Re: [Freesurfer] error in atlas creation

[Anthony Dick]

Hello Bruce,

We have tried running the atlas creation on newly freesurfed brains with 
the latest FS version and keep getting the same error. We have 
essentially replicated the error we get on our own manually edited 
volumes by copying the aparc+aseg.mgz and renaming it seg_edited.mgz. 
Thus, it is unlikely to be a problem with our manually edited brains. 
This results in the following error at the same place (running the 
rebuild_gca_atlas.csh script):

== Number of threads available to mri_em_register for OpenMP = 16 ==
reading 23 input volumes...
logging results to talairach_one.log
reading '/average/RB_one_2015-10-13.gca'...
average std = 9.8   using min determinant for regularization = 9.7
0 singular and 426 ill-conditioned covariance matrices regularized
reading '/009/mri/nu.mgz'...
reading '/average/RB_one_2015-10-13.gca'...
reading frame -1 of gca
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
reading '/009/mri/transforms/talairach_one.lta'...
mri_read(): couldn't determine type of file 
/009/mri/transforms/talairach_one.lta
mri_em_register: could not open input volume 
/009/mri/transforms/talairach_one.lta.

Perhaps the FS folks could try to replicate this error? You don't need 
my brains, just a couple of FS'd brains with a file called 
seg_edited.mgz. If you don't get the error, then maybe it is a problem 
with our local settings (although we get this error on multiple 
different computers). Thanks for any help!

Anthony



On 7/20/15 2:30 PM, Anthony Dick wrote:
> Hello,
>
> I was wondering if these got uploaded correctly. Please let me know if 
> I made a mistake and thanks,
>
> Anthony
>
> On 7/9/15 1:41 PM, Bruce Fischl wrote:
>> sure
>> On Thu, 9 Jul 2015, Anthony Dick wrote:
>>
>>> Hello Bruce,
>>>
>>> I am still getting this error after re-running autorecon1 in the newest
>>> version of FS. Can I upload two brains and see what is the issue? I'm a
>>> bit stumped on this one.
>>>
>>> Anthony
>>>
>>> On 5/26/15 12:21 PM, Bruce Fischl wrote:
 Hi Anthony

 sorry, I know you've posted this before. What version are you running?
 And what type is your labeled data? That is, are they uchar? int? 
 At some
 point this used to not work with non-uchar data, but I think I 
 fixed it a
 while ago. YOu might try downloading a beta of V6 and see if it 
 fixes your
 problem

 cheers
 Bruce


 On Tue, 26
 May 2015, Anthony Dick wrote:

> Hello,
>
> I have been stumped by this error I keep getting using the
> rebuild_gca_atlas.csh script. I am trying to build a cerebellar 
> atlas,
> so I am wondering if the problem is with the brains we 
> parcellated, or
> with my installation etc. The brains consist of manually segmented
> cerebellums from the original T1. The T1 is run through 
> Freesurfer, and
> the ROIs are made in Freeview. The edited file is called 
> seg_edited.mgz.
> Things run smoothly up until this error:
>
> using MR volume //subjects/4/mri/brain.mgz to mask input 
> volume...
> reading 23 input volumes...
> logging results to talairach_one.log
> reading 'subjects/average/RB_one_2015-05-14.gca'...
> gcaAllocMax: node dims 32 32 32
> gcaAllocMax: prior dims 128 128 128
> gcaAllocMax: max_labels 0
> average std = 8.4   using min determinant for regularization = 7.1
> 0 singular and 119 ill-conditioned covariance matrices regularized
> reading '//subjects/4/mri/nu.mgz'...
> reading '//subjects/average/RB_one_2015-05-14.gca'...
> gcaAllocMax: node dims 32 32 32
> gcaAllocMax: prior dims 128 128 128
> gcaAllocMax: max_labels 0
> reading frame -1 of gca
> MRIcopyFrame: src and dst must be same type
> reading '//subjects/4/mri/transforms/talairach_one.lta'...
> mri_read(): couldn't determine type of file
> //subjects/4/mri/transforms/talairach_one.lta
> mri_em_register: could not open input volume
> //subjects/4/mri/transforms/talairach_one.lta.
>
>
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

>>>
>>>
>> ___
>> 

Re: [Freesurfer] error in atlas creation

[Bruce Fischl]

HI Anthony

what is the full command line? Does it happen if you only train on a 
single subject instead of 23?
Bruce
On Tue, 13 Oct 2015, Anthony Dick wrote:

