subject:"\[Freesurfer\] Segmentation fault using mri

[Freesurfer] Segmentation fault using mri_label2vol

2015-10-14 Thread Syeda Wajiha Maryam

Hello Freesurfer experts,

I'm getting a segmentation fault when I use the mri_label2vol command to
push aseg labels from freesurfer space to my subject's original T1 space
(using the example given on the freesurfer website). I'm not sure why this
is happening...I've tried changing the parameters countless times but
nothing has worked. I also checked my "aseg.mgz" to make sure it's not
corrupted but that isn't the issue either. Any help would be highly
appreciated!! Thanks in advance

mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
--seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
/scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
/tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Number of labels: 0
Annot File:  (null)
Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   (null)
ProjTypeId: 0
ProjStart:  0
ProjStop:   0
ProjDelta:  0.1
Subject:  (null)
Hemi: (null)
UseNewASeg2Vol:  1
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
-0.000  -0.000  -0.985   128.000;
-0.000   0.833  -0.000   98.000;
 0.000   0.000   0.000   1.000;
Template Voxel Volume: 1.23773
nHits Thresh: 0
Computing registration based on header
RegMat: 
 1.000   0.000   0.000  -0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
Label RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
 0.000   0.000  -0.985   128.000;
 0.000   0.833   0.000   98.000;
 0.000   0.000   0.000   1.000;
ASeg2Vol: Building LUT
Segmentation fault
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Re: [Freesurfer] Segmentation fault using mri_label2vol

2015-10-14 Thread Syeda Maryam

So for some reason my mail with the attachments won't get delivered...the 
message size exceeds the limits. I was wondering if the segmentation fault 
error I'm getting might be do to some problem in the freesurfer version I'm 
running?
Thanks,Syeda

 On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam  
wrote:

 I'm not sure if my last message got delivered or not so I'll resend it.
Thanks very much for looking into this so quickly. Sure thing! I've 
attached the images here. The aseg file opens up with freeview, and the 
mri_label2vol command works fine on my local machine but when I try to 
implement it on our server using nipype, it gives me the error I mentioned. 

Best,Syeda 

 On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam  
wrote:

 Thanks very much for looking into this so quickly. Sure thing! I've attached 
the images here. The aseg file opens up with freeview, and the mri_label2vol 
command works fine on my local machine but when I try to implement it on our 
server using nipype, it gives me the error I mentioned. 

Best,Syeda

 On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl 
 wrote:

 Hi Syeda

that commnand doesn't segfault when I try it on another subject here. If 
you email me the aseg.mgz and the rawavg.mgz I'll take a look

cheers
Bruce

On Wed, 14 Oct 2015, Syeda 
Maryam wrote:

> Hello Freesurfer experts,
> 
> I'm getting a segmentation fault when I use the mri_label2vol command to push 
> aseg labels from freesurfer space to my
> subject's original T1 space (using the example given on the freesurfer 
> website). I'm not sure why this is
> happening...I've tried changing the parameters countless times but nothing 
> has worked. I also checked my "aseg.mgz" to
> make sure it's not corrupted but that isn't the issue either. Any help would 
> be highly appreciated!! Thanks in advance
> 
> mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg 
> /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o 
> /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> Number of labels: 0
> Annot File:  (null)
> Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> Registration File: (null)
> Fill Threshold: 0
> Label Vox Vol:  1
> ProjType:   (null)
> ProjTypeId: 0
> ProjStart:  0
> ProjStop:   0
> ProjDelta:  0.1
> Subject:  (null)
> Hemi: (null)
> UseNewASeg2Vol:  1
> DoLabelStatVol  0
> LabelCodeOffset  0
> setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> Template RAS-to-Vox: 
> -0.985   0.000   0.000   128.000;
> -0.000  -0.000  -0.985   128.000;
> -0.000   0.833  -0.000   98.000;
>  0.000   0.000   0.000   1.000;
> Template Voxel Volume: 1.23773
> nHits Thresh: 0
> Computing registration based on header
> RegMat: 
>  1.000   0.000   0.000  -0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> Label RAS-to-Vox: 
> -0.985   0.000   0.000   128.000;
>  0.000   0.000  -0.985   128.000;
>  0.000   0.833   0.000   98.000;
>  0.000   0.000   0.000   1.000;
> ASeg2Vol: Building LUT
> Segmentation fault
> 
> 
>

