Is there a way of making a volume like aparc+aseg with the defect labels so that cortical region where the defects are show up red?
Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.auhttp://www.mcri.edu.au/ E chris.adamson@mcri.edu.au T 03 9936 6780
______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________
have you tried mri_surf2vol? On Fri, 24 Jan 2014, Chris Adamson wrote:
Is there a way of making a volume like aparc+aseg with the defect labels so that cortical region where the defects are show up red?
Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children’s Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au
E chris.adamson@mcri.edu.au T 03 9936 6780
This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________
Dear experts, it seems that after the new apple update "Maverick" Matlab can not get access to Freesurfer. I already added the "recommended lines" from the homepage to matlab startup-file, but it is still not working. Im trying to estimate the local gyrification index. However when I type "recon-all -lgi -s G01"Im getting the following message: dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib Referenced from: /Users/dhirjak/freesurfer/bin/qdec.bin Reason: Incompatible library version: qdec.bin requires version 10.0.0 or later, but libX11.6.dylib provides version 9.0.0 Trace/BPT trap What is the problem with X11 and its library version, I already installed the latest version of X11 (2.7.5), but it is still not working. Can some help me??? Many thanks!!! DH
Hello Dusan,
When you say you installed "X11 (2.7.5)" does that mean you've installed the latest version of XQuartz (http://xquartz.macosforge.org/landing/)? If not, please do that first.
If you installed XQuartz, than can you please type the following on the command line and provide me with the output:
"otool -L /opt/X11/lib/libX11.dylib"
-Zeke
On 01/24/2014 11:02 AM, Dusan Hirjak wrote:
Dear experts,
it seems that after the new apple update "Maverick" Matlab can not get access to Freesurfer. I already added the "recommended lines" from the homepage to matlab startup-file, but it is still not working. Im trying to estimate the local gyrification index. However when I type "recon-all -lgi -s G01" Im getting the following message:
*dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib*
Referenced from: /Users/dhirjak/freesurfer/bin/qdec.bin*
Reason: Incompatible library version: qdec.bin requires version
10.0.0 or later, but libX11.6.dylib provides version 9.0.0*
*Trace/BPT trap*
What is the problem with X11 and its library version, I already installed the latest version of X11 (2.7.5), but it is still not working.
Can some help me???
Many thanks!!!
DH
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hallo Zeke, I did it as you told me and typed "otool -L /opt/X11/lib/libX11.dylib" in the command line, and got the following output: Usage: /Library/Developer/CommandLineTools/usr/bin/otool [-arch arch_type] [-fahlLDtdorSTMRIHGvVcXmqQj] [-mcpu=arg] <object file> ... -f print the fat headers -a print the archive header -h print the mach header -l print the load commands -L print shared libraries used -D print shared library id name -t print the text section (disassemble with -v) -p <routine name> start dissassemble from routine name -s <segname> <sectname> print contents of section -d print the data section -o print the Objective-C segment -r print the relocation entries -S print the table of contents of a library -T print the table of contents of a dynamic shared library -M print the module table of a dynamic shared library -R print the reference table of a dynamic shared library -I print the indirect symbol table -H print the two-level hints table -G print the data in code table -v print verbosely (symbolically) when possible -V print disassembled operands symbolically -c print argument strings of a core file -X print no leading addresses or headers -m don't use archive(member) syntax -B force Thumb disassembly (ARM objects only) -q use llvm's disassembler (the default) -Q use otool(1)'s disassembler -mcpu=arg use `arg' as the cpu for disassembly -j print opcode bytes (ARM64 objects only)
What should I do next to be able to use Freesurfer and Matlab on Maverick??? Many thanks!!! DH
Date: Fri, 24 Jan 2014 11:35:17 -0500 From: zkaufman@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
Hello Dusan,
When you say you installed "X11 (2.7.5)" does that mean you've installed the latest version of XQuartz (http://xquartz.macosforge.org/landing/)? If not, please do that first.
