Re: [Freesurfer] Hippocampal segmentation Matlab crash

[Hoopes, Andrew]

I’m not sure what the cause of this would be, unfortunately. The matlab runtime 
library errors become very difficult to track down. One thing you could do is 
try to run this in a singularity or docker container, if available on your 
cluster. You could use centos7 as the base image, and mount the paths to your 
freesurfer installation and your input/output data.
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Caitlin R Bowman 

Date: Wednesday, March 9, 2022 at 12:57 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash

External Email - Use Caution
Tried it, but I still get the same error.

--
Caitlin Bowman, Ph.D.
Assistant Professor of Psychology
University of Wisconsin-Milwaukee

From:  on behalf of "Hoopes, Andrew" 

Reply-To: Freesurfer support list 
Date: Tuesday, March 8, 2022 at 3:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash

Hi Cait,

Before running the command, can you try unsetting the LD_LIBRARY_PATH variable? 
You can do this in bash with:

unset LD_LIBRARY_PATH

or in cshell with:

unsetenv LD_LIBRARY_PATH

best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Caitlin R Bowman 

Date: Tuesday, March 8, 2022 at 3:14 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Hippocampal segmentation Matlab crash

External Email - Use Caution
Hello,

I am trying to run the hippocampal segmentation used in freesurfer 7. I have 
tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am 
running on a computing cluster, not locally. The same code works fine on my 
local computer. The managers of the computing cluster have tried to help but 
are stuck themselves. Find the command that I run below followed by the full 
error log.

Best,
Cait

Command:
segmentHA_T2.sh sub-110033 $ANATDIR/sub-110033_T2w.nii.gz T2 0

Error log:
--
USER bowman2
HOST compute-081.mortimer
PROCESSID 11325
PROCESSOR x86_64
OS Linux
Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
--
#
#@# Hippocampal Subfields processing (T2) left Thu Feb 24 14:14:35 CST 2022
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/os/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sharedapps/LS/psych_imaging/fsl/6.0.4/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/sys/os/glnxa64::/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/vtk/lib/vtk-5.6/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/tcltktixblt/lib/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/KWWidgets/lib/KWWidgets:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/mni/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib


  std::terminate() detected at Thu Feb 24 14:14:37 2022


Configuration:
  Crash Decoding : Disabled
  Default Encoding   : UTF-8
  GNU C Library  : 2.17 stable
  MATLAB Architecture: glnxa64
  MATLAB Root: 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Linux 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64
  Processor ID   : x86 Family 6 Model 63 Stepping 2, GenuineIntel

Fault Count: 1


Abnormal termination:
std::terminate()

Register State (captured):
  RAX =   RBX = 2baa657204e8
  RCX =   RDX = 2baa6570f758
  RSP = 2baa93ffb0b0  RBP = 2baa93ffb470
  RSI = 2baa654c3fb3  RDI = 2baa93ffb0c0

   R8 =    R9 = 2baa60271f90
  R10 =   R11 = 
  R12 = 2baa65730520  R13 = 2baa93ffc0b0
  R14 = 2baa93ffc090  R15 = 2baa93ffc470

  RIP = 2baa65422f4e  EFL = 

   CS =    FS =    GS = 

Stack Trace

Re: [Freesurfer] Hippocampal segmentation Matlab crash

[Caitlin R Bowman]

External Email - Use Caution

Tried it, but I still get the same error.

--
Caitlin Bowman, Ph.D.
Assistant Professor of Psychology
University of Wisconsin-Milwaukee

From:  on behalf of "Hoopes, Andrew" 

Reply-To: Freesurfer support list 
Date: Tuesday, March 8, 2022 at 3:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash

Hi Cait,

Before running the command, can you try unsetting the LD_LIBRARY_PATH variable? 
You can do this in bash with:

unset LD_LIBRARY_PATH

or in cshell with:

unsetenv LD_LIBRARY_PATH

best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Caitlin R Bowman 

Date: Tuesday, March 8, 2022 at 3:14 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Hippocampal segmentation Matlab crash

External Email - Use Caution
Hello,

I am trying to run the hippocampal segmentation used in freesurfer 7. I have 
tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am 
running on a computing cluster, not locally. The same code works fine on my 
local computer. The managers of the computing cluster have tried to help but 
are stuck themselves. Find the command that I run below followed by the full 
error log.

Best,
Cait

Command:
segmentHA_T2.sh sub-110033 $ANATDIR/sub-110033_T2w.nii.gz T2 0

Error log:
--
USER bowman2
HOST compute-081.mortimer
PROCESSID 11325
PROCESSOR x86_64
OS Linux
Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
--
#
#@# Hippocampal Subfields processing (T2) left Thu Feb 24 14:14:35 CST 2022
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/os/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sharedapps/LS/psych_imaging/fsl/6.0.4/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/sys/os/glnxa64::/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/vtk/lib/vtk-5.6/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/tcltktixblt/lib/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/KWWidgets/lib/KWWidgets:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/mni/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib


  std::terminate() detected at Thu Feb 24 14:14:37 2022


Configuration:
  Crash Decoding : Disabled
  Default Encoding   : UTF-8
  GNU C Library  : 2.17 stable
  MATLAB Architecture: glnxa64
  MATLAB Root: 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Linux 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64
  Processor ID   : x86 Family 6 Model 63 Stepping 2, GenuineIntel

Fault Count: 1


Abnormal termination:
std::terminate()

Register State (captured):
  RAX =   RBX = 2baa657204e8
  RCX =   RDX = 2baa6570f758
  RSP = 2baa93ffb0b0  RBP = 2baa93ffb470
  RSI = 2baa654c3fb3  RDI = 2baa93ffb0c0

   R8 =    R9 = 2baa60271f90
  R10 =   R11 = 
  R12 = 2baa65730520  R13 = 2baa93ffc0b0
  R14 = 2baa93ffc090  R15 = 2baa93ffc470

  RIP = 2baa65422f4e  EFL = 

   CS =    FS =    GS = 

Stack Trace (captured):
[  0] 0x2baa65422f4e 
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00966478
 _ZN2fl4diag5linux12context_base12capture_dataEv+0030
[  1] 0x2baa65420424 
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00955428
[  2] 0x2baa740ef0f5 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00868597
[  3] 0x2baa740f12ca 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+008

Re: [Freesurfer] Hippocampal segmentation Matlab crash

[Hoopes, Andrew]

Hi Cait,

Before running the command, can you try unsetting the LD_LIBRARY_PATH variable? 
You can do this in bash with:

unset LD_LIBRARY_PATH

or in cshell with:

unsetenv LD_LIBRARY_PATH

best,
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Caitlin R Bowman 

Date: Tuesday, March 8, 2022 at 3:14 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Hippocampal segmentation Matlab crash

External Email - Use Caution
Hello,

I am trying to run the hippocampal segmentation used in freesurfer 7. I have 
tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am 
running on a computing cluster, not locally. The same code works fine on my 
local computer. The managers of the computing cluster have tried to help but 
are stuck themselves. Find the command that I run below followed by the full 
error log.

