Re: [Freesurfer] Question longitudinal study about treatment effect with change of scanner and head coil?

[Markus Gschwind]

External Email - Use Caution

Thank you, Anastasia, that was my thoughts also.
So there is no way regressing this out, right?
Best, Markus

Le sam. 1 févr. 2020 à 00:10, Yendiki, Anastasia 
a écrit :

> Hi Markus - If you were to find longitudinal changes in this study, you
> would have no way of knowing if they are changes in the brain or changes in
> the instrument used to measure the brain.
>
> a.y
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Markus Gschwind <
> markus.gschw...@gmail.com>
> *Sent:* Friday, January 31, 2020 6:04 PM
> *To:* freesurfer 
> *Subject:* [Freesurfer] Question longitudinal study about treatment
> effect with change of scanner and head coil?
>
>
> External Email - Use Caution
>
> Dear experts,
>
> I am reviewing a study that proposes a longitudinal study in patients
> across several years on the effect of medical treatment in terms of fcMRI
> and DTI-connectivity measures.
>
> However, in several but not all patients, the scanner was upgraded from
> Trio to Prisma and the head coil was changed from a 12 to a 20-channel.
> Every patient had the upgrade at another time point.
>
> I would like to hear your opinion on this. In my experience,  the scanner
> upgrade and especially the head coil upgrade heavily affected the images.
>
> So I have fundamental doubts about the feasibility. What would be the
> conditions under which it could be acceptable?
>
> Thank you in advance!
> Best, Markus
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[Freesurfer] Question longitudinal study about treatment effect with change of scanner and head coil?

[Markus Gschwind]

External Email - Use Caution

Dear experts,

I am reviewing a study that proposes a longitudinal study in patients
across several years on the effect of medical treatment in terms of fcMRI
and DTI-connectivity measures.

However, in several but not all patients, the scanner was upgraded from
Trio to Prisma and the head coil was changed from a 12 to a 20-channel.
Every patient had the upgrade at another time point.

I would like to hear your opinion on this. In my experience,  the scanner
upgrade and especially the head coil upgrade heavily affected the images.

So I have fundamental doubts about the feasibility. What would be the
conditions under which it could be acceptable?

Thank you in advance!
Best, Markus
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Re: [Freesurfer] QDEC, order interpretationof Gracias @batmarandua for aqaa

[Markus Gschwind]

External Email - Use Caution

On Tue, May 29, 2018, 20:16 Avi Gharehgazlou  wrote:

> External Email - Use Caution
>
> Hello experts,
>
> I am using QDEC to compared LGI values between groups (typically develping
> and ASD). I made a "diagnosis.levels" file, putting my 2 groups in the
> following order:
>
> Typically developing
> ASD
>
> However, when I upload my qdec.table.dat file on QDEC, it recognizes my
> diagnosis levels in the following order:
>
> 1  Diagnosis  discrete 2
> 1  ASD
> 2  TD
> 2  age  continuous 0
> 3  SA  continuous 0
>
>
> Will you please tell me which order I have to interpret my results
> according to? i.e. significant regions in Blue colour would indicate less
> LGI in TD relative to ASD (if I consider TD first then ASD- like the order
> I designed my diagnosis.levels file) BUT blue regions would mean less LGI
> in ASD vs. TD if I consider order my groups appear on QDEC when I upload
> qdec.table.dat file.
>
> Would appreciate your reply,
>
> Avi
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>
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> 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
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Re: [Freesurfer] V6 Stable OSX software error v- muflagřú9diffusionltistripjsßsssssshg kkss muflagřú9diffusibltistripuuf67uwweďxu dvvnçuc uf7a çyrucuf fDddnnn6x7uf

[Markus Gschwind]

External Email - Use Caution

Ûghrf7f77f7f7ef

On Thu, May 3, 2018, 19:32 Matthew Grecsek  wrote:

> External Email - Use Caution
>
> I'm using the following flags on my recon -all:  -mprage -time -multistrip
> -subcortseg
>
> and getting the following errors at this section of the log file:
>
> mri_watershed -rusage
> /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat
> -brain_atlas
> /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca
> transforms/talairach_with_skull.lta -h 5 T1.mgz brainmask_T1_PFH5.auto.mgz
> \n
> \n mri_watershed -rusage
> /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat
> -brain_atlas
> /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca
> transforms/talairach_with_skull.lta -h 10 T1.mgz
> brainmask_T1_PFH10.auto.mgz \n
> \n mri_watershed -rusage
> /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat
> -brain_atlas
> /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca
> transforms/talairach_with_skull.lta -h 20 T1.mgz
> brainmask_T1_PFH20.auto.mgz \n
> \n mri_watershed -rusage
> /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat
> -brain_atlas
> /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca
> transforms/talairach_with_skull.lta -h 30 T1.mgz
> brainmask_T1_PFH30.auto.mgz \n
>
>  mri_watershed -rusage
> /Users/Matthew/Downloads/matt/mattmp/touch/rusage.mri_watershed.dat
> -brain_atlas
> /Applications/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca
> transforms/talairach_with_skull.lta -h 5 orig.mgz
> brainmask_orig_PFH5.auto.mgz
>
>
> Mode:  Use the information of atlas (default parms, --help for
> details)
> Mode:  Preflooding height manually specified
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> [... more of same ...]
>
> WARNING: Some multi-skullstrip operations may have failed!
>  Continuing multi-skullstrip with the others...
> ERROR: failure in calculating best preflood height param.
> Darwin Matthews-MacBook-Air.local 17.5.0 Darwin Kernel Version 17.5.0: Mon
> Mar  5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64
>
> recon-all -s mattmp exited with ERRORS at Thu May  3 12:57:24 EDT 2018
>
> Attached is my log file for reference. Any suggestions appreciated.
>
> Cheers,
>
> -Matt
>
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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] Freeview aborts under centos6

[Markus Gschwind]

-rwxr-xr-x 1 sagon unige 2425484 Sep 14  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6.0
lrwxrwxrwx 1 sagon unige  25 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so ->
libvtkWidgetsTCL.so.5.6.0
lrwxrwxrwx 1 sagon unige  25 Sep 21 14:46 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 ->
libvtkWidgetsTCL.so.5.6.0
-rwxr-xr-x 1 sagon unige 1227320 Sep 14  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6.0
-rwxr-xr-x 1 sagon unige   89056 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so
-rwxr-xr-x 1 sagon unige   89056 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6
-rwxr-xr-x 1 sagon unige   89056 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
6.0.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6.0

2017-09-19 20:10 GMT+02:00 Hoopes, Andrew <ahoo...@mgh.harvard.edu>:

> I've attached a tar of the vtk library (vtk.tar.gz). To reinstall this,
> the sys admin should run:
>
> tar -xzvf vtk.tar.gz
> rm -rf $FREESURFER_HOME/lib/vtk
> mv vtk  $FREESURFER_HOME/lib/
>
> after doing this, running the following command should display a bunch of
> symbolic links:
> ls -l $FREESURFER_HOME/lib/vtk/lib/vtk-5.6/libvtk*
>
> If that's the case, hopefully freeview will run... or at least throw a
> different error
>
> best
> Andrew
> 
> From: Hoopes, Andrew
> Sent: Tuesday, September 19, 2017 1:56 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Freeview aborts under centos6
>
> Hi Markus, okay - I'll directly send you a tar of the vtk library. A
> reinstall of vtk might work, because those shared objects that we
> distribute are usually sym-linked
>
> Can you also send the fs buildstamp? You can get this by running the
> command ‘bugr’ after sourcing freesurfer
>
> Andrew
>
> On Sep 19, 2017, at 11:02 AM, Markus Gschwind <markus.gschw...@gmail.com<
> mailto:markus.gschw...@gmail.com>> wrote:
>
> Dear Andrew,
>
> after the System admin executed your proposed commands, it stays the same,
> Freeview aborts.
>
> Is there anything else we could try?
>
> Thank you and best wishes,
>
> Markus
>
> 2017-09-15 20:06 GMT+02:00 Hoopes, Andrew <ahoo...@mgh.harvard.edu ahoo...@mgh.harvard.edu>>:
> Hm okay thanks - I’m curious what happens when you run:
>
> cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6
> # backup the shared objects
> mv libvtkverdict.so libvtkverdict.so.bk
> mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk
> # link them to 5.6
> ln -s libvtkverdict.so.5.6.0 libvtkverdict.so
> ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6
>
> then do you get the same error from freeview?
>
> -Andrew
>
> On Sep 15, 2017, at 12:10 PM, Markus Gschwind <markus.gschw...@gmail.com<
> mailto:markus.gschw...@gmail.com>> wrote:
>
> Dear Andrew,
>
> The command gives this result:
>
> [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<<
> $LD_LIBRARY_PATH) | grep libvtkverdict.so
> /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0-
> openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory
> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6:
> duplicate hwcap 1 nosegneg
> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6:
> duplicate hwcap 1 nosegneg
> /sbin/ldconfig: 
> /etc/ld.so.conf.d/kernel-2.6.32-642.6.2.el6.aufs21.x86_64.conf:6:
> duplicate hwcap 1 nosegneg
> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6:
> duplicate hwcap 1 nosegneg
> /sbin/ldconfig: Path `/usr/lib64' given more than once
> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/
> lib/vtk-5.6/libvtkalglib.so.5.6 is not a symbolic link
> /sbin/ldconfig: 
> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6
> is not a symbolic link
> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/
> lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not a symbolic link
> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/
> lib/vtk-5.6/libvtkWidgets.so.5.6 is not a symbolic link
> /sbin/ldconfig: 
> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6
> is not a symbolic link
> /sbin/ldconfig: 
> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6
> is not a symbolic link
> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/l

Re: [Freesurfer] Freeview aborts under centos6

[Markus Gschwind]

Hi Andrew,

Thank you!

Here is the output of bugr


> [gschwind@login1 ~]$ bugr
> Cut-and-paste the following info into your FreeSurfer problem report:
> -
> FREESURFER_HOME: /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64
> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> RedHat release: CentOS release 6.9 (Final)
> Kernel info: Linux 2.6.32-696.1.1.el6.x86_64 x86_64
> -


I'll tell the system admin to reinstall your new vtk libraries.

I'll come back to you.

Thanks again,
Markus


2017-09-19 19:56 GMT+02:00 Hoopes, Andrew <ahoo...@mgh.harvard.edu>:

> Hi Markus, okay - I'll directly send you a tar of the vtk library. A
> reinstall of vtk might work, because those shared objects that we
> distribute are usually sym-linked
>
> Can you also send the fs buildstamp? You can get this by running the
> command ‘bugr’ after sourcing freesurfer
>
> Andrew
>
>
> On Sep 19, 2017, at 11:02 AM, Markus Gschwind <markus.gschw...@gmail.com>
> wrote:
>
> Dear Andrew,
>
> after the System admin executed your proposed commands, it stays the same,
> Freeview aborts.
>
> Is there anything else we could try?
>
> Thank you and best wishes,
>
> Markus
>
> 2017-09-15 20:06 GMT+02:00 Hoopes, Andrew <ahoo...@mgh.harvard.edu>:
>
>> Hm okay thanks - I’m curious what happens when you run:
>>
>> cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6
>> # backup the shared objects
>> mv libvtkverdict.so libvtkverdict.so.bk
>> mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk
>> # link them to 5.6
>> ln -s libvtkverdict.so.5.6.0 libvtkverdict.so
>> ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6
>>
>> then do you get the same error from freeview?
>>
>> -Andrew
>>
>> On Sep 15, 2017, at 12:10 PM, Markus Gschwind <markus.gschw...@gmail.com>
>> wrote:
>>
>> Dear Andrew,
>>
>> The command gives this result:
>>
>> [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<<
>>> $LD_LIBRARY_PATH) | grep libvtkverdict.so
>>> /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0-openjd
>>> k-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory
>>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6:
>>> duplicate hwcap 1 nosegneg
>>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6:
>>> duplicate hwcap 1 nosegneg
>>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.3
>>> 2-642.6.2.el6.aufs21.x86_64.conf:6: duplicate hwcap 1 nosegneg
>>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6:
>>> duplicate hwcap 1 nosegneg
>>> /sbin/ldconfig: Path `/usr/lib64' given more than once
>>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5
>>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a
>>> symbolic link
>>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5
>>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a
>>> symbolic link
>>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5
>>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not
>>> a symbolic link
>>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5
>>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a
>>> symbolic link
>>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5
>>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a
>>> symbolic link
>>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5
>>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a
>>> symbolic link
>>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5
>>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is
>>> not a symbolic link
>>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5
>>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6
>>> is not a symbolic link
>>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5
>>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a
>>> symbolic link
>>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5
>>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a
>>> symbolic link
>>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/5
>>> .3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a
>>> symbolic link
>>> /sbin/ldconfig: /opt/ebsofts/Core/Free

Re: [Freesurfer] Freeview aborts under centos6

[Markus Gschwind]

Dear Andrew,

after the System admin executed your proposed commands, it stays the same,
Freeview aborts.

Is there anything else we could try?

Thank you and best wishes,

Markus

2017-09-15 20:06 GMT+02:00 Hoopes, Andrew <ahoo...@mgh.harvard.edu>:

> Hm okay thanks - I’m curious what happens when you run:
>
> cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6
> # backup the shared objects
> mv libvtkverdict.so libvtkverdict.so.bk
> mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk
> # link them to 5.6
> ln -s libvtkverdict.so.5.6.0 libvtkverdict.so
> ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6
>
> then do you get the same error from freeview?
>
> -Andrew
>
> On Sep 15, 2017, at 12:10 PM, Markus Gschwind <markus.gschw...@gmail.com>
> wrote:
>
> Dear Andrew,
>
> The command gives this result:
>
> [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<<
>> $LD_LIBRARY_PATH) | grep libvtkverdict.so
>> /sbin/ldconfig: Can't stat /usr/lib/jvm/java-1.7.0-
>> openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No such file or directory
>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6:
>> duplicate hwcap 1 nosegneg
>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6:
>> duplicate hwcap 1 nosegneg
>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.
>> 32-642.6.2.el6.aufs21.x86_64.conf:6: duplicate hwcap 1 nosegneg
>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6:
>> duplicate hwcap 1 nosegneg
>> /sbin/ldconfig: Path `/usr/lib64' given more than once
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not
>> a symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is
>> not a symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6
>> is not a symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is
>> not a symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not
>> a symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 is not a
>> symbolic link
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not
>> a symbolic link
>> libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0
>> /sbin/ldconfig: /opt/ebsofts/Core/FreeSurfer/
>> 5.3.

Re: [Freesurfer] Freeview aborts under centos6

[Markus Gschwind]

Thanks, I gave this to the system admin as I do not ave the sudo rights.

I’ll come back!

Best, Markus


> On 15 Sep 2017, at 20:06, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote:
> 
> Hm okay thanks - I’m curious what happens when you run:
> 
> cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6
> # backup the shared objects
> mv libvtkverdict.so libvtkverdict.so.bk
> mv libvtkverdict.so.5.6 libvtkverdict.so.5.6.bk
> # link them to 5.6
> ln -s libvtkverdict.so.5.6.0 libvtkverdict.so
> ln -s libvtkverdict.so.5.6.0 libvtkverdict.so.5.6
> 
> then do you get the same error from freeview?
> 
> -Andrew
> 
>> On Sep 15, 2017, at 12:10 PM, Markus Gschwind <markus.gschw...@gmail.com 
>> <mailto:markus.gschw...@gmail.com>> wrote:
>> 
>> Dear Andrew,
>> 
>> The command gives this result:
>> 
>> [gschwind@login1 ~]$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< 
>> $LD_LIBRARY_PATH) | grep libvtkverdict.so
>> /sbin/ldconfig: Can't stat 
>> /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.71.x86_64/jre/lib/amd64/server: No 
>> such file or directory
>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.1.1.el6.x86_64.conf:6: 
>> duplicate hwcap 1 nosegneg
>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-642.15.1.el6.x86_64.conf:6: 
>> duplicate hwcap 1 nosegneg
>> /sbin/ldconfig: 
>> /etc/ld.so.conf.d/kernel-2.6.32-642.6.2.el6.aufs21.x86_64.conf:6: duplicate 
>> hwcap 1 nosegneg
>> /sbin/ldconfig: /etc/ld.so.conf.d/kernel-2.6.32-696.1.1.el6.x86_64.conf:6: 
>> duplicate hwcap 1 nosegneg
>> /sbin/ldconfig: Path `/usr/lib64' given more than once
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6
>>  is not a symbolic link
>> /sbin/ldconfig: 
>> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6
>>  is not a symbolic link
>> libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0
&

Re: [Freesurfer] Freeview aborts under centos6

[Markus Gschwind]

ts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6
> is not a symbolic link
> /sbin/ldconfig:
> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6
> is not a symbolic link
> /sbin/ldconfig:
> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6
> is not a symbolic link
> /sbin/ldconfig:
> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6
> is not a symbolic link
> /sbin/ldconfig:
> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6
> is not a symbolic link
> /sbin/ldconfig:
> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6
> is not a symbolic link
> /sbin/ldconfig:
> /opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libMapReduceMPI.so.5.6
> is not a symbolic link



Thanks for your help!!

Markus

2017-09-15 17:49 GMT+02:00 Hoopes, Andrew <ahoo...@mgh.harvard.edu>:

> Hi Markus,
>
> What is the output when you run the following: (this will list libraries
> you have access to)
>
> /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep
> libvtkverdict.so
>
> best,
> Andrew
>
> On Sep 15, 2017, at 3:33 AM, Markus Gschwind <markus.gschw...@gmail.com>
> wrote:
>
> Hi experts,
>
> I am installing freeusrfer on our cluster which is running Centos6.
>
> [gschwind@login1 ~]$ uname -a
> Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24
> UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>
>
> Freeview aborts without any other complaint.
>
> [gschwind@login1 ~]$ freeview
> Abort
>
> When running freeview.bin it complains about a libraries error:
>
> [gschwind@login1 ~]$ freeview.bin
> freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6:
> cannot open shared object file: No such file or directory
>
> I searched the archives and found this info to be given,
>
> [gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/
> vtk-5.6/*libvtkverdict*
> -rwxr-xr-x 1 sagon unige 189017 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so
> -rwxr-xr-x 1 sagon unige 189017 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6
> -rwxr-xr-x 1 sagon unige 189017 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
> 5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0
>
>
> I then integrated this into bashrc
>
> export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6
>
> however, the problem persists.
>
> Any help is highly appreciated!
>
> Thanks you!
> Markus
> ___
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>
>
>
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>
>
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> 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
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> but does not contain patient information, please contact the sender and
> properly
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[Freesurfer] Freeview aborts under centos6

[Markus Gschwind]

Dear experts,

I am installing freeusrfer on our cluster which is running Centos6.

[gschwind@login1 ~]$ uname -a
Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux


Freeview aborts without any other complaint.

[gschwind@login1 ~]$ freeview
Abort

When running freeview.bin it complains about a libraries error:

[gschwind@login1 ~]$ freeview.bin
freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6:
cannot open shared object file: No such file or directory

I searched the archives and found this info to be given,

[gschwind@login1 ~]$ ls -l $FREESURFER_HOME/lib/vtk/lib/
vtk-5.6/*libvtkverdict*
-rwxr-xr-x 1 sagon unige 189017 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so
-rwxr-xr-x 1 sagon unige 189017 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6
-rwxr-xr-x 1 sagon unige 189017 Aug 17  2010 /opt/ebsofts/Core/FreeSurfer/
5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0


I then integrated this into bashrc

export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6

however, the problem persists.

Any help is highly appreciated!

Thanks you!
Markus
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[Freesurfer] Freeview aborts under centos6

[Markus Gschwind]

Hi experts,

I am installing freeusrfer on our cluster which is running Centos6.

[gschwind@login1 ~]$ uname -a
Linux login1.cluster 2.6.32-696.1.1.el6.x86_64 #1 SMP Tue Apr 11 17:13:24
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux


Freeview aborts without any other complaint.

[gschwind@login1 ~]$ freeview
Abort

When running freeview.bin it complains about a libraries error:

[gschwind@login1 ~]$ freeview.bin
freeview.bin: error while loading shared libraries: libvtkverdict.so.5.6:
cannot open shared object file: No such file or directory

I searched the archives and found this info to be given,

[gschwind@login1 ~]$ ls -l
$FREESURFER_HOME/lib/vtk/lib/vtk-5.6/*libvtkverdict*
-rwxr-xr-x 1 sagon unige 189017 Aug 17  2010
/opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so
-rwxr-xr-x 1 sagon unige 189017 Aug 17  2010
/opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6
-rwxr-xr-x 1 sagon unige 189017 Aug 17  2010
/opt/ebsofts/Core/FreeSurfer/5.3.0-centos6_x86_64/lib/vtk/lib/vtk-5.6/libvtkverdict.so.5.6.0


I then integrated this into bashrc

export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6

however, the problem persists.

Any help is highly appreciated!

Thanks you!
Markus
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Re: [Freesurfer] Error on Linux

[Markus Gschwind]

HI,
Please see the solution for this known error below, as given in this list
form Zeke some months ago:
Good luck, Markus

2015-09-22 6:05 GMT+02:00 :

> Hello,
>
> This is a known when running freesurfer on Ubuntu systems. The solution is
> addressed in the FAQ section on the frresurfer download page:
>
>   https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>
> pecifically, the solution is to go into you system's lib directory and
> create a symlink as follows:
>
>   $> cd /usr/lib/x86_64 (or something similar depending upon exact version)
>   $> sudo ln -s libjpeg.so.8 libjpeg.so.62
>   $> sudo ln -s libtiff.so.4 libtiff.so.3
>
> This should solve it. Best,
>
> -Zeke
>


2016-01-30 16:44 GMT+01:00 Ankita Chatterjee :

> Hello,
> I am hoping some freesurfer experts can help - I can't seem to be able to
> run qdec or freeview as I get an error - "error while loading shared
> libraries: libjpeg.so.62: cannot open shared object file: No such file or
> directory". I did run the command that probably links that library, but no
> luck.
>
> Any advice or direction?
>
> Thanks!
> Ankita
>
> On Wed, Jan 27, 2016 at 11:19 PM Ankita Chatterjee 
> wrote:
>
>> Hello,
>> I am trying to run freesurfer on a machine I got access to that has
>> Ubuntu (14.04) on it. When I run the tutorials and try to run qdec or
>> freeview, I get this error - qdec.bin: error while loading shared
>> libraries: libjpeg.so.62: cannot open shared object file: No such file or
>> directory
>> I tried running sudo ln -s libjpeg.so.8 libjpeg.so.62, but it says
>> libjpeg.so.62 already exists. Any ideas?
>> I ran tkmedit and tksurfer and those run fine - only freeview and qdec
>> are giving this error.
>>
>> Thanks!
>>
>> Ankita
>>
>
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Re: [Freesurfer] tksurfer

[Markus Gschwind]

Hi Isabel,

open a terminal and type:

cd /Applications/freesurfer
sudo mv license.txt .license
your_admin_password

That's it.

Best,
M

2015-06-17 22:19 GMT+02:00 isabel martinez tejada 
isa_martinez...@hotmail.com:

 I cannot put a . in the file name because Mac doesn't allow it. It says
 that a file that starts with a dot is an invisible file and there is no way
 I can do it, its only for special files of the system.

 Thanks,

 Isabel

 --
 From: bat...@gmail.com
 Date: Wed, 17 Jun 2015 06:58:03 -1000
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] tksurfer


 Dear Isabel,

 the “.” is part of the name of the file, that is why the system cannot
 find it.

 Hope this helps,

 Rodolphe.

 `·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·
 Rodolphe Nenert, Ph.D.
 Department of Neurology
 312 Civitan International Research Center
 1719 6th avenue south
 Birmingham, AL, 35294-0021

 Office: *205.975.3885 205.975.3885*
 Mob: *205.566.3854 205.566.3854*
 Web: http://www.rnenert.org

 `·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·

 On Jun 17, 2015, at 4:05 AM, isabel martinez tejada 
 isa_martinez...@hotmail.com wrote:

 Dear experts,

 I am using a Mac that runs bash shell. I have performed a group analysis
 and would like to visualize the results. When using tksurfer I come up with
 a license error.

 The lines of commands I am running are:
 export FREESURFER_HOME=/Applications/freesurfer
 source $FREESURFER_HOME/SetUpFreeSurfer.sh


 export SUBJECTS_DIR=/Users/IsabelMartinez/Documents/group1
 echo $SUBJECTS_DIR
 cd  $SUBJECTS_DIR




 tksurfer fsaverage lh inflated \
   -annot aparc.annot -fthresh 2 \
   -overlay lh.gender.glmdir/Contrast1/sig.mgh

 The error I get is the following:

 FreeSurfer license file /Applications/freesurfer/.license not found


 I have a license.txt (without the dot at the beginning) stored in that 
 folder, so I don't know what the problem is.


 Thank you for your attention,


 Isabel

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 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
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 ___ Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
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 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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 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
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 but does not contain patient information, please contact the sender and
 properly
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Qdec create stats tables error

[Markus Gschwind]

Dear all,

I am trying to make work Qdec on my system ubuntu 12.04.

freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

After I have loaded my qdec.table.dat and renamed the analysis folder ,
when I then try to create the stats tables, I get an error and it blocks
at 20% of the waiting bar.


Data table loading completed successfully.

 SUBJECTS_DIR is '~/Documents/ARNAUD/'

 mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/

 mkdir: cannot create directory `/usr/local/freesurfer/subjects/qdec':
 Permission denied

 ERROR: In
 /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
 line 230

 vtkKWQdecApp (0x289a94e0):

 Script:

 vtkTemp2 GenerateStatsDataTables

 Returned Error on line 1:

 Uncaught exception: command failed: mkdir -p
 /usr/local/freesurfer/subjects/qdec/stats_tables/


 Stack trace:

 Uncaught exception: command failed: mkdir -p
 /usr/local/freesurfer/subjects/qdec/stats_tables/


 while executing

 vtkTemp2 GenerateStatsDataTables


 It seems that it tries to write into the default SUBJECT_DIR, thing that I
do not understand as I put the actual SUBJECT_DIR in the top line of
qdec.table.dat (and it is correctly recognized in the qdec window
SUBJECTS_DIR).

How could I come around that problem?

Thanks in advance!
Markus
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Qdec create stats tables error

[Markus Gschwind]

Hi Martin!

Thanks!
Yes, indeed typing in the command
export SUBJECTS_DIR=subjectsdir before starting qdec solved the first
problem... there are others to follow...

When now writing the table stats file:

Data table loading completed successfully.

SUBJECTS_DIR is '~/Documents/ARNAUD/'

mkdir -p /home/user/Documents/ARNAUD/qdec/stats_tables/


 --

asegstats2table --common-segs --meas volume --tablefile
 /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat
 --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10
 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27

SUBJECTS_DIR : ~/Documents/ARNAUD/

Parsing the .stats files
 ERROR: The stats file ~/Documents/ARNAUD/s01/stats/aseg.stats is not found
 or is too small to be a valid statsfile
 Use --skip flag to automatically skip bad stats files
 ERROR: In
 /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
 line 230
 vtkKWQdecApp (0x28594510):
 Script:
 vtkTemp2 GenerateStatsDataTables
 Returned Error on line 1:
 Uncaught exception: command failed: asegstats2table --common-segs --meas
 volume --tablefile
 /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat
 --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10
 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27
 Stack trace:
 Uncaught exception: command failed: asegstats2table --common-segs --meas
 volume --tablefile
 /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat
 --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10
 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27
 while executing
 vtkTemp2 GenerateStatsDataTables


The file ~/Documents/ARNAUD/s01/stats/aseg.stats is very well there and
seems very normal, with plenty of numbers in it.

The /home/user/Documents/ARNAUD/qdec/stats_tables/ folders are created, but
empty.

Any further ideas?
Thanks !

Markus

2014-09-12 21:47 GMT+02:00 Martin Reuter mreu...@nmr.mgh.harvard.edu:

  Hi Markus,

 maybe for some weird reason it uses the subjects_dir from the environment
 variable instead of the qdec file (that would probably be a bug). If that's
 the case, try setting the subject dir on the command line before starting
 qdec:
 setenv SUBJECTS_DIR ~/Documents/ARNAUD/
 (or the full path). If you use a bash shell, use the equivalent export
 command for that.

 Best, Martin


 On 09/12/2014 03:30 PM, Markus Gschwind wrote:

 Dear all,

  I am trying to make work Qdec on my system ubuntu 12.04.

  freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

  After I have loaded my qdec.table.dat and renamed the analysis folder ,
 when I then try to create the stats tables, I get an error and it blocks
 at 20% of the waiting bar.


   Data table loading completed successfully.

 SUBJECTS_DIR is '~/Documents/ARNAUD/'

 mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/

 mkdir: cannot create directory `/usr/local/freesurfer/subjects/qdec':
 Permission denied

 ERROR: In
 /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
 line 230

 vtkKWQdecApp (0x289a94e0):

 Script:

 vtkTemp2 GenerateStatsDataTables

 Returned Error on line 1:

 Uncaught exception: command failed: mkdir -p
 /usr/local/freesurfer/subjects/qdec/stats_tables/


  Stack trace:

 Uncaught exception: command failed: mkdir -p
 /usr/local/freesurfer/subjects/qdec/stats_tables/


  while executing

 vtkTemp2 GenerateStatsDataTables


  It seems that it tries to write into the default SUBJECT_DIR, thing
 that I do not understand as I put the actual SUBJECT_DIR in the top line of
 qdec.table.dat (and it is correctly recognized in the qdec window
 SUBJECTS_DIR).

 How could I come around that problem?

 Thanks in advance!
 Markus


 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Dr. Martin Reuter

 Instructor in Neurology
   Harvard Medical School
 Assistant in Neuroscience
   Dept. of Radiology, Massachusetts General Hospital
   Dept. of Neurology, Massachusetts General Hospital
 Research Affiliate
   Computer Science and Artificial Intelligence Lab,
   Dept. of Electrical Engineering and Computer Science,
   Massachusetts Institute of Technology

 A.A.Martinos Center for Biomedical Imaging
 149 Thirteenth Street, Suite 2301
 Charlestown, MA 02129

 Phone: +1-617-724-5652
 Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
 Web  : http://reuter.mit.edu


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 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] Qdec create stats tables error

[Markus Gschwind]

Dear Martin,

Actually, I found that it doesn't like the ~/ for /home/username

When replacing the first line in the qdec.table.dat
SUBJECTS_DIR=/home/username/...

and also export the SUBJECTS_DIR in the terminal with the foll path, it
works nicley!

Thanks again!
Markus

2014-09-12 22:06 GMT+02:00 Markus Gschwind markus.gschw...@gmail.com:

 Hi Martin!

 Thanks!
 Yes, indeed typing in the command
 export SUBJECTS_DIR=subjectsdir before starting qdec solved the first
 problem... there are others to follow...

 When now writing the table stats file:

 Data table loading completed successfully.

 SUBJECTS_DIR is '~/Documents/ARNAUD/'

 mkdir -p /home/user/Documents/ARNAUD/qdec/stats_tables/


 --

 asegstats2table --common-segs --meas volume --tablefile
 /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat
 --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10
 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27

 SUBJECTS_DIR : ~/Documents/ARNAUD/

 Parsing the .stats files
 ERROR: The stats file ~/Documents/ARNAUD/s01/stats/aseg.stats is not
 found or is too small to be a valid statsfile
 Use --skip flag to automatically skip bad stats files
 ERROR: In
 /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
 line 230
 vtkKWQdecApp (0x28594510):
 Script:
 vtkTemp2 GenerateStatsDataTables
 Returned Error on line 1:
 Uncaught exception: command failed: asegstats2table --common-segs --meas
 volume --tablefile
 /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat
 --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10
 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27
 Stack trace:
 Uncaught exception: command failed: asegstats2table --common-segs --meas
 volume --tablefile
 /home/user/Documents/ARNAUD/qdec/stats_tables/aseg.volume.stats.dat
 --statsfile=aseg.stats --subjects s01 s02 s03 s04 s05 s06 s07 s08 s09 s10
 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27
 while executing
 vtkTemp2 GenerateStatsDataTables


 The file ~/Documents/ARNAUD/s01/stats/aseg.stats is very well there and
 seems very normal, with plenty of numbers in it.

 The /home/user/Documents/ARNAUD/qdec/stats_tables/ folders are created,
 but empty.

 Any further ideas?
 Thanks !

 Markus

 2014-09-12 21:47 GMT+02:00 Martin Reuter mreu...@nmr.mgh.harvard.edu:

  Hi Markus,

 maybe for some weird reason it uses the subjects_dir from the environment
 variable instead of the qdec file (that would probably be a bug). If that's
 the case, try setting the subject dir on the command line before starting
 qdec:
 setenv SUBJECTS_DIR ~/Documents/ARNAUD/
 (or the full path). If you use a bash shell, use the equivalent export
 command for that.

 Best, Martin


 On 09/12/2014 03:30 PM, Markus Gschwind wrote:

 Dear all,

  I am trying to make work Qdec on my system ubuntu 12.04.

  freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

  After I have loaded my qdec.table.dat and renamed the analysis folder ,
 when I then try to create the stats tables, I get an error and it blocks
 at 20% of the waiting bar.


   Data table loading completed successfully.

 SUBJECTS_DIR is '~/Documents/ARNAUD/'

 mkdir -p /usr/local/freesurfer/subjects/qdec/stats_tables/

 mkdir: cannot create directory `/usr/local/freesurfer/subjects/qdec':
 Permission denied

 ERROR: In
 /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx,
 line 230

 vtkKWQdecApp (0x289a94e0):

 Script:

 vtkTemp2 GenerateStatsDataTables

 Returned Error on line 1:

 Uncaught exception: command failed: mkdir -p
 /usr/local/freesurfer/subjects/qdec/stats_tables/


  Stack trace:

 Uncaught exception: command failed: mkdir -p
 /usr/local/freesurfer/subjects/qdec/stats_tables/


  while executing

 vtkTemp2 GenerateStatsDataTables


  It seems that it tries to write into the default SUBJECT_DIR, thing
 that I do not understand as I put the actual SUBJECT_DIR in the top line of
 qdec.table.dat (and it is correctly recognized in the qdec window
 SUBJECTS_DIR).

 How could I come around that problem?

 Thanks in advance!
 Markus


 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


 --
 Dr. Martin Reuter

 Instructor in Neurology
   Harvard Medical School
 Assistant in Neuroscience
   Dept. of Radiology, Massachusetts General Hospital
   Dept. of Neurology, Massachusetts General Hospital
 Research Affiliate
   Computer Science and Artificial Intelligence Lab,
   Dept. of Electrical Engineering and Computer Science,
   Massachusetts Institute of Technology

 A.A.Martinos Center for Biomedical Imaging
 149 Thirteenth Street, Suite 2301
 Charlestown, MA 02129

 Phone: +1-617-724-5652
 Email:
mreu...@nmr.mgh.harvard.edu
reu...@mit.edu
 Web  : http

Re: [Freesurfer] freesurfer commands from MATLAB

[Markus Gschwind]

Hi Barbara,

You haven't told us which OS you use.
For example in Mac OS it is necessary to start up MATLAB by typing matlab
into the X11 terminal, otherwise the system OS will not recognize the
commands given via matlab (e.g. system('mycommand') .)

Best,
Markus

2014-09-09 13:45 GMT+02:00 Barbara Kreilkamp bakk@googlemail.com:

 Dear Freesurfers,

 Is there a way of calling freesurfer-scripts from within MATLAB?
 I know there are some setups needed to make MATLAB understand where it can
 find the commands (I have done this before with FSL).
 I am using bash, and when I type the Freesurfer commands in a terminal by
 hand, they work. So I am guessing it must have to do with setting up the
 environment:

 freesurf_path ='Applications/freesurfer';
 setenv('FREESURFDIR',freesurf_path)

 setenv('FREESURFOUTPUTTYPE','NIFTI_GZ')
 curpath = getenv('PATH');
 setenv('PATH',sprintf('%s:%s',fullfile(freesurf_path,'bin'),curpath));

 Thanks a lot for any help,
 Barbara

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 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.


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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.

Re: [Freesurfer] a few short confirmatory questions

[Markus Gschwind]

Hi!

You probably mean

mris_expand

which creates a surf inside or outside of white, e.g.

mris_expand surf/lh.white -1 surf/lh.white_1mm_inside
# use positive values for outside ?h.white border

mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness
# this samples in % of GM thickness, use positive values for outside white

Best,
Markus




2014-08-13 20:57 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:


 You need a program whose name I can't remember. Bruce, what is the name
 of the program to create a surface midway between white and pial?

 Don, you can use this to create the mid surface (or project it to any
 depth) and to create a surface that is just inside the WM (use a
 negative projection distance). Then when you run mri_annotation2label
 specify each of these surfaces with --surf (you'll have to run it twice
 to get labels for each surface)



 On 08/13/2014 02:31 PM, Krieger, Donald N. wrote:
  Thanks for posting back so quickly and for the clarifications.
  What I am looking for is a list of vectors which are in the gray matter
 and a 2nd list that are inside the nearby white matter.
 
  It sounds like the white are inside the white matter but near the
 boundary with the gray.
  Is it reasonable to rely on each of these to be inside the white matter
 for at least say 1/2 mm in all directions from its xyz coordinate?
 
  You mention lists of nearest neighbors ... where may these be found as I
 definitely would like to use them or else likely must generate my own.
  In order to get the coordinates of a vector within the nearby gray
 matter, I was thinking to use a neighbor, perhaps not nearest but certainly
 close, in the direction of the nearest pial vector.  What do you think?
 
  An alternative is to use a nearby vector from the list in ribbon for
 the gray matter.
 
  Regards,
 
  Don
 
  -Original Message-
  From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
  boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
  Sent: Wednesday, August 13, 2014 2:21 PM
  To: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] a few short confirmatory questions
 
 
  On 08/13/2014 02:11 PM, Krieger, Donald N. wrote:
  mri_annotation2label enables extraction of vectors from .annot files
  to .label files, one file per label.
 
  One may choose orig, white, or pial vectors.
 
  (1)orig vectors are on the cortical surface. The gray scale value for
  each of these is that of gray matter, correct? And these are inside
  the pia and outside white, correct?
 
  orig is the first surface created by tessellating the white matter. It
 is a coarse,
  jagged surface on the voxel boundary. The white is the orig refined to
 follow
  the GM/WM boundary better. The orig is definitely inside the pia, but
 one
  cannot make a statement about its position relative to the white. I
 don't
  know what you mean by the gray scale value. The surface just has xyz
 values
  and lists of nearest neighbors.
  (2)white vectors are at the surface of the white matter just below the
  orig layer, correct? Their gray scale value is that of white matter,
  correct?
 
  Thanks,
 
  Don
 
 
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  --
  Douglas N. Greve, Ph.D.
  MGH-NMR Center
  gr...@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358
  Fax: 617-726-7422
 
  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
  ___
  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.
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 

 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 

Re: [Freesurfer] free surfer

[Markus Gschwind]

Hi,

You can see here what to do:
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
no 4., 5 and 6 especailly.

Cheers,
M


2014-06-18 0:45 GMT+02:00 Sam Raby rabysa...@gmail.com:

 I have downloaded the following file

 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

 and have extracted the contained files, and I was wondering where the
 binary file is so that I can open the freesurfer with?
 https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall

 thanks
 -S



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 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
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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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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Fwd: How to improve/fix TKMEDIT lag

[Markus Gschwind]

Hi Vy,

This is what my 2011 MBP gives:
$ glxgears
10235 frames in 5.0 seconds = 2046.978 FPS
10612 frames in 5.0 seconds = 2122.353 FPS
10689 frames in 5.0 seconds = 2137.778 FPS
14639 frames in 5.0 seconds = 2927.775 FPS
14584 frames in 5.0 seconds = 2915.777 FPS
14437 frames in 5.0 seconds = 2885.138 FPS

So yours is quite slow. Did you see the gears move smoothly or where they
stuttering?

What gives glxgears on your local terminal (without ssh to your server)?
You'll probably see the difference...

Best,
M





2014-06-03 23:39 GMT+02:00 Vy Dinh vdi...@wisc.edu:

  Hi Markus,

 Thanks for your help!

 Here's what I have after typing glxgears:

 16523 frames in 5.5 seconds = 3013.267 FPS
 362 frames in 5.4 seconds = 66.654 FPS
 367 frames in 6.5 seconds = 56.306 FPS
 381 frames in 277.1 seconds =  1.375 FPS
 16640 frames in 5.2 seconds = 3201.886 FPS
 262 frames in 6.1 seconds = 43.029 FPS
 372 frames in 5.4 seconds = 69.340 FPS
 262 frames in 5.7 seconds = 45.837 FPS
 383 frames in 6.4 seconds = 59.809 FPS
 382 frames in 6.7 seconds = 56.849 FPS
 369 frames in 5.4 seconds = 68.384 FPS
 364 frames in 6.4 seconds = 57.207 FPS
 370 frames in 5.7 seconds = 65.105 FPS
 263 frames in 5.4 seconds = 48.992 FPS
 381 frames in 6.4 seconds = 59.994 FPS
 381 frames in 5.7 seconds = 67.056 FPS
 253 frames in 5.3 seconds = 47.457 FPS
 383 frames in 6.3 seconds = 60.355 FPS
 383 frames in 6.7 seconds = 57.111 FPS
 394 frames in 6.3 seconds = 62.099 FPS
 385 frames in 6.7 seconds = 57.298 FPS
 325 frames in 5.4 seconds = 59.984 FPS
 372 frames in 6.7 seconds = 55.758 FPS
 408 frames in 6.4 seconds = 64.083 FPS
 391 frames in 6.7 seconds = 58.364 FPS
 340 frames in 5.4 seconds = 63.223 FPS
 374 frames in 6.3 seconds = 58.905 FPS

 Best,
 Vy


 On Tue, Jun 3, 2014 at 4:27 PM, Markus Gschwind markus.gschw...@gmail.com
  wrote:

 Hi!

 Can the connection be slow?

 Can you type in your local terminal and also in the ssh remote terminal
 the following:

 glxgears

 and let it run a while and past here the output.

 Cheers!
 Markus


 2014-06-03 23:16 GMT+02:00 Vy Dinh vdi...@wisc.edu:

 Hi,

 I discovered that installing Freesurfer onto my local workstation and
 running Tkmedit from there has resolved my issue. It doesn't explain why
 tkmedit is so slow when run from our server, so if you have some ideas
 please let me know. Thank you all for your help.

 Best,

 Vy


 On Tue, Jun 3, 2014 at 12:39 PM, Vy Dinh vydi...@gmail.com wrote:

 Thank you for your reply. All of our Freesurfer commands, including
 Tkmedit are run from the servers on the RedHat Machine. We use the ssh -Y
 syntax (not -X), and when I tried using -X instead, it doesn't change the
 speed of tkmedit.

 Additionally, I tried copying my data to another (department's) server
 at our institution and running tkmedit from there. We didn't experience any
 lag here, so this suggests that our department's dedicated server is
 somehow dealing with tkmedit differently. However, when our server expert
 checked the CPU usage, it appears that OUR department's server is using
 less RAM overall (so it if anything, our data should process more
 quickly.). In other words, we can't figure out how Tkmedit is utilized by
 the servers differently.

 -Vy


 On Tue, Jun 3, 2014 at 11:13 AM, dgw dgwake...@gmail.com wrote:

 Hi,

 What machine are you actually running tkmedit on?

 more specifically:
 You appear to be using a mac. Do you run tkmedit directly on the mac?

 or are you using ssh -X (or something like it to run it) on the Red
 Hat machines?

 Thanks,
 D


 On Tue, Jun 3, 2014 at 11:55 AM, Vy Dinh vdi...@wisc.edu wrote:


 Greetings Freesurfer developers,

 I'm looking for ways to improve the speed of TKMEDIT for Freesurfer
 5.3. Specifically, the GUI interface is abnormally slow; edits made to a
 voxel takes 1-2 seconds to show up on the screen. Interesting, the
 recon-all doesn't appear to be slow (as each subject has been processed
 within a 24 hr period), so I wonder if this problem has something to do
 with TKMEDIT's GUI  my current setup.

 Although I SSH into our server for data processing, here are the
 specs for my local workstation:

 Mac OSX 10.9.2
 2.7 GHz Intel Core i5 Determine how many cores (Apple icon  About
 this Mac  More Info)
 4 GB 1333 MHz DDR3

 Server Specs:

 Our App servers have 4 Xeon CPUs apiece, each with 8 cores running at
 2.7GHz, for a total of 32 cores (I was told that this shouldn't be the
 cause as the point of multi-core and multi-threading is not dependent on
 speed only). As well, each server has 94 GB of RAM.

 Our App servers mount shares via NFS from our file servers. All
 servers are the same version of Red Hat Linux, so there is no differences
 there. According to the server expert at our institution, the tkmedit 
 does
 not appear to surpass a CPU *utilization* of 8*%* of a single core,
 so the programs running off the server should be able to utilize its
 maximum speed.

 I am working closely with our server expert

Re: [Freesurfer] wm and pial edits - what to correct and what not?

[Markus Gschwind]

Dear Louis (and Bruce),

So I have run

recon-all -skullstrip -clean-bm -gcut -subjid subjid

on my subjects where remaining pieces of dura after a normal recon-all got
included into pial surface. I am having a look at the result before
continuing with autorecon2 etc.

Results are not yet satisfactory as there is still several centimeters of
dura included in the brainmask, mostly on the convex part of central regions

Is there a possibility to make graph-cut slightly more agressive?

Thank you for help!
Markus


 2014-04-07 22:40 GMT+02:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu
 :

 Hi Markus,
 It will only skullstrip the T1 and generate a new brainmask.mgz. So
 you'll need to run autorecon2 and 3 afterwards.
 -Louis


 On Mon, 7 Apr 2014, Markus Gschwind wrote:

  Dear Louis!
 Thank you for the link.

