[Freesurfer] Error in running make_average_subject

2018-12-07 Thread Emanuel Alvaredo 
External Email - Use Caution

Hello!, I am getting the following error using the
command make_average_subject

mri/norm.mgz: could not load norm volume from (null)

I have found this page with a path for de issue

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html

But I dont know how to apply the path. Can you give some information about
this?

Thanks!



Emanuel
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[Freesurfer] Error in running make_average_subject

2019-09-15 Thread Himanshu Aggarwal 
External Email - Use Caution

Hello Freesurfer Developers

I am trying to create an average subject for 20 subjects using the function 
make_average_subject. But I keep running into a segmentation fault. I have 
attached the recon-all.log file.

I found a few other posts about the same problem which direct the users to the 
following patch:
 https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ 
(https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/)

But this patch does not have a readme file which can instruct the users about 
the steps that need to be followed to get rid of this bug. However, I have 
replaced the files in /usr/local/freesurfer/bin/ (i.e. the $FREESURFER_HOME) 
with the files given in this patch directory. But the problem still persists. 
Kindly provide the steps that need to be followed to make use of this patch 
properly.

Regards

Himanshu
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[Freesurfer] Error in running make_average_subject

2019-09-15 Thread Himanshu Aggarwal 
External Email - Use Caution

Hello Freesurfer Developers

I am trying to create an average subject for 20 subjects using the function 
make_average_subject. But I keep running into a segmentation fault. I have 
attached the recon-all.log file.

I found a few other posts about the same problem which direct the users to the 
following patch:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ 
(https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/)

But this patch does not have a readme file which can instruct the users about 
the steps that need to be followed to get rid of this bug. However, I have 
replaced the files in /usr/local/freesurfer/bin/ (i.e. the $FREESURFER_HOME) 
with the files given in this patch directory. But the problem still persists. 
Kindly provide the steps that need to be followed to make use of this patch 
properly.

Regards

Himanshu
Sun Sep 15 16:15:08 IST 2019
/home/leesa/Desktop/freesurfer_outputs/avgsubject
/home/leesa/freesurfer/bin/recon-all
-s avgsubject -cortribbon -aparc2aseg
subjid avgsubject
setenv SUBJECTS_DIR /home/leesa/Desktop/freesurfer_outputs
FREESURFER_HOME /home/leesa/freesurfer
Actual FREESURFER_HOME /home/leesa/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux sinha-Lenovo-Product 4.15.0-62-generic #69-Ubuntu SMP Wed Sep 4 20:55:53 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 16384 kbytes
maxproc  96050 
maxlocks unlimited
maxsignal96050 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   24633364 321609613523204   84196 789406420933832
Swap:  18431996   018431996


program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info 
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2019/09/15-10:45:08-GMT  BuildTimeStamp: Jan 18 
2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp 
$  User: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version 
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2019/09/15-10:45:09-GMT  BuildTimeStamp: Jan 18 
2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve 
Exp $  User: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier 
(x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2019/09/15-10:45:09-GMT  BuildTimeStamp: Jan 18 
2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ 
 User: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2019/09/15-10:45:09-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  
CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: 
leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:09-GMT  BuildTimeStamp: Jan 18 2017 
16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp 
$  User: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:09-GMT  BuildTimeStamp: Jan 18 2017 
16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: 
leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2019/09/15-10:45:09-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  
CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: 
leesa  Machine: sinha-Lenovo-Product  Platform

[Freesurfer] Error in running make_average_subject

2018-02-19 Thread M Janani 
Dear FreeSurfer Experts,

 I’m recently getting an error in make_average_subject and can’t find
 the reason.

 Please see the following for the error log from recon-all.log:


 mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel 
mri/norm.mgz mri/transforms/talairach.m3z 
/home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca 
mri/aseg.auto_noCCseg.label_intensities.txt

relabeling unlikely voxels interior to white matter surface:
norm: mri/norm.mgz
 XFORM: mri/transforms/talairach.m3z
GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca
label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /home/lakshman/freesurfer/subjects
subject avgsubject1
outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white

Reading lh pial surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial

Loading lh annotations from 
/home/lakshman/freesurfer/subjects/avgsubject1/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)

Reading rh white surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white

Reading rh pial surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial

Loading rh annotations from 
/home/lakshman/freesurfer/subjects/avgsubject1/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from 
/home/lakshman/freesurfer/subjects/avgsubject1/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from 
/home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from

Could you please help us in resolving the issue.

Have also attached the recon-all log for reference.

Thanks & Regards,
Janani


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Re: [Freesurfer] Error in running make_average_subject

2018-12-07 Thread Bruce Fischl 

Hi Emanuel

you need to send us the full command you ran and output of it if you want 
us to be able to help you


cheers
Bruce
On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:



External Email - Use Caution

Hello!, I am getting the following error using the command make_average_subject 

mri/norm.mgz: could not load norm volume from (null)

I have found this page with a path for de issue

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html

But I dont know how to apply the path. Can you give some information about this?

Thanks!



Emanuel

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Re: [Freesurfer] Error in running make_average_subject

2018-12-10 Thread Emanuel Alvaredo 
External Email - Use Caution

Thanks Bruce. The following is the command.


 make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects
subject1  subject2 subject3


And I made a mistake in may last mail. I use the word path instead of patch

I have found this page with a *patch* for de issue

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html

But I dont know how to apply the *patch*. Can you give some information
about this?


Emanuel


On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl 
wrote:

> Hi Emanuel
>
> you need to send us the full command you ran and output of it if you want
> us to be able to help you
>
> cheers
> Bruce
> On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:
>
> >
> > External Email - Use Caution
> >
> > Hello!, I am getting the following error using the
> command make_average_subject
> >
> > mri/norm.mgz: could not load norm volume from (null)
> >
> > I have found this page with a path for de issue
> >
> >
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
> >
> > But I dont know how to apply the path. Can you give some information
> about this?
> >
> > Thanks!
> >
> >
> >
> > Emanuel
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Error in running make_average_subject

2018-12-11 Thread Greve, Douglas N.,Ph.D. 
Sorry, the disk that held that patch failed and we did not have a backup so not 
everything was restored. I just put this file there:

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface

Copy it to $FREESURFER_HOME/bin. Let me know how it goes


On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:

External Email - Use Caution

Thanks Bruce. The following is the command.


 make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects  subject1  
subject2 subject3


And I made a mistake in may last mail. I use the word path instead of patch

I have found this page with a patch for de issue

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html

But I dont know how to apply the patch. Can you give some information about 
this?


Emanuel


On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Emanuel

you need to send us the full command you ran and output of it if you want
us to be able to help you

cheers
Bruce
On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:

>
> External Email - Use Caution
>
> Hello!, I am getting the following error using the command 
> make_average_subject
>
> mri/norm.mgz: could not load norm volume from (null)
>
> I have found this page with a path for de issue
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>
> But I dont know how to apply the path. Can you give some information about 
> this?
>
> Thanks!
>
>
>
> Emanuel
>
>___
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Re: [Freesurfer] Error in running make_average_subject

2018-12-12 Thread Emanuel Alvaredo 
External Email - Use Caution

Thanks for your answer Douglas. I replaced the make_average_surface  file
with the new one but  I have the same message error.

ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from (null)

Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2
17:16:02 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

Thanks

Emanuel


On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Sorry, the disk that held that patch failed and we did not have a backup
> so not everything was restored. I just put this file there:
>
>
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
>
> Copy it to $FREESURFER_HOME/bin. Let me know how it goes
>
>
> On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:
>
> External Email - Use Caution
> Thanks Bruce. The following is the command.
>
>
>  make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects
> subject1  subject2 subject3
>
>
> And I made a mistake in may last mail. I use the word path instead of patch
>
> I have found this page with a *patch* for de issue
>
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>
> But I dont know how to apply the *patch*. Can you give some information
> about this?
>
>
> Emanuel
>
>
> On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl 
> wrote:
>
>> Hi Emanuel
>>
>> you need to send us the full command you ran and output of it if you want
>> us to be able to help you
>>
>> cheers
>> Bruce
>> On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Hello!, I am getting the following error using the
>> command make_average_subject
>> >
>> > mri/norm.mgz: could not load norm volume from (null)
>> >
>> > I have found this page with a path for de issue
>> >
>> >
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>> >
>> > But I dont know how to apply the path. Can you give some information
>> about this?
>> >
>> > Thanks!
>> >
>> >
>> >
>> > Emanuel
>> >
>> >___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing 
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>
>
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Re: [Freesurfer] Error in running make_average_subject

2018-12-12 Thread Bruce Fischl 

Hi Emanuel,

can you include the full command line and output?

cheers
Bruce
On Wed, 12 Dec 2018, 
Emanuel Alvaredo wrote:




External Email - Use Caution

Thanks for your answer Douglas. I replaced the make_average_surface  file with 
the new one but  I
have the same message error.
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from (null)

Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 
UTC 2018 x86_64 x86_64
x86_64 GNU/Linux

Thanks

Emanuel


On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. 
 wrote:
  Sorry, the disk that held that patch failed and we did not have a backup 
so not
  everything was restored. I just put this file there:

  
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface

  Copy it to $FREESURFER_HOME/bin. Let me know how it goes


  On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:

  External Email - Use Caution

  Thanks Bruce. The following is the command.

 make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects  subject1 
subject2 subject3


And I made a mistake in may last mail. I use the word path instead of patch

I have found this page with a patch for de issue

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html

But I dont know how to apply the patch. Can you give some information about 
this?


Emanuel


On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl  wrote:
  Hi Emanuel

  you need to send us the full command you ran and output of it if you want
  us to be able to help you

  cheers
  Bruce
  On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:

  >
  > External Email - Use Caution
  >
  > Hello!, I am getting the following error using the
  command make_average_subject 
  >
  > mri/norm.mgz: could not load norm volume from (null)
  >
  > I have found this page with a path for de issue
  >
  >
  
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
  >
  > But I dont know how to apply the path. Can you give some information 
about
  this?
  >
  > Thanks!
  >
  >
  >
  > Emanuel
  >
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Re: [Freesurfer] Error in running make_average_subject

2018-12-13 Thread Emanuel Alvaredo 
External Email - Use Caution

Hello Bruce, thanks for your anwer. Sure. The command is

*make_average_subject --out avgsubjectPRUEBAESTASI! --subjects
Bartley_Recon Baez_Recon Bonilla_Recon*

The output is in the attached file

Thanks!

Emanuel


On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl 
wrote:

> Hi Emanuel,
>
> can you include the full command line and output?
>
> cheers
> Bruce
> On Wed, 12 Dec 2018,
> Emanuel Alvaredo wrote:
>
> >
> > External Email - Use Caution
> >
> > Thanks for your answer Douglas. I replaced the make_average_surface
> file with the new one but  I
> > have the same message error.
> > ASeg Vox2RAS: ---
> > -1.0   0.0   0.0   128.0;
> >  0.0   0.0   1.0  -128.0;
> >  0.0  -1.0   0.0   128.0;
> >  0.0   0.0   0.0   1.0;
> > mghRead(mri/norm.mgz, -1): could not open file
> > -
> >
> > Labeling Slice
> > relabeling unlikely voxels in interior of white matter
> > mri/norm.mgz: could not load norm volume from (null)
> >
> > Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2
> 17:16:02 UTC 2018 x86_64 x86_64
> > x86_64 GNU/Linux
> >
> > Thanks
> >
> > Emanuel
> >
> >
> > On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
> >   Sorry, the disk that held that patch failed and we did not have a
> backup so not
> >   everything was restored. I just put this file there:
> >
> >
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
> >
> >   Copy it to $FREESURFER_HOME/bin. Let me know how it goes
> >
> >
> >   On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:
> >
> >   External Email - Use Caution
> >
> >   Thanks Bruce. The following is the command.
> >
> >  make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects
> subject1
> > subject2 subject3
> >
> >
> > And I made a mistake in may last mail. I use the word path instead of
> patch
> >
> > I have found this page with a patch for de issue
> >
> >
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
> >
> > But I dont know how to apply the patch. Can you give some information
> about this?
> >
> >
> > Emanuel
> >
> >
> > On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl 
> wrote:
> >   Hi Emanuel
> >
> >   you need to send us the full command you ran and output of it if
> you want
> >   us to be able to help you
> >
> >   cheers
> >   Bruce
> >   On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hello!, I am getting the following error using the
> >   command make_average_subject
> >   >
> >   > mri/norm.mgz: could not load norm volume from (null)
> >   >
> >   > I have found this page with a path for de issue
> >   >
> >   >
> >
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
> >   >
> >   > But I dont know how to apply the path. Can you give some
> information about
> >   this?
> >   >
> >   > Thanks!
> >   >
> >   >
> >   >
> >   > Emanuel
> >   >
> >   >___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Wed Dec 12 15:07:35 -03 2018
/usr/local/freesurfer/subjects/avgsubjectPRUEBAESTASI!
/usr/local/freesurfer/bin/recon-all
-s avgsubjectPRUEBAESTASI! -cortribbon -aparc2aseg
subjid avgsubjectPRUEBAESTASI!
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  127892 
maxlocks unlimited
maxsignal127892 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   32782796131

Re: [Freesurfer] Error in running make_average_subject

2018-12-14 Thread Greve, Douglas N.,Ph.D. 
 can you include the full terminal output?

On 12/13/18 7:45 AM, Emanuel Alvaredo wrote:

External Email - Use Caution

Hello Bruce, thanks for your anwer. Sure. The command is

make_average_subject --out avgsubjectPRUEBAESTASI! --subjects  Bartley_Recon 
Baez_Recon Bonilla_Recon

The output is in the attached file

Thanks!

Emanuel


On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi Emanuel,

can you include the full command line and output?

cheers
Bruce
On Wed, 12 Dec 2018,
Emanuel Alvaredo wrote:

>
> External Email - Use Caution
>
> Thanks for your answer Douglas. I replaced the make_average_surface  file 
> with the new one but  I
> have the same message error.
> ASeg Vox2RAS: ---
> -1.0   0.0   0.0   128.0;
>  0.0   0.0   1.0  -128.0;
>  0.0  -1.0   0.0   128.0;
>  0.0   0.0   0.0   1.0;
> mghRead(mri/norm.mgz, -1): could not open file
> -
>
> Labeling Slice
> relabeling unlikely voxels in interior of white matter
> mri/norm.mgz: could not load norm volume from (null)
>
> Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 
> UTC 2018 x86_64 x86_64
> x86_64 GNU/Linux
>
> Thanks
>
> Emanuel
>
>
> On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>   Sorry, the disk that held that patch failed and we did not have a 
> backup so not
>   everything was restored. I just put this file there:
>
>   
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
>
>   Copy it to $FREESURFER_HOME/bin. Let me know how it goes
>
>
>   On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:
>
>   External Email - Use Caution
>
>   Thanks Bruce. The following is the command.
>
>  make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects  subject1
> subject2 subject3
>
>
> And I made a mistake in may last mail. I use the word path instead of patch
>
> I have found this page with a patch for de issue
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>
> But I dont know how to apply the patch. Can you give some information about 
> this?
>
>
> Emanuel
>
>
> On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>   Hi Emanuel
>
>   you need to send us the full command you ran and output of it if you 
> want
>   us to be able to help you
>
>   cheers
>   Bruce
>   On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:
>
>   >
>   > External Email - Use Caution
>   >
>   > Hello!, I am getting the following error using the
>   command make_average_subject
>   >
>   > mri/norm.mgz: could not load norm volume from (null)
>   >
>   > I have found this page with a path for de issue
>   >
>   >
>   
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>   >
>   > But I dont know how to apply the path. Can you give some information 
> about
>   this?
>   >
>   > Thanks!
>   >
>   >
>   >
>   > Emanuel
>   >
>   >___
>   Freesurfer mailing list
>   Freesurfer@nmr.mgh.harvard.edu
>   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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

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

Re: [Freesurfer] Error in running make_average_subject

2019-01-17 Thread Korom, Marta 
External Email - Use Caution

Hello Bruce, Greve and Emanuel,

I have an identical problem. Have you found a solution to this issue? I'm
attaching my recon-all.log, as well, in case you need it.

Thank you!
Marta

On Fri, Dec 14, 2018 at 1:44 PM Emanuel Alvaredo 
wrote:

> External Email - Use Caution
>
> Thanks Greve. The output is attached  now.
>
>
> Emanuel
>
>
> On Fri, Dec 14, 2018 at 1:01 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>>  can you include the full terminal output?
>>
>> On 12/13/18 7:45 AM, Emanuel Alvaredo wrote:
>>
>> External Email - Use Caution
>> Hello Bruce, thanks for your anwer. Sure. The command is
>>
>> *make_average_subject --out avgsubjectPRUEBAESTASI! --subjects
>> Bartley_Recon Baez_Recon Bonilla_Recon*
>>
>> The output is in the attached file
>>
>> Thanks!
>>
>> Emanuel
>>
>>
>> On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl 
>> wrote:
>>
>>> Hi Emanuel,
>>>
>>> can you include the full command line and output?
>>>
>>> cheers
>>> Bruce
>>> On Wed, 12 Dec 2018,
>>> Emanuel Alvaredo wrote:
>>>
>>> >
>>> > External Email - Use Caution
>>> >
>>> > Thanks for your answer Douglas. I replaced the make_average_surface
>>> file with the new one but  I
>>> > have the same message error.
>>> > ASeg Vox2RAS: ---
>>> > -1.0   0.0   0.0   128.0;
>>> >  0.0   0.0   1.0  -128.0;
>>> >  0.0  -1.0   0.0   128.0;
>>> >  0.0   0.0   0.0   1.0;
>>> > mghRead(mri/norm.mgz, -1): could not open file
>>> > -
>>> >
>>> > Labeling Slice
>>> > relabeling unlikely voxels in interior of white matter
>>> > mri/norm.mgz: could not load norm volume from (null)
>>> >
>>> > Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2
>>> 17:16:02 UTC 2018 x86_64 x86_64
>>> > x86_64 GNU/Linux
>>> >
>>> > Thanks
>>> >
>>> > Emanuel
>>> >
>>> >
>>> > On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D. <
>>> dgr...@mgh.harvard.edu> wrote:
>>> >   Sorry, the disk that held that patch failed and we did not have
>>> a backup so not
>>> >   everything was restored. I just put this file there:
>>> >
>>> >
>>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
>>> >
>>> >   Copy it to $FREESURFER_HOME/bin. Let me know how it goes
>>> >
>>> >
>>> >   On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:
>>> >
>>> >   External Email - Use Caution
>>> >
>>> >   Thanks Bruce. The following is the command.
>>> >
>>> >  make_average_subject --out avgsubjectPRUEBAESTASIEmac --subjects
>>> subject1
>>> > subject2 subject3
>>> >
>>> >
>>> > And I made a mistake in may last mail. I use the word path instead of
>>> patch
>>> >
>>> > I have found this page with a patch for de issue
>>> >
>>> >
>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>>> >
>>> > But I dont know how to apply the patch. Can you give some information
>>> about this?
>>> >
>>> >
>>> > Emanuel
>>> >
>>> >
>>> > On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl <
>>> fis...@nmr.mgh.harvard.edu> wrote:
>>> >   Hi Emanuel
>>> >
>>> >   you need to send us the full command you ran and output of it if
>>> you want
>>> >   us to be able to help you
>>> >
>>> >   cheers
>>> >   Bruce
>>> >   On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:
>>> >
>>> >   >
>>> >   > External Email - Use Caution
>>> >   >
>>> >   > Hello!, I am getting the following error using the
>>> >   command make_average_subject
>>> >   >
>>> >   > mri/norm.mgz: could not load norm volume from (null)
>>> >   >
>>> >   > I have found this page with a path for de issue
>>> >   >
>>> >   >
>>> >
>>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>>> >   >
>>> >   > But I dont know how to apply the path. Can you give some
>>> information about
>>> >   this?
>>> >   >
>>> >   > Thanks!
>>> >   >
>>> >   >
>>> >   >
>>> >   > Emanuel
>>> >   >
>>> >   >___
>>> >   Freesurfer mailing list
>>> >   Freesurfer@nmr.mgh.harvard.edu
>>> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >
>>> >
>>> >
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >
>>> >
>>> > ___
>>> > Freesurfer mailing list
>>> > Freesurfer@nmr.mgh.harvard.edu
>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> >
>>> >
>>> >___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>> ___
>> Free

Re: [Freesurfer] Error in running make_average_subject

2019-01-22 Thread Greve, Douglas N.,Ph.D. 
This has been fixed in our development version. I can give you a new 
script or you can try this:
cd $SUBJECTS_DIR/*avgsubjectPRUEBAESTASI!
ln -s orig.mgz norm.mgz
Then re-run make_average_subject




*
On 12/14/18 1:43 PM, Emanuel Alvaredo wrote:
>
> External Email - Use Caution
>
> Thanks Greve. The output is attached  now.
>
>
> Emanuel
>
>
> On Fri, Dec 14, 2018 at 1:01 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
>  can you include the full terminal output?
>
> On 12/13/18 7:45 AM, Emanuel Alvaredo wrote:
>>
>> External Email - Use Caution
>>
>> Hello Bruce, thanks for your anwer. Sure. The command is
>>
>> *make_average_subject --out avgsubjectPRUEBAESTASI! --subjects 
>> Bartley_Recon Baez_Recon Bonilla_Recon*
>>
>> The output is in the attached file
>>
>> Thanks!
>>
>> Emanuel
>>
>>
>> On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl
>> mailto:fis...@nmr.mgh.harvard.edu>>
>> wrote:
>>
>> Hi Emanuel,
>>
>> can you include the full command line and output?
>>
>> cheers
>> Bruce
>> On Wed, 12 Dec 2018,
>> Emanuel Alvaredo wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Thanks for your answer Douglas. I replaced the
>> make_average_surface  file with the new one but  I
>> > have the same message error.
>> > ASeg Vox2RAS: ---
>> > -1.0   0.0   0.0   128.0;
>> >  0.0   0.0   1.0  -128.0;
>> >  0.0  -1.0   0.0   128.0;
>> >  0.0   0.0   0.0   1.0;
>> > mghRead(mri/norm.mgz, -1): could not open file
>> > -
>> >
>> > Labeling Slice
>> > relabeling unlikely voxels in interior of white matter
>> > mri/norm.mgz: could not load norm volume from (null)
>> >
>> > Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP
>> Tue Oct 2 17:16:02 UTC 2018 x86_64 x86_64
>> > x86_64 GNU/Linux
>> >
>> > Thanks
>> >
>> > Emanuel
>> >
>> >
>> > On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D.
>> mailto:dgr...@mgh.harvard.edu>> wrote:
>> >       Sorry, the disk that held that patch failed and we
>> did not have a backup so not
>> >       everything was restored. I just put this file there:
>> >
>> >
>> 
>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
>> >
>> >       Copy it to $FREESURFER_HOME/bin. Let me know how it goes
>> >
>> >
>> >       On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:
>> >
>> >       External Email - Use Caution
>> >
>> >       Thanks Bruce. The following is the command.
>> >
>> >  make_average_subject --out avgsubjectPRUEBAESTASIEmac
>> --subjects  subject1
>> > subject2 subject3
>> >
>> >
>> > And I made a mistake in may last mail. I use the word path
>> instead of patch
>> >
>> > I have found this page with a patch for de issue
>> >
>> >
>> 
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>> >
>> > But I dont know how to apply the patch. Can you give some
>> information about this?
>> >
>> >
>> > Emanuel
>> >
>> >
>> > On Fri, Dec 7, 2018 at 4:54 PM Bruce Fischl
>> > > wrote:
>> >       Hi Emanuel
>> >
>> >       you need to send us the full command you ran and
>> output of it if you want
>> >       us to be able to help you
>> >
>> >       cheers
>> >       Bruce
>> >       On Fri, 7 Dec 2018, Emanuel Alvaredo wrote:
>> >
>> >       >
>> >       > External Email - Use Caution
>> >       >
>> >       > Hello!, I am getting the following error using the
>> >       command make_average_subject
>> >       >
>> >       > mri/norm.mgz: could not load norm volume from (null)
>> >       >
>> >       > I have found this page with a path for de issue
>> >       >
>> >       >
>> >
>> 
>> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
>> >       >
>> >       > But I dont know how to apply the path. Can you give
>> some information about
>> >       this?
>> >       >
>> >       > Thanks!
>> >       >
>> >       >
>> >       >
>> >       > Emanuel
>> >       >
>> >  >_

