[Freesurfer] Path Problem

[LIEWALD David]

Environment : Opensuse 13.2 Freesurver Version 6 (Beta)


Hi I hope you can help with this problem


I'm using the version 6 Beta due to problems with license authentication. 
Freesurfer runs but bails out with a file not found error :



Iteration 1 Fri Dec  4 09:38:57 GMT 2015
nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc 
./tmp.mri_nu_correct.mni.24767/nu1.mnc -tmpdir 
./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 -distance 200 
-shrink 2



ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist!
Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 
(ec183cc) x86_64 x86_64 x86_64 GNU/Linux



on examination of the file structure a directory named 
"tmp.mri_nu_correct.mni.24767" has been created under the "mri"directory and 
nothing has been created under the "tmp" directory  in the subject root. I am 
guessing that this is the cause of the error.


any advice on correcting this would be extremely useful


Dave Liewald

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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[Freesurfer] g-w.pct vs. g-w. ratio

[Andrews, Derek]

>Dear FreeSurfer Support team,
>
>Thank you for your quick response.
>
>Is it fair to present both g-w.pct (100*(w-g)/((w+g)/2)) and g-w.ratio
>(g/w) as GWR? I have seen the pct calculation presented as GWR in an
>abstract that cited Salat (2009) in its introduction text.

>Also, is it fair to say that decreases in in g-w.pct indicate less
>definition between
>the g/w matter boundary as a decrease in g-w.ratio would indicate? If I
>want to make a statement about reduced definition between the g/w matter
>boundary, what calculation would you suggest?
>
>Thank you very much for your clarifications on this.
>
>Best, Derek 
>
>
>
>
>
>Derek Sayre Andrews, MSc
>PhD Candidate
>
>The Sackler Institute for Translational Neurodevelopment
>Department of Forensic and Neurodevelopmental Sciences
>Institute of Psychiatry, Psychology & Neuroscience, King's College London
>
>Telephone: +44 (0)20 7848 5701
>Email: derek.andr...@kcl.ac.uk
>
>
>
>
>
>On 03/12/2015 17:26, "Douglas N Greve"  wrote:
>
>>g-w.pct is computed as
>>
>>pct = 100*(w-g)/((w+g)/2)
>>
>>in the pctsurfcon script
>>
>>
>>On 12/03/2015 12:18 PM, Andrews, Derek wrote:
>>> Dear FreeSurfer Support team and Community
>>>
>>> I am wondering if someone can give me an explanation of the difference
>>> between g-w.pct and g:w ratio (as calculated by; fscalc lh.gm.mgh div
>>> lh.wm.mgh -o lh.ratio.mgh)
>>> Will both these measures essentially measure the relationship between
>>> grey and white matter signal intensity but in a different way?
>>>
>>>
>>> Best, Derek
>>>
>>>
>>> 
>>>
>>>
>>> *Derek Sayre Andrews, MSc*
>>> PhD Candidate
>>>
>>> The Sackler Institute for Translational Neurodevelopment
>>>
>>> Department of Forensic and Neurodevelopmental Sciences
>>>
>>> Institute of Psychiatry, Psychology & Neuroscience, King's College
>>>London
>>>
>>> Telephone: +44 (0)20 7848 5701
>>> Email: derek.andr...@kcl.ac.uk
>>>
>>>
>>>
>>>
>>> ___
>>> 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.
>>
>


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[Freesurfer] ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***

[Matthieu Vanhoutte]

Dear experts,

I am confronted with some problem in the "recon-all" of a few subjects
concerning Talairach space, but don't know how to manage these.

Please find below the recon-all log with errors :

#
#@# Talairach Failure Detection Fri Dec  4 15:29:38 CET 2015
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm

talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6911,
pval=0.4932 >= threshold=0.0050)

 awk -f /home/global//freesurfer5.3//bin/extract_talairach_avi_QA.awk
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log


 tal_QC_AZS
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log

TalAviQA: 0.93027
z-score: -10
ERROR: Talairach QA check failed!
   z-score = -10 <= -9 = threshold
   atlas xform error = 0 < -60 | > 24
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
INFO: Attempting MINC mritotal to perform Talairach align
#
#@# Talairach Fri Dec  4 15:29:39 CET 2015
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz


 talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm

/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
/home/global//freesurfer5.3//bin/talairach
--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
$Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $
Linux wutang 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014
x86_64 x86_64 x86_64 GNU/Linux
Fri Dec  4 15:31:35 CET 2015
tmpdir is transforms/tmp.talairach.13347
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
mri_convert orig_nu.mgz transforms/tmp.talairach.13347/src.mnc
mri_convert orig_nu.mgz transforms/tmp.talairach.13347/src.mnc
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from orig_nu.mgz...
TR=9.90, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (7.45058e-09, 1, 0)
writing to transforms/tmp.talairach.13347/src.mnc...