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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
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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
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[Freesurfer] Segmentation fault using mri_label2vol

2015-10-14 Thread Syeda Maryam

Hello Freesurfer experts,
I'm getting a segmentation fault when I use the mri_label2vol command to push 
aseg labels from freesurfer space to my subject's original T1 space (using the 
example given on the freesurfer website). I'm not sure why this is 
happening...I've tried changing the parameters countless times but nothing has 
worked. I also checked my "aseg.mgz" to make sure it's not corrupted but that 
isn't the issue either. Any help would be highly appreciated!! Thanks in advance

mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg 
/tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp 
/scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o 
/tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Number of labels: 0
Annot File:  (null)
Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   (null)
ProjTypeId: 0
ProjStart:  0
ProjStop:   0
ProjDelta:  0.1
Subject:  (null)
Hemi: (null)
UseNewASeg2Vol:  1
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
-0.000  -0.000  -0.985   128.000;
-0.000   0.833  -0.000   98.000;
 0.000   0.000   0.000   1.000;
Template Voxel Volume: 1.23773
nHits Thresh: 0
Computing registration based on header
RegMat: 
 1.000   0.000   0.000  -0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
Label RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
 0.000   0.000  -0.985   128.000;
 0.000   0.833   0.000   98.000;
 0.000   0.000   0.000   1.000;
ASeg2Vol: Building LUT
Segmentation fault

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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
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] Segmentation fault using mri_label2vol

2015-10-14 Thread Bruce Fischl


Hi Syeda

that commnand doesn't segfault when I try it on another subject here. If 
you email me the aseg.mgz and the rawavg.mgz I'll take a look


cheers
Bruce

On Wed, 14 Oct 2015, Syeda 
Maryam wrote:



Hello Freesurfer experts,

I'm getting a segmentation fault when I use the mri_label2vol command to push 
aseg labels from freesurfer space to my
subject's original T1 space (using the example given on the freesurfer 
website). I'm not sure why this is
happening...I've tried changing the parameters countless times but nothing has worked. I 
also checked my "aseg.mgz" to
make sure it's not corrupted but that isn't the issue either. Any help would be 
highly appreciated!! Thanks in advance

mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg 
/tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
/scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o 
/tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Number of labels: 0
Annot File:  (null)
Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   (null)
ProjTypeId: 0
ProjStart:  0
ProjStop:   0
ProjDelta:  0.1
Subject:  (null)
Hemi: (null)
UseNewASeg2Vol:  1
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
-0.000  -0.000  -0.985   128.000;
-0.000   0.833  -0.000   98.000;
 0.000   0.000   0.000   1.000;
Template Voxel Volume: 1.23773
nHits Thresh: 0
Computing registration based on header
RegMat: 
 1.000   0.000   0.000  -0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
Label RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
 0.000   0.000  -0.985   128.000;
 0.000   0.833   0.000   98.000;
 0.000   0.000   0.000   1.000;
ASeg2Vol: Building LUT
Segmentation fault


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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
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] Segmentation fault using mri_label2vol

2015-10-14 Thread Bruce Fischl

it's possible, or something to do with your images. You can use either 
our filedrop or ftp site to send them to me if you want
On Wed, 14 Oct 2015, 
Syeda Maryam wrote:

So for some reason my mail with the attachments won't get delivered...the
message size exceeds the limits. I was wondering if the segmentation fault
error I'm getting might be do to some problem in the freesurfer version I'm
running?

Thanks,
Syeda

On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam 
wrote:

I'm not sure if my last message got delivered or not so I'll resend it.

