External Email - Use Caution

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 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: 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

External Email - Use Caution 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.ukmailto:e.iglesias@ucl.ac.uk> wrote:

External Email - Use Caution 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 http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Pradeep <tpradeep@gmail.commailto:tpradeep@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 4 October 2018 at 19:12 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

External Email - Use Caution 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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

External Email - Use Caution

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

External Email - Use Caution 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.ukmailto:e.iglesias@ucl.ac.uk> wrote:

External Email - Use Caution 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 http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Pradeep <tpradeep@gmail.commailto:tpradeep@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 4 October 2018 at 19:21 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

External Email - Use Caution 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.ukmailto:e.iglesias@ucl.ac.uk> wrote:

External Email - Use Caution 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 http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Pradeep <tpradeep@gmail.commailto:tpradeep@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 4 October 2018 at 19:12 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

External Email - Use Caution 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

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer