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Glad to hear.
As much as it exists to solve problems, it’s also nice to get positive news on the list every once in a while.
Cheers,
/E
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Pradeep <tpradeep@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Monday, 8 October 2018 at 18:51
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab
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Hi Iglesias,
It turns out that my input images are in different orientation and I had a hard time reorienting them.
Starting from dicom images and using mri_convert to bring them to nifti format seem to fix the problem
The hippocampal subfiled segmentation program with the additional high resolution scan works!
Thank you for all the help!
Pradeep
On Thu, Oct 4, 2018 at 11:28 AM Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:
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Thanks!
Did you check whether the T2 and the T1 were correctly registered? You can check out the animated gif under mri/transforms in the subject’s directory.
Cheers,
/E
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Pradeep <tpradeep@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 4 October 2018 at 19:21
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab
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I have tried this for two subjects and got the same error.
Thanks,
Pradeep
On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:
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Dear Pradeep,
Did you get this error on several subjects, or only one?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Pradeep <tpradeep@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 4 October 2018 at 19:12
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab
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Hello,
I am trying to run the hippocampal segmentation with an additional Hi-res scan using the following command
recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of additional scan> <analysisID>and got the following error
Error using kvlGEMSMatlab
/autofs/cluster/koen/eugenio/InsightToolkit-4.9.1/Modules/Core/Common/include/itkImageConstIterator.h:211:
itk::ERROR: Region ImageRegion (0x7f67011c5dd0)
Dimension: 3
Index: [0, 845, 0]
Size: [105, 18446744073709550952, 20]
is outside of buffered region ImageRegion (0x7f6573ca8bb8)
Dimension: 3
Index: [0, 0, 0]
Size: [526, 181, 526]
Error in kvlReadCroppedImage (line 11)
Error in segmentSubjectT2_autoEstimateAlveusML (line 838)
Started at Thu Oct 4 09:35:38 MST 2018
Ended at Thu Oct 4 09:57:35 MST 2018
#@#%# recon-all-run-time-hours 0.366
recon-all -s subject_id finished without error at Thu Oct 4 09:57:36 MST 2018
done
I came across a similar error in the forums and using the most recent version seem to have worked for some, but it did not help in my case.
Freesurfer version I am using
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
with matlab run time from 2012b as suggested
I have also tried to use 2014b runtime which exited right away.
Thank you for your help,
Pradeep
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