mritotal -verbose -debug -clobber -modeldir
/home/global//freesurfer5.3//mni/bin/../share/mni_autoreg -protocol icbm
transforms/tmp.talairach.13347/src.mnc transforms/talairach.auto.xfm


Fri Dec  4 15:31:58 CET 2015
talairach done

 cp transforms/talairach.auto.xfm transforms/talairach.xfm

#
#@# Talairach Failure Detection Fri Dec  4 15:31:59 CET 2015
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm

ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0039, pval=0. < threshold=0.0050)
Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Linux wutang 3.13.0-24-generic #47-Ubuntu SMP Fri May 2 23:30:00 UTC 2014
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s M0_2011-02-23 exited with ERRORS at Fri Dec  4 15:32:00 CET
2015

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Thanks in advance for helping !

Best regards,
Matthieu
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Re: [Freesurfer] Path Problem

[LIEWALD David]

Hi Bruce

here's the output

CCACE-PROC5:/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri # nu_correct 
-clobber ./tmp.mri_nu_correct.mni.24649/nu0.mnc 
./tmp.mri_nu_correct.mni.24649/nu1.mnc -tmpdir 
./tmp.mri_nu_correct.mni.24649/0/ -iterations 1000 -stop 1e-4 -distance 200 
-shrink 2

CCACE-PROC5:/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri # nu_correct 
-version

CCACE-PROC5:/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri # which 
nu_correct/home/freesurfer/mni/bin/nu_correct

CCACE-PROC5:/UK_Biobank_MRI/FS_Output/1493335_20216_2_0/mri # 

1st command: No output
2nd command: No output
3rd Command : freesurfer has never been installed on this machine before and 
there is no freesurfer entries in the home directory

thanks

Dave



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: 04 December 2015 14:04
To: Freesurfer support list
Subject: Re: [Freesurfer] Path Problem

Hi Dave

that is pretty puzzling. The nu1.mnc is the output of the command that is
failing, so I don't see why it complains that it doesn't exist. The same
command:

  nu_correct -clobber ./tmp.mri_nu_correct.mni.24649/nu0.mnc
./tmp.mri_nu_correct.mni.24649/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.24649/0/ -iterations 1000 -stop 1e-4 -distance 200
-shrink 2

works fine for me. Can you try it from the command line (from the mri dir)?
If it fails, can you run:

nu_correct -version

and

which nu_correct?

cheers
Bruce



On Fri, 4
Dec 2015, LIEWALD David wrote:

> Hi Bruce
>
> Yes the dir is writable and the echo command does create the test.dat in the 
> subdir.
>
> I have attached a recon-all log as requested
>
> Many Thanks
>
> Dave
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: 04 December 2015 13:36
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Path Problem
>
> HI David
>
> can you write to that dir? For example, does
>
> echo test >  ./tmp.mri_nu_correct.mni.24767/test.dat
>
>
> work properly (from the mri dir)? Also, please send us the entire
> recon-all.log so we can have a look
>
> cheers
> Bruce
>
> On Fri, 4 Dec 2015,
> LIEWALD
> David wrote:
>
>>
>> Environment : Opensuse 13.2 Freesurver Version 6 (Beta)
>>
>>
>> Hi I hope you can help with this problem
>>
>>
>> I'm using the version 6 Beta due to problems with license authentication. 
>> Freesurfer runs but bails
>> out with a file not found error :
>>
>>
>>
>> Iteration 1 Fri Dec  4 09:38:57 GMT 2015
>> nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc 
>> ./tmp.mri_nu_correct.mni.24767/nu1.mnc
>> -tmpdir ./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 
>> -distance 200 -shrink 2
>>
>>
>>
>> ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist!
>> Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 
>> 2015 (ec183cc) x86_64
>> x86_64 x86_64 GNU/Linux
>>
>>
>>
>> on examination of the file structure a directory named 
>> "tmp.mri_nu_correct.mni.24767" has been
>> created under the "mri"directory and nothing has been created under the 
>> "tmp" directory  in the
>> subject root. I am guessing that this is the cause of the error.
>>
>>
>> any advice on correcting this would be extremely useful
>>
>>
>> Dave Liewald
>>
>>
>>
>
>
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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.


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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Re: [Freesurfer] Path Problem

[LIEWALD David]

Hi Bruce

Just checked the actual location of the file is

/UK_Biobank_MRI/freesurfer/mni/bin/nu_correct

i.e. FREESURFER_HOME/mni/bin

Dave


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: 04 December 2015 14:04
To: Freesurfer support list
Subject: Re: [Freesurfer] Path Problem

Hi Dave

that is pretty puzzling. The nu1.mnc is the output of the command that is
failing, so I don't see why it complains that it doesn't exist. The same
command:

  nu_correct -clobber ./tmp.mri_nu_correct.mni.24649/nu0.mnc
./tmp.mri_nu_correct.mni.24649/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.24649/0/ -iterations 1000 -stop 1e-4 -distance 200
-shrink 2

works fine for me. Can you try it from the command line (from the mri dir)?
If it fails, can you run:

nu_correct -version

and

which nu_correct?

cheers
Bruce



On Fri, 4
Dec 2015, LIEWALD David wrote:

> Hi Bruce
>
> Yes the dir is writable and the echo command does create the test.dat in the 
> subdir.
>
> I have attached a recon-all log as requested
>
> Many Thanks
>
> Dave
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: 04 December 2015 13:36
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Path Problem
>
> HI David
>
> can you write to that dir? For example, does
>
> echo test >  ./tmp.mri_nu_correct.mni.24767/test.dat
>
>
> work properly (from the mri dir)? Also, please send us the entire
> recon-all.log so we can have a look
>
> cheers
> Bruce
>
> On Fri, 4 Dec 2015,
> LIEWALD
> David wrote:
>
>>
>> Environment : Opensuse 13.2 Freesurver Version 6 (Beta)
>>
>>
>> Hi I hope you can help with this problem
>>
>>
>> I'm using the version 6 Beta due to problems with license authentication. 
>> Freesurfer runs but bails
>> out with a file not found error :
>>
>>
>>
>> Iteration 1 Fri Dec  4 09:38:57 GMT 2015
>> nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc 
>> ./tmp.mri_nu_correct.mni.24767/nu1.mnc
>> -tmpdir ./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 
>> -distance 200 -shrink 2
>>
>>
>>
>> ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist!
>> Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 
>> 2015 (ec183cc) x86_64
>> x86_64 x86_64 GNU/Linux
>>
>>
>>
>> on examination of the file structure a directory named 
>> "tmp.mri_nu_correct.mni.24767" has been
>> created under the "mri"directory and nothing has been created under the 
>> "tmp" directory  in the
>> subject root. I am guessing that this is the cause of the error.
>>
>>
>> any advice on correcting this would be extremely useful
>>
>>
>> Dave Liewald
>>
>>
>>
>
>
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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.


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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Re: [Freesurfer] Path Problem

[LIEWALD David]

Hi Bruce

Yes the dir is writable and the echo command does create the test.dat in the 
subdir.

I have attached a recon-all log as requested

Many Thanks

Dave

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: 04 December 2015 13:36
To: Freesurfer support list
Subject: Re: [Freesurfer] Path Problem

HI David

can you write to that dir? For example, does

echo test >  ./tmp.mri_nu_correct.mni.24767/test.dat


work properly (from the mri dir)? Also, please send us the entire
recon-all.log so we can have a look

cheers
Bruce

On Fri, 4 Dec 2015,
LIEWALD
David wrote:

>
> Environment : Opensuse 13.2 Freesurver Version 6 (Beta)
>
>
> Hi I hope you can help with this problem
>
>
> I'm using the version 6 Beta due to problems with license authentication. 
> Freesurfer runs but bails
> out with a file not found error :
>
>
>
> Iteration 1 Fri Dec  4 09:38:57 GMT 2015
> nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc 
> ./tmp.mri_nu_correct.mni.24767/nu1.mnc
> -tmpdir ./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 
> -distance 200 -shrink 2
>
>
>
> ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist!
> Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 
> 2015 (ec183cc) x86_64
> x86_64 x86_64 GNU/Linux
>
>
>
> on examination of the file structure a directory named 
> "tmp.mri_nu_correct.mni.24767" has been
> created under the "mri"directory and nothing has been created under the "tmp" 
> directory  in the
> subject root. I am guessing that this is the cause of the error.
>
>
> any advice on correcting this would be extremely useful
>
>
> Dave Liewald
>
>
>