 It says I should use


 recon-all -skullstrip -clean-bm -gcut -subjid subjid
 My question is if this command only skullstrips and then stops and I
 would have to resume with
 autorecon2 etc. or if it continues until the end and overwrites the
 whole processing (I'd like to
 know before I mess up with te subject and have a further 16 hours
 processing for nothing... ;-)

 Thanks!
 Markus


 2014-04-07 20:01 GMT+02:00 Louis Nicholas Vinke 
 vi...@nmr.mgh.harvard.edu:
   Hi Markus,
   Instructions for using gcut within recon-all can be found on this
 wiki page, near the
   bottom.

   https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/
 SkullStripFix_freeview

   -Louis

   On Mon, 7 Apr 2014, Bruce Fischl wrote:

 Hi Markus

 that looks pretty blurry and low contrast, although it's
 hard to tell
 without windowing it. Does the intensity normalization
 remove the contrast?
 If so, you can try making it less aggressive with the
 -gentle flag or
 playing with individual parameters (like -b).

 I can't remember the graph cuts stuff. Hopefully Nick or
 Zeke or someone
 will point you in the right direction
 Bruce


 On Mon, 7 Apr 2014, Markus Gschwind wrote:

   Dear Bruce,

   Thanks for your detailed answer!

  it's tough to tell for sure on just a single
 slice,
   particularly if it is the intensity normalized one that
 removes a lot of the contrast if it is (as you
 suspect)
   doing the wrong thing. What does the orig look like?
 We try
 pretty hard to avoid including deep, highly
 myelinated
   gray matter inside the white matter surface, but of
 course if
 the contrast is low enough we can fail. If you
 scroll
   backwards and forward a few slices does or look in a
 different
 orientation does it look different/better?
 Sometimes the
   surface is curving sharply and this kind of thing will
 show
 up on a single slice, but actually isn't a
 significant
   inaccuracy.



   Yes, when scrolling throug the slides it really appears
   consistent across several slides (actually the attached
   screenshots
   showed Freeview in coronal, sagittal and axial
 perspective of
   the same region). Here is the orig attached together
 with the
   wm,
   pial and white.
   So how should I treat it?

  As for the dura, that certainly looks like a
 problem for
   thickness estimates. Have you tried using the graph
 cuts
 skull stripping? That is more aggressive than
   mri_watershed. You can also play with the watershed
 parameters
   to try
 to get more dura removed. Finally, if you have a
 T2-space
   FLAIR scan we can use that to properly reposition the
 surfaces (or less ideally, a T2-space scan
 without a FLAIR
   inversion).



   No, unfortunately there are no other images at
 disposition.

   How would one go with the graph cuts ?
   I found mri_gcut [-110| -mult filename |-T value]
   in_filename out_filename,

   but how is it run within recon-all in order to repair
 (FS
   version 5.3)?

   Thank you so much!
   Markus


   2014-04-07 14:47 GMT+02:00 Bruce Fischl
   fis...@nmr.mgh.harvard.edu:
 Hi Markus

 it's tough to tell for sure on just a single
 slice,
   particularly if it is the intensity normalized one
 that removes
 a lot of the contrast if it is (as you

Re: [Freesurfer] wm and pial edits - what to correct and what not?

[Markus Gschwind]

Thanks Louis!

Great. It seems I need -T 0.65. That looks fine.

Is it necessary
- to name the modified brainmask.gcuts.T065.mgz?
- and keep both brainmask.mgz and brainmask.gcuts.mgz in the mri folder?

And then continue with
recon-all autorecon2 autorecon3 -s subjectid

Is that correct?

Thank you so much!
Markus


2014-04-11 17:23 GMT+02:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu:

 Hi Markus,
 You can try running mri_gcut with a slightly higher T value, default is
 0.4.

 command would be something like (running from within subject's mri dir):
 mri_gcut -T 0.5 T1.mgz brainmask.gcuts.T-0.5.mgz

 Carefully inspect the output, overlaid as a heatmap on the T1 and/or
 previous brainmask.mgz.  You might have to clone back in some brain voxels.

 -Louis


 On Fri, 11 Apr 2014, Markus Gschwind wrote:

  Dear Louis (and Bruce),
 So I have run

 recon-all -skullstrip -clean-bm -gcut -subjid subjid
 on my subjects where remaining pieces of dura after a normal recon-all got
 included into pial surface. I am having a look at the result before
 continuing with autorecon2 etc.

 Results are not yet satisfactory as there is still several centimeters of
 dura included in the brainmask, mostly on the convex part of central
 regions

 Is there a possibility to make graph-cut slightly more agressive?

 Thank you for help!
 Markus


   2014-04-07 22:40 GMT+02:00 Louis Nicholas Vinke
   vi...@nmr.mgh.harvard.edu:
 Hi Markus,
 It will only skullstrip the T1 and generate a new
 brainmask.mgz. So you'll need to run autorecon2 and
 3 afterwards.
 -Louis

 On Mon, 7 Apr 2014, Markus Gschwind wrote:

   Dear Louis!
   Thank you for the link.

   It says I should use


   recon-all -skullstrip -clean-bm -gcut
   -subjid subjid
   My question is if this command only
   skullstrips and then stops and I would
   have to resume with
   autorecon2 etc. or if it continues until
   the end and overwrites the whole
   processing (I'd like to
   know before I mess up with te subject
   and have a further 16 hours processing
   for nothing... ;-)

   Thanks!
   Markus


   2014-04-07 20:01 GMT+02:00 Louis
   Nicholas Vinke
   vi...@nmr.mgh.harvard.edu:
 Hi Markus,
 Instructions for using gcut within
   recon-all can be found on this wiki
   page, near the
 bottom.

https://surfer.nmr.mgh.
 harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview


 -Louis

 On Mon, 7 Apr 2014, Bruce Fischl
   wrote:

   Hi Markus

   that looks pretty blurry and
   low contrast, although it's hard to tell
   without windowing it. Does
   the intensity normalization remove the
   contrast?
   If so, you can try making it
   less aggressive with the -gentle flag or
   playing with individual
   parameters (like -b).

   I can't remember the graph
   cuts stuff. Hopefully Nick or Zeke or
   someone
   will point you in the right
   direction
   Bruce


   On Mon, 7 Apr 2014, Markus
   Gschwind wrote:

 Dear Bruce,

 Thanks for your
   detailed answer!

it's tough to
   tell for sure on just a single slice,
 particularly if it is
   the intensity normalized one that
   removes a lot of
   the contrast if it is (as you suspect)
 doing the wrong thing.
   What does the orig look like? We try
   pretty hard to
   avoid including deep, highly myelinated
 gray matter inside the
   white matter surface, but of course if
   the contrast is
   low enough we can fail. If you scroll
 backwards and forward
   a few slices does or look in a different

Re: [Freesurfer] Mac OSX installations incomplete? What to do?

[Markus Gschwind]

Thank you Zeke, that seems to work all fine!
Best, Markus


2014-04-08 21:17 GMT+02:00 Z K zkauf...@nmr.mgh.harvard.edu:

 Markus,

 Thanks for pointing that out. I have added those files to the ftp link.

 -Zeke


 On 04/04/2014 04:16 PM, Markus Gschwind wrote:

 Thank you Zeke,

 What about these?

 /usr/local/freesurfer/bin/bet.fsl
 /usr/local/freesurfer/bin/flirt.fsl
 /usr/local/freesurfer/bin/slicetimer.fsl

 They are not there neither compared to the ubuntu install.

 Best,
 Markus




 2014-04-04 19:05 GMT+02:00 Z K zkauf...@nmr.mgh.harvard.edu
 mailto:zkauf...@nmr.mgh.harvard.edu:


 There are 3 missing fsl files from the OSX snow leopard installation.
 They can be downloaded from here:

 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/fsl

 Copy them into your $FREESURFER_HOME/bin directory.

 -Zeke



 On 04/04/2014 12:32 PM, Markus Gschwind wrote:
   Dear Freesurfers,
  
   As discovered here,
  
  
 http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.
 edu/msg35160.html
  
   it seams that some Mac OSX installations suffered from incomplete
 files.
  
   I just veryfied that I had downloaded the complete image and wget
 says yes:
  
   Logging in as anonymous ... Logged in!
   == SYST ... done.== PWD ... done.
   == TYPE I ... done.  == CWD (1) /pub/dist/freesurfer/5.3.0
 ... done.
   == SIZE freesurfer-Darwin-snowleopard-
 i686-stable-pub-v5.3.0.dmg
   ... 3394499614
   File has already been retrieved.
   2014-04-04 18:24:26 (0.00 B/s) -
   'freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg'
 saved
   [3394499614]
  
  
   So this is what I installed recently and it seems that there are
 some
   files missing (at least some of the fsl-functions in bin).
  
   Doug, you said that you suspected that it could be a problem of the
   installer script?
  
   What should we do (also Eiran) in order to complete the
 installation?
  
   Thanks for you work!
   Markus
  
  
   ___
   Freesurfer mailing list
   Freesurfer@nmr.mgh.harvard.edu
 mailto:Freesurfer@nmr.mgh.harvard.edu

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




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


___
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.

Re: [Freesurfer] wm and pial edits - what to correct and what not?

[Markus Gschwind]

Dear Louis!

Thank you for the link.

It says I should use


recon-all -skullstrip -clean-bm -gcut -subjid subjid

My question is if this command only skullstrips and then stops and I would
have to resume with autorecon2 etc. or if it continues until the end and
overwrites the whole processing (I'd like to know before I mess up with te
subject and have a further 16 hours processing for nothing... ;-)

Thanks!
Markus


2014-04-07 20:01 GMT+02:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu:

 Hi Markus,
 Instructions for using gcut within recon-all can be found on this wiki
 page, near the bottom.

 https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/
 SkullStripFix_freeview

 -Louis


 On Mon, 7 Apr 2014, Bruce Fischl wrote:

  Hi Markus

 that looks pretty blurry and low contrast, although it's hard to tell
 without windowing it. Does the intensity normalization remove the contrast?
 If so, you can try making it less aggressive with the -gentle flag or
 playing with individual parameters (like -b).

 I can't remember the graph cuts stuff. Hopefully Nick or Zeke or someone
 will point you in the right direction
 Bruce


 On Mon, 7 Apr 2014, Markus Gschwind wrote:

  Dear Bruce,

 Thanks for your detailed answer!

it's tough to tell for sure on just a single slice, particularly
 if it is the intensity normalized one that
   removes a lot of the contrast if it is (as you suspect) doing the
 wrong thing. What does the orig look like? We try
   pretty hard to avoid including deep, highly myelinated gray matter
 inside the white matter surface, but of course if
   the contrast is low enough we can fail. If you scroll backwards
 and forward a few slices does or look in a different
   orientation does it look different/better? Sometimes the surface
 is curving sharply and this kind of thing will show
   up on a single slice, but actually isn't a significant inaccuracy.



 Yes, when scrolling throug the slides it really appears consistent
 across several slides (actually the attached screenshots
 showed Freeview in coronal, sagittal and axial perspective of the same
 region). Here is the orig attached together with the wm,
 pial and white.
 So how should I treat it?

As for the dura, that certainly looks like a problem for
 thickness estimates. Have you tried using the graph cuts
   skull stripping? That is more aggressive than mri_watershed. You
 can also play with the watershed parameters to try
   to get more dura removed. Finally, if you have a T2-space FLAIR
 scan we can use that to properly reposition the
   surfaces (or less ideally, a T2-space scan without a FLAIR
 inversion).



 No, unfortunately there are no other images at disposition.

 How would one go with the graph cuts ?
 I found mri_gcut [-110| -mult filename |-T value] in_filename
 out_filename,

 but how is it run within recon-all in order to repair (FS version 5.3)?

 Thank you so much!
 Markus


 2014-04-07 14:47 GMT+02:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:
   Hi Markus

   it's tough to tell for sure on just a single slice, particularly
 if it is the intensity normalized one that removes
   a lot of the contrast if it is (as you suspect) doing the wrong
 thing. What does the orig look like? We try pretty
   hard to avoid including deep, highly myelinated gray matter inside
 the white matter surface, but of course if the
   contrast is low enough we can fail. If you scroll backwards and
 forward a few slices does or look in a different
   orientation does it look different/better? Sometimes the surface
 is curving sharply and this kind of thing will show
   up on a single slice, but actually isn't a significant inaccuracy.


   As for the dura, that certainly looks like a problem for thickness
 estimates. Have you tried using the graph cuts
   skull stripping? That is more aggressive than mri_watershed. You
 can also play with the watershed parameters to try
   to get more dura removed. Finally, if you have a T2-space FLAIR
 scan we can use that to properly reposition the
   surfaces (or less ideally, a T2-space scan without a FLAIR
 inversion).

   cheers
   Bruce


   On Mon, 7 Apr 2014, Markus Gschwind wrote:

 Dear all,
 I would like to show some very frequent and typical cases of
 segmentation
 problems in my bunch of data of normal subjects (after
 recon-all), of which
 I couldn't find a description in the
 wiki(http://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/
 FreeviewWorkingWith
 Data/FreeviewEditingaRecon).

 I am therefore not sure if these types of error are serious
 and will affect
 later results like thickness, curvature, GWR, etc.

 Here are the examples (c.f. attached screenshots from
 Freeview)

 1) In the primary sensory-motor cortex it frequently happens
 that the
 ?h.white

Re: [Freesurfer] wm and pial edits - what to correct and what not?

[Markus Gschwind]

Great, thanks! I'll give it a try!
Best, Markus


2014-04-07 22:40 GMT+02:00 Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu:

 Hi Markus,
 It will only skullstrip the T1 and generate a new brainmask.mgz. So you'll
 need to run autorecon2 and 3 afterwards.
 -Louis


 On Mon, 7 Apr 2014, Markus Gschwind wrote:

  Dear Louis!
 Thank you for the link.

 It says I should use


 recon-all -skullstrip -clean-bm -gcut -subjid subjid
 My question is if this command only skullstrips and then stops and I
 would have to resume with
 autorecon2 etc. or if it continues until the end and overwrites the whole
 processing (I'd like to
 know before I mess up with te subject and have a further 16 hours
 processing for nothing... ;-)

 Thanks!
 Markus


 2014-04-07 20:01 GMT+02:00 Louis Nicholas Vinke 
 vi...@nmr.mgh.harvard.edu:
   Hi Markus,
   Instructions for using gcut within recon-all can be found on this
 wiki page, near the
   bottom.

   https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/
 SkullStripFix_freeview

   -Louis

   On Mon, 7 Apr 2014, Bruce Fischl wrote:

 Hi Markus

 that looks pretty blurry and low contrast, although it's hard
 to tell
 without windowing it. Does the intensity normalization remove
 the contrast?
 If so, you can try making it less aggressive with the -gentle
 flag or
 playing with individual parameters (like -b).

 I can't remember the graph cuts stuff. Hopefully Nick or Zeke
 or someone
 will point you in the right direction
 Bruce


 On Mon, 7 Apr 2014, Markus Gschwind wrote:

   Dear Bruce,

   Thanks for your detailed answer!

  it's tough to tell for sure on just a single
 slice,
   particularly if it is the intensity normalized one that
 removes a lot of the contrast if it is (as you
 suspect)
   doing the wrong thing. What does the orig look like? We
 try
 pretty hard to avoid including deep, highly
 myelinated
   gray matter inside the white matter surface, but of
 course if
 the contrast is low enough we can fail. If you
 scroll
   backwards and forward a few slices does or look in a
 different
 orientation does it look different/better?
 Sometimes the
   surface is curving sharply and this kind of thing will
 show
 up on a single slice, but actually isn't a
 significant
   inaccuracy.



   Yes, when scrolling throug the slides it really appears
   consistent across several slides (actually the attached
   screenshots
   showed Freeview in coronal, sagittal and axial
 perspective of
   the same region). Here is the orig attached together
 with the
   wm,
   pial and white.
   So how should I treat it?

  As for the dura, that certainly looks like a
 problem for
   thickness estimates. Have you tried using the graph cuts
 skull stripping? That is more aggressive than
   mri_watershed. You can also play with the watershed
 parameters
   to try
 to get more dura removed. Finally, if you have a
 T2-space
   FLAIR scan we can use that to properly reposition the
 surfaces (or less ideally, a T2-space scan
 without a FLAIR
   inversion).



   No, unfortunately there are no other images at
 disposition.

   How would one go with the graph cuts ?
   I found mri_gcut [-110| -mult filename |-T value]
   in_filename out_filename,

   but how is it run within recon-all in order to repair
 (FS
   version 5.3)?

   Thank you so much!
   Markus


   2014-04-07 14:47 GMT+02:00 Bruce Fischl
   fis...@nmr.mgh.harvard.edu:
 Hi Markus

 it's tough to tell for sure on just a single
 slice,
   particularly if it is the intensity normalized one that
 removes
 a lot of the contrast if it is (as you suspect)
 doing the
   wrong thing. What does the orig look like? We try pretty
 hard to avoid including deep, highly myelinated
 gray
   matter inside the white matter surface, but of course
 if the
 contrast is low enough we can fail. If you scroll
   backwards and forward a few slices does or look in a
 different
 orientation does it look

[Freesurfer] Mac OSX installations incomplete? What to do?

[Markus Gschwind]

Dear Freesurfers,

As discovered here,

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35160.html

it seams that some Mac OSX installations suffered from incomplete files.

I just veryfied that I had downloaded the complete image and wget says yes:

Logging in as anonymous ... Logged in!
 == SYST ... done.== PWD ... done.
 == TYPE I ... done.  == CWD (1) /pub/dist/freesurfer/5.3.0 ... done.
 == SIZE freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg ...
 3394499614
 File has already been retrieved.
 2014-04-04 18:24:26 (0.00 B/s) -
 'freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg' saved
 [3394499614]


So this is what I installed recently and it seems that there are some files
missing (at least some of the fsl-functions in bin).

Doug, you said that you suspected that it could be a problem of the
installer script?

What should we do (also Eiran) in order to complete the installation?

Thanks for you work!
Markus
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Re: [Freesurfer] Mac OSX installations incomplete? What to do?

[Markus Gschwind]

Thank you Zeke,

What about these?

/usr/local/freesurfer/bin/bet.fsl
/usr/local/freesurfer/bin/flirt.fsl
/usr/local/freesurfer/bin/slicetimer.fsl

They are not there neither compared to the ubuntu install.

Best,
Markus




2014-04-04 19:05 GMT+02:00 Z K zkauf...@nmr.mgh.harvard.edu:

 There are 3 missing fsl files from the OSX snow leopard installation.
 They can be downloaded from here:

 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/fsl

 Copy them into your $FREESURFER_HOME/bin directory.

 -Zeke



 On 04/04/2014 12:32 PM, Markus Gschwind wrote:
  Dear Freesurfers,
 
  As discovered here,
 
  http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35160.html
 
  it seams that some Mac OSX installations suffered from incomplete files.
 
  I just veryfied that I had downloaded the complete image and wget says
 yes:
 
  Logging in as anonymous ... Logged in!
  == SYST ... done.== PWD ... done.
  == TYPE I ... done.  == CWD (1) /pub/dist/freesurfer/5.3.0 ...
 done.
  == SIZE freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg
  ... 3394499614
  File has already been retrieved.
  2014-04-04 18:24:26 (0.00 B/s) -
  'freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg' saved
  [3394499614]
 
 
  So this is what I installed recently and it seems that there are some
  files missing (at least some of the fsl-functions in bin).
 
  Doug, you said that you suspected that it could be a problem of the
  installer script?
 
  What should we do (also Eiran) in order to complete the installation?
 
  Thanks for you work!
  Markus
 
 
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  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
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 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
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 properly
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Re: [Freesurfer] preprocessing question

[Markus Gschwind]

Hi Eiran and Doug,

I do not have bet.fsl neither (c.f. previous mail with the list of what I
had).

It seems that there is quite some more missing in the mac build...

This is what I find on my ubuntu
installation freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

$ ls $FREESURFER_HOME/bin/*.fsl
/usr/local/freesurfer/bin/bet.fsl
/usr/local/freesurfer/bin/epidewarp.fsl
/usr/local/freesurfer/bin/flirt.fsl
/usr/local/freesurfer/bin/fscalc.fsl
/usr/local/freesurfer/bin/fslmaths.fsl
/usr/local/freesurfer/bin/fslorient.fsl
/usr/local/freesurfer/bin/fslswapdim.fsl
/usr/local/freesurfer/bin/mri_motion_correct.fsl
/usr/local/freesurfer/bin/slicetimer.fsl

$ ls $FREESURFER_HOME/bin/fsl*
/usr/local/freesurfer/bin/fsl_label2voxel
/usr/local/freesurfer/bin/fslmaths.fsl
/usr/local/freesurfer/bin/fslorient.fsl
/usr/local/freesurfer/bin/fslregister
/usr/local/freesurfer/bin/fsl_rigid_register
/usr/local/freesurfer/bin/fsl_sub_mgh
/usr/local/freesurfer/bin/fslswapdim.fsl


And this is what I have on my Mac OSX installation (freesurfer-Darwin-
snowleopard-i686-stable-pub-v5.3.0)


 $ which $FREESURFER_HOME/bin/fsl*
 /Applications/freesurfer/bin/fsl_label2voxel
 /Applications/freesurfer/bin/fsl_rigid_register
 /Applications/freesurfer/bin/fsl_sub_mgh
 /Applications/freesurfer/bin/fslregister



 $ which $FREESURFER_HOME/bin/*.fsl
 /Applications/freesurfer/bin/epidewarp.fsl
 /Applications/freesurfer/bin/fscalc.fsl
 /Applications/freesurfer/bin/mri_motion_correct.fsl



Best,
Markus




2014-04-03 13:35 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il:

 Hi Doug,
 I changed the file permissions to be executable and it passed this stage.
 It then gets stuck when looking for bet.fsl:

 # -- Using FSL's BET to Extract Brain-- #
 /applications/freesurfer/BSMT_project/bsmt103/bold
 bet.fsl /tmp/mkbrainmask_76128/in.nii /tmp/mkbrainmask_76128/brain -m -f
 0.1
 bet.fsl: Command not found.
 ERROR: bet failed

 Was there something wrong in the insatallation that it is missing those
 files?
 Thanks!
 Eiran

 From: freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [
 gr...@nmr.mgh.harvard.edu]
 Sent: Wednesday, April 02, 2014 5:21 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] preprocessing question

 a couple of thiings to check: make sure it is exectuable and make sure
 that you rehash your path. Make sure that if you type fslmaths.fsl that
 it runs something

 On 04/02/2014 03:23 AM, Eiran Harel wrote:
  Thanks Doug, i downloaded it and now the file exists:
 
  $FREESURFER_HOME/bin/fslmaths.fsl
 
  Unfortuantely it is still not running and gives the same error when
 running preproc-sess:
 
  mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1
 -nerode 0
  ERROR: cannot find either fslmaths for avwmaths
 
  How can i proceed?
  Thanks,
  Eiran
  
  From: freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [
 gr...@nmr.mgh.harvard.edu]
  Sent: Wednesday, April 02, 2014 12:41 AM
  To: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] preprocessing question
 
  thanks, it must be something in our distribution script affecting mac
 
  On 04/01/2014 05:13 PM, Markus Gschwind wrote:
  Thanks Doug,
 
  I notice that on my Mac
  build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
 
  ...I don't have fslmaths.fsl neither. There are only
 
   $ which $FREESURFER_HOME/bin/fsl*
   /Applications/freesurfer/bin/fsl_label2voxel
   /Applications/freesurfer/bin/fsl_rigid_register
   /Applications/freesurfer/bin/fsl_sub_mgh
   /Applications/freesurfer/bin/fslregister
 
   $ which $FREESURFER_HOME/bin/*.fsl
   /Applications/freesurfer/bin/epidewarp.fsl
   /Applications/freesurfer/bin/fscalc.fsl
   /Applications/freesurfer/bin/mri_motion_correct.fsl
 
  (I never executed the above mentioned process of Eiran thoug...)
 
  Best,
  Markus
 
 
 
 
 
  2014-04-01 18:36 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu:
 
   That is weird. You can get a copy from here
 
 
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac
 
   copy it to
 
   $FREESURFER_HOME/bin/fslmaths.fsl
 
 
   On 04/01/2014 12:25 PM, Eiran Harel wrote:
Hi Doug,
No, it does not exist.
What should i do?
Thanks,
Eiran

From: freesurfer-boun...@nmr.mgh.harvard.edu
   mailto:freesurfer-boun...@nmr.mgh.harvard.edu
   [freesurfer-boun...@nmr.mgh.harvard.edu
   mailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of
   Douglas N Greve [gr...@nmr.mgh.harvard.edu
   mailto:gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, April 01, 2014 7:16 PM
To: freesurfer@nmr.mgh.harvard.edu
   mailto:freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Display tkmedit image of surface after mri_vol2surf with projfrac or projdist

[Markus Gschwind]

Hi Ruthger!

Use mris_expand to create a surf inside or outside of white

e.g.

mris_expand surf/lh.white -1 surf/lh.white_1mm_inside
# use positive values for outside ?h.white border

mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness
# this samples in % of GM thickness, use positive values for outside white

Cheers!
Markus


2014-04-03 16:24 GMT+02:00 Righart, Ruthger righ...@lrz.tu-muenchen.de:

 Hi All,

 mri_vol2surf has the flags --projfrac and --projdist. If I understand
 these flags correctly, the volume is sampled inbetween the white-matter
 surface and the pial surface (for ex. --projfrac 0.5 is midway). Is
 there a possibility in tkmedit/Freeview to display with a colored line
 for ex. --projfrac 0.5 for a given subject? (actually similar to what
 was done by Salat et al., NeuroImage 2009, 48, p23, fig 1A,
 http://surfer.nmr.mgh.harvard.edu/pub/articles/salat_2009.pdf).

 Thank you very much in advance for your help!

 All the best,

 Ruthger
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 e-mail
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Re: [Freesurfer] preprocessing question

[Markus Gschwind]

Hi!

Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)
What happens if you type in your terminal
fslmaths
?

Best,
Markus
2014-04-01 9:59 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il:

Dear freesurfers,
 I have installed freesurfer and fsl on my Mac:

  * freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 *
 *Setting up environment for FreeSurfer/FS-FAST (and FSL)*
 *FREESURFER_HOME   /Applications/freesurfer*
 *FSFAST_HOME   /Applications/freesurfer/fsfast*
 *FSF_OUTPUT_FORMAT nii.gz*
 *SUBJECTS_DIR  /Applications/freesurfer/subjects*
 *MNI_DIR   /Applications/freesurfer/mni*
 *FSL_DIR   /usr/local/fsl*

 I am trying to run Preproc-sess command:

  *preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm 5 -fsd
 bold -stc odd -per-run -force*

 and get this error:

  *mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil
 1 -nerode 0*
 *ERROR: cannot find either fslmaths for avwmaths*

  Any suggestions?
 Thanks!
 Eiran




   http://www.tasmc.org.il/be-well/Pages/default.aspx
 https://www.facebook.com/ichilov.medical http://twitter.com/tasmc1
 http://www.youtube.com/tasmc1
 http://www.tasmc.org.il/sites/en/Pages/default.aspx

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 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
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 HelpLine at
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Re: [Freesurfer] preprocessing question

[Markus Gschwind]

Hi,

Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that
can be used in FSL, I think it is not necessary to have matlab working for
FSL to work.

There are many more matlab utils in Freesurfer ($FREESURFER_HOME/matlab).

The error message tells you that freesurfer doesn't find fslmaths in the
fsl directory...

Can you post here the exact result of

 more $FSL_DIR/etc/fslversion

and

echo $FSLDIR #(without the _ between FSL and DIR!)

Best,
Markus











2014-04-01 12:13 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il:

 Hi Markus,
 Thanks, it's is in FSL_DIR   /usr/local/fsl.
 Is MATLAB necessary to run FSL?
 EIran




 *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [
 markus.gschw...@gmail.com]
 *Sent:* Tuesday, April 01, 2014 12:55 PM

 *To:* Freesurfer support list
 *Subject:* Re: [Freesurfer] preprocessing question

   Hi,
 what does it say when you type
 which fsl
 which fslmath
 ?

  It mud be the same thing as
 FSL_DIR   /usr/local/fsl

  It is possible that the FSL_DIR specified in the freesurfersetup is not
 the good one...

 Best,
 Markus


 2014-04-01 10:25 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il:

 Hi Markus,
 Thanks, i did install fsl and when i type fslmaths it gives me the help
 for that command.
 Any other suggestions?
 Eiran
  --




 *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [
 markus.gschw...@gmail.com]
 *Sent:* Tuesday, April 01, 2014 11:11 AM
 *To:* Freesurfer support list
 *Subject:* Re: [Freesurfer] preprocessing question

Hi!

 Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)
 What happens if you type in your terminal
 fslmaths
 ?

 Best,
 Markus
  2014-04-01 9:59 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il:

 Dear freesurfers,
 I have installed freesurfer and fsl on my Mac:

  * freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
 *
 *Setting up environment for FreeSurfer/FS-FAST (and FSL)*
 *FREESURFER_HOME   /Applications/freesurfer*
 *FSFAST_HOME   /Applications/freesurfer/fsfast*
 *FSF_OUTPUT_FORMAT nii.gz*
 *SUBJECTS_DIR  /Applications/freesurfer/subjects*
 *MNI_DIR   /Applications/freesurfer/mni*
 *FSL_DIR   /usr/local/fsl*

  I am trying to run Preproc-sess command:

  *preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm 5 -fsd
 bold -stc odd -per-run -force*

  and get this error:

  *mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1
 -ndil 1 -nerode 0*
 *ERROR: cannot find either fslmaths for avwmaths*

  Any suggestions?
 Thanks!
 Eiran




   http://www.tasmc.org.il/be-well/Pages/default.aspx
 https://www.facebook.com/ichilov.medical http://twitter.com/tasmc1
 http://www.youtube.com/tasmc1
 http://www.tasmc.org.il/sites/en/Pages/default.aspx

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 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
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 in error
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Re: [Freesurfer] preprocessing question

[Markus Gschwind]

Well, Eiran,

That seems all fine.

Maybe Bruce or Doug can jump in and help?

Sorry!
Markus



2014-04-01 15:25 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il:

Hi Markus,

  [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran%
 more $FSL_DIR/etc/fslversion
 5.0.6
 [Eran-Harels-MacBook-Pro:/Applications/freesurfer/BSMT_PROJECT] eiran%
 echo $FSLDIR
 /usr/local/fsl

 Thanks!
 Eiran




  *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [
 markus.gschw...@gmail.com]
 *Sent:* Tuesday, April 01, 2014 2:48 PM

 *To:* Freesurfer support list
 *Subject:* Re: [Freesurfer] preprocessing question

   Hi,

 Although there are matlab utils as part of FSL in $FSL_DIR/etc/matlab that
 can be used in FSL, I think it is not necessary to have matlab working for
 FSL to work.

 There are many more matlab utils in Freesurfer ($FREESURFER_HOME/matlab).

 The error message tells you that freesurfer doesn't find fslmaths in the
 fsl directory...