Thanks very much for looking into this so quickly. Sure thing! I've
attached the images here. The aseg file opens up with freeview, and the
mri_label2vol command works fine on my local machine but when I try to
implement it on our server using nipype, it gives me the error I mentioned.

Best,
Syeda

On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam 
wrote:

Thanks very much for looking into this so quickly. Sure thing! I've attached
the images here. The aseg file opens up with freeview, and the mri_label2vol
command works fine on my local machine but when I try to implement it on our
server using nipype, it gives me the error I mentioned.

Best,
Syeda

On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
 wrote:

Hi Syeda

that commnand doesn't segfault when I try it on another subject here. If
you email me the aseg.mgz and the rawavg.mgz I'll take a look

cheers
Bruce

On Wed, 14 Oct 2015, Syeda
Maryam wrote:

> Hello Freesurfer experts,
>
> I'm getting a segmentation fault when I use the mri_label2vol command to
push aseg labels from freesurfer space to my
> subject's original T1 space (using the example given on the freesurfer
website). I'm not sure why this is
> happening...I've tried changing the parameters countless times but nothing
has worked. I also checked my "aseg.mgz" to
> make sure it's not corrupted but that isn't the issue either. Any help
would be highly appreciated!! Thanks in advance
>
> mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
--seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
/tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> Number of labels: 0
> Annot File:  (null)
> Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> Registration File: (null)
> Fill Threshold: 0
> Label Vox Vol:  1
> ProjType:   (null)
> ProjTypeId: 0
> ProjStart:  0
> ProjStop:   0
> ProjDelta:  0.1
> Subject:  (null)
> Hemi: (null)
> UseNewASeg2Vol:  1
> DoLabelStatVol  0
> LabelCodeOffset  0
> setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> Template RAS-to-Vox: 
> -0.985   0.000   0.000   128.000;
> -0.000  -0.000  -0.985   128.000;
> -0.000   0.833  -0.000   98.000;
>  0.000   0.000   0.000   1.000;
> Template Voxel Volume: 1.23773
> nHits Thresh: 0
> Computing registration based on header
> RegMat: 
>  1.000   0.000   0.000  -0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> Label RAS-to-Vox: 
> -0.985   0.000   0.000   128.000;
>  0.000   0.000  -0.985   128.000;
>  0.000   0.833   0.000   98.000;
>  0.000   0.000   0.000   1.000;
> ASeg2Vol: Building LUT
> Segmentation fault

>
>
>

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

___
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Freesurfer@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] Segmentation fault using mri_label2vol

2015-10-14 Thread Syeda Maryam

So the strangest thing happened. Just on a hunch, I logged out of the server 
then logged back in, and now it's running! It's a mystery to me. Thanks again, 
I'll check the RAM specs and get back to you. For now though it seems to be 
working. Hope it stays that way!
Best,Syeda
 


 On Wednesday, October 14, 2015 12:48 PM, Bruce Fischl 
 wrote:
   

 Hi Syeda

it doesn't die when I run it locally. How much RAM do you have on the 
machine that it crashes on? If you want a new version we can send you one.
cheers
Bruce


On Wed, 14 Oct 2015, Syeda Maryam wrote:

> Hi Bruce,
> I just sent you the files on filedrop! I thought it might have something to 
> do with the freesurfer version since the
> mri_label2vol comman works fine on my local machine and the segmentation 
> fault I was talking about only happens when I
> try to run it on the server our research group is using. But when I checked 
> the freesurfer versions, turns out the same
> version is installed on both machines: 
> freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> 
> Needless to say, I'm well and truly stumped right now.
> Really appreciate your help in this matter!
> 
> Best,
> Syeda
> 
> 
> 
> 
> 
> On Wednesday, October 14, 2015 12:20 PM, Bruce Fischl 
>  wrote:
> 
> 
> it's possible, or something to do with your images. You can use either
> our filedrop or ftp site to send them to me if you want
> On Wed, 14 Oct 2015,
> Syeda Maryam wrote:
> 
> > So for some reason my mail with the attachments won't get delivered...the
> > message size exceeds the limits. I was wondering if the segmentation fault
> > error I'm getting might be do to some problem in the freesurfer version I'm
> > running?
> >
> > Thanks,
> > Syeda
> >
> >
> >
> > On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam 
> > wrote:
> >
> >
> > I'm not sure if my last message got delivered or not so I'll resend it.
> > 
> > Thanks very much for looking into this so quickly. Sure thing! I've
> > attached the images here. The aseg file opens up with freeview, and the
> > mri_label2vol command works fine on my local machine but when I try to
> > implement it on our server using nipype, it gives me the error I mentioned.
> >
> > Best,
> > Syeda
> >
> >
> >
> > On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam 
> > wrote:
> >
> >
> > Thanks very much for looking into this so quickly. Sure thing! I've attached
> > the images here. The aseg file opens up with freeview, and the mri_label2vol
> > command works fine on my local machine but when I try to implement it on our
> > server using nipype, it gives me the error I mentioned.
> >
> > Best,
> > Syeda
> >
> >
> >
> > On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
> >  wrote:
> >
> >
> > Hi Syeda
> >
> > that commnand doesn't segfault when I try it on another subject here. If
> > you email me the aseg.mgz and the rawavg.mgz I'll take a look
> >
> > cheers
> > Bruce
> >
> > On Wed, 14 Oct 2015, Syeda
> > Maryam wrote:
> >
> > > Hello Freesurfer experts,
> > >
> > > I'm getting a segmentation fault when I use the mri_label2vol command to
> > push aseg labels from freesurfer space to my
> > > subject's original T1 space (using the example given on the freesurfer
> > website). I'm not sure why this is
> > > happening...I've tried changing the parameters countless times but nothing
> > has worked. I also checked my "aseg.mgz" to
> > > make sure it's not corrupted but that isn't the issue either. Any help
> > would be highly appreciated!! Thanks in advance
> > >
> > > mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
> > --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> > > /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
> > /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > > Number of labels: 0
> > > Annot File:  (null)
> > > Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> > > Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > > Registration File: (null)
> > > Fill Threshold: 0
> > > Label Vox Vol:  1
> > > ProjType:   (null)
> > > ProjTypeId: 0
> > > ProjStart:  0
> > > ProjStop:   0
> > > ProjDelta:  0.1
> > > Subject:  (null)
> > > Hemi: (null)
> > > UseNewASeg2Vol:  1
> > > DoLabelStatVol  0
> > > LabelCodeOffset  0
> > > setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> > > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> > > Template RAS-to-Vox: 
> > > -0.985   0.000   0.000   128.000;
> > > -0.000  -0.000  -0.985   128.000;
> > > -0.000   0.833  -0.000   98.000;
> > >  0.000   0.000   0.000   1.000;
> > > Template Voxel Volume: 1.23773
> > > nHits Thresh: 0
> > > Computing registration based on header
> > > RegMat: 
> > >  1.000   0.000   0.000  -0.000;
> > >  0.000   1.000   0.000   0.000;
> > >  0.000   0.000   1.000   0.000;
> > >  0.000   0.000   0.000   1.000;
>

Re: [Freesurfer] Segmentation fault using mri_label2vol

2015-10-14 Thread Bruce Fischl


Hi Syeda

it doesn't die when I run it locally. How much RAM do you have on the 
machine that it crashes on? If you want a new version we can send you one.

cheers
Bruce


On Wed, 14 Oct 2015, Syeda Maryam wrote:


Hi Bruce,
I just sent you the files on filedrop! I thought it might have something to do 
with the freesurfer version since the
mri_label2vol comman works fine on my local machine and the segmentation fault 
I was talking about only happens when I
try to run it on the server our research group is using. But when I checked the 
freesurfer versions, turns out the same
version is installed on both machines: 
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Needless to say, I'm well and truly stumped right now.
Really appreciate your help in this matter!