Re: [Freesurfer] Error in running make_average_subject

2019-01-25 Thread Korom, Marta 
External Email - Use Caution

Hello Bruce, Doug and Emanuel,

I tried what you suggested (ln -s orig.mgz norm.mgz), and I also downloaded
the development version and tried that, but neither procedures fixed
the problem.

In the meantime, my father-in-law took a week and fixed the script and now
it runs smoothly and finishes without error. The following code segment of
the make_average_subject file needed to be fixed:

*Erroneous code segment: *
…
if($DoSurfaces && $DoVolumes) then
  set cmd = (recon-all -s $average_subject -cortribbon -aparc2aseg)
  echo $cmd
  $cmd
  if($status) exit 1;
endif
…

*New, corrected code segment: *

if($DoSurfaces && $DoVolumes) then
  *#set cmd = (recon-all -s $average_subject -cortribbon -aparc2aseg)*
*  set cmd = (recon-all -s $average_subject -nuintensitycor -gcareg -canorm
-careg -calabel -cortribbon -aparc2aseg)*
  echo $cmd
  $cmd
  if($status) exit 1;
endif
…

The code that is highlighted with red and a hashtag is what caused the
script to exit with errors. The one below that (highlighted with green) is
the fixed line of code that finishes without errors.

The patched make_average_subject file is also attached. Feel free to use
it.

Best,
Marta (and my father-in-law)


On Tue, Jan 22, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> This has been fixed in our development version. I can give you a new
> script or you can try this:
> cd $SUBJECTS_DIR/*avgsubjectPRUEBAESTASI!
> ln -s orig.mgz norm.mgz
> Then re-run make_average_subject
>
>
>
>
> *
> On 12/14/18 1:43 PM, Emanuel Alvaredo wrote:
> >
> > External Email - Use Caution
> >
> > Thanks Greve. The output is attached  now.
> >
> >
> > Emanuel
> >
> >
> > On Fri, Dec 14, 2018 at 1:01 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> >  can you include the full terminal output?
> >
> > On 12/13/18 7:45 AM, Emanuel Alvaredo wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Hello Bruce, thanks for your anwer. Sure. The command is
> >>
> >> *make_average_subject --out avgsubjectPRUEBAESTASI! --subjects
> >> Bartley_Recon Baez_Recon Bonilla_Recon*
> >>
> >> The output is in the attached file
> >>
> >> Thanks!
> >>
> >> Emanuel
> >>
> >>
> >> On Wed, Dec 12, 2018 at 7:05 PM Bruce Fischl
> >> mailto:fis...@nmr.mgh.harvard.edu>>
> >> wrote:
> >>
> >> Hi Emanuel,
> >>
> >> can you include the full command line and output?
> >>
> >> cheers
> >> Bruce
> >> On Wed, 12 Dec 2018,
> >> Emanuel Alvaredo wrote:
> >>
> >> >
> >> > External Email - Use Caution
> >> >
> >> > Thanks for your answer Douglas. I replaced the
> >> make_average_surface  file with the new one but  I
> >> > have the same message error.
> >> > ASeg Vox2RAS: ---
> >> > -1.0   0.0   0.0   128.0;
> >> >  0.0   0.0   1.0  -128.0;
> >> >  0.0  -1.0   0.0   128.0;
> >> >  0.0   0.0   0.0   1.0;
> >> > mghRead(mri/norm.mgz, -1): could not open file
> >> > -
> >> >
> >> > Labeling Slice
> >> > relabeling unlikely voxels in interior of white matter
> >> > mri/norm.mgz: could not load norm volume from (null)
> >> >
> >> > Linux neuroWorkstation00 4.4.0-138-generic #164-Ubuntu SMP
> >> Tue Oct 2 17:16:02 UTC 2018 x86_64 x86_64
> >> > x86_64 GNU/Linux
> >> >
> >> > Thanks
> >> >
> >> > Emanuel
> >> >
> >> >
> >> > On Tue, Dec 11, 2018 at 1:10 PM Greve, Douglas N.,Ph.D.
> >> mailto:dgr...@mgh.harvard.edu>> wrote:
> >> >   Sorry, the disk that held that patch failed and we
> >> did not have a backup so not
> >> >   everything was restored. I just put this file there:
> >> >
> >> >
> >>
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface
> >> >
> >> >   Copy it to $FREESURFER_HOME/bin. Let me know how it goes
> >> >
> >> >
> >> >   On 12/10/18 12:48 PM, Emanuel Alvaredo wrote:
> >> >
> >> >   External Email - Use Caution
> >> >
> >> >   Thanks Bruce. The following is the command.
> >> >
> >> >  make_average_subject --out avgsubjectPRUEBAESTASIEmac
> >> --subjects  subject1
> >> > subject2 subject3
> >> >
> >> >
> >> > And I made a mistake in may last mail. I use the word path
> >> instead of patch
> >> >
> >> > I have found this page with a patch for de issue
> >> >
> >> >
> >>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-February/056008.html
> >> >
> >> > B

Re: [Freesurfer] Error in running make_average_subject

2019-10-10 Thread Hoopes, Andrew 
Hi Himanshu,

Our pub disk went down a while ago and we lost the 6.0 patch files, but I've 
just updated that link with the necessary executables and README file. 
Following the readme instructions should fix your issue.

best
Andrew

From:  on behalf of Himanshu Aggarwal 

Reply-To: FS Help 
Date: Sunday, September 15, 2019 at 12:25 PM
To: FS Help 
Subject: [Freesurfer] Error in running make_average_subject


External Email - Use Caution

Hello Freesurfer Developers

I am trying to create an average subject for 20 subjects using the function 
make_average_subject. But I keep running into a segmentation fault. I have 
attached the recon-all.log file.