Best,
Cait

Command:
segmentHA_T2.sh sub-110033 $ANATDIR/sub-110033_T2w.nii.gz T2 0

Error log:
--
USER bowman2
HOST compute-081.mortimer
PROCESSID 11325
PROCESSOR x86_64
OS Linux
Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
--
#
#@# Hippocampal Subfields processing (T2) left Thu Feb 24 14:14:35 CST 2022
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/os/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sharedapps/LS/psych_imaging/fsl/6.0.4/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/sys/os/glnxa64::/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/vtk/lib/vtk-5.6/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/tcltktixblt/lib/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/KWWidgets/lib/KWWidgets:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/mni/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib


  std::terminate() detected at Thu Feb 24 14:14:37 2022


Configuration:
  Crash Decoding : Disabled
  Default Encoding   : UTF-8
  GNU C Library  : 2.17 stable
  MATLAB Architecture: glnxa64
  MATLAB Root: 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Linux 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64
  Processor ID   : x86 Family 6 Model 63 Stepping 2, GenuineIntel

Fault Count: 1


Abnormal termination:
std::terminate()

Register State (captured):
  RAX =   RBX = 2baa657204e8
  RCX =   RDX = 2baa6570f758
  RSP = 2baa93ffb0b0  RBP = 2baa93ffb470
  RSI = 2baa654c3fb3  RDI = 2baa93ffb0c0

   R8 =    R9 = 2baa60271f90
  R10 =   R11 = 
  R12 = 2baa65730520  R13 = 2baa93ffc0b0
  R14 = 2baa93ffc090  R15 = 2baa93ffc470

  RIP = 2baa65422f4e  EFL = 

   CS =    FS =    GS = 

Stack Trace (captured):
[  0] 0x2baa65422f4e 
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00966478
 _ZN2fl4diag5linux12context_base12capture_dataEv+0030
[  1] 0x2baa65420424 
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00955428
[  2] 0x2baa740ef0f5 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00868597
[  3] 0x2baa740f12ca 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877258
[  4] 0x2baa740f13c1 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877505
[  5] 0x2baa740f1743 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878403
[  6] 0x2baa740f17b3 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878515
[  7

[Freesurfer] Hippocampal segmentation Matlab crash

[Caitlin R Bowman]

External Email - Use Caution

Hello,

I am trying to run the hippocampal segmentation used in freesurfer 7. I have 
tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am 
running on a computing cluster, not locally. The same code works fine on my 
local computer. The managers of the computing cluster have tried to help but 
are stuck themselves. Find the command that I run below followed by the full 
error log.

Best,
Cait

Command:
segmentHA_T2.sh sub-110033 $ANATDIR/sub-110033_T2w.nii.gz T2 0

Error log:
--
USER bowman2
HOST compute-081.mortimer
PROCESSID 11325
PROCESSOR x86_64
OS Linux
Linux compute-081.mortimer 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
--
#
#@# Hippocampal Subfields processing (T2) left Thu Feb 24 14:14:35 CST 2022
--
Setting up environment variables
---
LD_LIBRARY_PATH is 
.:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/os/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/sharedapps/LS/psych_imaging/fsl/6.0.4/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/sys/os/glnxa64::/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/runtime/glnxa64:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/vtk/lib/vtk-5.6/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/tcltktixblt/lib/:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib/KWWidgets/lib/KWWidgets:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/mni/lib:/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/lib


  std::terminate() detected at Thu Feb 24 14:14:37 2022


Configuration:
  Crash Decoding : Disabled
  Default Encoding   : UTF-8
  GNU C Library  : 2.17 stable
  MATLAB Architecture: glnxa64
  MATLAB Root: 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84
  MATLAB Version : 8.4.0.150421 (R2014b)
  Operating System   : Linux 3.10.0-1160.49.1.el7.x86_64 #1 SMP Tue Nov 30 
15:51:32 UTC 2021 x86_64
  Processor ID   : x86 Family 6 Model 63 Stepping 2, GenuineIntel

Fault Count: 1


Abnormal termination:
std::terminate()

Register State (captured):
  RAX =   RBX = 2baa657204e8
  RCX =   RDX = 2baa6570f758
  RSP = 2baa93ffb0b0  RBP = 2baa93ffb470
  RSI = 2baa654c3fb3  RDI = 2baa93ffb0c0

   R8 =    R9 = 2baa60271f90
  R10 =   R11 = 
  R12 = 2baa65730520  R13 = 2baa93ffc0b0
  R14 = 2baa93ffc090  R15 = 2baa93ffc470

  RIP = 2baa65422f4e  EFL = 

   CS =    FS =    GS = 

Stack Trace (captured):
[  0] 0x2baa65422f4e 
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00966478
 _ZN2fl4diag5linux12context_base12capture_dataEv+0030
[  1] 0x2baa65420424 
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwfl.so+00955428
[  2] 0x2baa740ef0f5 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00868597
[  3] 0x2baa740f12ca 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877258
[  4] 0x2baa740f13c1 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00877505
[  5] 0x2baa740f1743 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878403
[  6] 0x2baa740f17b3 
/raid-07/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84/bin/glnxa64/libmwmcr.so+00878515
[  7] 0x2baa5ffe4a06  
/lib64/libstdc++.so.6+00387590
[  8] 0x2baa5ffe4a33  
/lib64/libstdc++.so.6+00387635
[  9] 0x2baa5ffe4c53  
/lib64/libstdc++.so.6+00388179
[ 10] 0x2baa60fe3822 
/sharedapps/LS/psych_imaging/freesurfer/7.2.0/freesurfer/MCRv84//bin/glnxa64/libmwi18n.so+00325666
 

Re: [Freesurfer] hippocampal segmentation differences pediatric sample

[Douglas N. Greve]

I would not expect the different subjects to be the same (they are 
different subjects). I don't know how you'd get them back to native 
space. The opposite of how you normalized them I guess.


On 2/12/2022 8:15 AM, Aleksandra Lecei wrote:


External Email - Use Caution

Hi,

I'm new to this and was wondering if someone could help me out?
I used a T1 preprocessed image (fmriprep), normalized to the NIH 
pediatric cohort 6 (13-18.5 years) template to do recon-all and then 
used the hippocampal segmentation tool v.7.
I have two questions: a) wouldn't one expect the segmentation to be 
the same for different individuals if the normalized T1's are used 
(registration seems to be well aligned to the same space when checked 
in SPM but when looking into the .txt files the volumes are 
different)? and b) (how) do I need to use the -custom-tal-atlas flag 
to get the estimates back to the NIH pediatric atlas (cohort 6) and 
can I make masks from the hippocampal segmentations for ROI analysis 
in other software for this study population?


Thank you!

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[Freesurfer] hippocampal segmentation differences pediatric sample

[Aleksandra Lecei]

External Email - Use Caution

Hi,

I'm new to this and was wondering if someone could help me out?
I used a T1 preprocessed image (fmriprep), normalized to the NIH pediatric
cohort 6 (13-18.5 years) template to do recon-all and then used the
hippocampal segmentation tool v.7.
I have two questions: a) wouldn't one expect the segmentation to be the
same for different individuals if the normalized T1's are used
(registration seems to be well aligned to the same space when checked in
SPM but when looking into the .txt files the volumes are different)? and b)
(how) do I need to use the -custom-tal-atlas flag to get the estimates back
to the NIH pediatric atlas (cohort 6) and can I make masks from the
hippocampal segmentations for ROI analysis in other software for this study
population?

Thank you!
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Re: [Freesurfer] Hippocampal segmentation - data processed in different fs version

[Iglesias Gonzalez, Juan E.]

Yes! As long as you explain it clearly in whatever paper you may write with the 
results ;-)

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On Jan 10, 2022, at 23:28, Katarina Vulić 
mailto:vulic.katari...@gmail.com>> wrote:


External Email - Use Caution

Hello Freesurfer Developers,

We have data that has been initially processed by Freesurfer v6.0.1.
Is it ok if we run hippocampal subfield segmentation (MailScanner has detected 
a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala)
 with v7.1.1 that we currently have on our machine?

Thanks in advance,
Katarina
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[Freesurfer] Hippocampal segmentation - data processed in different fs version

[Katarina Vulić]

External Email - Use Caution

Hello Freesurfer Developers,

We have data that has been initially processed by Freesurfer v6.0.1.
Is it ok if we run hippocampal subfield segmentation (
https://secure-web.cisco.com/1jE-n3Hq6P8vcsBZUmGPkR42g9WznVSWKUxrDeSXYoSnRiQ7w9sPdFxkojCvOKSo7MwK2yxjWiL_dOWKwm3TSkiyIW2o5SZP_vM93pe9jws3DKRsSEz1mSMqpCIceNcJIyPe2LlgE56f8lZYOHJkVluik1MP-Zz5RXAckFBYX2RtE-sd7PD-5hk2yGonbMxiwF5289LFQleIvmATT5uDH_sZj5ndSZ1f1XNTSZ0L5OXFfoAlxRxVf2EN3i2Rsq9Q91RICL1dwFy9vGTl9jqmIRwZWgsdD5vQLXQpnGBASku7ncsLZ0Fx-9eaWd4NJWLuBWIZXYJSA25g5JAMV-70_8A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala)
with v7.1.1 that we currently have on our machine?