> Hello Bruce,
>
> We have tried running the atlas creation on newly freesurfed brains with
> the latest FS version and keep getting the same error. We have
> essentially replicated the error we get on our own manually edited
> volumes by copying the aparc+aseg.mgz and renaming it seg_edited.mgz.
> Thus, it is unlikely to be a problem with our manually edited brains.
> This results in the following error at the same place (running the
> rebuild_gca_atlas.csh script):
>
> == Number of threads available to mri_em_register for OpenMP = 16 ==
> reading 23 input volumes...
> logging results to talairach_one.log
> reading '/average/RB_one_2015-10-13.gca'...
> average std = 9.8   using min determinant for regularization = 9.7
> 0 singular and 426 ill-conditioned covariance matrices regularized
> reading '/009/mri/nu.mgz'...
> reading '/average/RB_one_2015-10-13.gca'...
> reading frame -1 of gca
> INFO: MRImask() using MRImaskDifferentGeometry()
> INFO: MRImask() using MRImaskDifferentGeometry()
> INFO: MRImask() using MRImaskDifferentGeometry()
> INFO: MRImask() using MRImaskDifferentGeometry()
> INFO: MRImask() using MRImaskDifferentGeometry()
> reading '/009/mri/transforms/talairach_one.lta'...
> mri_read(): couldn't determine type of file
> /009/mri/transforms/talairach_one.lta
> mri_em_register: could not open input volume
> /009/mri/transforms/talairach_one.lta.
>
> Perhaps the FS folks could try to replicate this error? You don't need
> my brains, just a couple of FS'd brains with a file called
> seg_edited.mgz. If you don't get the error, then maybe it is a problem
> with our local settings (although we get this error on multiple
> different computers). Thanks for any help!
>
> Anthony
>
>
>
> On 7/20/15 2:30 PM, Anthony Dick wrote:
>> Hello,
>>
>> I was wondering if these got uploaded correctly. Please let me know if
>> I made a mistake and thanks,
>>
>> Anthony
>>
>> On 7/9/15 1:41 PM, Bruce Fischl wrote:
>>> sure
>>> On Thu, 9 Jul 2015, Anthony Dick wrote:
>>>
 Hello Bruce,

 I am still getting this error after re-running autorecon1 in the newest
 version of FS. Can I upload two brains and see what is the issue? I'm a
 bit stumped on this one.

 Anthony

 On 5/26/15 12:21 PM, Bruce Fischl wrote:
> Hi Anthony
>
> sorry, I know you've posted this before. What version are you running?
> And what type is your labeled data? That is, are they uchar? int?
> At some
> point this used to not work with non-uchar data, but I think I
> fixed it a
> while ago. YOu might try downloading a beta of V6 and see if it
> fixes your
> problem
>
> cheers
> Bruce
>
>
> On Tue, 26
> May 2015, Anthony Dick wrote:
>
>> Hello,
>>
>> I have been stumped by this error I keep getting using the
>> rebuild_gca_atlas.csh script. I am trying to build a cerebellar
>> atlas,
>> so I am wondering if the problem is with the brains we
>> parcellated, or
>> with my installation etc. The brains consist of manually segmented
>> cerebellums from the original T1. The T1 is run through
>> Freesurfer, and
>> the ROIs are made in Freeview. The edited file is called
>> seg_edited.mgz.
>> Things run smoothly up until this error:
>>
>> using MR volume //subjects/4/mri/brain.mgz to mask input
>> volume...
>> reading 23 input volumes...
>> logging results to talairach_one.log
>> reading 'subjects/average/RB_one_2015-05-14.gca'...
>> gcaAllocMax: node dims 32 32 32
>> gcaAllocMax: prior dims 128 128 128
>> gcaAllocMax: max_labels 0
>> average std = 8.4   using min determinant for regularization = 7.1
>> 0 singular and 119 ill-conditioned covariance matrices regularized
>> reading '//subjects/4/mri/nu.mgz'...
>> reading '//subjects/average/RB_one_2015-05-14.gca'...
>> gcaAllocMax: node dims 32 32 32
>> gcaAllocMax: prior dims 128 128 128
>> gcaAllocMax: max_labels 0
>> reading frame -1 of gca
>> MRIcopyFrame: src and dst must be same type
>> reading '//subjects/4/mri/transforms/talairach_one.lta'...
>> mri_read(): couldn't determine type of file
>> //subjects/4/mri/transforms/talairach_one.lta
>> mri_em_register: could not open input volume
>> //subjects/4/mri/transforms/talairach_one.lta.
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> 

Re: [Freesurfer] error in atlas creation

[Anthony Dick]

Hello Bruce,

I used the rebuild_gca_atlas.csh script (attached). I only commented out 
the cluster configuration options. Otherwise the script is unchanged.


The process fails in the same place when we use one subject.

Thanks!