If you installed XQuartz, than can you please type the following on the command line and provide me with the output:
"otool -L /opt/X11/lib/libX11.dylib"
-Zeke
On 01/24/2014 11:02 AM, Dusan Hirjak wrote:
Dear experts,
it seems that after the new apple update "Maverick" Matlab can not get access to Freesurfer. I already added the "recommended lines" from the homepage to matlab startup-file, but it is still not working. Im trying to estimate the local gyrification index. However when I type "recon-all -lgi -s G01" Im getting the following message:
*dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib*
Referenced from: /Users/dhirjak/freesurfer/bin/qdec.bin*
Reason: Incompatible library version: qdec.bin requires version
10.0.0 or later, but libX11.6.dylib provides version 9.0.0*
*Trace/BPT trap*
What is the problem with X11 and its library version, I already installed the latest version of X11 (2.7.5), but it is still not working.
Can some help me???
Many thanks!!!
DH
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 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.
Hello Dusan,
Are you sure you typed the entire command? Because your system is supposed ouput information about that particular file. Instead you got the help information, which is output when you only type "otool" instead of ""otool -L /opt/X11/lib/libX11.dylib"
Also, did you install XQuartz?
-Zeke
On 01/24/2014 04:35 PM, Dusan Hirjak wrote:
Hallo Zeke,
I did it as you told me and typed "otool -L /opt/X11/lib/libX11.dylib" in the command line, and got the following output:
Usage: /Library/Developer/CommandLineTools/usr/bin/otool [-arch arch_type] [-fahlLDtdorSTMRIHGvVcXmqQj] [-mcpu=arg] <object file> ... -f print the fat headers -a print the archive header -h print the mach header -l print the load commands -L print shared libraries used -D print shared library id name -t print the text section (disassemble with -v) -p <routine name> start dissassemble from routine name -s <segname> <sectname> print contents of section -d print the data section -o print the Objective-C segment -r print the relocation entries -S print the table of contents of a library -T print the table of contents of a dynamic shared library -M print the module table of a dynamic shared library -R print the reference table of a dynamic shared library -I print the indirect symbol table -H print the two-level hints table -G print the data in code table -v print verbosely (symbolically) when possible -V print disassembled operands symbolically -c print argument strings of a core file -X print no leading addresses or headers -m don't use archive(member) syntax -B force Thumb disassembly (ARM objects only) -q use llvm's disassembler (the default) -Q use otool(1)'s disassembler -mcpu=arg use `arg' as the cpu for disassembly -j print opcode bytes (ARM64 objects only)
What should I do next to be able to use Freesurfer and Matlab on Maverick???
Many thanks!!!
DH
Date: Fri, 24 Jan 2014 11:35:17 -0500 From: zkaufman@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
Hello Dusan,
When you say you installed "X11 (2.7.5)" does that mean you've installed the latest version of XQuartz (http://xquartz.macosforge.org/landing/)? If not, please do that first.
If you installed XQuartz, than can you please type the following on the command line and provide me with the output:
"otool -L /opt/X11/lib/libX11.dylib"
-Zeke
On 01/24/2014 11:02 AM, Dusan Hirjak wrote:
Dear experts,
it seems that after the new apple update "Maverick" Matlab can not get access to Freesurfer. I already added the "recommended lines" from the homepage to matlab startup-file, but it is still not working. Im trying to estimate the local gyrification index. However when I type
"recon-all
-lgi -s G01" Im getting the following message:
*dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib*
Referenced from: /Users/dhirjak/freesurfer/bin/qdec.bin*
Reason: Incompatible library version: qdec.bin requires version
10.0.0 or later, but libX11.6.dylib provides version 9.0.0*
*Trace/BPT trap*
What is the problem with X11 and its library version, I already installed the latest version of X11 (2.7.5), but it is still not
working.
Can some help me???
Many thanks!!!
DH
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 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.
Hi Zeke, sorry, I did it again and got the following output: /opt/x11/lib/libx11.dylib: /usr/X11/lib/libX11.6.dylib (compatibility version 9.0.0, current version 9.0.0) /usr/X11/lib/libXau.6.dylib (compatibility version 7.0.0, current version 7.0.0) /usr/X11/lib/libXdmcp.6.dylib (compatibility version 7.0.0, current version 7.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 125.2.11)
What should I do now. XQuartz is already installed. I did not have any problems using Freesurfer until I installed Maverick:-) Thanks! DH
Date: Fri, 24 Jan 2014 17:07:08 -0500 From: zkaufman@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
Hello Dusan,
Are you sure you typed the entire command? Because your system is supposed ouput information about that particular file. Instead you got the help information, which is output when you only type "otool" instead of ""otool -L /opt/X11/lib/libX11.dylib"
Also, did you install XQuartz?