Thanks in advance,
Katarina
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Re: [Freesurfer] Hippocampal segmentation

[Douglas N. Greve]

It segments the whole hippocampus (ie, assigns voxels as either hippo or 
something else), then counts up the voxels to get the voume (also 
applies partial volume correction). It does not compute curvature of 
hippo. Hippo does form part of the boundary of the surface, but we 
exclude it from further analysis.


On 2/26/2021 9:12 AM, Alberto Del Cerro Leon wrote:


External Email - Use Caution

Then How FreeSurfer calculates the volume, curvature etc from 
Hippocampus and How could I check it?


El vie, 26 feb 2021 a las 14:44, Douglas N. Greve 
(mailto:dgr...@mgh.harvard.edu>>) escribió:


Hippocampus is not part of the surface

On 2/24/2021 10:40 AM, Alberto Del Cerro Leon wrote:


External Email - Use Caution

Hello Freesurfers, I am doing an AAL atlas on freesurfer using
mri_vol2surf and editing the labels manually. However when I was
editing the labels in tksurfer the hippocampal field is quite
bad. I tried to look the segmentation used by you in labels but I
didn't find it. How could I segment the Hippocampus

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Re: [Freesurfer] Hippocampal segmentation

[Alberto Del Cerro Leon]

External Email - Use Caution

Then How FreeSurfer calculates the volume, curvature etc from
Hippocampus and How could I check it?

El vie, 26 feb 2021 a las 14:44, Douglas N. Greve ()
escribió:

> Hippocampus is not part of the surface
>
> On 2/24/2021 10:40 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Hello Freesurfers, I am doing an AAL atlas on freesurfer using
> mri_vol2surf and editing the labels manually. However when I was editing
> the labels in tksurfer the hippocampal field is quite bad. I tried to look
> the segmentation used by you in labels but I didn't find it. How could I
> segment the Hippocampus
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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Re: [Freesurfer] Hippocampal segmentation

[Douglas N. Greve]

Hippocampus is not part of the surface

On 2/24/2021 10:40 AM, Alberto Del Cerro Leon wrote:


External Email - Use Caution

Hello Freesurfers, I am doing an AAL atlas on freesurfer using 
mri_vol2surf and editing the labels manually. However when I was 
editing the labels in tksurfer the hippocampal field is quite bad. I 
tried to look the segmentation used by you in labels but I didn't find 
it. How could I segment the Hippocampus


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[Freesurfer] Hippocampal segmentation

[Alberto Del Cerro Leon]

External Email - Use Caution

Hello Freesurfers, I am doing an AAL atlas on freesurfer using mri_vol2surf
and editing the labels manually. However when I was editing the labels in
tksurfer the hippocampal field is quite bad. I tried to look the
segmentation used by you in labels but I didn't find it. How could I
segment the Hippocampus
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[Freesurfer] HIppocampal segmentation failure with FS 7.1.1

[Mukaino Takahiko]

External Email - Use Caution

Dear experts,

I'm currently using FS 7.1.1 and have already done hippocampal segmentation
with segmentHA_T2.sh command for over 100 subjects.
Most results are excellent but some segmentations are inaccurate, for
example, including neighbouring white and gray matter as CA1, even though
T2 images are clear enough and the pial surface results show recon-all has
successfully segmented hippocampus and parahippocampal gyrus.

I'm wondering if there is any way to fix them, but I couldn't find any
official writing to deal with this issue.

Is there any method to fix this?
Or the only way is to exclude these subjects?

Best regards,

Taka
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Re: [Freesurfer] hippocampal segmentation freesurfer 7.1.0

[Angela Favaro]

External Email - Use Caution

ok thank you!
Can you help me with my question about the longitudinal script?
My message is reported below


Dear Freesurfer experts,
I am trying to process a dataset with a longitudinal design.

However, after building the template, at the “recon-all -long” command
I got this error:





longmc Done

/Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri

\n cp -f --preserve=timestamps
/Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz
./brainmask_template4.mgz \n

cp: illegal option -- -

usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file

cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ...
target_directory

ERROR:

Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu
Oct 17 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64




recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23
03:47:31 CEST 2020




For more details, see the log file
/Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log







Thank you for any help!




Angela
"Hoopes, Andrew"  ha scritto:

> Hi Angela,
>
> This is a bit odd. It looks like
> segmentSubjectT1_autoEstimateAlveusML.app exists in the release tar,
> but doesn’t get installed by the pkg installer. Thanks for pointing
> this out, we’ll look into it. In the meantime, you can reinstall FS
> from the tar at
> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-darwin-macOS-7.1.0.tar.gz
> instead.
>
> Best
> Andrew
>
> From:  on behalf of Angela
> Favaro 
> Reply-To: FS Help 
> Date: Sunday, May 24, 2020 at 3:58 AM
> To: FS Help 
> Subject: [Freesurfer] hippocampal segmentation freesurfer 7.1.0
>
>
> External Email - Use Caution
> Hi all,
> I realized that in the MacOS version of freesurfer 7.1.0 there is a
> file (for hippocampal segmentation) that is lacking. How can I
> obtain it?
>
> The file is a Matlab script:
>
> segmentSubjectT1_autoEstimateAlveusML.app
>
>
> That should be in /Applications/freesurfer/7.1.0/bin/
>
> Thank you for any help!
>
> Angela



--
Angela Favaro
Professore di Psichiatria
Direttore UOC Psichiatria
Azienda Ospedale Università di Padova
Direttore Scuola di Specializzazione in Psichiatria
Dipartimento di Neuroscienze
Padova Neuroscience Center
Universita’ di Padova
Via Giustiniani, 2 - 35128 Padova, Italy


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Re: [Freesurfer] hippocampal segmentation freesurfer 7.1.0

[Hoopes, Andrew]

Hi Angela,

This is a bit odd. It looks like segmentSubjectT1_autoEstimateAlveusML.app 
exists in the release tar, but doesn’t get installed by the pkg installer. 
Thanks for pointing this out, we’ll look into it. In the meantime, you can 
reinstall FS from the tar at 
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-darwin-macOS-7.1.0.tar.gz
 instead.

Best
Andrew

From:  on behalf of Angela Favaro 

Reply-To: FS Help 
Date: Sunday, May 24, 2020 at 3:58 AM
To: FS Help 
Subject: [Freesurfer] hippocampal segmentation freesurfer 7.1.0


External Email - Use Caution
Hi all,
I realized that in the MacOS version of freesurfer 7.1.0 there is a file (for 
hippocampal segmentation) that is lacking. How can I obtain it?

The file is a Matlab script:

segmentSubjectT1_autoEstimateAlveusML.app


That should be in /Applications/freesurfer/7.1.0/bin/

Thank you for any help!

Angela
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[Freesurfer] hippocampal segmentation freesurfer 7.1.0

[Angela Favaro]

External Email - Use Caution

Hi all, 
I realized that in the MacOS version of freesurfer 7.1.0 there is a file (for 
hippocampal segmentation) that is lacking. How can I obtain it?

The file is a Matlab script:

segmentSubjectT1_autoEstimateAlveusML.app

That should be in /Applications/freesurfer/7.1.0/bin/

Thank you for any help!

Angela___
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[Freesurfer] Freesurfer hippocampal segmentation in patient with temporal lesion

[Linda Zhang]

External Email - Use Caution

Dear all,

I have a subject for whom I need to segment the right hippocampal and
amygdalar subfields.  However, they have a significant white matter
lesion and large ventricles in the right temporal lobe, such that
skull-stripping consistently cuts away the cortex in that region, and
subsequent aseg and surface reconstruction is inaccurate.

My question is, does the hippocampal subfield module (I'm using the
old segmentHA_T1.sh for consistency with our other subjects) use the
aseg froom recon-all as a basis for its segmentation?  If I just
manually correct the
hippocampus in the aseg and try running the subfields again, would it
work?  I've tried adjusting the skull-strip and no combination of
wsthresh and no-wgcsaatlas has helped.  I'm running FS6.0 on Ubuntu
18.

Thank you!