Anthony

On 10/13/15 12:07 PM, Bruce Fischl wrote:

and how did you create the gca?
On Tue, 13 Oct 2015, Anthony Dick wrote:


Hello Bruce,

I will try a single subject. When I run the following command line 
(i.e.,

right out of recon-all) it works:

mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
$FREESURFER_HOME/average/RB_all_2014-08-21.gca transforms/talairach.lta


When I replace the Freesurfer-shipped .gca with the script created 
one I get

the following:

mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
//average/RB_one_2015-10-13.gca transforms/talairach.lta
setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_em_register for OpenMP = 16 ==
reading 1 input volumes...
logging results to talairach.log
reading '/average/RB_one_2015-10-13.gca'...
average std = 9.8   using min determinant for regularization = 9.7
0 singular and 426 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 18.3 or > 695.1
Segmentation fault


So it appears to be a problem with the gca creation? However, 
mri_info on

both RB_all_2014-08-21.gca and RB_one_2015-10-13.gca look identical.

Anthony


On 10/13/15 11:54 AM, Bruce Fischl wrote:

HI Anthony

what is the full command line? Does it happen if you only train on a 
single subject instead of 23?

Bruce
On Tue, 13 Oct 2015, Anthony Dick wrote:

Hello Bruce,

We have tried running the atlas creation on newly freesurfed brains with
the latest FS version and keep getting the same error. We have
essentially replicated the error we get on our own manually edited
volumes by copying the aparc+aseg.mgz and renaming it seg_edited.mgz.
Thus, it is unlikely to be a problem with our manually edited brains.
This results in the following error at the same place (running the
rebuild_gca_atlas.csh script):

== Number of threads available to mri_em_register for OpenMP = 16 ==
reading 23 input volumes...
logging results to talairach_one.log
reading '/average/RB_one_2015-10-13.gca'...
average std = 9.8   using min determinant for regularization = 9.7
0 singular and 426 ill-conditioned covariance matrices regularized
reading '/009/mri/nu.mgz'...
reading '/average/RB_one_2015-10-13.gca'...
reading frame -1 of gca
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
reading '/009/mri/transforms/talairach_one.lta'...
mri_read(): couldn't determine type of file
/009/mri/transforms/talairach_one.lta
mri_em_register: could not open input volume
/009/mri/transforms/talairach_one.lta.

Perhaps the FS folks could try to replicate this error? You don't need
my brains, just a couple of FS'd brains with a file called
seg_edited.mgz. If you don't get the error, then maybe it is a problem
with our local settings (although we get this error on multiple
different computers). Thanks for any help!

Anthony



On 7/20/15 2:30 PM, Anthony Dick wrote:

Hello,

I was wondering if these got uploaded correctly. Please let me know if
I made a mistake and thanks,

Anthony

On 7/9/15 1:41 PM, Bruce Fischl wrote:

sure
On Thu, 9 Jul 2015, Anthony Dick wrote:

Hello Bruce,

I am still getting this error after re-running autorecon1 in the newest
version of FS. Can I upload two brains and see what is the issue? I'm a
bit stumped on this one.

Anthony

On 5/26/15 12:21 PM, Bruce Fischl wrote:

Hi Anthony

sorry, I know you've posted this before. What version are you running?
And what type is your labeled data? That is, are they uchar? int?
At some
point this used to not work with non-uchar data, but I think I
fixed it a
while ago. YOu might try downloading a beta of V6 and see if it
fixes your
problem

cheers
Bruce


On Tue, 26
May 2015, Anthony Dick wrote:

Hello,

I have been stumped by this error I keep getting using the
rebuild_gca_atlas.csh script. I am trying to build a cerebellar
atlas,
so I am wondering if the problem is with the brains we
parcellated, or
with my installation etc. The brains consist of manually segmented
cerebellums from the original T1. The T1 is run through
Freesurfer, and
the ROIs are made in Freeview. The edited file is called
seg_edited.mgz.
Things run smoothly up until this error:

using MR volume //subjects/4/mri/brain.mgz to mask input
volume...
reading 23 input volumes...
logging results to talairach_one.log
reading 'subjects/average/RB_one_2015-05-14.gca'...
gcaAllocMax: node dims 32 32 32
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
average std = 8.4   using min determinant for regularization = 7.1
0 

Re: [Freesurfer] error in atlas creation

[Bruce Fischl]

and how did you create the gca?
On Tue, 13 Oct 2015, Anthony Dick wrote:


Hello Bruce,

I will try a single subject. When I run the following command line (i.e.,
right out of recon-all) it works:

mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
$FREESURFER_HOME/average/RB_all_2014-08-21.gca transforms/talairach.lta


When I replace the Freesurfer-shipped .gca with the script created one I get
the following:

mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
//average/RB_one_2015-10-13.gca transforms/talairach.lta
setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_em_register for OpenMP = 16 ==
reading 1 input volumes...
logging results to talairach.log
reading '/average/RB_one_2015-10-13.gca'...
average std = 9.8   using min determinant for regularization = 9.7
0 singular and 426 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 18.3 or > 695.1
Segmentation fault


So it appears to be a problem with the gca creation? However, mri_info on
both RB_all_2014-08-21.gca and RB_one_2015-10-13.gca look identical.