-Zeke
On 01/24/2014 04:35 PM, Dusan Hirjak wrote:
Hallo Zeke,
I did it as you told me and typed "otool -L /opt/X11/lib/libX11.dylib" in the command line, and got the following output:
Usage: /Library/Developer/CommandLineTools/usr/bin/otool [-arch arch_type] [-fahlLDtdorSTMRIHGvVcXmqQj] [-mcpu=arg] <object file> ... -f print the fat headers -a print the archive header -h print the mach header -l print the load commands -L print shared libraries used -D print shared library id name -t print the text section (disassemble with -v) -p <routine name> start dissassemble from routine name -s <segname> <sectname> print contents of section -d print the data section -o print the Objective-C segment -r print the relocation entries -S print the table of contents of a library -T print the table of contents of a dynamic shared library -M print the module table of a dynamic shared library -R print the reference table of a dynamic shared library -I print the indirect symbol table -H print the two-level hints table -G print the data in code table -v print verbosely (symbolically) when possible -V print disassembled operands symbolically -c print argument strings of a core file -X print no leading addresses or headers -m don't use archive(member) syntax -B force Thumb disassembly (ARM objects only) -q use llvm's disassembler (the default) -Q use otool(1)'s disassembler -mcpu=arg use `arg' as the cpu for disassembly -j print opcode bytes (ARM64 objects only)
What should I do next to be able to use Freesurfer and Matlab on Maverick???
Many thanks!!!
DH
Date: Fri, 24 Jan 2014 11:35:17 -0500 From: zkaufman@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
Hello Dusan,
When you say you installed "X11 (2.7.5)" does that mean you've installed the latest version of XQuartz (http://xquartz.macosforge.org/landing/)? If not, please do that first.
If you installed XQuartz, than can you please type the following on the command line and provide me with the output:
"otool -L /opt/X11/lib/libX11.dylib"
-Zeke
On 01/24/2014 11:02 AM, Dusan Hirjak wrote:
Dear experts,
it seems that after the new apple update "Maverick" Matlab can not get access to Freesurfer. I already added the "recommended lines" from the homepage to matlab startup-file, but it is still not working. Im trying to estimate the local gyrification index. However when I type
"recon-all
-lgi -s G01" Im getting the following message:
*dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib*
Referenced from: /Users/dhirjak/freesurfer/bin/qdec.bin*
Reason: Incompatible library version: qdec.bin requires version
10.0.0 or later, but libX11.6.dylib provides version 9.0.0*
*Trace/BPT trap*
What is the problem with X11 and its library version, I already installed the latest version of X11 (2.7.5), but it is still not
working.
Can some help me???
Many thanks!!!
DH
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 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.
If you previously had XQuartz installed, then upgraded to Mavericks, it may have written over the relevant files. Please install Xquartz and give it another try. Thanks.
-Zeke
On 01/24/2014 05:33 PM, Dusan Hirjak wrote:
Hi Zeke,
sorry, I did it again and got the following output:
/opt/x11/lib/libx11.dylib: /usr/X11/lib/libX11.6.dylib (compatibility version 9.0.0, current version 9.0.0) /usr/X11/lib/libXau.6.dylib (compatibility version 7.0.0, current version 7.0.0) /usr/X11/lib/libXdmcp.6.dylib (compatibility version 7.0.0, current version 7.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 125.2.11)
What should I do now. XQuartz is already installed. I did not have any problems using Freesurfer until I installed Maverick:-)
Thanks!
DH
Date: Fri, 24 Jan 2014 17:07:08 -0500 From: zkaufman@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
Hello Dusan,
Are you sure you typed the entire command? Because your system is supposed ouput information about that particular file. Instead you got the help information, which is output when you only type "otool" instead of ""otool -L /opt/X11/lib/libX11.dylib"
Also, did you install XQuartz?