Best,
Syeda





On Wednesday, October 14, 2015 12:20 PM, Bruce Fischl 
 wrote:


it's possible, or something to do with your images. You can use either
our filedrop or ftp site to send them to me if you want
On Wed, 14 Oct 2015,
Syeda Maryam wrote:

> So for some reason my mail with the attachments won't get delivered...the
> message size exceeds the limits. I was wondering if the segmentation fault
> error I'm getting might be do to some problem in the freesurfer version I'm
> running?
>
> Thanks,
> Syeda
>
>
>
> On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam 
> wrote:
>
>
> I'm not sure if my last message got delivered or not so I'll resend it.
> 
> Thanks very much for looking into this so quickly. Sure thing! I've
> attached the images here. The aseg file opens up with freeview, and the
> mri_label2vol command works fine on my local machine but when I try to
> implement it on our server using nipype, it gives me the error I mentioned.
>
> Best,
> Syeda
>
>
>
> On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam 
> wrote:
>
>
> Thanks very much for looking into this so quickly. Sure thing! I've attached
> the images here. The aseg file opens up with freeview, and the mri_label2vol
> command works fine on my local machine but when I try to implement it on our
> server using nipype, it gives me the error I mentioned.
>
> Best,
> Syeda
>
>
>
> On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
>  wrote:
>
>
> Hi Syeda
>
> that commnand doesn't segfault when I try it on another subject here. If
> you email me the aseg.mgz and the rawavg.mgz I'll take a look
>
> cheers
> Bruce
>
> On Wed, 14 Oct 2015, Syeda
> Maryam wrote:
>
> > Hello Freesurfer experts,
> >
> > I'm getting a segmentation fault when I use the mri_label2vol command to
> push aseg labels from freesurfer space to my
> > subject's original T1 space (using the example given on the freesurfer
> website). I'm not sure why this is
> > happening...I've tried changing the parameters countless times but nothing
> has worked. I also checked my "aseg.mgz" to
> > make sure it's not corrupted but that isn't the issue either. Any help
> would be highly appreciated!! Thanks in advance
> >
> > mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
> --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> > /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
> /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Number of labels: 0
> > Annot File:  (null)
> > Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> > Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Registration File: (null)
> > Fill Threshold: 0
> > Label Vox Vol:  1
> > ProjType:   (null)
> > ProjTypeId: 0
> > ProjStart:  0
> > ProjStop:   0
> > ProjDelta:  0.1
> > Subject:  (null)
> > Hemi: (null)
> > UseNewASeg2Vol:  1
> > DoLabelStatVol  0
> > LabelCodeOffset  0
> > setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> > Template RAS-to-Vox: 
> > -0.985   0.000   0.000   128.000;
> > -0.000  -0.000  -0.985   128.000;
> > -0.000   0.833  -0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > Template Voxel Volume: 1.23773
> > nHits Thresh: 0
> > Computing registration based on header
> > RegMat: 
> >  1.000   0.000   0.000  -0.000;
> >  0.000   1.000   0.000   0.000;
> >  0.000   0.000   1.000   0.000;
> >  0.000   0.000   0.000   1.000;
> > Label RAS-to-Vox: 
> > -0.985   0.000   0.000   128.000;
> >  0.000   0.000  -0.985   128.000;
> >  0.000   0.833   0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > ASeg2Vol: Building LUT
> > Segmentation fault
>
> >
> >
> >
>
>
> 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

Re: [Freesurfer] Segmentation fault using mri_label2vol

2015-10-14 Thread Syeda Maryam

Hi Bruce,I just sent you the files on filedrop! I thought it might have 
something to do with the freesurfer version since the mri_label2vol comman 
works fine on my local machine and the segmentation fault I was talking about 
only happens when I try to run it on the server our research group is using. 
But when I checked the freesurfer versions, turns out the same version is 
installed on both machines: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Needless to say, I'm well and truly stumped right now.Really appreciate your 
help in this matter!
Best,Syeda