Anthony


On 10/13/15 11:54 AM, Bruce Fischl wrote:

HI Anthony

what is the full command line? Does it happen if you only train on a 
single subject instead of 23?

Bruce
On Tue, 13 Oct 2015, Anthony Dick wrote:

Hello Bruce,

We have tried running the atlas creation on newly freesurfed brains with
the latest FS version and keep getting the same error. We have
essentially replicated the error we get on our own manually edited
volumes by copying the aparc+aseg.mgz and renaming it seg_edited.mgz.
Thus, it is unlikely to be a problem with our manually edited brains.
This results in the following error at the same place (running the
rebuild_gca_atlas.csh script):

== Number of threads available to mri_em_register for OpenMP = 16 ==
reading 23 input volumes...
logging results to talairach_one.log
reading '/average/RB_one_2015-10-13.gca'...
average std = 9.8   using min determinant for regularization = 9.7
0 singular and 426 ill-conditioned covariance matrices regularized
reading '/009/mri/nu.mgz'...
reading '/average/RB_one_2015-10-13.gca'...
reading frame -1 of gca
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
reading '/009/mri/transforms/talairach_one.lta'...
mri_read(): couldn't determine type of file
/009/mri/transforms/talairach_one.lta
mri_em_register: could not open input volume
/009/mri/transforms/talairach_one.lta.

Perhaps the FS folks could try to replicate this error? You don't need
my brains, just a couple of FS'd brains with a file called
seg_edited.mgz. If you don't get the error, then maybe it is a problem
with our local settings (although we get this error on multiple
different computers). Thanks for any help!

Anthony



On 7/20/15 2:30 PM, Anthony Dick wrote:

Hello,

I was wondering if these got uploaded correctly. Please let me know if
I made a mistake and thanks,

Anthony

On 7/9/15 1:41 PM, Bruce Fischl wrote:

sure
On Thu, 9 Jul 2015, Anthony Dick wrote:

Hello Bruce,

I am still getting this error after re-running autorecon1 in the newest
version of FS. Can I upload two brains and see what is the issue? I'm a
bit stumped on this one.

Anthony

On 5/26/15 12:21 PM, Bruce Fischl wrote:

Hi Anthony

sorry, I know you've posted this before. What version are you running?
And what type is your labeled data? That is, are they uchar? int?
At some
point this used to not work with non-uchar data, but I think I
fixed it a
while ago. YOu might try downloading a beta of V6 and see if it
fixes your
problem

cheers
Bruce


On Tue, 26
May 2015, Anthony Dick wrote:

Hello,

I have been stumped by this error I keep getting using the
rebuild_gca_atlas.csh script. I am trying to build a cerebellar
atlas,
so I am wondering if the problem is with the brains we
parcellated, or
with my installation etc. The brains consist of manually segmented
cerebellums from the original T1. The T1 is run through
Freesurfer, and
the ROIs are made in Freeview. The edited file is called
seg_edited.mgz.
Things run smoothly up until this error:

using MR volume //subjects/4/mri/brain.mgz to mask input
volume...
reading 23 input volumes...
logging results to talairach_one.log
reading 'subjects/average/RB_one_2015-05-14.gca'...
gcaAllocMax: node dims 32 32 32
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
average std = 8.4   using min determinant for regularization = 7.1
0 singular and 119 ill-conditioned covariance matrices regularized
reading '//subjects/4/mri/nu.mgz'...
reading '//subjects/average/RB_one_2015-05-14.gca'...
gcaAllocMax: node dims 32 32 32
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
reading frame -1 of gca
MRIcopyFrame: src and 

Re: [Freesurfer] error in atlas creation

[Anthony Dick]

Hello Bruce,

I will try a single subject. When I run the following command line 
(i.e., right out of recon-all) it works:


mri_em_register 
 -uns 3 -mask 
brainmask.mgz nu.mgz $FREESURFER_HOME/average/RB_all_2014-08-21.gca 
transforms/talairach.lta



When I replace the Freesurfer-shipped .gca with the script created one I 
get the following:


mri_em_register -uns 3 -mask brainmask.mgz nu.mgz 
//average/RB_one_2015-10-13.gca transforms/talairach.lta

setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input volume...

== Number of threads available to mri_em_register for OpenMP = 16 ==
reading 1 input volumes...
logging results to talairach.log
reading '/average/RB_one_2015-10-13.gca'...
average std = 9.8   using min determinant for regularization = 9.7
0 singular and 426 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 18.3 or > 695.1
Segmentation fault


So it appears to be a problem with the gca creation? However, mri_info 
on both RB_all_2014-08-21.gca and RB_one_2015-10-13.gca look identical.


Anthony


On 10/13/15 11:54 AM, Bruce Fischl wrote:

HI Anthony

what is the full command line? Does it happen if you only train on a
single subject instead of 23?
Bruce
On Tue, 13 Oct 2015, Anthony Dick wrote:


Hello Bruce,

We have tried running the atlas creation on newly freesurfed brains with
the latest FS version and keep getting the same error. We have
essentially replicated the error we get on our own manually edited
volumes by copying the aparc+aseg.mgz and renaming it seg_edited.mgz.
Thus, it is unlikely to be a problem with our manually edited brains.
This results in the following error at the same place (running the
rebuild_gca_atlas.csh script):

== Number of threads available to mri_em_register for OpenMP = 16 ==
reading 23 input volumes...
logging results to talairach_one.log
reading '/average/RB_one_2015-10-13.gca'...
average std = 9.8   using min determinant for regularization = 9.7
0 singular and 426 ill-conditioned covariance matrices regularized
reading '/009/mri/nu.mgz'...
reading '/average/RB_one_2015-10-13.gca'...
reading frame -1 of gca
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
reading '/009/mri/transforms/talairach_one.lta'...
mri_read(): couldn't determine type of file
/009/mri/transforms/talairach_one.lta
mri_em_register: could not open input volume
/009/mri/transforms/talairach_one.lta.

Perhaps the FS folks could try to replicate this error? You don't need
my brains, just a couple of FS'd brains with a file called
seg_edited.mgz. If you don't get the error, then maybe it is a problem
with our local settings (although we get this error on multiple
different computers). Thanks for any help!

Anthony



On 7/20/15 2:30 PM, Anthony Dick wrote:

Hello,

I was wondering if these got uploaded correctly. Please let me know if
I made a mistake and thanks,

Anthony

On 7/9/15 1:41 PM, Bruce Fischl wrote:

sure
On Thu, 9 Jul 2015, Anthony Dick wrote:


Hello Bruce,

I am still getting this error after re-running autorecon1 in the newest
version of FS. Can I upload two brains and see what is the issue? I'm a
bit stumped on this one.

Anthony

On 5/26/15 12:21 PM, Bruce Fischl wrote:

Hi Anthony

sorry, I know you've posted this before. What version are you running?
And what type is your labeled data? That is, are they uchar? int?
At some
point this used to not work with non-uchar data, but I think I
fixed it a
while ago. YOu might try downloading a beta of V6 and see if it
fixes your
problem

cheers
Bruce


On Tue, 26
May 2015, Anthony Dick wrote:


Hello,

I have been stumped by this error I keep getting using the
rebuild_gca_atlas.csh script. I am trying to build a cerebellar
atlas,
so I am wondering if the problem is with the brains we
parcellated, or
with my installation etc. The brains consist of manually segmented
cerebellums from the original T1. The T1 is run through
Freesurfer, and
the ROIs are made in Freeview. The edited file is called
seg_edited.mgz.
Things run smoothly up until this error:

using MR volume //subjects/4/mri/brain.mgz to mask input
volume...
reading 23 input volumes...
logging results to talairach_one.log
reading 'subjects/average/RB_one_2015-05-14.gca'...
gcaAllocMax: node dims 32 32 32
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
average std = 8.4   using min determinant for regularization = 7.1
0 singular and 119 ill-conditioned covariance matrices regularized
reading '//subjects/4/mri/nu.mgz'...
reading '//subjects/average/RB_one_2015-05-14.gca'...
gcaAllocMax: node dims 32 32 32
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
reading frame -1 of gca
MRIcopyFrame: src and 

Re: [Freesurfer] error in atlas creation

[Bruce Fischl]

Hi Anthony

feel free to email me the .gca and I'll take a look

cheers
Bruce
On Tue, 13 Oct 2015, 
Anthony Dick wrote:



Hello Bruce,

I used the rebuild_gca_atlas.csh script (attached). I only commented out the
cluster configuration options. Otherwise the script is unchanged.

The process fails in the same place when we use one subject.

Thanks!

Anthony

On 10/13/15 12:07 PM, Bruce Fischl wrote:
  and how did you create the gca?
  On Tue, 13 Oct 2015, Anthony Dick wrote:

Hello Bruce,

I will try a single subject. When I run the
following command line (i.e.,
right out of recon-all) it works:

mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
$FREESURFER_HOME/average/RB_all_2014-08-21.gca
transforms/talairach.lta


When I replace the Freesurfer-shipped .gca with the
script created one I get
the following:

mri_em_register -uns 3 -mask brainmask.mgz nu.mgz
//average/RB_one_2015-10-13.gca
transforms/talairach.lta
setting unknown_nbr_spacing = 3
using MR volume brainmask.mgz to mask input
volume...