-Zeke
On 01/24/2014 04:35 PM, Dusan Hirjak wrote:
Hallo Zeke,
I did it as you told me and typed "otool -L /opt/X11/lib/libX11.dylib" in the command line, and got the following output:
Usage: /Library/Developer/CommandLineTools/usr/bin/otool [-arch arch_type] [-fahlLDtdorSTMRIHGvVcXmqQj] [-mcpu=arg] <object file> ... -f print the fat headers -a print the archive header -h print the mach header -l print the load commands -L print shared libraries used -D print shared library id name -t print the text section (disassemble with -v) -p <routine name> start dissassemble from routine name -s <segname> <sectname> print contents of section -d print the data section -o print the Objective-C segment -r print the relocation entries -S print the table of contents of a library -T print the table of contents of a dynamic shared library -M print the module table of a dynamic shared library -R print the reference table of a dynamic shared library -I print the indirect symbol table -H print the two-level hints table -G print the data in code table -v print verbosely (symbolically) when possible -V print disassembled operands symbolically -c print argument strings of a core file -X print no leading addresses or headers -m don't use archive(member) syntax -B force Thumb disassembly (ARM objects only) -q use llvm's disassembler (the default) -Q use otool(1)'s disassembler -mcpu=arg use `arg' as the cpu for disassembly -j print opcode bytes (ARM64 objects only)
What should I do next to be able to use Freesurfer and Matlab on
Maverick???
Many thanks!!!
DH
Date: Fri, 24 Jan 2014 11:35:17 -0500 From: zkaufman@nmr.mgh.harvard.edu To: dusanhirjak@hotmail.com; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
Hello Dusan,
When you say you installed "X11 (2.7.5)" does that mean you've
installed
the latest version of XQuartz
(http://xquartz.macosforge.org/landing/)?
If not, please do that first.
If you installed XQuartz, than can you please type the following
on the
command line and provide me with the output:
"otool -L /opt/X11/lib/libX11.dylib"
-Zeke
On 01/24/2014 11:02 AM, Dusan Hirjak wrote:
Dear experts,
it seems that after the new apple update "Maverick" Matlab can
not get
access to Freesurfer. I already added the "recommended lines"
from the
homepage to matlab startup-file, but it is still not working.
Im trying
to estimate the local gyrification index. However when I type
"recon-all
-lgi -s G01" Im getting the following message:
*dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib*
Referenced from: /Users/dhirjak/freesurfer/bin/qdec.bin*
Reason: Incompatible library version: qdec.bin requires version
10.0.0 or later, but libX11.6.dylib provides version 9.0.0*
*Trace/BPT trap*
What is the problem with X11 and its library version, I already installed the latest version of X11 (2.7.5), but it is still not
working.
Can some help me???
Many thanks!!!
DH
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 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.
Hi Zeke, I have one more question: It seems that I did not copied the the "recommended lines" from thehomepage to matlab startup-file correct. when I type "recon-all -lgi -s G01" Im getting the following message: ERROR: Matlab is required to run mris_compute_lgi!
When Im trying to run Qdec, then I get the already mentioned message: *dyld: Library not loaded: /opt/X11/lib/libX11.6.dylib*
* Referenced from: /Users/dhirjak/freesurfer/bin/qdec.bin*
* Reason: Incompatible library version: qdec.bin requires version 10.0.0 or later, but libX11.6.dylib provides version 9.0.0* *Trace/BPT trap*
Sorry for the mistake:-( But it is still not working. Best regards, DH
Defect-seg is what I was looking for. Thanks Bruce.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Saturday, 25 January 2014 12:36 AM To: Chris Adamson Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] defect_labels to volume
have you tried mri_surf2vol? On Fri, 24 Jan 2014, Chris Adamson wrote:
Is there a way of making a volume like aparc+aseg with the defect labels so that cortical region where the defects are show up red?
Dr Chris Adamson Research Officer, Developmental Imaging, Murdoch Childrens Research Institute Murdoch Childrens Research Institute Royal Children’s Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au
E chris.adamson@mcri.edu.au T 03 9936 6780
This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________
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.
______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com
If you have any question, please contact MCRI IT Helpdesk for further assistance. ______________________________________________________________________
______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________
Have you tried running the defect-seg script? It creates annotations of the defects. Look at the --help doug
On 1/24/14 1:03 AM, Chris Adamson wrote:
Is there a way of making a volume like aparc+aseg with the defect labels so that cortical region where the defects are show up red?
*Dr **Chris Adamson *Research Officer, Developmental Imaging, *Murdoch Childrens Research Institute *Murdoch Childrens Research Institute Royal Children's Hospital Flemington Road, Parkville, Victoria 3052, Australia www.mcri.edu.au http://www.mcri.edu.au/
E chris.adamson@mcri.edu.au T 03 9936 6780
This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Chris Adamson -
Douglas Greve -
Dusan Hirjak -
Z K