Regards,
Linda

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Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Iglesias Gonzalez, Eugenio]

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:  on behalf of Pradeep 

Reply-To: Freesurfer support list 
Date: Monday, 8 October 2018 at 18:51
To: Freesurfer support list 
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 
mailto:e.igles...@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: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Pradeep mailto:tprad...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 4 October 2018 at 19:21
To: Freesurfer support list 
mailto: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 
mailto:e.igles...@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: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Pradeep mailto:tprad...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 4 October 2018 at 19:12
To: Freesurfer support list 
mailto: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  -hippocampal-subfields-T2   
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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Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Pradeep]

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.igles...@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: * on behalf of Pradeep <
> tprad...@gmail.com>
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, 4 October 2018 at 19:21
> *To: *Freesurfer support list 
> *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.igles...@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: * on behalf of Pradeep <
> tprad...@gmail.com>
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, 4 October 2018 at 19:12
> *To: *Freesurfer support list 
> *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  -hippocampal-subfields-T2  additional scan>  
>
> 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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>
> ___
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Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Iglesias Gonzalez, Eugenio]

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:  on behalf of Pradeep 

Reply-To: Freesurfer support list 
Date: Thursday, 4 October 2018 at 19:21
To: Freesurfer support list 
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 
mailto:e.igles...@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: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Pradeep mailto:tprad...@gmail.com>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, 4 October 2018 at 19:12
To: Freesurfer support list 
mailto: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  -hippocampal-subfields-T2   
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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Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Pradeep]

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.igles...@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: * on behalf of Pradeep <
> tprad...@gmail.com>
> *Reply-To: *Freesurfer support list 
> *Date: *Thursday, 4 October 2018 at 19:12
> *To: *Freesurfer support list 
> *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  -hippocampal-subfields-T2  additional scan>  
>
> 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.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Iglesias Gonzalez, Eugenio]

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:  on behalf of Pradeep 

Reply-To: Freesurfer support list 
Date: Thursday, 4 October 2018 at 19:12
To: Freesurfer support list 
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  -hippocampal-subfields-T2   
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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[Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

[Pradeep]

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  -hippocampal-subfields-T2   

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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[Freesurfer] hippocampal segmentation development version question

[Maureen McHugo]

Hi,

I am interested in using the head/body/tail output from the hippocampal
subfield segmentation module. Is there a reference or description of what
landmarks were used to separate head/body and body/tail? Thanks!

Maureen
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Re: [Freesurfer] Hippocampal segmentation flips on the left side

[Hoopes, Andrew]

Hi Lauri,

This error is occurring because the libstdc++.so.6 library included with the 
linked matlab is older than the version shipped with centos7. While I think 
about the best way to resolve this, setting the following environment variable 
before running recon-all should clear everything up for now:

export LD_PRELOAD=/usr/lib64/libstdc++.so.6   # (with bash)

or

setenv LD_PRELOAD /usr/lib64/libstdc++.so.6   # (with tcsh)

best
Andrew


On Jan 11, 2018, at 2:43 PM, Hoopes, Andrew 
> wrote:

I think this is related to a matlab incompatibility. Can I see a copy of the 
log?
Andrew


On Jan 11, 2018, at 12:09 PM, Iglesias Gonzalez, Eugenio 
> wrote:

Dear Lauri,
Your problem is that GLIBCXX_3.4.15 was not found by kvlApplyTransform, so the 
left model was not successfully flipped to create the right model – which is 
why your right hippocampus appears flipped.
Andrew: any ideas on how to fix this?
Cheers,
/Eugenio
PS: the dev version does not depend on this executable anymore

--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 10/01/2018, 21:29, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Iglesias Gonzalez, Eugenio"  wrote:

  Dear Lauri,
  Would you mind sending me the log of the subfield segmentation?
  Cheers,
  /Eugenio

  --
  Juan Eugenio Iglesias
  ERC Senior Research Fellow
  Translational Imaging Group
  University College London
  http://www.jeiglesias.com
  http://cmictig.cs.ucl.ac.uk/


  On 08/01/2018, 22:04, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Tuominen, Lauri Johannes"  wrote:

  Dear Freesurfers,
  When I run freesurfer 6.0 recon-all -hippocampal-subfields-T1 command to 
segment an MNI152 template, the resulting segmentation of left hippocampus got 
flipped in left-right dimension. Otherwise the right hippocampus and other 
subcortical segmentations in the aseg-file look fine. I encountered a similar 
problem when I tried to segment a T1 acquired at 7T. I run the command both 
locally and then on launchpad. Would you know how to fix this?

  Thanks so much for your advice!
  Lauri Tuominen
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is
  addressed. If you believe this e-mail was sent to you in error and the 
e-mail
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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] Hippocampal segmentation flips on the left side

[Hoopes, Andrew]

I think this is related to a matlab incompatibility. Can I see a copy of the 
log?
Andrew


> On Jan 11, 2018, at 12:09 PM, Iglesias Gonzalez, Eugenio 
>  wrote:
> 
> Dear Lauri,
> Your problem is that GLIBCXX_3.4.15 was not found by kvlApplyTransform, so 
> the left model was not successfully flipped to create the right model – which 
> is why your right hippocampus appears flipped. 
> Andrew: any ideas on how to fix this?
> Cheers,
> /Eugenio
> PS: the dev version does not depend on this executable anymore 
> 
> -- 
> Juan Eugenio Iglesias
> ERC Senior Research Fellow
> Translational Imaging Group
> University College London
> http://www.jeiglesias.com
> http://cmictig.cs.ucl.ac.uk/
> 
> 
> On 10/01/2018, 21:29, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Iglesias Gonzalez, Eugenio"  of e.igles...@ucl.ac.uk> wrote:
> 
>Dear Lauri,
>Would you mind sending me the log of the subfield segmentation?
>Cheers,
>/Eugenio
> 
>-- 
>Juan Eugenio Iglesias
>ERC Senior Research Fellow
>Translational Imaging Group
>University College London
>http://www.jeiglesias.com
>http://cmictig.cs.ucl.ac.uk/
> 
> 
>On 08/01/2018, 22:04, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Tuominen, Lauri Johannes"  of ltuomi...@mgh.harvard.edu> wrote:
> 
>Dear Freesurfers,
>When I run freesurfer 6.0 recon-all -hippocampal-subfields-T1 command 
> to segment an MNI152 template, the resulting segmentation of left hippocampus 
> got flipped in left-right dimension. Otherwise the right hippocampus and 
> other subcortical segmentations in the aseg-file look fine. I encountered a 
> similar problem when I tried to segment a T1 acquired at 7T. I run the 
> command both locally and then on launchpad. Would you know how to fix this? 
> 
>Thanks so much for your advice!  
>Lauri Tuominen
>___
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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.
> 
> 
> 
> 
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> 
> 


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Re: [Freesurfer] Hippocampal segmentation flips on the left side

[Iglesias Gonzalez, Eugenio]

Dear Lauri,
Your problem is that GLIBCXX_3.4.15 was not found by kvlApplyTransform, so the 
left model was not successfully flipped to create the right model – which is 
why your right hippocampus appears flipped. 
Andrew: any ideas on how to fix this?
Cheers,
/Eugenio
PS: the dev version does not depend on this executable anymore 

-- 
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
 

On 10/01/2018, 21:29, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Iglesias Gonzalez, Eugenio"  wrote:

Dear Lauri,
Would you mind sending me the log of the subfield segmentation?
Cheers,
/Eugenio

-- 
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
 

On 08/01/2018, 22:04, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Tuominen, Lauri Johannes"  wrote:

Dear Freesurfers,
When I run freesurfer 6.0 recon-all -hippocampal-subfields-T1 command 
to segment an MNI152 template, the resulting segmentation of left hippocampus 
got flipped in left-right dimension. Otherwise the right hippocampus and other 
subcortical segmentations in the aseg-file look fine. I encountered a similar 
problem when I tried to segment a T1 acquired at 7T. I run the command both 
locally and then on launchpad. Would you know how to fix this? 

Thanks so much for your advice!  
Lauri Tuominen
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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.