 Can you post here the exact result of

  more $FSL_DIR/etc/fslversion

 and

 echo $FSLDIR #(without the _ between FSL and DIR!)

 Best,
 Markus











 2014-04-01 12:13 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il:

Hi Markus,
 Thanks, it's is in FSL_DIR   /usr/local/fsl.
 Is MATLAB necessary to run FSL?
 EIran




  *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [
 markus.gschw...@gmail.com]
 *Sent:* Tuesday, April 01, 2014 12:55 PM

 *To:* Freesurfer support list
 *Subject:* Re: [Freesurfer] preprocessing question

   Hi,
 what does it say when you type
 which fsl
 which fslmath
 ?

 It mud be the same thing as
 FSL_DIR   /usr/local/fsl

 It is possible that the FSL_DIR specified in the freesurfersetup is not
 the good one...

 Best,
 Markus


 2014-04-01 10:25 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il:

Hi Markus,
 Thanks, i did install fsl and when i type fslmaths it gives me the help
 for that command.
 Any other suggestions?
 Eiran
  --




 *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Markus Gschwind [
 markus.gschw...@gmail.com]
 *Sent:* Tuesday, April 01, 2014 11:11 AM
 *To:* Freesurfer support list
 *Subject:* Re: [Freesurfer] preprocessing question

   Hi!

 Have you installed FSL? (http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)
 What happens if you type in your terminal
 fslmaths
 ?

 Best,
 Markus
 2014-04-01 9:59 GMT+02:00 Eiran Harel eir...@tlvmc.gov.il:

Dear freesurfers,
 I have installed freesurfer and fsl on my Mac:

  * freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
 *
 *Setting up environment for FreeSurfer/FS-FAST (and FSL)*
 *FREESURFER_HOME   /Applications/freesurfer*
 *FSFAST_HOME   /Applications/freesurfer/fsfast*
 *FSF_OUTPUT_FORMAT nii.gz*
 *SUBJECTS_DIR  /Applications/freesurfer/subjects*
 *MNI_DIR   /Applications/freesurfer/mni*
 *FSL_DIR   /usr/local/fsl*

 I am trying to run Preproc-sess command:

  *preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm 5 -fsd
 bold -stc odd -per-run -force*

 and get this error:

  *mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1
 -ndil 1 -nerode 0*
 *ERROR: cannot find either fslmaths for avwmaths*

  Any suggestions?
 Thanks!
 Eiran




   http://www.tasmc.org.il/be-well/Pages/default.aspx
 https://www.facebook.com/ichilov.medical http://twitter.com/tasmc1
 http://www.youtube.com/tasmc1
 http://www.tasmc.org.il/sites/en/Pages/default.aspx

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 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
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Re: [Freesurfer] preprocessing question

[Markus Gschwind]

Thanks Doug,

I notice that on my Mac
build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0

...I don't have fslmaths.fsl neither. There are only

$ which $FREESURFER_HOME/bin/fsl*
 /Applications/freesurfer/bin/fsl_label2voxel
 /Applications/freesurfer/bin/fsl_rigid_register
 /Applications/freesurfer/bin/fsl_sub_mgh
 /Applications/freesurfer/bin/fslregister



 $ which $FREESURFER_HOME/bin/*.fsl
 /Applications/freesurfer/bin/epidewarp.fsl
 /Applications/freesurfer/bin/fscalc.fsl
 /Applications/freesurfer/bin/mri_motion_correct.fsl


(I never executed the above mentioned process of Eiran thoug...)

Best,
Markus





2014-04-01 18:36 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:

 That is weird. You can get a copy from here


 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac

 copy it to

 $FREESURFER_HOME/bin/fslmaths.fsl


 On 04/01/2014 12:25 PM, Eiran Harel wrote:
  Hi Doug,
  No, it does not exist.
  What should i do?
  Thanks,
  Eiran
  
  From: freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [
 gr...@nmr.mgh.harvard.edu]
  Sent: Tuesday, April 01, 2014 7:16 PM
  To: freesurfer@nmr.mgh.harvard.edu
  Subject: Re: [Freesurfer] preprocessing question
 
  does $FREESURFER_HOME/bin/fslmaths.fsl exist?
 
  On 04/01/2014 03:59 AM, Eiran Harel wrote:
  Dear freesurfers,
  I have installed freesurfer and fsl on my Mac:
  *
  *
  * freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 *
  *Setting up environment for FreeSurfer/FS-FAST (and FSL)*
  *FREESURFER_HOME   /Applications/freesurfer*
  *FSFAST_HOME   /Applications/freesurfer/fsfast*
  *FSF_OUTPUT_FORMAT nii.gz*
  *SUBJECTS_DIR  /Applications/freesurfer/subjects*
  *MNI_DIR   /Applications/freesurfer/mni*
  *FSL_DIR   /usr/local/fsl*
 
  I am trying to run Preproc-sess command:
 
  *preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm 5 -fsd
  bold -stc odd -per-run -force*
 
  and get this error:
 
  *mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1
  -ndil 1 -nerode 0*
  *ERROR: cannot find either fslmaths for avwmaths*
  *
  *
  Any suggestions?
  Thanks!
  Eiran
 
 
 
 
  http://www.tasmc.org.il/be-well/Pages/default.aspx
  https://www.facebook.com/ichilov.medical
  http://twitter.com/tasmc1   http://www.youtube.com/tasmc1
  http://www.tasmc.org.il/sites/en/Pages/default.aspx
 
 
 
 
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  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
  --
  Douglas N. Greve, Ph.D.
  MGH-NMR Center
  gr...@nmr.mgh.harvard.edu
  Phone Number: 617-724-2358
  Fax: 617-726-7422
 
  Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
  FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
  www.nmr.mgh.harvard.edu/facility/filedrop/index.html
  Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 
  ___
  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.
 
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 

 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] how to capture blurred GM/WM junction?

[Markus Gschwind]

Thank you Bruce, this works great.

This is just for the records:

$ mris_expand -thickness surf/lh.white 0.35 surf/lh.white_outer0.35GM
 using distance as a % of thickness
 expanding surface surf/lh.white by 35.0% of thickness and writing it to
 surf/lh.white_outer0.35GM



 $ mris_expand surf/lh.white -1 surf/lh.white_inner1mmWM
 expanding surface surf/lh.white by -1.0 mm and writing it to
 surf/lh.white_inner1mmWM


Thanks again!



2014-03-27 13:29 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:

 Hi Markus

 use mris_expand.

 cheers
 Bruce

 On Thu, 27 Mar 2014, Markus Gschwind wrote:

  Thank you, Doug!
 One last question:
 - Using which command would one construct the ?h.white -1mm surface and
 the ?h.white+30%GM surface for visualisation purposes as in Salat
  Figure
 1(http://www.sciencedirect.com/science/article/pii/
 S1053811910013261?via=ihu
 b)?

 Thank you!
 Markus



 2014-03-26 15:36 GMT+01:00 Douglas Greve gr...@nmr.mgh.harvard.edu:

   On 3/26/14 8:24 AM, Markus Gschwind wrote:
   Dear Doug and Bruce,
 I have three more questions concerning 'pctsurfcon'.

 1) The inner sampling distance is set to 1mm by default, but the
 outer sampling is done at a 30% of the cortical thickness. I saw
 that I could easily change the parameters or modify the script,
 but I wonder why this has been chosen like this. What was the
 rationale?

 A fixed distance of 1mm was used to help prevent the WM sample from
 projecting so far back that it samples GM behind it. I can't
 remember how I choose 30% (instead of 50%). I think David Salat used
 slightly different parameters in his paper.



 2) I think it is possible to run glmfit on the ?h.w-g.pct.mgh
 file in order to get some group stats, right?

 Yes

 3) Is it also possibe to run the xhemi on the w-g.pct.mgh file?

 Yes
 doug


 Thank you so much!
 Markus


 2014-03-24 23:51 GMT+01:00 Markus Gschwind
 markus.gschw...@gmail.com:
   Whow that is great!! Thank you so much Doug, I was
   not aware of this! That's what I needed it seems.
   Thanks Bruce and Doug!
 Markus


 2014-03-24 23:21 GMT+01:00 Douglas N Greve
 gr...@nmr.mgh.harvard.edu:

   you might want to look at the pctsurfcon
   script to see if that gets you
   where you want to be

   On 03/24/2014 06:18 PM, Bruce Fischl wrote:
it really depends on the size of the
   abnormality. I would guess 2 is
too big, and you want something more like 1,
   and sampling not averaging
On Mon, 24 Mar 2014, Markus Gschwind wrote:
   
Hi Bruce!
Ok I see, great! Tank you!
   
So to double check, this will be something
   like :
   
mri_vol2surf \
   
   
  --mov /mri/nu.mgz \
  --ref /mri/nu.mgz \
   
  --surf /surf/lh.white
  --projdist mmdist -2 \ # for inside white
   
   
  # --projdist mmdist 2 \ # for outside
   white
  --interp trilinear \
  --hemi lh \
  --out lh.nu_inside_white.mgh
   
   
I am not sure which one to use from those,
   as I want to compare stable
values but distant from white.
   
   
   --projfrac-avg min max del : average
   along normal
   --projdist mmdist : distance projection
   along normal
   --projdist-avg min max del : average
   along normal
   
What would you recommend?
Thank you again!
Markus
   
   
   
   
   
   
   
2014-03-24 21:29 GMT+01:00 Bruce Fischl
   fis...@nmr.mgh.harvard.edu:
  Hi Markus
   
  I wouldn't use brainmask as it has
   been normalized too
  aggressivley. Maybe the nu.mgz. Look
   at the difference between
  values just outside of it and just
   inside of it
   
  cheers
  Bruce
   
   
  On Mon, 24 Mar 2014, Markus Gschwind
   wrote:
   
Dear Bruce,
Thanks for the rapid answer!
   
Do you mean that I take the
   voxel values of
brainmask.mgz at the place
   where
the ?h.white surface passes,
   right?
   
I thought that the ?l.white
   surface marks the limit
between GM and WM as a
result of a binary decision.
I would be interested in the
   local certainty of this
decision. I thought
this is represented by the
   slope between the values
around 70 and those
100.
   
Thanks again,
Markus
   
   
   
   
   
   
2014-03-24 19:26 GMT+01:00
   Bruce Fischl
fis...@nmr.mgh.harvard.edu

Re: [Freesurfer] how to capture blurred GM/WM junction?

[Markus Gschwind]

Dear Doug and Bruce,

I have three more questions concerning 'pctsurfcon'.

1) The inner sampling distance is set to 1mm by default, but the outer
sampling is done at a 30% of the cortical thickness. I saw that I could
easily change the parameters or modify the script, but I wonder why this
has been chosen like this. What was the rationale?

2) I think it is possible to run glmfit on the ?h.w-g.pct.mgh file in order
to get some group stats, right?

3) Is it also possibe to run the xhemi on the w-g.pct.mgh file?

Thank you so much!
Markus


2014-03-24 23:51 GMT+01:00 Markus Gschwind markus.gschw...@gmail.com:

 Whow that is great!! Thank you so much Doug, I was not aware of this!
 That's what I needed it seems.
 Thanks Bruce and Doug!
 Markus


 2014-03-24 23:21 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:


 you might want to look at the pctsurfcon script to see if that gets you
 where you want to be

 On 03/24/2014 06:18 PM, Bruce Fischl wrote:
  it really depends on the size of the abnormality. I would guess 2 is
  too big, and you want something more like 1, and sampling not averaging
  On Mon, 24 Mar 2014, Markus Gschwind wrote:
 
  Hi Bruce!
  Ok I see, great! Tank you!
 
  So to double check, this will be something like :
 
  mri_vol2surf \
 
 
--mov /mri/nu.mgz \
--ref /mri/nu.mgz \
 
--surf /surf/lh.white
--projdist mmdist -2 \ # for inside white
 
 
# --projdist mmdist 2 \ # for outside white
--interp trilinear \
--hemi lh \
--out lh.nu_inside_white.mgh
 
 
  I am not sure which one to use from those, as I want to compare stable
  values but distant from white.
 
 
 --projfrac-avg min max del : average along normal
 --projdist mmdist : distance projection along normal
 --projdist-avg min max del : average along normal
 
  What would you recommend?
  Thank you again!
  Markus
 
 
 
 
 
 
 
  2014-03-24 21:29 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Markus
 
I wouldn't use brainmask as it has been normalized too
aggressivley. Maybe the nu.mgz. Look at the difference between
values just outside of it and just inside of it
 
cheers
Bruce
 
 
On Mon, 24 Mar 2014, Markus Gschwind wrote:
 
  Dear Bruce,
  Thanks for the rapid answer!
 
  Do you mean that I take the voxel values of
  brainmask.mgz at the place where
  the ?h.white surface passes, right?
 
  I thought that the ?l.white surface marks the limit
  between GM and WM as a
  result of a binary decision.
  I would be interested in the local certainty of this
  decision. I thought
  this is represented by the slope between the values
  around 70 and those
  100.
 
  Thanks again,
  Markus
 
 
 
 
 
 
  2014-03-24 19:26 GMT+01:00 Bruce Fischl
  fis...@nmr.mgh.harvard.edu:
Hi Markus
 
I would think that looking at the gray/white
  contrast across the
?h.white surface would be more informative
 
cheers
Bruce
On Mon, 24 Mar 2014, Markus Gschwind wrote:
 
  Dear all,
  I would like to capture regions where
  the gray
  matter/ white matter junction is blurred
  in order to
  detect possible focal
  cortical dysplasias.
 
  As I understood the WM/GM segmentation
  is done by
  the script mri_segment.
 
  Would it be possible detect those
  regions where the
  gradient between GM and WM regions is
  low?
 
  I imagined that running mri_segment
  several times,
  with each time a different lower GM
  threshold and
  higher WM threshold, and
  then calculating the diference between
  the results,
  might give such information.
 
  I am very much interested in what you
  think about
  this approach and how to do it
  practically.
 
  For info here are the optional flags of
  mri_segment:
 
  -slope s
 
  set the curvature slope (both n and p)
 
  -pslope p
 
  set the curvature pslope (default=1.0)
 
  -nslope n
 
  set the curvature nslope (default=1.0)
 
  -debug_voxel x y z
 
  set voxel

[Freesurfer] how to capture blurred GM/WM junction?

[Markus Gschwind]

Dear all,

I would like to capture regions where the gray matter/ white matter
junction is blurred in order to detect possible focal cortical dysplasias.

As I understood the WM/GM segmentation is done by the script mri_segment.

Would it be possible detect those regions where the gradient between GM and
WM regions is low?

I imagined that running mri_segment several times, with each time a
different lower GM threshold and higher WM threshold, and then calculating
the diference between the results, might give such information.

I am very much interested in what you think about this approach and how to
do it practically.

For info here are the optional flags of mri_segment:

-slope s

set the curvature slope (both n and p)

-pslope p

set the curvature pslope (default=1.0)

-nslope n

set the curvature nslope (default=1.0)

-debug_voxel x y z

set voxel for debugging

-auto

automatically detect class statistics (default)

-noauto

don't automatically detect class statistics

-log

log to ./segment.dat

-keep

keep wm edits. maintains all values of 0 and 255

-ghi, -gray_hi h

set the gray matter high limit (default=100.000)

-wlo, -wm_low l

set the white matter low limit (default=90.000)

-whi, -wm_hi h

set the white matter high limit (default=125.000)

-nseg n

thicken the n largest thin strands (default=20)

-thicken

toggle thickening step (default=ON)

-fillbg

toggle filling of the basal ganglia (default=OFF)

-fillv

toggle filling of the ventricles (default=OFF)

-b s

set blur sigma (default=0.25)

-n i

set # iterations of border classification (default=1)

-t t

set limit to thin strands in mm (default=4)

-v

verbose

-p p

set % threshold (default=0.80)

-x filename

extract options from filename

-w w

set wsize (default=11)

-u

usage


Thank you very much for all comments!