I found a few other posts about the same problem which direct the users to the 
following patch:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/

But this patch does not have a readme file which can instruct the users about 
the steps that need to be followed to get rid of this bug. However, I have 
replaced the files in /usr/local/freesurfer/bin/ (i.e. the $FREESURFER_HOME) 
with the files given in this patch directory. But the problem still persists. 
Kindly provide the steps that need to be followed to make use of this patch 
properly.

Regards

Himanshu

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Re: [Freesurfer] Error in running make_average_subject

2018-02-20 Thread Hoopes, Andrew 
Hi Janani,

We have a patch for this bug here:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/

The second part of the readme file in that directory provides instructions for 
resolving this.

best
Andrew



On February 19, 2018 at 9:40:22 AM, M Janani 
(janan...@hcl.com) wrote:

Dear FreeSurfer Experts,

 I’m recently getting an error in make_average_subject and can’t find
 the reason.

 Please see the following for the error log from recon-all.log:



 mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel 
mri/norm.mgz mri/transforms/talairach.m3z 
/home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca 
mri/aseg.auto_noCCseg.label_intensities.txt

relabeling unlikely voxels interior to white matter surface:
norm: mri/norm.mgz
XFORM: mri/transforms/talairach.m3z
GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca
label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /home/lakshman/freesurfer/subjects
subject avgsubject1
outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white

Reading lh pial surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial

Loading lh annotations from 
/home/lakshman/freesurfer/subjects/avgsubject1/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)

Reading rh white surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white

Reading rh pial surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial

Loading rh annotations from 
/home/lakshman/freesurfer/subjects/avgsubject1/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from 
/home/lakshman/freesurfer/subjects/avgsubject1/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from 
/home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from

Could you please help us in resolving the issue.

Have also attached the recon-all log for reference.

Thanks & Regards,
Janani

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Re: [Freesurfer] Error in running make_average_subject

2018-02-20 Thread Pruett, Scott 
Hey Andrew,

I am running FreeSurfer 6.0 on MacOS X and ran into the exact same issue as
Janani, so I installed this patch. However, now I am getting the following
error:

#@# AParc-to-ASeg aparc Tue Feb 20 11:04:08 EST 2018

/Users/scottpruett/Desktop/CSMRI/Freesurfer/601_10y_av

\n mri_aparc2aseg --s 601_10y_av --volmask --aseg aseg.presurf.hypos
--relabel mri/norm.mgz mri/transforms/talairach.m3z
/Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca
mri/aseg.auto_noCCseg.label_intensities.txt --no-relabel \n

/Applications/freesurfer/bin/mri_aparc2aseg: Exec format error. Binary file
not executable.

Darwin scott-pruetts-computer.local 17.3.0 Darwin Kernel Version 17.3.0:
Thu Nov  9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64 x86_64


recon-all -s 601_10y_av exited with ERRORS at Tue Feb 20 11:04:10 EST 2018

I've attached the recon-all.log file. Any help would be greatly appreciated.

Best,

Scott

On Tue, Feb 20, 2018 at 10:25 AM, Hoopes, Andrew 
wrote:

> Hi Janani,
>
> We have a patch for this bug here:
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
>
> The second part of the readme file in that directory provides instructions
> for resolving this.
>
> best
> Andrew
>
>
> On February 19, 2018 at 9:40:22 AM, M Janani (janan...@hcl.com) wrote:
>
> Dear FreeSurfer Experts,
>
>  I’m recently getting an error in make_average_subject and can’t find
>  the reason.
>
>  Please see the following for the error log from recon-all.log:
>
>mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos
> --relabel mri/norm.mgz mri/transforms/talairach.m3z
> /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca
> mri/aseg.auto_noCCseg.label_intensities.txt
>
> relabeling unlikely voxels interior to white matter surface:
> norm: mri/norm.mgz
> XFORM: mri/transforms/talairach.m3z
> GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca
> label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
> SUBJECTS_DIR /home/lakshman/freesurfer/subjects
> subject avgsubject1
> outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz
> useribbon 0
> baseoffset 0
> RipUnknown 0
>
> Reading lh white surface
>  /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white
>
> Reading lh pial surface
>  /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial
>
> Loading lh annotations from /home/lakshman/freesurfer/
> subjects/avgsubject1/label/lh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally /home/lakshman/freesurfer/
> subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.
> MRI-98004548-1c415d596e6fc5f9.ctab)
>
> Reading rh white surface
>  /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white
>
> Reading rh pial surface
>  /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial
>
> Loading rh annotations from /home/lakshman/freesurfer/
> subjects/avgsubject1/label/rh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally /home/lakshman/freesurfer/
> subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.
> MRI-98004548-1c415d596e6fc5f9.ctab)
> Have color table for lh white annotation
> Have color table for rh white annotation
> Loading ribbon segmentation from /home/lakshman/freesurfer/
> subjects/avgsubject1/mri/ribbon.mgz
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
>
> Loading aseg from /home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg.
> presurf.hypos.mgz
> ASeg Vox2RAS: ---
> -1.0   0.0   0.0   128.0;
>  0.0   0.0   1.0  -128.0;
>  0.0  -1.0   0.0   128.0;
>  0.0   0.0   0.0   1.0;
> mghRead(mri/norm.mgz, -1): could not open file
> -
>
> Labeling Slice
> relabeling unlikely voxels in interior of white matter
> *mri/norm.mgz: could not load norm volume from *
>
> Could you please help us in resolving the issue.
>
> Have also attached the recon-all log for reference.
>
> Thanks & Regards,
> Janani
>
> ::DISCLAIMER::
> 
> 
> 
> 
> --
> The contents of this e-mail and any attachment(s) are confidential and
> intended for the named recipient(s) only. E-mail transmission is not
> guaranteed to be secure or error-free as information could be intercepted,
> corrupted, lost, destroyed, arrive late or incomplete, or may contain
> viruses in transmission. The e mail and its contents (with or without
> referred errors) shall therefore not attach any liability on the originator
> or HCL or its affiliates. Views or opinions, if any, presented in this
> email are solely