== Number of threads available to mri_em_register
for OpenMP = 16 ==
reading 1 input volumes...
logging results to talairach.log
reading '/average/RB_one_2015-10-13.gca'...
average std = 9.8   using min determinant for
regularization = 9.7
0 singular and 426 ill-conditioned covariance
matrices regularized
reading 'nu.mgz'...
freeing gibbs priors...done.
bounding unknown intensity as < 18.3 or > 695.1
Segmentation fault


So it appears to be a problem with the gca creation?
However, mri_info on
both RB_all_2014-08-21.gca and RB_one_2015-10-13.gca
look identical.

Anthony


On 10/13/15 11:54 AM, Bruce Fischl wrote:

HI Anthony

what is the full command line? Does it happen if you
only train on a single subject instead of 23?
Bruce
On Tue, 13 Oct 2015, Anthony Dick wrote:

Hello Bruce,

We have tried running the atlas creation on newly
freesurfed brains with
the latest FS version and keep getting the same
error. We have
essentially replicated the error we get on our own
manually edited
volumes by copying the aparc+aseg.mgz and renaming
it seg_edited.mgz.
Thus, it is unlikely to be a problem with our
manually edited brains.
This results in the following error at the same
place (running the
rebuild_gca_atlas.csh script):

== Number of threads available to mri_em_register
for OpenMP = 16 ==
reading 23 input volumes...
logging results to talairach_one.log
reading '/average/RB_one_2015-10-13.gca'...
average std = 9.8   using min determinant for
regularization = 9.7
0 singular and 426 ill-conditioned covariance
matrices regularized
reading '/009/mri/nu.mgz'...
reading '/average/RB_one_2015-10-13.gca'...
reading frame -1 of gca
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
INFO: MRImask() using MRImaskDifferentGeometry()
reading
'/009/mri/transforms/talairach_one.lta'...
mri_read(): couldn't determine type of file
/009/mri/transforms/talairach_one.lta
mri_em_register: could not open input volume
/009/mri/transforms/talairach_one.lta.

Perhaps the FS folks could try to replicate this
error? You don't need
my brains, just a couple of FS'd brains with a file
called
seg_edited.mgz. If you don't get the error, then
maybe it is a problem
with our local settings (although we get this error
on multiple
different computers). Thanks for any help!

Anthony



On 7/20/15 2:30 PM, Anthony Dick wrote:

Hello,

I was wondering if these got uploaded correctly.
Please let me know if
I made a mistake and thanks,

Anthony

On 7/9/15 1:41 PM, Bruce Fischl wrote:

sure
On Thu, 9 Jul 2015, Anthony Dick wrote:

Hello Bruce,

I am still getting this error after re-running
autorecon1 in the newest
version of FS. 

Re: [Freesurfer] error in atlas creation

[Anthony Dick]

Hello,

I was wondering if these got uploaded correctly. Please let me know if I 
made a mistake and thanks,

Anthony

On 7/9/15 1:41 PM, Bruce Fischl wrote:
 sure
 On Thu, 9 Jul 2015, Anthony Dick wrote:

 Hello Bruce,

 I am still getting this error after re-running autorecon1 in the newest
 version of FS. Can I upload two brains and see what is the issue? I'm a
 bit stumped on this one.

 Anthony

 On 5/26/15 12:21 PM, Bruce Fischl wrote:
 Hi Anthony

 sorry, I know you've posted this before. What version are you running?
 And what type is your labeled data? That is, are they uchar? int? At some
 point this used to not work with non-uchar data, but I think I fixed it a
 while ago. YOu might try downloading a beta of V6 and see if it fixes your
 problem

 cheers
 Bruce


 On Tue, 26
 May 2015, Anthony Dick wrote:

 Hello,

 I have been stumped by this error I keep getting using the
 rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas,
 so I am wondering if the problem is with the brains we parcellated, or
 with my installation etc. The brains consist of manually segmented
 cerebellums from the original T1. The T1 is run through Freesurfer, and
 the ROIs are made in Freeview. The edited file is called seg_edited.mgz.
 Things run smoothly up until this error:

 using MR volume /path/subjects/4/mri/brain.mgz to mask input volume...
 reading 23 input volumes...
 logging results to talairach_one.log
 reading 'subjects/average/RB_one_2015-05-14.gca'...
 gcaAllocMax: node dims 32 32 32
 gcaAllocMax: prior dims 128 128 128
 gcaAllocMax: max_labels 0
 average std = 8.4   using min determinant for regularization = 7.1
 0 singular and 119 ill-conditioned covariance matrices regularized
 reading '/path/subjects/4/mri/nu.mgz'...
 reading '/path/subjects/average/RB_one_2015-05-14.gca'...
 gcaAllocMax: node dims 32 32 32
 gcaAllocMax: prior dims 128 128 128
 gcaAllocMax: max_labels 0
 reading frame -1 of gca
 MRIcopyFrame: src and dst must be same type
 reading '/path/subjects/4/mri/transforms/talairach_one.lta'...
 mri_read(): couldn't determine type of file
 /path/subjects/4/mri/transforms/talairach_one.lta
 mri_em_register: could not open input volume
 /path/subjects/4/mri/transforms/talairach_one.lta.


