and
 how to deal with it?


 Best,

 EK




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




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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


Re: [Freesurfer] WM/GM boundary changes and control points

2012-10-10 Thread EK Kim
Thank you for your answer.
I'm not sure I understand your question right,
but I just processed the file using following procedures.
1. recon-all -autorecon1 -nuintensitycor-3T (because mine was 3T)
2. skullstripping brain mask using gcuts
3. adding control points (only on the left hemisphere)
4. recon-all -autorecon2-cp
and this figure was made by a commnad line, [tkmedit wm.mgz -aux brain.mgz
-surfs].
 Best,
EK.

2012/10/10 Bruce Fischl fis...@nmr.mgh.harvard.edu

 what was the name of the file that you transferred?

 On Wed, 10 Oct 2012, EK Kim wrote:

  I already uploaded this problem 2 days ago, reprocessing the subject to
 make
 sure about control points.
 However when I added the control points to the left hemisphere,
 the right hemisphere surface was changed severely.
 I used the command line, recon-all -autorecon2-cp -s subjectID.
 Could you tell me why does it occur and how to deal with it?


 Best,

 EK




 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/**compliancelinehttp://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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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.


[Freesurfer] anisotropic input data

2012-05-04 Thread EK Kim
Dear freesurfers,

I wondered is it okay to analyze isotropic data which was converted to the
anisotropic one.

The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512, 104)
voxels.
It obtained from 3T scanner.

I know the Freesurfer recommend isotropic data (1,1,1)mm.
Does it have any problem to use the data I just transformed?

To do this, I rescaled the images and did bilinear interpolation to create
an isotropic 8-bit version of images.


Thanks for any help.

EK
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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] anisotropic input data

2012-05-04 Thread EK Kim
Thank you for the answer. But I still confuse to convert the data.
Does this mean is it 'not okay' to convert the anisotropic data to the
isotropic?
Then should I analyze the original one?

2012년 5월 4일 금요일에 Bruce Fischlfis...@nmr.mgh.harvard.edu님이 작성:
 Hi EK

 it's an empirical question. That is *very* anisotropic, so I suspect that
there will be unavoidable biases in things like thickness maps which will
be more accurate in regions in which the folds happen to place the cortex
in the high resolution plane. That said, if the CNR is good enough it will
probably generate reasonable surfaces.

 cheers
 Bruce
 On Fri, 4 May 2012, EK Kim wrote:

 Dear freesurfers,

 I wondered is it okay to analyze isotropic data which was converted to
the
 anisotropic one.

 The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512,
104)
 voxels.
 It obtained from 3T scanner.

 I know the Freesurfer recommend isotropic data (1,1,1)mm.
 Does it have any problem to use the data I just transformed?

 To do this, I rescaled the images and did bilinear interpolation to
create
 an isotropic 8-bit version of images.


 Thanks for any help.

 EK





 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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


Re: [Freesurfer] anisotropic input data

2012-05-04 Thread EK Kim
Thank you, but again I think that there might be no internal convert in my
data from the recon-all log files.

The other data set I used had records about internal convert in their
recon-all log file representing as (1 1 1)mm but this data was not.

So I worry about whether correct internal convert was preprocessed or not.
How can I confirm the processes?

Sorry for bothering you.
Thank you in advance.

2012년 5월 4일 금요일에 Bruce Fischlfis...@nmr.mgh.harvard.edu님이 작성:
 if you give it to recon-all it will convert it internally, so you don't
need to convert it yourself
 On Fri, 4 May 2012, EK Kim wrote:

 Thank you for the answer. But I still confuse to convert the data.
 Does this mean is it 'not okay' to convert the anisotropic data to the
 isotropic?
 Then should I analyze the original one?

 2012? 5?4?Bruce Fischlfis...@nmr.mgh.harvard.edu?? ??:
  Hi EK
 
  it's an empirical question. That is *very* anisotropic, so I suspect
that
 there will be unavoidable biases in things like thickness maps which
will be
 more accurate in regions in which the folds happen to place the cortex in
 the high resolution plane. That said, if the CNR is good enough it will
 probably generate reasonable surfaces.
 
  cheers
  Bruce
  On Fri, 4 May 2012, EK Kim wrote:
 
  Dear freesurfers,
 
  I wondered is it okay to analyze isotropic data which was converted to
 the
  anisotropic one.
 
  The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512,
 104)
  voxels.
  It obtained from 3T scanner.
 
  I know the Freesurfer recommend isotropic data (1,1,1)mm.
  Does it have any problem to use the data I just transformed?
 
  To do this, I rescaled the images and did bilinear interpolation to
 create
  an isotropic 8-bit version of images.
 
 
  Thanks for any help.
 
  EK
 
 
 
 
 
  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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


Re: [Freesurfer] anisotropic input data

2012-05-04 Thread EK Kim
Yes I found it :)
Thank you for your help!

Sincerely,

EK.

2012/5/4 Bruce Fischl fis...@nmr.mgh.harvard.edu

 run:

 mri_info $SUBJECTS_DIR/$subject/mri/**orig.mgz

 and you should see that it is 1mm isotropic


 cheers
 Bruce
 On Fri, 4 May 2012, EK Kim wrote:

  Thank you, but again I think that there might be no internal convert in
 my
 data from the recon-all log files.

 The other data set I used had records about internal convert in their
 recon-all log file representing as (1 1 1)mm but this data was not.

 So I worry about whether correct internal convert was preprocessed or not.
 How can I confirm the processes?

 Sorry for bothering you.
 Thank you in advance.

  2012? 5?4?Bruce 
 Fischlfis...@nmr.mgh.harvard.**edufis...@nmr.mgh.harvard.edu??
 ??:
  if you give it to recon-all it will convert it internally, so you don't
 need to convert it yourself
  On Fri, 4 May 2012, EK Kim wrote:
 
  Thank you for the answer. But I still confuse to convert the data.
  Does this mean is it 'not okay' to convert the anisotropic data to the
  isotropic?
  Then should I analyze the original one?
 
  2012? 5?4?Bruce 
  Fischlfis...@nmr.mgh.harvard.**edufis...@nmr.mgh.harvard.edu??
 ??:
   Hi EK
  
   it's an empirical question. That is *very* anisotropic, so I suspect
 that
  there will be unavoidable biases in things like thickness maps which
 will
 be
  more accurate in regions in which the folds happen to place the cortex
 in
  the high resolution plane. That said, if the CNR is good enough it will
  probably generate reasonable surfaces.
  
   cheers
   Bruce
   On Fri, 4 May 2012, EK Kim wrote:
  
   Dear freesurfers,
  
   I wondered is it okay to analyze isotropic data which was converted
 to
  the
   anisotropic one.
  
   The original data has (0.390625, 0.390625, 1.5) mm size and (512,
 512,
  104)
   voxels.
   It obtained from 3T scanner.
  
   I know the Freesurfer recommend isotropic data (1,1,1)mm.
   Does it have any problem to use the data I just transformed?
  
   To do this, I rescaled the images and did bilinear interpolation to
  create
   an isotropic 8-bit version of images.
  
  
   Thanks for any help.
  
   EK
  
  
  
  
  
   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/**compliancelinehttp://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] recon-all error (nu_correct problem)

2012-02-14 Thread EK Kim
Hello, Freesurfers,

I got an error message when I trying to use recon-all function in
freesurfer
on the XUbuntu system installed on the VirtualBox on a Windows 7 machine.
I searched the e-mailing list but I can't find any answers.

My problem is related to the nu_correct and nu_estimate_np_and_em.
However, nu_correct and nu_estimate_np_and_em were located to exact path
(/home/virtualuser/freesurfer/mni/bin).
echo $MNI_DATAPATH, echo $MNI_PERL5LIB showed exact path.
In addition, I already tried to use fixup_mni_paths.

Could anyone give me an advice for fixing up this problem?

Thanks in advance.

Cheers,

EK


error message!


#@# Nu Intensity Correction Wed Feb 15 01:23:24 EST 2012
 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar
transforms/talairach.xfm --n 2
/home/virtualuser/Desktop/DATA/30664304/mri
/home/virtualuser/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC
2009 i686 GNU/Linux
Wed Feb 15 01:23:25 EST 2012
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.17682
/home/virtualuser/Desktop/DATA/30664304/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17682/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.17682/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.17682/nu0.mnc...


Iteration 1 Wed Feb 15 01:23:37 EST 2012
nu_correct -clobber ./tmp.mri_nu_correct.mni.17682/nu0.mnc
./tmp.mri_nu_correct.mni.17682/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.17682/0/
[virtualuser@FreeSurfer:/home/virtualuser/Desktop/DATA/30664304/mri/]
[2012-02-15 01:23:37] running:
  /home/virtualuser/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log
-sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask
-nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp
-tmpdir ./tmp.mri_nu_correct.mni.17682/0/
./tmp.mri_nu_correct.mni.17682/nu0.mnc
./tmp.mri_nu_correct.mni.17682/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: nu_correct
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC
2009 i686 GNU/Linux
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