External Email - Use Caution
---------- Forwarded message --------- From: Dalton Bermudez daltonhbermudez@gmail.com Date: Wed, Nov 13, 2019 at 1:54 PM Subject: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm To: freesurfer@nmr.mgh.harvard.edu
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
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 daltonhbermudez@gmail.com Date: Wed, Nov 13, 2019 at 1:54 PM Subject: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm To: freesurfer@nmr.mgh.harvard.edu
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
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 fischl@nmr.mgh.harvard.edu 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 daltonhbermudez@gmail.com Date: Wed, Nov 13, 2019 at 1:54 PM Subject: recon-all error: ltMNIreadEx: could not open file
transforms/talairach.xfm
To: freesurfer@nmr.mgh.harvard.edu
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
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* <daltonhbermudez@gmail.com mailto:daltonhbermudez@gmail.com> Date: Wed, Nov 13, 2019 at 1:54 PM Subject: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm To: <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Dalton Bermudez -
Greve, Douglas N.,Ph.D.