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 e-mail
 contains patient information, please contact the Partners Compliance 
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 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Anthony Steven Dick, Ph.D.
Assistant Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu
Webpage: faculty.fiu.edu/~adick

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

Re: [Freesurfer] error in atlas creation

[Bruce Fischl]

sure
On Thu, 9 Jul 2015, Anthony Dick wrote:

 Hello Bruce,

 I am still getting this error after re-running autorecon1 in the newest
 version of FS. Can I upload two brains and see what is the issue? I'm a
 bit stumped on this one.

 Anthony

 On 5/26/15 12:21 PM, Bruce Fischl wrote:
 Hi Anthony

 sorry, I know you've posted this before. What version are you running?
 And what type is your labeled data? That is, are they uchar? int? At some
 point this used to not work with non-uchar data, but I think I fixed it a
 while ago. YOu might try downloading a beta of V6 and see if it fixes your
 problem

 cheers
 Bruce


 On Tue, 26
 May 2015, Anthony Dick wrote:

 Hello,

 I have been stumped by this error I keep getting using the
 rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas,
 so I am wondering if the problem is with the brains we parcellated, or
 with my installation etc. The brains consist of manually segmented
 cerebellums from the original T1. The T1 is run through Freesurfer, and
 the ROIs are made in Freeview. The edited file is called seg_edited.mgz.
 Things run smoothly up until this error:

 using MR volume /path/subjects/4/mri/brain.mgz to mask input volume...
 reading 23 input volumes...
 logging results to talairach_one.log
 reading 'subjects/average/RB_one_2015-05-14.gca'...
 gcaAllocMax: node dims 32 32 32
 gcaAllocMax: prior dims 128 128 128
 gcaAllocMax: max_labels 0
 average std = 8.4   using min determinant for regularization = 7.1
 0 singular and 119 ill-conditioned covariance matrices regularized
 reading '/path/subjects/4/mri/nu.mgz'...
 reading '/path/subjects/average/RB_one_2015-05-14.gca'...
 gcaAllocMax: node dims 32 32 32
 gcaAllocMax: prior dims 128 128 128
 gcaAllocMax: max_labels 0
 reading frame -1 of gca
 MRIcopyFrame: src and dst must be same type
 reading '/path/subjects/4/mri/transforms/talairach_one.lta'...
 mri_read(): couldn't determine type of file
 /path/subjects/4/mri/transforms/talairach_one.lta
 mri_em_register: could not open input volume
 /path/subjects/4/mri/transforms/talairach_one.lta.


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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.




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Re: [Freesurfer] error in atlas creation

[Bruce Fischl]

Hi Anthony

sorry, I know you've posted this before. What version are you running? 
And what type is your labeled data? That is, are they uchar? int? At some 
point this used to not work with non-uchar data, but I think I fixed it a 
while ago. YOu might try downloading a beta of V6 and see if it fixes your 
problem

cheers
Bruce


On Tue, 26 
May 2015, Anthony Dick wrote:

 
 Hello,
 
 I have been stumped by this error I keep getting using the 
 rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas, 
 so I am wondering if the problem is with the brains we parcellated, or 
 with my installation etc. The brains consist of manually segmented 
 cerebellums from the original T1. The T1 is run through Freesurfer, and 
 the ROIs are made in Freeview. The edited file is called seg_edited.mgz. 
 Things run smoothly up until this error:
 
 using MR volume /path/subjects/4/mri/brain.mgz to mask input volume...
 reading 23 input volumes...
 logging results to talairach_one.log
 reading 'subjects/average/RB_one_2015-05-14.gca'...
 gcaAllocMax: node dims 32 32 32
 gcaAllocMax: prior dims 128 128 128
 gcaAllocMax: max_labels 0
 average std = 8.4   using min determinant for regularization = 7.1
 0 singular and 119 ill-conditioned covariance matrices regularized
 reading '/path/subjects/4/mri/nu.mgz'...
 reading '/path/subjects/average/RB_one_2015-05-14.gca'...
 gcaAllocMax: node dims 32 32 32
 gcaAllocMax: prior dims 128 128 128
 gcaAllocMax: max_labels 0
 reading frame -1 of gca
 MRIcopyFrame: src and dst must be same type
 reading '/path/subjects/4/mri/transforms/talairach_one.lta'...
 mri_read(): couldn't determine type of file 
 /path/subjects/4/mri/transforms/talairach_one.lta
 mri_em_register: could not open input volume 
 /path/subjects/4/mri/transforms/talairach_one.lta.
 

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


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

[Freesurfer] error in atlas creation

[Anthony Dick]

Hello,

I have been stumped by this error I keep getting using the
rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas,
so I am wondering if the problem is with the brains we parcellated, or
with my installation etc. The brains consist of manually segmented
cerebellums from the original T1. The T1 is run through Freesurfer, and
the ROIs are made in Freeview. The edited file is called seg_edited.mgz.
Things run smoothly up until this error:

using MR volume /path/subjects/4/mri/brain.mgz to mask input volume...
reading 23 input volumes...
logging results to talairach_one.log
reading 'subjects/average/RB_one_2015-05-14.gca'...
gcaAllocMax: node dims 32 32 32
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
average std = 8.4   using min determinant for regularization = 7.1
0 singular and 119 ill-conditioned covariance matrices regularized
reading '/path/subjects/4/mri/nu.mgz'...
reading '/path/subjects/average/RB_one_2015-05-14.gca'...
gcaAllocMax: node dims 32 32 32
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
reading frame -1 of gca
MRIcopyFrame: src and dst must be same type
reading '/path/subjects/4/mri/transforms/talairach_one.lta'...
mri_read(): couldn't determine type of file
/path/subjects/4/mri/transforms/talairach_one.lta
mri_em_register: could not open input volume
/path/subjects/4/mri/transforms/talairach_one.lta.


--
Anthony Steven Dick, Ph.D.
Assistant Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu
Webpage: faculty.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu
Join the Society for the Study of Human Development: http://www.sshdonline.org

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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] error in atlas creation

[Anthony Dick]

Hello,

I just wanted to give this message a bump. Thanks!

Anthony

On 5/15/15 9:49 AM, Anthony Dick wrote:
 Hello,

 I have been stumped by this error I keep getting using the 
 rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas, 
 so I am wondering if the problem is with the brains we parcellated, or 
 with my installation etc. The brains consist of manually segmented 
 cerebellums from the original T1. The T1 is run through Freesurfer, 
 and the ROIs are made in Freeview. The edited file is called 
 seg_edited.mgz. Things run smoothly up until this error:

 using MR volume /path/subjects/4/mri/brain.mgz to mask input volume...
 reading 23 input volumes...
 logging results to talairach_one.log
 reading 'subjects/average/RB_one_2015-05-14.gca'...
 gcaAllocMax: node dims 32 32 32
 gcaAllocMax: prior dims 128 128 128
 gcaAllocMax: max_labels 0
 average std = 8.4   using min determinant for regularization = 7.1
 0 singular and 119 ill-conditioned covariance matrices regularized
 reading '/path/subjects/4/mri/nu.mgz'...
 reading '/path/subjects/average/RB_one_2015-05-14.gca'...
 gcaAllocMax: node dims 32 32 32
 gcaAllocMax: prior dims 128 128 128
 gcaAllocMax: max_labels 0
 reading frame -1 of gca
 MRIcopyFrame: src and dst must be same type
 reading '/path/subjects/4/mri/transforms/talairach_one.lta'...
 mri_read(): couldn't determine type of file 
 /path/subjects/4/mri/transforms/talairach_one.lta
 mri_em_register: could not open input volume 
 /path/subjects/4/mri/transforms/talairach_one.lta.


-- 
Anthony Steven Dick, Ph.D.
Assistant Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu
Webpage: faculty.fiu.edu/~adick

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

[Freesurfer] error in atlas creation

[Anthony Dick]

Hello,

I have been stumped by this error I keep getting using the 
rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas, 
so I am wondering if the problem is with the brains we parcellated, or 
with my installation etc. The brains consist of manually segmented 
cerebellums from the original T1. The T1 is run through Freesurfer, and 
the ROIs are made in Freeview. The edited file is called seg_edited.mgz. 
Things run smoothly up until this error:

using MR volume /path/subjects/4/mri/brain.mgz to mask input volume...
reading 23 input volumes...
logging results to talairach_one.log
reading 'subjects/average/RB_one_2015-05-14.gca'...
gcaAllocMax: node dims 32 32 32
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
average std = 8.4   using min determinant for regularization = 7.1
0 singular and 119 ill-conditioned covariance matrices regularized
reading '/path/subjects/4/mri/nu.mgz'...
reading '/path/subjects/average/RB_one_2015-05-14.gca'...
gcaAllocMax: node dims 32 32 32
gcaAllocMax: prior dims 128 128 128
gcaAllocMax: max_labels 0
reading frame -1 of gca
MRIcopyFrame: src and dst must be same type
reading '/path/subjects/4/mri/transforms/talairach_one.lta'...
mri_read(): couldn't determine type of file 
/path/subjects/4/mri/transforms/talairach_one.lta
mri_em_register: could not open input volume 
/path/subjects/4/mri/transforms/talairach_one.lta.

-- 
Anthony Steven Dick, Ph.D.
Assistant Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu
Webpage: faculty.fiu.edu/~adick

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