 


 On Wednesday, October 14, 2015 12:20 PM, Bruce Fischl 
 wrote:
   

 it's possible, or something to do with your images. You can use either 
our filedrop or ftp site to send them to me if you want
On Wed, 14 Oct 2015, 
Syeda Maryam wrote:

> So for some reason my mail with the attachments won't get delivered...the
> message size exceeds the limits. I was wondering if the segmentation fault
> error I'm getting might be do to some problem in the freesurfer version I'm
> running?
> 
> Thanks,
> Syeda
> 
> 
> 
> On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam 
> wrote:
> 
> 
> I'm not sure if my last message got delivered or not so I'll resend it.
> 
> Thanks very much for looking into this so quickly. Sure thing! I've
> attached the images here. The aseg file opens up with freeview, and the
> mri_label2vol command works fine on my local machine but when I try to
> implement it on our server using nipype, it gives me the error I mentioned.
> 
> Best,
> Syeda
> 
> 
> 
> On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam 
> wrote:
> 
> 
> Thanks very much for looking into this so quickly. Sure thing! I've attached
> the images here. The aseg file opens up with freeview, and the mri_label2vol
> command works fine on my local machine but when I try to implement it on our
> server using nipype, it gives me the error I mentioned.
> 
> Best,
> Syeda
> 
> 
> 
> On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
>  wrote:
> 
> 
> Hi Syeda
> 
> that commnand doesn't segfault when I try it on another subject here. If
> you email me the aseg.mgz and the rawavg.mgz I'll take a look
> 
> cheers
> Bruce
> 
> On Wed, 14 Oct 2015, Syeda
> Maryam wrote:
> 
> > Hello Freesurfer experts,
> >
> > I'm getting a segmentation fault when I use the mri_label2vol command to
> push aseg labels from freesurfer space to my
> > subject's original T1 space (using the example given on the freesurfer
> website). I'm not sure why this is
> > happening...I've tried changing the parameters countless times but nothing
> has worked. I also checked my "aseg.mgz" to
> > make sure it's not corrupted but that isn't the issue either. Any help
> would be highly appreciated!! Thanks in advance
> >
> > mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
> --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> > /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
> /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Number of labels: 0
> > Annot File:  (null)
> > Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> > Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Registration File: (null)
> > Fill Threshold: 0
> > Label Vox Vol:  1
> > ProjType:   (null)
> > ProjTypeId: 0
> > ProjStart:  0
> > ProjStop:   0
> > ProjDelta:  0.1
> > Subject:  (null)
> > Hemi: (null)
> > UseNewASeg2Vol:  1
> > DoLabelStatVol  0
> > LabelCodeOffset  0
> > setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> > Template RAS-to-Vox: 
> > -0.985   0.000   0.000   128.000;
> > -0.000  -0.000  -0.985   128.000;
> > -0.000   0.833  -0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > Template Voxel Volume: 1.23773
> > nHits Thresh: 0
> > Computing registration based on header
> > RegMat: 
> >  1.000   0.000   0.000  -0.000;
> >  0.000   1.000   0.000   0.000;
> >  0.000   0.000   1.000   0.000;
> >  0.000   0.000   0.000   1.000;
> > Label RAS-to-Vox: 
> > -0.985   0.000   0.000   128.000;
> >  0.000   0.000  -0.985   128.000;
> >  0.000   0.833   0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > ASeg2Vol: Building LUT
> > Segmentation fault
> 
> >
> >
> >
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
> 
> 
> 
> 
> 
> 
> 
>
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[Freesurfer] Segmentation fault using mri_label2vol

Re: [Freesurfer] Segmentation fault using mri_label2vol

Re: [Freesurfer] Segmentation fault using mri_label2vol

Re: [Freesurfer] Segmentation fault using mri_label2vol

Re: [Freesurfer] Segmentation fault using mri_label2vol

Re: [Freesurfer] Segmentation fault using mri_label2vol

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