Markus
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] how to capture blurred GM/WM junction?

[Markus Gschwind]

Dear Bruce,

Thanks for the rapid answer!

Do you mean that I take the voxel values of brainmask.mgz at the place
where the ?h.white surface passes, right?

I thought that the ?l.white surface marks the limit between GM and WM as a
result of a binary decision.
I would be interested in the local certainty of this decision. I thought
this is represented by the slope between the values around 70 and those
100.

Thanks again,
Markus






2014-03-24 19:26 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:

 Hi Markus

 I would think that looking at the gray/white contrast across the ?h.white
 surface would be more informative

 cheers
 Bruce

 On Mon, 24 Mar 2014, Markus Gschwind wrote:

  Dear all,
 I would like to capture regions where the gray matter/ white matter
 junction is blurred in order to detect possible focal
 cortical dysplasias.

 As I understood the WM/GM segmentation is done by the script mri_segment.

 Would it be possible detect those regions where the gradient between GM
 and WM regions is low?

 I imagined that running mri_segment several times, with each time a
 different lower GM threshold and higher WM threshold, and
 then calculating the diference between the results, might give such
 information.

 I am very much interested in what you think about this approach and how
 to do it practically.

 For info here are the optional flags of mri_segment:

 -slope s

 set the curvature slope (both n and p)

 -pslope p

 set the curvature pslope (default=1.0)

 -nslope n

 set the curvature nslope (default=1.0)

 -debug_voxel x y z

 set voxel for debugging

 -auto

 automatically detect class statistics (default)

 -noauto

 don't automatically detect class statistics

 -log

 log to ./segment.dat

 -keep

 keep wm edits. maintains all values of 0 and 255

 -ghi, -gray_hi h

 set the gray matter high limit (default=100.000)

 -wlo, -wm_low l

 set the white matter low limit (default=90.000)

 -whi, -wm_hi h

 set the white matter high limit (default=125.000)

 -nseg n

 thicken the n largest thin strands (default=20)

 -thicken

 toggle thickening step (default=ON)

 -fillbg

 toggle filling of the basal ganglia (default=OFF)

 -fillv

 toggle filling of the ventricles (default=OFF)

 -b s

 set blur sigma (default=0.25)

 -n i

 set # iterations of border classification (default=1)

 -t t

 set limit to thin strands in mm (default=4)

 -v

 verbose

 -p p

 set % threshold (default=0.80)

 -x filename

 extract options from filename

 -w w

 set wsize (default=11)

 -u

 usage



 Thank you very much for all comments!

 Markus


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 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.


___
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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.

Re: [Freesurfer] how to capture blurred GM/WM junction?

[Markus Gschwind]

Hi Bruce!

Ok I see, great! Tank you!

So to double check, this will be something like :

mri_vol2surf \


  --mov /mri/nu.mgz \
  --ref /mri/nu.mgz \

  --surf /surf/lh.white
  --projdist mmdist -2 \ # for inside white


  # --projdist mmdist 2 \ # for outside white
  --interp trilinear \
  --hemi lh \
  --out lh.nu_inside_white.mgh



I am not sure which one to use from those, as I want to compare stable
values but distant from white.

   --projfrac-avg min max del : average along normal
   --projdist mmdist : distance projection along normal
   --projdist-avg min max del : average along normal

What would you recommend?

Thank you again!
Markus








2014-03-24 21:29 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:

 Hi Markus

 I wouldn't use brainmask as it has been normalized too aggressivley. Maybe
 the nu.mgz. Look at the difference between values just outside of it and
 just inside of it


 cheers
 Bruce


 On Mon, 24 Mar 2014, Markus Gschwind wrote:

  Dear Bruce,
 Thanks for the rapid answer!

 Do you mean that I take the voxel values of brainmask.mgz at the place
 where
 the ?h.white surface passes, right?

 I thought that the ?l.white surface marks the limit between GM and WM as a
 result of a binary decision.
 I would be interested in the local certainty of this decision. I thought
 this is represented by the slope between the values around 70 and those
 100.

 Thanks again,
 Markus






 2014-03-24 19:26 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:
   Hi Markus

   I would think that looking at the gray/white contrast across the
   ?h.white surface would be more informative

   cheers
   Bruce
   On Mon, 24 Mar 2014, Markus Gschwind wrote:

 Dear all,
 I would like to capture regions where the gray
 matter/ white matter junction is blurred in order to
 detect possible focal
 cortical dysplasias.

 As I understood the WM/GM segmentation is done by
 the script mri_segment.

 Would it be possible detect those regions where the
 gradient between GM and WM regions is low?

 I imagined that running mri_segment several times,
 with each time a different lower GM threshold and
 higher WM threshold, and
 then calculating the diference between the results,
 might give such information.

 I am very much interested in what you think about
 this approach and how to do it practically.

 For info here are the optional flags of mri_segment:

 -slope s

 set the curvature slope (both n and p)

 -pslope p

 set the curvature pslope (default=1.0)

 -nslope n

 set the curvature nslope (default=1.0)

 -debug_voxel x y z

 set voxel for debugging

 -auto

 automatically detect class statistics (default)

 -noauto

 don't automatically detect class statistics

 -log

 log to ./segment.dat

 -keep

 keep wm edits. maintains all values of 0 and 255

 -ghi, -gray_hi h

 set the gray matter high limit (default=100.000)

 -wlo, -wm_low l

 set the white matter low limit (default=90.000)

 -whi, -wm_hi h

 set the white matter high limit (default=125.000)

 -nseg n

 thicken the n largest thin strands (default=20)

 -thicken

 toggle thickening step (default=ON)

 -fillbg

 toggle filling of the basal ganglia (default=OFF)

 -fillv

 toggle filling of the ventricles (default=OFF)

 -b s

 set blur sigma (default=0.25)

 -n i

 set # iterations of border classification
 (default=1)

 -t t

 set limit to thin strands in mm (default=4)

 -v

 verbose

 -p p

 set % threshold (default=0.80)

 -x filename

 extract options from filename

 -w w

 set wsize (default=11)

 -u

 usage



 Thank you very much for all comments!

 Markus


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Re: [Freesurfer] how to capture blurred GM/WM junction?

[Markus Gschwind]

Whow that is great!! Thank you so much Doug, I was not aware of this!
That's what I needed it seems.
Thanks Bruce and Doug!
Markus


2014-03-24 23:21 GMT+01:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:


 you might want to look at the pctsurfcon script to see if that gets you
 where you want to be

 On 03/24/2014 06:18 PM, Bruce Fischl wrote:
  it really depends on the size of the abnormality. I would guess 2 is
  too big, and you want something more like 1, and sampling not averaging
  On Mon, 24 Mar 2014, Markus Gschwind wrote:
 
  Hi Bruce!
  Ok I see, great! Tank you!
 
  So to double check, this will be something like :
 
  mri_vol2surf \
 
 
--mov /mri/nu.mgz \
--ref /mri/nu.mgz \
 
--surf /surf/lh.white
--projdist mmdist -2 \ # for inside white
 
 
# --projdist mmdist 2 \ # for outside white
--interp trilinear \
--hemi lh \
--out lh.nu_inside_white.mgh
 
 
  I am not sure which one to use from those, as I want to compare stable
  values but distant from white.
 
 
 --projfrac-avg min max del : average along normal
 --projdist mmdist : distance projection along normal
 --projdist-avg min max del : average along normal
 
  What would you recommend?
  Thank you again!
  Markus
 
 
 
 
 
 
 
  2014-03-24 21:29 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:
Hi Markus
 
I wouldn't use brainmask as it has been normalized too
aggressivley. Maybe the nu.mgz. Look at the difference between
values just outside of it and just inside of it
 
cheers
Bruce
 
 
On Mon, 24 Mar 2014, Markus Gschwind wrote:
 
  Dear Bruce,
  Thanks for the rapid answer!
 
  Do you mean that I take the voxel values of
  brainmask.mgz at the place where
  the ?h.white surface passes, right?
 
  I thought that the ?l.white surface marks the limit
  between GM and WM as a
  result of a binary decision.
  I would be interested in the local certainty of this
  decision. I thought
  this is represented by the slope between the values
  around 70 and those
  100.
 
  Thanks again,
  Markus
 
 
 
 
 
 
  2014-03-24 19:26 GMT+01:00 Bruce Fischl
  fis...@nmr.mgh.harvard.edu:
Hi Markus
 
I would think that looking at the gray/white
  contrast across the
?h.white surface would be more informative
 
cheers
Bruce
On Mon, 24 Mar 2014, Markus Gschwind wrote:
 
  Dear all,
  I would like to capture regions where
  the gray
  matter/ white matter junction is blurred
  in order to
  detect possible focal
  cortical dysplasias.
 
  As I understood the WM/GM segmentation
  is done by
  the script mri_segment.
 
  Would it be possible detect those
  regions where the
  gradient between GM and WM regions is
  low?
 
  I imagined that running mri_segment
  several times,
  with each time a different lower GM
  threshold and
  higher WM threshold, and
  then calculating the diference between
  the results,
  might give such information.
 
  I am very much interested in what you
  think about
  this approach and how to do it
  practically.
 
  For info here are the optional flags of
  mri_segment:
 
  -slope s
 
  set the curvature slope (both n and p)
 
  -pslope p
 
  set the curvature pslope (default=1.0)
 
  -nslope n
 
  set the curvature nslope (default=1.0)
 
  -debug_voxel x y z
 
  set voxel for debugging
 
  -auto
 
  automatically detect class statistics
  (default)
 
  -noauto
 
  don't automatically detect class
  statistics
 
  -log
 
  log to ./segment.dat
 
  -keep
 
  keep wm edits. maintains all values of 0
  and 255
 
  -ghi, -gray_hi h
 
  set the gray matter high limit
  (default=100.000

Re: [Freesurfer] brain.mgz image error

[markus . gschwind]

Hi,

Can you send us a screenshot of the original MRI before skull stripping?

Thanks!
Markus

On 20 mars 2014, at 14:46, Saurabh Thakur srbht...@gmail.com wrote:

 Hello Freesurfer expert ,
 
 I am sending you the image of brain.mgz screen-shot.
 
 Is the area highlighted is part of cortex or it is due to skull stripping 
 error.
 
 Please clarify.
 
 Thanks in advance,
 
 cheers
 Saurabh Thakur,
 
 
 
 
 brain_01.png
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[Freesurfer] fsaverage_sym in xhemi commands

[Markus Gschwind]

Dear all,

I have a question concerning the xhemi commands as explained here:

http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi

2.  The command
  surfreg --s $subject --t fsaverage_sym --lh

is absolutely searching for fsaverage_sym in the $SUBJECTS_DIR.

Do I really have to copy the whole fsaverage_sym folder from
$FREESUERFER_HOME/subjects into each subject's directory once again?


Thank you very much!
Markus
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[Freesurfer] creating a multi-scanner template?

[Markus Gschwind]

Dear all,

I am planning to create a local cortical thickness normal template in
order to test single patients against it.

For that purpose I was planning to use 50-100 MPRAGE scans of healthy
subjects (balanced for age range and sex).

My question is, if I should worry about the scanner where the data comes
form. We have three Siemens Trios, the MPRAGES are more or less the same
protocols.

- when the created template with standart deviation map comes from all
three scanners, can I test patients coming from all three scanners? Will it
reduce sensitivity?

- when the created template comes from only one scanner, it is clear that I
will not be able to compare patients coming from another scanner against it.

Thank you!

Markus
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Re: [Freesurfer] creating a multi-scanner template?

[Markus Gschwind]

Thank you Bruce!
Good! So, at least it doesn't seem an impossible thing to achieve!!
Best,
Markus


2014-03-12 13:21 GMT+01:00 Bruce Fischl fis...@nmr.mgh.harvard.edu:

 Hi Markus

 there is no way to know until you try it. There are many possible sources
 of variance depending on e.g. how uniformly they are calibrated, but you
 have to try and see.

 cheers
 Bruce

 On Wed, 12 Mar 2014, Markus Gschwind wrote:

  Dear all,
 I am planning to create a local cortical thickness normal template in
 order to test single patients against it.

 For that purpose I was planning to use 50-100 MPRAGE scans of healthy
 subjects (balanced for age range and sex).

 My question is, if I should worry about the scanner where the data comes
 form. We have three Siemens Trios, the MPRAGES are more or less the same
 protocols.

 - when the created template with standart deviation map comes from all
 three
 scanners, can I test patients coming from all three scanners? Will it
 reduce
 sensitivity?

 - when the created template comes from only one scanner, it is clear that
 I
 will not be able to compare patients coming from another scanner against
 it.

 Thank you!

 Markus






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Re: [Freesurfer] Matlab help

[markus . gschwind]

Hi!

Can you specify what happens when you try to read the files?




On 4 mars 2014, at 06:44, Saurabh Thakur srbht...@gmail.com wrote:

 Hello Freesurfer,
 
 I am trying to runs MRIread.m file in matlab.
 
 But it is not reading the brain.mgz or any other format.
 
 Can u help  in this regards.
 
 Thanks in advance,
 
 cheers
 Saurabh Thakur,
 
 
 
 
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Re: [Freesurfer] Create a surf from a special volume?

[Markus Gschwind]

Hi again,

It is certainly a beginners question, and probably the code examples given
below are not right...

Is there anyone that could advice me how to do this?

Thanks so much!
Markus


2014-02-01 Markus Gschwind markus.gschw...@gmail.com:

 Dear all,

 I want to create a surface of a partially altered brain T1 (temporal lobe
 cut away by hand).

 I figured out that this would be done with mri_vol2surf.

 This command asks for a register.dat file.

 I think that I can get it using this command:

 SUBJECT_DIR=/Users/FREESURFER

 bbregister --s /mri/brain_T1.mgz  --mov
 /Users/FREESURFER/mri/brain_T1_ins.mgz --reg /FREESURFER/mri/register.dat
 --t1 --init-spm

 I well starts calculation, but suddenly stops and complains that there is
 no brainmask /Users/FREESURFER/mri/brain_T1.mgz/mri/brainmask.mgz

 which makes somehow no sense as the brainmask is in
 /Users/FREESURFER/mri/brainmask.mgz of course.

 But I don't find a option to specify the brainmask in bbregister.

 What am I doing wrong?

 Thanks for any help!
 Markus




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Re: [Freesurfer] Create a surf from a special volume?

[Markus Gschwind]

Hi Bruce,

Thank you! The creation of register.data worked perfectly.

Now in order to create the mesh file (I suppose .w) of the altered brain
with cut out temporal lobe (brain_T1fin), would this command be OK?

mri_vol2surf --src FREESURFER/mri/brain_T1fin.nii.gz --srcreg
FREESURFER/mri/register2.dat --hemi lh --projfrac 0.5 --out
FREESURFER/mri/brain_T1fin_surf.w --out_type nifti

...however I get
ERROR: could not determine type of FREESURFER/mri/brain_T1fin_surf.w

And when using output_type 'paint' or 'gii' (without the ' ' ) it is
calculating something, but freeview crashes when I try to look at it...
Actually I have no clue what the output_type should be...

Thanks so much!
Markus


2014-02-03 Bruce Fischl fis...@nmr.mgh.harvard.edu:

 Hi Markus

 the --s option should be a subject name, not a path to a volume

 cheers
 Bruce

 On Mon, 3 Feb 2014, Markus Gschwind wrote:

  Hi again,
 It is certainly a beginners question, and probably the code examples given
 below are not right...

 Is there anyone that could advice me how to do this?

 Thanks so much!
 Markus


 2014-02-01 Markus Gschwind markus.gschw...@gmail.com:
   Dear all,
 I want to create a surface of a partially altered brain T1 (temporal
 lobe cut away by hand).

 I figured out that this would be done with mri_vol2surf.

 This command asks for a register.dat file.

 I think that I can get it using this command:

 SUBJECT_DIR=/Users/FREESURFER

 bbregister --s /mri/brain_T1.mgz  --mov
 /Users/FREESURFER/mri/brain_T1_ins.mgz --reg
 /FREESURFER/mri/register.dat --t1 --init-spm

 I well starts calculation, but suddenly stops and complains that there
 is no brainmask /Users/FREESURFER/mri/brain_T1.mgz/mri/brainmask.mgz

 which makes somehow no sense as the brainmask is in
 /Users/FREESURFER/mri/brainmask.mgz of course.

 But I don't find a option to specify the brainmask in bbregister.

 What am I doing wrong?

 Thanks for any help!
 Markus








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[Freesurfer] Create a surf from a special volume?

[Markus Gschwind]

Dear all,

I want to create a surface of a partially altered brain T1 (temporal lobe
cut away by hand).

I figured out that this would be done with mri_vol2surf.

This command asks for a register.dat file.

I think that I can get it using this command:

SUBJECT_DIR=/Users/FREESURFER

bbregister --s /mri/brain_T1.mgz  --mov
/Users/FREESURFER/mri/brain_T1_ins.mgz --reg /FREESURFER/mri/register.dat
--t1 --init-spm

I well starts calculation, but suddenly stops and complains that there is
no brainmask /Users/FREESURFER/mri/brain_T1.mgz/mri/brainmask.mgz

which makes somehow no sense as the brainmask is in
/Users/FREESURFER/mri/brainmask.mgz of course.

But I don't find a option to specify the brainmask in bbregister.

What am I doing wrong?

Thanks for any help!
Markus
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[Freesurfer] freeview porblem under ubuntu 12.04

[Markus Gschwind]

Dear Experts,

I have installed Freesurfer 5.3 under ubuntu 12.04.

It is running fine except for Freeview which is causing heavy graphic
trouble (thousands of colored squares in the black fields where the brains
should be displayed.

Tksurfer is working fine.

Glxgears is showing the rotating blue, red and green gears.

There is no error in the terminal.

What could I do to track down the problem?

Thanks for help!
Markus
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Re: [Freesurfer] Installation problem on ubuntu 12.04.

[Markus Gschwind]

Dear all,

For the error

 freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot
 open shared object file: No such file or directory


sudo apt-get install libjpeg62

did the trick. Freeview is running fine

For the error
*libGL error: failed to load driver: swrast*
*libGL error: Try again with LIBGL_DEBUG=verbose for more details.*

Any ideas?

Thank you in advance!
Markus

2014/1/27 Markus Gschwind markus.gschw...@gmail.com

 Dear experts!

 I installed freesurfer on a machine running Ubuntu 12.04.

 I have got some error messages when testing:

 ~$ freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v
 $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
 $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
 $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f
 $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f
 $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
 *freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot
 open shared object file: No such file or directory*


 ~$ tkmedit bert orig.mgz
 *libGL error: failed to load driver: swrast*
 *libGL error: Try again with LIBGL_DEBUG=verbose for more details.*

 and the same error also for tkurfer.

 Thank you for your help!

 Kind regards,
 Markus


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Re: [Freesurfer] Installation problem on ubuntu 12.04.

[Markus Gschwind]

Dear Zeke,

Thanks for stepping in!

$ LIBGL_DEBUG=verbose tkmedit bert orig.mgz
libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/tls/swrast_dri.so
libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so
libGL error: failed to load driver: swrast
Reading /usr/local/freesurfer/tktools/tkm_common.tcl
Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl
Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /usr/local/freesurfer/tktools/tkUtils.tcl

tkmedit seems fine though.


~$ glxgears
libGL error: failed to load driver: swrast
libGL error: Try again with LIBGL_DEBUG=verbose for more details.
21147 frames in 5.1 seconds = 4139.989 FPS
5715 frames in 5.0 seconds = 1135.272 FPS
5716 frames in 5.2 seconds = 1108.204 FPS
5715 frames in 5.1 seconds = 1110.123 FPS
5716 frames in 5.2 seconds = 1104.290 FPS
5455 frames in 5.2 seconds = 1058.021 FPS
etc.

I see three 3D gears (blue, red and green) which kind of wiggle...

I mean, is this error really a problem or could I possible live with it?

Thank you!

Makrus

2014/1/28 Z K zkauf...@nmr.mgh.harvard.edu

 Markus,

 I have never seen those errors before. But a little googling suggested
 perhaps running the program as follows:

 ~$ LIBGL_DEBUG=verbose ./tkmedit bert orig.mgz

 Im a little at a lose at what else to try because we have freesurfer
 installed on pretty much stock Ubuntu platforms and it runs as expected.
 Could you also try typing glxgears and tell me if a 3D window popups
 up displaying turning gears, or perhaps an error message is displayed?

 -Zeke

 On 01/28/2014 03:40 AM, Markus Gschwind wrote:
  Dear all,
 
  For the error
 
  freeview.bin: error while loading shared libraries: libjpeg.so.62:
  cannot open shared object file: No such file or directory
 
 
  sudo apt-get install libjpeg62
 
  did the trick. Freeview is running fine
 
  For the error
  *libGL error: failed to load driver: swrast*
  *libGL error: Try again with LIBGL_DEBUG=verbose for more details.*
  *
  *
  Any ideas?
 
  Thank you in advance!
  Markus
 
  2014/1/27 Markus Gschwind markus.gschw...@gmail.com
  mailto:markus.gschw...@gmail.com
 
  Dear experts!
 
  I installed freesurfer on a machine running Ubuntu 12.04.
 
  I have got some error messages when testing:
 
  ~$ freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v
  $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
  $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
  $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f
  $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f
  $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
  *freeview.bin: error while loading shared libraries: libjpeg.so.62:
  cannot open shared object file: No such file or directory*
 
 
  ~$ tkmedit bert orig.mgz
  *libGL error: failed to load driver: swrast*
  *libGL error: Try again with LIBGL_DEBUG=verbose for more details.*
 
  and the same error also for tkurfer.
 
  Thank you for your help!
 
  Kind regards,
  Markus
 
 
 
 
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[Freesurfer] Installation problem on ubuntu 12.04.

[Markus Gschwind]

Dear experts!

I installed freesurfer on a machine running Ubuntu 12.04.

I have got some error messages when testing:

~$ freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v
$SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
$SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
$SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f
$SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f
$SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
*freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot
open shared object file: No such file or directory*


~$ tkmedit bert orig.mgz
*libGL error: failed to load driver: swrast*
*libGL error: Try again with LIBGL_DEBUG=verbose for more details.*

and the same error also for tkurfer.

Thank you for your help!

Kind regards,
Markus
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Re: [Freesurfer] problem creating annotation using mri_sample_parc?

[Markus Gschwind]

Dear Bruce or someone else,

would you mind answering a little more in detail, please? I am stuck. There
is hardly any thread about the command mris_sample_parc, but I need this
function.

1) This file called cma_parcellation_colors.txt, is an option for
mris_sample_parc. Where does that file come from? How am I supposed to
create it?

2) What is missing if the loading of the created annotation file onto a
surface (in freeview) gives the following error, repeating for infinity
CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory

What does this error mean, at all?

Thank you and please excuse my insisting!
Markus


2013/12/14 Markus Gschwind markus.gschw...@gmail.com

 Thank you Bruce,

 I read that mris_sample_parc samples a volumetric parcellation onto a
 surface.

 I understand that this is like creating from a file of the type of aseg a
 corresponding file of the type of aparc.annot.ctab.

 Is this not true? Do I actually  have to create the aparc.annot.ctab type
 file manually and give this as the above mentionned file to the command?
 The file is only an optional arguement though?

 Thanks again, Markus


 2013/12/14 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Hi Markus

 you need to create that file (or update FreeSurferColorLUT.txt) to
 reflect whatever you have in /Documents/myROIfile.mgz

 cheers
 Bruce


 On Sat, 14 Dec 2013, Markus Gschwind wrote:

  Dear Bruce,
 Thank you for your answer. I have not yet gotten it correctly.

 1) Where does that file come from? Should I create it? how?

 2) what is missing in the command of mris_sample_parc? Why does it now
 work?

 3) what does the second error mean?
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory

 Thanks in advance!
 [cleardot.gif]

 Markus


 2013/12/13 Bruce Fischl fis...@nmr.mgh.harvard.edu
   Hi Markus

   that file translates indices/annotations into colors to display
   and human reasable names.

   cheers
   Bruce
   On Fri, 13 Dec 2013, Markus Gschwind wrote:

 I can precise the question, actually there are
 three:

 1) ist the command correct?

   mris_sample_parc -v -sdir subject001 rh
   ~/Documents/myROIfile.mgz rh.myROIfile.annot


 2) I do not understand the meaning of this claimed
 file
 cma_parcellation_colors.txt

 Actually this does not exist. In the Wiki
 (http://surfer.nmr.mgh.harvard.edu/fswiki/mris_sample_parc)
 it says that
 there was an optional arguement

 -file filename

 use filename as translation (default:
 'cma_parcellation_colors.txt')


 If I understand correctly, translation points ot a
 problem of different
 spaces, but the filename rather seems something like
 a parcellation/atlas
 color table?

 3) The result of this problem seems to be that I
 cannot annotate the surface
 using the created annotation file. It gives this
 error, which i do not
 understand.



 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 ... etc.

 Can anyone help me find the problem?


 Thank you in advance!

 Markus




 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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dispose of the e

Re: [Freesurfer] problem creating annotation using mri_sample_parc?

[Markus Gschwind]

I can precise the question, actually there are three:

1) ist the command correct?

mris_sample_parc -v -sdir subject001 rh ~/Documents/myROIfile.mgz
 rh.myROIfile.annot


2) I do not understand the meaning of this claimed file
cma_parcellation_colors.txt

Actually this does not exist. In the Wiki (
http://surfer.nmr.mgh.harvard.edu/fswiki/mris_sample_parc) it says that
there was an optional arguement

-file filename

use filename as translation (default: 'cma_parcellation_colors.txt')

If I understand correctly, translation points ot a problem of different
spaces, but the filename rather seems something like a parcellation/atlas
color table?

3) The result of this problem seems to be that I cannot annotate the
surface using the created annotation file. It gives this error, which i do
not understand.




 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 ... etc.

 Can anyone help me find the problem?


Thank you in advance!

Markus
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] problem creating annotation using mri_sample_parc?

[Markus Gschwind]

Dear Bruce,

Thank you for your answer. I have not yet gotten it correctly.

1) Where does that file come from? Should I create it? how?

2) what is missing in the command of mris_sample_parc? Why does it now
work?

3) what does the second error mean?
CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory

Thanks in advance!
Markus


2013/12/13 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Hi Markus

 that file translates indices/annotations into colors to display and human
 reasable names.

 cheers
 Bruce

 On Fri, 13 Dec 2013, Markus Gschwind wrote:

  I can precise the question, actually there are three:

 1) ist the command correct?

   mris_sample_parc -v -sdir subject001 rh
   ~/Documents/myROIfile.mgz rh.myROIfile.annot


 2) I do not understand the meaning of this claimed file
 cma_parcellation_colors.txt

 Actually this does not exist. In the Wiki
 (http://surfer.nmr.mgh.harvard.edu/fswiki/mris_sample_parc) it says that
 there was an optional arguement

 -file filename

 use filename as translation (default: 'cma_parcellation_colors.txt')


 If I understand correctly, translation points ot a problem of different
 spaces, but the filename rather seems something like a parcellation/atlas
 color table?

 3) The result of this problem seems to be that I cannot annotate the
 surface
 using the created annotation file. It gives this error, which i do not
 understand.



 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 ... etc.

 Can anyone help me find the problem?


 Thank you in advance!

 Markus




 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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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.

Re: [Freesurfer] problem creating annotation using mri_sample_parc?

[Markus Gschwind]

Thank you Bruce,

I read that mris_sample_parc samples a volumetric parcellation onto a
surface.

I understand that this is like creating from a file of the type of aseg a
corresponding file of the type of aparc.annot.ctab.

Is this not true? Do I actually  have to create the aparc.annot.ctab type
file manually and give this as the above mentionned file to the command?
The file is only an optional arguement though?

Thanks again, Markus


2013/12/14 Bruce Fischl fis...@nmr.mgh.harvard.edu

 Hi Markus

 you need to create that file (or update FreeSurferColorLUT.txt) to reflect
 whatever you have in /Documents/myROIfile.mgz

 cheers
 Bruce


 On Sat, 14 Dec 2013, Markus Gschwind wrote:

  Dear Bruce,
 Thank you for your answer. I have not yet gotten it correctly.

 1) Where does that file come from? Should I create it? how?

 2) what is missing in the command of mris_sample_parc? Why does it now
 work?

 3) what does the second error mean?
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory

 Thanks in advance!
 [cleardot.gif]

 Markus


 2013/12/13 Bruce Fischl fis...@nmr.mgh.harvard.edu
   Hi Markus

   that file translates indices/annotations into colors to display
   and human reasable names.

   cheers
   Bruce
   On Fri, 13 Dec 2013, Markus Gschwind wrote:

 I can precise the question, actually there are
 three:

 1) ist the command correct?

   mris_sample_parc -v -sdir subject001 rh
   ~/Documents/myROIfile.mgz rh.myROIfile.annot


 2) I do not understand the meaning of this claimed
 file
 cma_parcellation_colors.txt

 Actually this does not exist. In the Wiki
 (http://surfer.nmr.mgh.harvard.edu/fswiki/mris_sample_parc)
 it says that
 there was an optional arguement

 -file filename

 use filename as translation (default:
 'cma_parcellation_colors.txt')


 If I understand correctly, translation points ot a
 problem of different
 spaces, but the filename rather seems something like
 a parcellation/atlas
 color table?

 3) The result of this problem seems to be that I
 cannot annotate the surface
 using the created annotation file. It gives this
 error, which i do not
 understand.



 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 CTABfindAnnotation: ct was NULL
 No such file or directory
 ... etc.

 Can anyone help me find the problem?


 Thank you in advance!

 Markus




 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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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.

[Freesurfer] problem creating annotation using mri_sample_parc?

[Markus Gschwind]

Dear all,

I am trying to create a annotation file from a ROI_file with multiple ROIs
with values form 1:10 using mris_sample_parc

I had verified that myROIfile and subject001/surf/rh.white and also
mri/T1.mgz loadable together in freeview (=same space).

when running the command

mris_sample_parc -v -sdir subject001 rh ~/Documents/myROIfile.mgz
rh.myROIfile.annot

it first starts well, but then complains about

could not open translation file
/Applications/freesurfer/cma_parcellation_colors.txt


However when trying to load the created annotation file it gives me the
same never endign error:

CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory
CTABfindAnnotation: ct was NULL
No such file or directory
... etc.

I guess that the annotation is not on the surface, but what am I doing
wrong?

Thank you in advance,
Markus
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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
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but does not contain patient information, please contact the sender and properly
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