Re: [Freesurfer] Error in running make_average_subject

2018-02-20 Thread M Janani 
Thanks andrew... I will try this

From: Hoopes, Andrew 
Sent: Tuesday, February 20, 2018 8:55:47 PM
To: M Janani; Freesurfer support list
Cc: Sasikala Sethu
Subject: Re: [Freesurfer] Error in running make_average_subject

Hi Janani,

We have a patch for this bug here:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/

The second part of the readme file in that directory provides instructions for 
resolving this.

best
Andrew



On February 19, 2018 at 9:40:22 AM, M Janani 
(janan...@hcl.com<mailto:janan...@hcl.com>) wrote:

Dear FreeSurfer Experts,

 I’m recently getting an error in make_average_subject and can’t find
 the reason.

 Please see the following for the error log from recon-all.log:



 mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel 
mri/norm.mgz mri/transforms/talairach.m3z 
/home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca 
mri/aseg.auto_noCCseg.label_intensities.txt

relabeling unlikely voxels interior to white matter surface:
norm: mri/norm.mgz
XFORM: mri/transforms/talairach.m3z
GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca
label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /home/lakshman/freesurfer/subjects
subject avgsubject1
outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white

Reading lh pial surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial

Loading lh annotations from 
/home/lakshman/freesurfer/subjects/avgsubject1/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)

Reading rh white surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white

Reading rh pial surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial

Loading rh annotations from 
/home/lakshman/freesurfer/subjects/avgsubject1/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from 
/home/lakshman/freesurfer/subjects/avgsubject1/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from 
/home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from

Could you please help us in resolving the issue.

Have also attached the recon-all log for reference.

Thanks & Regards,
Janani

::DISCLAIMER::
--
The contents of this e-mail and any attachment(s) are confidential and intended 
for the named recipient(s) only. E-mail transmission is not guaranteed to be 
secure or error-free as information could be intercepted, corrupted, lost, 
destroyed, arrive late or incomplete, or may contain viruses in transmission. 
The e mail and its contents (with or without referred errors) shall therefore 
not attach any liability on the originator or HCL or its affiliates. Views or 
opinions, if any, presented in this email are solely those of the author and 
may not necessarily reflect the views or opinions of HCL or its affiliates. Any 
form of reproduction, dissemination, copying, disclosure, modification, 
distribution and / or publication of this message without the prior written 
consent of authorized representative of HCL is strictly prohibited. If you have 
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Re: [Freesurfer] Error in running make_average_subject

2018-02-20 Thread Hoopes, Andrew 
Hi Scott,

It looks like the mri_aparc2aseg binary in that patch directory was compiled 
for centos. The version at the following link was compiled on OS X:  
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/OSX-ElCapitan/mri_aparc2aseg

If you download this new mri_aparc2aseg into your $FREESURFER_HOME/bin, it 
should fix the issue.

best
Andrew



On February 20, 2018 at 11:22:20 AM, Pruett, Scott 
(brandon_pru...@brown.edu) wrote:

Hey Andrew,

I am running FreeSurfer 6.0 on MacOS X and ran into the exact same issue as 
Janani, so I installed this patch. However, now I am getting the following 
error:


#@# AParc-to-ASeg aparc Tue Feb 20 11:04:08 EST 2018

/Users/scottpruett/Desktop/CSMRI/Freesurfer/601_10y_av

\n mri_aparc2aseg --s 601_10y_av --volmask --aseg aseg.presurf.hypos --relabel 
mri/norm.mgz mri/transforms/talairach.m3z 
/Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca 
mri/aseg.auto_noCCseg.label_intensities.txt --no-relabel \n

/Applications/freesurfer/bin/mri_aparc2aseg: Exec format error. Binary file not 
executable.

Darwin scott-pruetts-computer.local 17.3.0 Darwin Kernel Version 17.3.0: Thu 
Nov  9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64 x86_64


recon-all -s 601_10y_av exited with ERRORS at Tue Feb 20 11:04:10 EST 2018

I've attached the recon-all.log file. Any help would be greatly appreciated.

Best,

Scott

On Tue, Feb 20, 2018 at 10:25 AM, Hoopes, Andrew 
mailto:ahoo...@mgh.harvard.edu>> wrote:
Hi Janani,

We have a patch for this bug here:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/

The second part of the readme file in that directory provides instructions for 
resolving this.

best
Andrew



On February 19, 2018 at 9:40:22 AM, M Janani 
(janan...@hcl.com) wrote:

Dear FreeSurfer Experts,

 I’m recently getting an error in make_average_subject and can’t find
 the reason.

 Please see the following for the error log from recon-all.log:



 mri_aparc2aseg --s avgsubject1 --volmask --aseg aseg.presurf.hypos --relabel 
mri/norm.mgz mri/transforms/talairach.m3z 
/home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca 
mri/aseg.auto_noCCseg.label_intensities.txt

relabeling unlikely voxels interior to white matter surface:
norm: mri/norm.mgz
XFORM: mri/transforms/talairach.m3z
GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca
label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /home/lakshman/freesurfer/subjects
subject avgsubject1
outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white

Reading lh pial surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial

Loading lh annotations from 
/home/lakshman/freesurfer/subjects/avgsubject1/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)

Reading rh white surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white

Reading rh pial surface
 /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial

Loading rh annotations from 
/home/lakshman/freesurfer/subjects/avgsubject1/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/home/lakshman/freesurfer/subjects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI-98004548-1c415d596e6fc5f9.ctab)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from 
/home/lakshman/freesurfer/subjects/avgsubject1/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from 
/home/lakshman/freesurfer/subjects/avgsubject1/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
mri/norm.mgz: could not load norm volume from

Could you please help us in resolving the issue.