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Re: [Freesurfer] Hippocampal segmentation flips on the left side

[Iglesias Gonzalez, Eugenio]

Dear Lauri,
Would you mind sending me the log of the subfield segmentation?
Cheers,
/Eugenio

-- 
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
 

On 08/01/2018, 22:04, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Tuominen, Lauri Johannes"  wrote:

Dear Freesurfers,
When I run freesurfer 6.0 recon-all -hippocampal-subfields-T1 command to 
segment an MNI152 template, the resulting segmentation of left hippocampus got 
flipped in left-right dimension. Otherwise the right hippocampus and other 
subcortical segmentations in the aseg-file look fine. I encountered a similar 
problem when I tried to segment a T1 acquired at 7T. I run the command both 
locally and then on launchpad. Would you know how to fix this? 

Thanks so much for your advice!  
Lauri Tuominen
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[Freesurfer] Hippocampal segmentation flips on the left side

[Tuominen, Lauri Johannes]

Dear Freesurfers,
When I run freesurfer 6.0 recon-all -hippocampal-subfields-T1 command to 
segment an MNI152 template, the resulting segmentation of left hippocampus got 
flipped in left-right dimension. Otherwise the right hippocampus and other 
subcortical segmentations in the aseg-file look fine. I encountered a similar 
problem when I tried to segment a T1 acquired at 7T. I run the command both 
locally and then on launchpad. Would you know how to fix this? 

Thanks so much for your advice!  
Lauri Tuominen
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Re: [Freesurfer] Hippocampal segmentation flips on the left side

[Iglesias Gonzalez, Eugenio]

Very weird! Can you please send us the log files?
Cheers,
/Eugenio

-- 
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/
 

On 21/12/2017, 17:51, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Lauri Tuominen"  wrote:

Dear Freesurfers,
When I run the freesurfer 6.0 recon-all -hippocampal-subfields-T1 command 
to segment a MNI152 template, the resulting segmentation of the left 
hippocampus is flipped in right-left dimension. Otherwise the right hippocampus 
and the subcortical segmentations in the aseg-file look fine. I encountered a 
similar problem when I segmented a 7T scan. Would you know what might cause 
this how to fix it? Thanks so much for your advice!  

Lauri Tuominen 





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Re: [Freesurfer] Hippocampal Segmentation

[Iglesias Gonzalez, Eugenio]

Yes, it's the tail.
All subfield are segmented jointly.
Cheers
E

Sent from my phone, please excuse brevity and typos


From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Jessica Sevick 
<jessica.sevi...@ucalgary.ca>
Sent: Sunday, February 26, 2017 7:54:28 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Segmentation

Hi Eugenio,

Thanks for getting back to me and yes it is version 5.1-5.3. I will speak to my 
IT department about upgrading to version 6.0, but can you let me know about the 
processing details for the older version in the meantime? We have already 
processed a group of subjects and my Investigator would like to know.

Thanks,
Jessica

Sent from my iPhone

On Feb 24, 2017, at 9:51 PM, Iglesias Gonzalez, Eugenio 
<e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> wrote:

Hi Jessica,
I believe that those are the old labels. What version of FreeSurfer are you 
using? 5.1 - 5.3? If so, you should upgrade to 6.0.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 24 Feb 2017, at 19:18, Jessica Sevick 
<jessica.sevi...@ucalgary.ca<mailto:jessica.sevi...@ucalgary.ca>> wrote:

Hello FreeSurfer Team ,

I was wondering if you could explain to me what the “Left-Hippocampus” and 
“Right-Hippocampus” labels in the subfield segmentation are? Are they the tail 
of the hippocampi? Or everything that is not assigned to one of the other seven 
labels?

Additionally I am wondering how the hippocampal subfields are ordered in terms 
of their determination? Is it a particular order or is it randomized?

Thanks,

Jessica Sevick
MRI Research Assistant
Seaman Family MR Research Centre
T: 403.944.8652
C: 587.576.
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Re: [Freesurfer] Hippocampal Segmentation

[Jessica Sevick]

Hi Eugenio,

Thanks for getting back to me and yes it is version 5.1-5.3. I will speak to my 
IT department about upgrading to version 6.0, but can you let me know about the 
processing details for the older version in the meantime? We have already 
processed a group of subjects and my Investigator would like to know.

Thanks,
Jessica

Sent from my iPhone

On Feb 24, 2017, at 9:51 PM, Iglesias Gonzalez, Eugenio 
> wrote:

Hi Jessica,
I believe that those are the old labels. What version of FreeSurfer are you 
using? 5.1 - 5.3? If so, you should upgrade to 6.0.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 24 Feb 2017, at 19:18, Jessica Sevick 
> wrote:

Hello FreeSurfer Team ,

I was wondering if you could explain to me what the “Left-Hippocampus” and 
“Right-Hippocampus” labels in the subfield segmentation are? Are they the tail 
of the hippocampi? Or everything that is not assigned to one of the other seven 
labels?

Additionally I am wondering how the hippocampal subfields are ordered in terms 
of their determination? Is it a particular order or is it randomized?

Thanks,

Jessica Sevick
MRI Research Assistant
Seaman Family MR Research Centre
T: 403.944.8652
C: 587.576.
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dispose of the e-mail.

Re: [Freesurfer] Hippocampal Segmentation

[Iglesias Gonzalez, Eugenio]

Hi Jessica,
I believe that those are the old labels. What version of FreeSurfer are you 
using? 5.1 - 5.3? If so, you should upgrade to 6.0.
Cheers,
/Eugenio

Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 24 Feb 2017, at 19:18, Jessica Sevick 
> wrote:

Hello FreeSurfer Team ,

I was wondering if you could explain to me what the “Left-Hippocampus” and 
“Right-Hippocampus” labels in the subfield segmentation are? Are they the tail 
of the hippocampi? Or everything that is not assigned to one of the other seven 
labels?

Additionally I am wondering how the hippocampal subfields are ordered in terms 
of their determination? Is it a particular order or is it randomized?

Thanks,

Jessica Sevick
MRI Research Assistant
Seaman Family MR Research Centre
T: 403.944.8652
C: 587.576.
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[Freesurfer] Hippocampal Segmentation

[Jessica Sevick]

Hello FreeSurfer Team ,

I was wondering if you could explain to me what the “Left-Hippocampus” and 
“Right-Hippocampus” labels in the subfield segmentation are? Are they the tail 
of the hippocampi? Or everything that is not assigned to one of the other seven 
labels?

Additionally I am wondering how the hippocampal subfields are ordered in terms 
of their determination? Is it a particular order or is it randomized?

Thanks,

Jessica Sevick
MRI Research Assistant
Seaman Family MR Research Centre
T: 403.944.8652
C: 587.576.
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[Freesurfer] Hippocampal segmentation

[Rowa Aljondi]

Hello Freesurfer Developers,

I'm willing to use the new released version from Freesurfer (6.7.0) to
measure the hippocampal volumes.

Is that able to provide me the volumes of the anterior (hippocampal head)
and posterior (hippocampal tail) parts of the Hippocampus and segmented
these parts separately?

Thanks,
Rowa

-- 
Rowa Aljondi
PhD Candidate
Faculty of Medicine, Dentistry and Health Sciences
The University of Melbourne
M: +61 416565756
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Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

[Eugenio Iglesias]

Hi Alexandra,
Thanks for your email. We have identified the problem an it will be fixed for 
the next build of our development version. 
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: Alexandra De Araujo deara...@uoregon.edu
To: Z K zkauf...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu
Cc: e iglesias e.igles...@bcbl.eu
Sent: Thursday, August 20, 2015 2:29:16 PM
Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - 
missing files?

Hi Zeke and Eugenio,

Thanks for your quick answers.
I removed the maverick distribution and installed the lion one pointed 
by Zeke.

Running the segmentation, I get the same message as before:

/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: 
line 35: 
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
 
No such file or directory

Here is were the symbolic link is pointing:

segmentSubjectT1_autoEstimateAlveusML - 
../../../../../.git/annex/objects/gj/5f/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a

It is pointing to a directory which is outside of freesurfer's.

-Alexandra

On 8/20/15 9:38 AM, Z K wrote:
 Hi Alexandra,

 The mavericks build that you downloaded was an experimental build that 
 hasnt been updated for awhile. Please remove that version and download 
 and install the lion version instead. That version is more up-to-date. 
 Sorry for the confusion.

 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz
  


 -Zeke





 On 08/20/2015 04:42 AM, Eugenio Iglesias wrote:
 Hi Alexandra,
 that's weird. Where is the symbolic link pointing?
 Cheers,
 Eugenio

 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu

 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


 - Original Message -
 From: Alexandra De Araujo deara...@uoregon.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Thursday, August 20, 2015 1:45:02 AM
 Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 
 Beta -missing files?


 Hello,

 I have installed FreeSurfer v6 
 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new 
 hippocampal segmentation modules. I have installed it in my folder 
 Application. Now, when I tried to run a hippocampal segmentation, I 
 get the following error:

 /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: 
 line 35: 
 /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
  
 No such file or directory

 Looking into 
 bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find 
 segmentSubjectT1_autoEstimateAlveusML that looks like to be a 
 symbolic link pointing to no existing file. I have similar problems 
 when I try to run a T1T2 or a T2.

 Can someone help me with this issue?

 Thanks,

 Alex
 --
 Alexandra De Araujo
 Adjunct research assistant
 Brain and memory lab
 University of Oregon
 (+1) 541-346-6733
 --

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 the e-mail
 contains patient information, please contact the Partners Compliance 
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 dispose of the e-mail.
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Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

[Eugenio Iglesias]

Hi Alexandra,
that's weird. Where is the symbolic link pointing?
Cheers,
Eugenio

Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


- Original Message -
From: Alexandra De Araujo deara...@uoregon.edu
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thursday, August 20, 2015 1:45:02 AM
Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta -
missing files?


Hello, 

I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in 
order to try the new hippocampal segmentation modules. I have installed it in 
my folder Application. Now, when I tried to run a hippocampal segmentation, I 
get the following error: 

/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 
35: 
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
 No such file or directory 

Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I 
find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic 
link pointing to no existing file. I have similar problems when I try to run a 
T1T2 or a T2. 

Can someone help me with this issue? 

Thanks, 

Alex 
-- 
Alexandra De Araujo 
Adjunct research assistant 
Brain and memory lab 
University of Oregon 
(+1) 541-346-6733 
-- 

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Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

[Alexandra De Araujo]

Hi Zeke and Eugenio,

Thanks for your quick answers.
I removed the maverick distribution and installed the lion one pointed 
by Zeke.

Running the segmentation, I get the same message as before:

/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: 
line 35: 
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
 
No such file or directory

Here is were the symbolic link is pointing:

segmentSubjectT1_autoEstimateAlveusML - 
../../../../../.git/annex/objects/gj/5f/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a

It is pointing to a directory which is outside of freesurfer's.

-Alexandra

On 8/20/15 9:38 AM, Z K wrote:
 Hi Alexandra,

 The mavericks build that you downloaded was an experimental build that 
 hasnt been updated for awhile. Please remove that version and download 
 and install the lion version instead. That version is more up-to-date. 
 Sorry for the confusion.

 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz
  


 -Zeke





 On 08/20/2015 04:42 AM, Eugenio Iglesias wrote:
 Hi Alexandra,
 that's weird. Where is the symbolic link pointing?
 Cheers,
 Eugenio

 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu

 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


 - Original Message -
 From: Alexandra De Araujo deara...@uoregon.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Thursday, August 20, 2015 1:45:02 AM
 Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 
 Beta -missing files?


 Hello,

 I have installed FreeSurfer v6 
 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new 
 hippocampal segmentation modules. I have installed it in my folder 
 Application. Now, when I tried to run a hippocampal segmentation, I 
 get the following error:

 /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: 
 line 35: 
 /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
  
 No such file or directory

 Looking into 
 bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find 
 segmentSubjectT1_autoEstimateAlveusML that looks like to be a 
 symbolic link pointing to no existing file. I have similar problems 
 when I try to run a T1T2 or a T2.

 Can someone help me with this issue?

 Thanks,

 Alex
 --
 Alexandra De Araujo
 Adjunct research assistant
 Brain and memory lab
 University of Oregon
 (+1) 541-346-6733
 --

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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 
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 but does not contain patient information, please contact the sender 
 and properly
 dispose of the e-mail.
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Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

[zkaufman]

Ah, I see. This issue must have arisen due to some changes I made in the
freesurfer git repository.

Eugenio, I should have this resolved by tomorrows build.

Alexandra, thanks for pointing this out. It should be fixed in tomorrows
daily build. Ill send you an email to confirm.

-Zeke


 Hi Zeke and Eugenio,

 Thanks for your quick answers.
 I removed the maverick distribution and installed the lion one pointed
 by Zeke.

 Running the segmentation, I get the same message as before:

 /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 35:
 /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
 No such file or directory

 Here is were the symbolic link is pointing:

 segmentSubjectT1_autoEstimateAlveusML -
 ../../../../../.git/annex/objects/gj/5f/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a/SHA256-s5032153--a43ec180ffefc9c94e74bc34d78c108b37736f8b11ea6cacfbd982abdd90dd0a

 It is pointing to a directory which is outside of freesurfer's.

 -Alexandra

 On 8/20/15 9:38 AM, Z K wrote:
 Hi Alexandra,

 The mavericks build that you downloaded was an experimental build that
 hasnt been updated for awhile. Please remove that version and download
 and install the lion version instead. That version is more up-to-date.
 Sorry for the confusion.

 ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz


 -Zeke





 On 08/20/2015 04:42 AM, Eugenio Iglesias wrote:
 Hi Alexandra,
 that's weird. Where is the symbolic link pointing?
 Cheers,
 Eugenio

 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu

 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


 - Original Message -
 From: Alexandra De Araujo deara...@uoregon.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Thursday, August 20, 2015 1:45:02 AM
 Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6
 Beta -missing files?


 Hello,

 I have installed FreeSurfer v6
 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new
 hippocampal segmentation modules. I have installed it in my folder
 Application. Now, when I tried to run a hippocampal segmentation, I
 get the following error:

 /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 35:
 /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
 No such file or directory

 Looking into
 bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find
 segmentSubjectT1_autoEstimateAlveusML that looks like to be a
 symbolic link pointing to no existing file. I have similar problems
 when I try to run a T1T2 or a T2.

 Can someone help me with this issue?

 Thanks,

 Alex
 --
 Alexandra De Araujo
 Adjunct research assistant
 Brain and memory lab
 University of Oregon
 (+1) 541-346-6733
 --

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Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

[Z K]

Hi Alexandra,

The mavericks build that you downloaded was an experimental build that 
hasnt been updated for awhile. Please remove that version and download 
and install the lion version instead. That version is more up-to-date. 
Sorry for the confusion.

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-Darwin-lion-dev.tar.gz

-Zeke





On 08/20/2015 04:42 AM, Eugenio Iglesias wrote:
 Hi Alexandra,
 that's weird. Where is the symbolic link pointing?
 Cheers,
 Eugenio

 Juan Eugenio Iglesias
 Postdoctoral researcher BCBL
 www.jeiglesias.com
 www.bcbl.eu

 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer


 - Original Message -
 From: Alexandra De Araujo deara...@uoregon.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Thursday, August 20, 2015 1:45:02 AM
 Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta -  
 missing files?


 Hello,

 I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in 
 order to try the new hippocampal segmentation modules. I have installed it in 
 my folder Application. Now, when I tried to run a hippocampal segmentation, I 
 get the following error:

 /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: 
 line 35: 
 /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
  No such file or directory

 Looking into bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I 
 find segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic 
 link pointing to no existing file. I have similar problems when I try to run 
 a T1T2 or a T2.

 Can someone help me with this issue?

 Thanks,

 Alex
 --
 Alexandra De Araujo
 Adjunct research assistant
 Brain and memory lab
 University of Oregon
 (+1) 541-346-6733
 --

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Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

[Alexandra De Araujo]

Hello,

I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) 
in order to try the new hippocampal segmentation modules. I have 
installed it in my folder Application. Now, when I tried to run a 
hippocampal segmentation, I get the following error:


/Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: 
line 35: 
/Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML: 
No such file or directory


Looking into 
bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/, I find 
segmentSubjectT1_autoEstimateAlveusML that looks like to be a symbolic 
link pointing to no existing file. I have similar problems when I try to 
run a T1T2 or a T2.


Can someone help me with this issue?

Thanks,

Alex
--
Alexandra De Araujo
Adjunct research assistant
Brain and memory lab
University of Oregon
(+1) 541-346-6733
--
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Re: [Freesurfer] hippocampal segmentation converting mgz to nii

[Koen Van Leemput]

Hi Lorenzo,

The correct way to calculate the expected (not an integer value) number of
voxels belonging to a subfield is by summing ( intensity / 255 ) across all
voxels. Not sure where things go wrong: the integer values you report are a
bit suspicious, or perhaps some rescaling of image intensities is done
during the conversion. You should also be able to convert from .mgz to .nii
using the command kvlConvert

Cheers,

Koen



On Wed, Nov 28, 2012 at 8:21 AM, lorenzo pasquini lollopasqu...@yahoo.itwrote:

 Dear freesurfer users,

 I have used freesurfer to segment hippocampal subfields. Then I used
 freeview to convert the derived .mgz files in .nii files for further
 analysis. I estimated the hippocampal subfields volumes with the command:

 kvlQuantifyPosteriorProbabilityImages $ FREESURFER_HOME/ data/ GEMS/
 compressionLookupTable.txt  posterior_right_*
 posterior_Right-Hippocampus.mgz

 I have calculated the number of voxels in the converted .nii files using
 SPM and realized that they do not fit the estimated volumes through
 freesurfer
 Example

 for CA2-2
 estimated voxel number though freesurfer:   6851
 voxels found in .nii file: 15812

 Did somebody had similar problems? Do you have any suggestion? Are there
 any incompatibilities between SPM and freesurfer? I did not find any
 apparent error in my counting script.
 Thank you very much and regards,

 Lorenzo Pasquini

 *Can. Ph. D., Medical Life Science and Technology (**Technische
 Universität Muenchen)
 Neuroimaging Lab, Neuroradiology
 Klinikum r. d. Isar (Technische Universität)*
 81675 München
 Tel.: 0049 (0) 89 4140-7666

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 e-mail
 contains patient information, please contact the Partners Compliance
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[Freesurfer] hippocampal segmentation converting mgz to nii

[lorenzo pasquini]

Dear freesurfer users,

I have used freesurfer to segment hippocampal subfields. Then I used freeview 
to convert the derived .mgz files in .nii files for further analysis. I 
estimated the hippocampal subfields volumes with the command:

kvlQuantifyPosteriorProbabilityImages $ FREESURFER_HOME/ data/ GEMS/ 
compressionLookupTable.txt  posterior_right_* posterior_Right-Hippocampus.mgz

I have calculated the number of voxels in the converted .nii files using SPM 
and realized that they do not fit the estimated volumes through freesurfer
Example

for CA2-2
estimated voxel number though freesurfer:   6851
voxels found in .nii file: 15812

Did somebody had similar problems? Do you have any suggestion? Are there any 
incompatibilities between SPM and freesurfer? I did not find any apparent error 
in my counting script.
Thank you very much and regards,

Lorenzo Pasquini

Can. Ph. D., Medical Life Science and Technology (Technische Universität 
Muenchen)

Neuroimaging Lab, Neuroradiology

Klinikum r. d. Isar (Technische Universität)

81675
 München

Tel.: 0049 (0) 89 4140-7666
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Re: [Freesurfer] hippocampal segmentation

[Bruce Fischl]

Hi Hugh,

no attachments came through. Do you mean the segmentation of the 
hippocampus in the aseg? What version are you running?

cheers
Bruce

On Wed, 10 Oct 2012, Hugh Pemberton wrote:

 Dear freesurfer crew,
 I'm having a few issues with segmentation around the hippocampus, I have
 included a few screenshots of main and aux vol where the hippocampus has
 been excluded even with the addition of control points. Have you got any
 tips for rectifying this? It's happened a fair few times with my subjects.
 
 Thanks very much in advance and all the best,
 Hugh
 

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[Freesurfer] hippocampal segmentation

[Hugh Pemberton]

Dear freesurfer crew,

I'm having a few issues with segmentation around the hippocampus, I have
included a few screenshots of main and aux vol where the hippocampus has
been excluded even with the addition of control points. Have you got any
tips for rectifying this? It's happened a fair few times with my subjects.

Thanks very much in advance and all the best,
Hugh
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Re: [Freesurfer] Hippocampal segmentation doubts

[Gabriel Gonzalez Escamilla]

Thank you so much for your answer Koen,I understand, but now I'm having some trouble when running the command on one subject, hope you can help me.I have tried to perform the hippocampal subfields segmentation by running:recon-all -s MySubject -hippo-subfields and also:kvlSegmentHippocampalSubfields.sh MySubject left /root/trabajo/freesurfer/subjects /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults 
But I always get the following error:maximalDeformation: 75.1793Transforming meshDone transforming meshRasterizing Levenberg-Marquardt...numberOfEntries: 24131/root/trabajo/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 23175 Segmentation fault      kvlSegmentWithoutGUI configurationFileDeformableRegistration.txtfailed to do kvlSegmentWithoutGUI configurationFileDeformableRegistration.txtLinux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s MySubject exited with ERRORS at Tue Jul  3 15:54:39 CEST 2012For more details, see the log file /root/trabajo/freesurfer/subjects/MySubject/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportingThe recon-all.log says:##@# Hippocampal Subfields processing Tue Jul  3 15:48:33 CEST 2012 mkdir -p /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults kvlSegmentHippocampalSubfields.sh MySubject left /root/trabajo/freesurfer/subjects /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s MySubject exited with ERRORS at Tue Jul  3 15:54:39 CEST 2012To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting This error occurres only on this subject and for the left hemisphere, not like this for the right hemisphere, which ends perfectly when running the second command. I'm sending you the configurationFileDeformation for the left hemisphere, in case it may help. Any help will be so appreciatedBest Regards,GabrielEl 04/07/12, Koen Van Leemput  k...@nmr.mgh.harvard.edu escribió:Hi Gabriel,1. Using pre-processed data obtained with an older version ofFreeSurfer should be OK, as long as you remember that the obtainedresults might/will be different from the ones you'd get if you had runthe whole analysis from scratch.2. The generic label hippocampus is used to denote the tail of thehippocampus, where no attempt is made to further subdivide between thedifferent subfields. This is admittedly not a great naming convention- sorry for the confusion.3. You should not do any correction on the obtained volumes: partialvolume here merely means the effect of voxels containing a mix ofdifferent subfields simultaneously. The non-partial volume resultshere only indicate that this effect is not explicitly modeled when youcall the hippocampal subfield segmentation routine with its defaultsettings.Hope this helps,KoenOn Thu, Jun 28, 2012 at 5:29 AM, Gabriel Gonzalez Escamillaggon...@upo.es wrote: Dear Freesurfer experts I'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts... If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields? I'm guessing not, but I wanna be sure. Because, as I've looked the -hippo-subfields recon seems to not modify the whole brain segmentation, am I right? second, when I apply the kvlQuantifyHippocampalSubfieldSegmentations.sh I do obtain two txt files containing such segmentation of the 8 hippocampal subfields, but at the beggining it appear a field for the left and right hippocampus, but I don't know exactly what does this column represents, because if I sum the other colums the subfield sums are so much bigger than the hippocampus field; i.e. volume_in_number_of_voxels   Left-Hippocampus   left_presubiculum   left_CA1 left_CA2-3   left_fimbria   left_subiculum   left_CA4-DG left_hippocampal_fissure c_12_hipo    3789.97    3215.08    2654.65    7705.2    336.857    4841.63 4158.49    356.626 and last. Do I need to somehow do some partial volume corrections to this output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw on the page that the output is 0.5*0.5*0.5mm^3. Many thanks in advanced, Gabriel -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ 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 

Re: [Freesurfer] Hippocampal segmentation doubts

[Koen Van Leemput]

Hi Gabriel,

1. Using pre-processed data obtained with an older version of
FreeSurfer should be OK, as long as you remember that the obtained
results might/will be different from the ones you'd get if you had run
the whole analysis from scratch.

2. The generic label hippocampus is used to denote the tail of the
hippocampus, where no attempt is made to further subdivide between the
different subfields. This is admittedly not a great naming convention
- sorry for the confusion.

3. You should not do any correction on the obtained volumes: partial
volume here merely means the effect of voxels containing a mix of
different subfields simultaneously. The non-partial volume results
here only indicate that this effect is not explicitly modeled when you
call the hippocampal subfield segmentation routine with its default
settings.

Hope this helps,

Koen


On Thu, Jun 28, 2012 at 5:29 AM, Gabriel Gonzalez Escamilla
ggon...@upo.es wrote:

 Dear Freesurfer experts

 I'm starting to deal with the FS v5.1 hippocampal subfields segmentation,
 and I have a couple doubts...

 If I have my subjects segmented from an older FS version, Would be any
 problem when running the -hippo-subfields?
 I'm guessing not, but I wanna be sure. Because, as I've looked the
 -hippo-subfields recon seems to not modify the whole brain segmentation, am
 I right?

 second, when I apply the kvlQuantifyHippocampalSubfieldSegmentations.sh I
 do obtain two txt files containing such segmentation of the 8 hippocampal
 subfields, but at the beggining it appear a field for the left and right
 hippocampus, but I don't know exactly what does this column represents,
 because if I sum the other colums the subfield sums are so much bigger than
 the hippocampus field; i.e.
 volume_in_number_of_voxels   Left-Hippocampus   left_presubiculum   left_CA1
 left_CA2-3   left_fimbria   left_subiculum   left_CA4-DG
 left_hippocampal_fissure
 c_12_hipo3789.973215.082654.657705.2336.8574841.63
 4158.49356.626


 and last. Do I need to somehow do some partial volume corrections to this
 output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw
 on the page that the output is 0.5*0.5*0.5mm^3.


 Many thanks in advanced,
 Gabriel





 --
 --
 PhD. student Gabriel González-Escamilla
 Laboratory of Functional Neuroscience
 Department of Physiology, Anatomy, and Cell Biology
 University Pablo de Olavide
 Ctra. de Utrera, Km.1
 41013 - Seville
 - Spain -

 Email: ggon...@upo.es
 http://www.upo.es/neuroaging/es/

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[Freesurfer] Hippocampal segmentation: version needed

[lorenzo pasquini]

Dear Freesurfer experts,

I used freesurfer v4.3.0 on anatomical data (T1).
I am trying to segment hippocampal subfields with the following command: 

recon-all -s subjname -hippo-subfields
unfortunately I get the following error:
ERROR: Flag -hippo-subfields unrecognized
I have already the files aseg.mgz, nu.mgz, talairach.xfm

Does this error occur because I am using an old Freesurfer version?
If this is the case which is the optimal version to run hippocampal 
segmentation? Should I process my whole data again with the newest version? 
Unfortunately I did not find any convincing answer from the posting list where 
I had the impression that version 5.1 is facing some problems regarding 
hippocampal segmentation. 

Thank you very much and kind regards,

Lorenzo Pasquini___
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Re: [Freesurfer] Hippocampal segmentation: version needed

[Koen Van Leemput]

Hi Lorenzo,

The hippocampal subfield segmentation routines are only available from
FreeSurfer 5.1, so you'll need that version to run the code.

If all your data is already pre-processed with an older version of
FreeSurfer, you might be able to simply run the hippocampal subfield
segmentation routines only using 5.1, although your version (4.3.0)
sounds very old (and therefore might not produce the correct output
files needed by the hippocampal subfield stuff). The safest is to
re-analyze everything from scratch using 5.1.

Hope this helps,

Koen


On Wed, Jul 4, 2012 at 10:43 AM, lorenzo pasquini
lollopasqu...@yahoo.it wrote:
 Dear Freesurfer experts,

 I used freesurfer v4.3.0 on anatomical data (T1).
 I am trying to segment hippocampal subfields with the following command:

 recon-all -s subjname -hippo-subfields
 unfortunately I get the following error:
 ERROR: Flag -hippo-subfields unrecognized
 I have already the files aseg.mgz, nu.mgz, talairach.xfm

 Does this error occur because I am using an old Freesurfer version?
 If this is the case which is the optimal version to run hippocampal
 segmentation? Should I process my whole data again with the newest version?
 Unfortunately I did not find any convincing answer from the posting list
 where I had the impression that version 5.1 is facing some problems
 regarding hippocampal segmentation.
 Thank you very much and kind regards,

 Lorenzo Pasquini


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[Freesurfer] Hippocampal segmentation doubts

[Gabriel Gonzalez Escamilla]

Dear Freesurfer expertsI'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts...If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields?I'm guessing not, but I wanna be sure. Because, as I've looked the -hippo-subfields recon seems to not modify the whole brain segmentation, am I right?second, when I apply the kvlQuantifyHippocampalSubfieldSegmentations.sh I do obtain two txt files containing such segmentation of the 8 hippocampal subfields, but at the beggining it appear a field for the left and right hippocampus, but I don't know exactly what does this column represents, because if I sum the other colums the subfield sums are so much bigger than the hippocampus field; i.e.volume_in_number_of_voxels   Left-Hippocampus   left_presubiculum   left_CA1   left_CA2-3   left_fimbria   left_subiculum   left_CA4-DG   left_hippocampal_fissurec_12_hipo    3789.97    3215.08    2654.65    7705.2    336.857    4841.63    4158.49    356.626and last. Do I need to somehow do some partial volume corrections to this output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw on the page that the output is 0.5*0.5*0.5mm^3. Many thanks in advanced,Gabriel
-- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/
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[Freesurfer] Hippocampal segmentation

[Gabriel Gonzalez Escamilla]

Dear FreesurfersI'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts...If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields?I'm guessing not, but I wanna be sure. Because, as I've looked the -hippo-subfields recon seems to not modify the whole brain segmentation, am I right?second, when I apply the kvlQuantifyHippocampalSubfieldSegmentations.sh I do obtain two txt files containing such segmentation of the 8 hippocampal subfields, but at the beggining it appear a field for the left and right hippocampus, but I don't know exactly what does this column represents, because if I sum the other colums the subfield sums are so much bigger than the hippocampus field; i.e.volume_in_number_of_voxels   Left-Hippocampus   left_presubiculum   left_CA1   left_CA2-3   left_fimbria   left_subiculum   left_CA4-DG   left_hippocampal_fissurec_12_hipo    3789.97    3215.08    2654.65    7705.2    336.857    4841.63    4158.49    356.626and last. Do I need to somehow do some partial volume corrections to this output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw on the page that the output is 0.5*0.5*0.5mm^3. Many thanks in advanced,Gabriel
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[Freesurfer] hippocampal segmentation

[Rashmi Singh]

Hello,
 I converted the aseg. mgz files to nii format and created a hippcampal mask 
with 3dcalc.
Using AFNI I opened the hippocampal mask as overlay on the brainmask .nii image 
 as underlay.  For some subjects the hippocampus is not at the correct position.
Please advise.
Thanks,
Rashmi.




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Re: [Freesurfer] hippocampal segmentation

[Bruce Fischl]

Hi Rashmi

does it look correct in our visualization tools? If so, you'll need to talk 
to the AFNI folks.


cheers
Bruce


On Wed, 4 Apr 2012, Rashmi Singh wrote:


Hello,
 I converted the aseg. mgz files to nii format and created a hippcampal mask
with 3dcalc.
Using AFNI I opened the hippocampal mask as overlay on the brainmask .nii
image  as underlay.  For some subjects the hippocampus is not at the correct
position.
Please advise.
Thanks,
Rashmi.




This document may contain information covered under the Privacy Act, 5 USC
552(a), and/or the Health Insurance Portability and Accountability Act (PL
104-191) and its various implementing regulations and must be protected in
accordance with those provisions. Healthcare information is personal and
sensitive and must be treated accordingly. If this correspondence contains
healthcare information it is being provided to you after appropriate
authorization from the patient or under circumstances that don't require
patient authorization. You, the recipient, are obligated to maintain it in a
safe, secure and confidential manner. Redisclosure without additional
patient consent or as permitted by law is prohibited. Unauthorized
redisclosure or failure to maintain confidentiality subjects you to
application of appropriate sanction. If you have received this
correspondence in error, please notify the sender at once and destroy any
copies you have made.

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