Re: [Freesurfer] Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm

[Greve, Douglas N.,Ph.D.]

You did not tell recon-all to do anything:)
Try adding -all to your command line

On 11/13/19 2:10 PM, Dalton Bermudez wrote:
>
> External Email - Use Caution
>
>
>
> -- Forwarded message -
> From: *Dalton Bermudez*  >
> Date: Wed, Nov 13, 2019 at 1:54 PM
> Subject: recon-all error: ltMNIreadEx: could not open file 
> transforms/talairach.xfm
> To:  >
>
>
> Dear FreeSurfer Developers,
>
> I am attempting to obtain a average cortical surface for two 
> structural MRI nii dataset. However, when I run the command, I obtain 
> the following errors.
>
> error: No such file or directory
> error: ltMNIreadEx: could not open file transforms/talairach.xfm
> error: 
> mghRead(/home/dbermudez/Documents/subjects/00_0086/mri/orig.mgz, -1): 
> could not open file
> ERROR readMNI: cannot read src MRIorig.mgz
>
> FreeSurfer version: freesurfer-linux-centos6_x86_64-dev
> Platform: Linux Ubuntu 18.05
> recon-all.log: see attachment
>
>
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Re: [Freesurfer] Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm

[Dalton Bermudez]

External Email - Use Caution

Dear Bruce,
This is the command I ran with my own data:
recon-all -subjid 00_0086 -i RAW/00_0086/ns_00_0086_3T_T1w_MPR1.nii -i
RAW/00_0086/ns_00_0086_3T_T1w_MPR2.nii
The whole output can be found in the recon-all.log attached below

On Wed, Nov 13, 2019 at 2:24 PM Bruce Fischl 
wrote:

> Hi Dalton
>
> you need to give us a lot more information. What command did you run?
> What was the full output?
>
> cheers
> Bruce
> On Wed, 13 Nov 2019, Dalton Bermudez wrote:
>
> >
> > External Email - Use Caution
> >
> >
> >
> > -- Forwarded message -
> > From: Dalton Bermudez 
> > Date: Wed, Nov 13, 2019 at 1:54 PM
> > Subject: recon-all error: ltMNIreadEx: could not open file
> transforms/talairach.xfm
> > To: 
> >
> >
> > Dear FreeSurfer Developers,
> >
> > I am attempting to obtain a average cortical surface for two structural
> MRI nii dataset. However,
> > when I run the command, I obtain the following errors.
> >
> > error: No such file or directory
> > error: ltMNIreadEx: could not open file transforms/talairach.xfm
> > error: mghRead(/home/dbermudez/Documents/subjects/00_0086/mri/orig.mgz,
> -1): could not open file
> > ERROR readMNI: cannot read src MRIorig.mgz
> >
> > FreeSurfer version: freesurfer-linux-centos6_x86_64-dev
> > Platform: Linux Ubuntu 18.05
> > recon-all.log: see attachment
> >
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Wed Nov 13 13:43:32 EST 2019
/home/dbermudez/Documents/subjects/00_0086
/usr/local/freesurfer/bin/recon-all
-subjid 00_0086 -i RAW/00_0086/ns_00_0086_3T_T1w_MPR1.nii -i RAW/00_0086/ns_00_0086_3T_T1w_MPR2.nii
subjid 00_0086
setenv SUBJECTS_DIR /home/dbermudez/Documents/subjects
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-local-build-dev-20191112
Linux dbermudez-XPS-15-9550 5.0.0-32-generic #34~18.04.2-Ubuntu SMP Thu Oct 10 10:36:02 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  62333 
maxlocks unlimited
maxsignal62333 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   16005232 237583610735724  212276 289367213070860
Swap:   2097148   0 2097148


program versions used
$Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $
$Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $

ProgramName: lta_convert  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2019/11/13-18:43:32-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.0.0-32-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2019/11/13-18:43:32-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.0.0-32-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_annotation2label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2019/11/13-18:43:32-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_annotation2label.c,v 1.32 2016/08/02 21:20:27 nicks Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.0.0-32-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_aparc2aseg  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2019/11/13-18:43:32-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_aparc2aseg.c,v 1.54 2016/12/26 15:29:30 fischl Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.0.0-32-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_aparc2wmseg  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2019/11/13-18:43:32-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_aparc2wmseg.c,v 1.6 2011/03/02 00:04:13 nicks Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.0.0-32-generic  CompilerName: GCC  CompilerVersion: 40900 
ProgramName: mri_binarize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2019/11/13-18:43:32-GMT  BuildTimeStamp: Nov 12 2019 00:45:11  Id: $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $  User: dbermudez  Machine: dbermudez-XPS-15-9550  Platform: Linux  PlatformVersion: 5.0.0-32-generic  

Re: [Freesurfer] Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm

[Bruce Fischl]

Hi Dalton

you need to give us a lot more information. What command did you run? 
What was the full output?


cheers
Bruce
On Wed, 13 Nov 2019, Dalton Bermudez wrote:



External Email - Use Caution



-- Forwarded message -
From: Dalton Bermudez 
Date: Wed, Nov 13, 2019 at 1:54 PM
Subject: recon-all error: ltMNIreadEx: could not open file 
transforms/talairach.xfm
To: 


Dear FreeSurfer Developers,

I am attempting to obtain a average cortical surface for two structural MRI nii 
dataset. However,
when I run the command, I obtain the following errors.

error: No such file or directory
error: ltMNIreadEx: could not open file transforms/talairach.xfm
error: mghRead(/home/dbermudez/Documents/subjects/00_0086/mri/orig.mgz, -1): 
could not open file
ERROR readMNI: cannot read src MRIorig.mgz

FreeSurfer version: freesurfer-linux-centos6_x86_64-dev
Platform: Linux Ubuntu 18.05
recon-all.log: see attachment


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