Have also attached the recon-all log for reference.

Thanks & Regards,
Janani

::DISCLAIMER::
--
The contents of this e-mail and any attachment(s) are confidential and intended 
for the named recipient(s) only. E-mail transmission is not guaranteed to be 
secure

Re: [Freesurfer] Error in running make_average_subject

2018-02-20 Thread Pruett, Scott 
Thanks, Andrew!

On Tue, Feb 20, 2018 at 11:42 AM, Hoopes, Andrew 
wrote:

> Hi Scott,
>
> It looks like the mri_aparc2aseg binary in that patch directory was
> compiled for centos. The version at the following link was compiled on OS
> X:  https://surfer.nmr.mgh.harvard.edu/pub/dist/
> freesurfer/dev_binaries/OSX-ElCapitan/mri_aparc2aseg
>
> If you download this new mri_aparc2aseg into your $FREESURFER_HOME/bin,
> it should fix the issue.
>
> best
> Andrew
>
>
> On February 20, 2018 at 11:22:20 AM, Pruett, Scott (
> brandon_pru...@brown.edu) wrote:
>
> Hey Andrew,
>
> I am running FreeSurfer 6.0 on MacOS X and ran into the exact same issue
> as Janani, so I installed this patch. However, now I am getting the
> following error:
>
> #@# AParc-to-ASeg aparc Tue Feb 20 11:04:08 EST 2018
>
> /Users/scottpruett/Desktop/CSMRI/Freesurfer/601_10y_av
>
> \n mri_aparc2aseg --s 601_10y_av --volmask --aseg aseg.presurf.hypos
> --relabel mri/norm.mgz mri/transforms/talairach.m3z
> /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca
> mri/aseg.auto_noCCseg.label_intensities.txt --no-relabel \n
>
> /Applications/freesurfer/bin/mri_aparc2aseg: Exec format error. Binary
> file not executable.
>
> Darwin scott-pruetts-computer.local 17.3.0 Darwin Kernel Version 17.3.0:
> Thu Nov  9 18:09:22 PST 2017; root:xnu-4570.31.3~1/RELEASE_X86_64 x86_64
>
>
> recon-all -s 601_10y_av exited with ERRORS at Tue Feb 20 11:04:10 EST 2018
>
> I've attached the recon-all.log file. Any help would be greatly
> appreciated.
>
> Best,
>
> Scott
>
> On Tue, Feb 20, 2018 at 10:25 AM, Hoopes, Andrew 
> wrote:
>
>> Hi Janani,
>>
>> We have a patch for this bug here:
>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/
>>
>> The second part of the readme file in that directory provides
>> instructions for resolving this.
>>
>> best
>> Andrew
>>
>>
>> On February 19, 2018 at 9:40:22 AM, M Janani (janan...@hcl.com) wrote:
>>
>> Dear FreeSurfer Experts,
>>
>>  I’m recently getting an error in make_average_subject and can’t find
>>  the reason.
>>
>>  Please see the following for the error log from recon-all.log:
>>
>>mri_aparc2aseg --s avgsubject1 --volmask --aseg
>> aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z
>> /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca
>> mri/aseg.auto_noCCseg.label_intensities.txt
>>
>> relabeling unlikely voxels interior to white matter surface:
>> norm: mri/norm.mgz
>> XFORM: mri/transforms/talairach.m3z
>> GCA: /home/lakshman/freesurfer/average/RB_all_2016-05-10.vc700.gca
>> label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
>> SUBJECTS_DIR /home/lakshman/freesurfer/subjects
>> subject avgsubject1
>> outvol /home/lakshman/freesurfer/subjects/avgsubject1/mri/aparc+aseg.mgz
>> useribbon 0
>> baseoffset 0
>> RipUnknown 0
>>
>> Reading lh white surface
>>  /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.white
>>
>> Reading lh pial surface
>>  /home/lakshman/freesurfer/subjects/avgsubject1/surf/lh.pial
>>
>> Loading lh annotations from /home/lakshman/freesurfer/subj
>> ects/avgsubject1/label/lh.aparc.annot
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally /home/lakshman/freesurfer/subj
>> ects/avgsubject1/label/tmpdir.annot2std.30180/seg.1.MRI-
>> 98004548-1c415d596e6fc5f9.ctab)
>>
>> Reading rh white surface
>>  /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.white
>>
>> Reading rh pial surface
>>  /home/lakshman/freesurfer/subjects/avgsubject1/surf/rh.pial
>>
>> Loading rh annotations from /home/lakshman/freesurfer/subj
>> ects/avgsubject1/label/rh.aparc.annot
>> reading colortable from annotation file...
>> colortable with 36 entries read (originally /home/lakshman/freesurfer/subj
>> ects/avgsubject1/label/tmpdir.annot2std.33768/seg.1.MRI-
>> 98004548-1c415d596e6fc5f9.ctab)
>> Have color table for lh white annotation
>> Have color table for rh white annotation
>> Loading ribbon segmentation from /home/lakshman/freesurfer/subj
>> ects/avgsubject1/mri/ribbon.mgz
>>
>> Building hash of lh white
>>
>> Building hash of lh pial
>>
>> Building hash of rh white
>>
>> Building hash of rh pial
>>
>> Loading aseg from /home/lakshman/freesurfer/subj
>> ects/avgsubject1/mri/aseg.presurf.hypos.mgz
>> ASeg Vox2RAS: ---
>> -1.0   0.0   0.0   128.0;
>>  0.0   0.0   1.0  -128.0;
>>  0.0  -1.0   0.0   128.0;
>>  0.0   0.0   0.0   1.0;
>> mghRead(mri/norm.mgz, -1): could not open file
>> -
>>
>> Labeling Slice
>> relabeling unlikely voxels in interior of white matter
>> *mri/norm.mgz: could not load norm volume from *
>>
>> Could you please help us in resolving the issue.
>>
>> Have also attached the recon-all log for reference.
>>
>> Thanks & Regards,
>> Janani
>>
>> ::DISCLAIMER::
>> 
>> --