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Fri Dec  4 11:11:10 GMT 2015
/UK_Biobank_MRI/FS_Output/1493335_20216_2_0
/UK_Biobank_MRI/freesurfer/bin/recon-all
-i 
/UK_Biobank_MRI/WorkDir/1493335_20216_2_0/1.3.12.2.1107.5.2.19.45594.2014102612140161812159407.dcm
 -s 1493335_20216_2_0 -sd /UK_Biobank_MRI/FS_Output -no-isrunning -all
subjid 1493335_20216_2_0
setenv SUBJECTS_DIR /UK_Biobank_MRI/FS_Output
FREESURFER_HOME /UK_Biobank_MRI/freesurfer
Actual FREESURFER_HOME /UK_Biobank_MRI/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015
Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 
(ec183cc) x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  387206 
maxlocks unlimited
maxsignal387206 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:  99140516   53688556   45451960  95916 418652   51296424
-/+ buffers/cache:1973480   97167036
Swap:1258290761818048  124011028


program versions used
$Id: recon-all,v 1.515.2.24 2015/10/01 21:23:52 greve Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info 
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2015/12/04-11:11:10-GMT  BuildTimeStamp: Oct 15 2015 01:03:13  
CVS: $Id: mri_convert.c,v 1.221.2.2 2015/10/02 16:39:36 zkaufman Exp $  User: 
root  Machine: CCACE-PROC5  Platform: Linux  PlatformVersion: 3.16.7-24-desktop 
 CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 5.5
$Id: talairach_avi,v 1.11 2015/01/13 20:22:51 nicks Exp $
mri_convert --version 
dev build (use --all-info flag for full version info)
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2015/12/04-11:11:10-GMT  BuildTimeStamp: Oct 15 
2015 01:03:13  CVS: $Id: tkregister2.c,v 1.129 2014/02/26 21:31:58 greve Exp $  
User: root  Machine: CCACE-PROC5  Platform: Linux  PlatformVersion: 
3.16.7-24-desktop  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2015/12/04-11:11:10-GMT  BuildTimeStamp: Oct 15 
2015 01:03:13  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ 
 User: root  Machine: CCACE-PROC5  Platform: Linux  PlatformVersion: 
3.16.7-24-desktop  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2015/12/04-11:11:10-GMT  BuildTimeStamp: Oct 15 2015 01:03:13  
CVS: $Id: mri_normalize.c,v 1.84.2.1 2015/08/13 17:12:10 zkaufman Exp $  User: 
root  Machine: CCACE-PROC5  Platform: Linux  PlatformVersion: 3.16.7-24-desktop 
 CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info 

Re: [Freesurfer] Path Problem

[Bruce Fischl]

Hi Dave

that is pretty puzzling. The nu1.mnc is the output of the command that is 
failing, so I don't see why it complains that it doesn't exist. The same 
command:

  nu_correct -clobber ./tmp.mri_nu_correct.mni.24649/nu0.mnc 
./tmp.mri_nu_correct.mni.24649/nu1.mnc -tmpdir 
./tmp.mri_nu_correct.mni.24649/0/ -iterations 1000 -stop 1e-4 -distance 200 
-shrink 2

works fine for me. Can you try it from the command line (from the mri dir)? 
If it fails, can you run:

nu_correct -version

and

which nu_correct?

cheers
Bruce



On Fri, 4 
Dec 2015, LIEWALD David wrote:

> Hi Bruce
>
> Yes the dir is writable and the echo command does create the test.dat in the 
> subdir.
>
> I have attached a recon-all log as requested
>
> Many Thanks
>
> Dave
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Bruce Fischl 
> 
> Sent: 04 December 2015 13:36
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Path Problem
>
> HI David
>
> can you write to that dir? For example, does
>
> echo test >  ./tmp.mri_nu_correct.mni.24767/test.dat
>
>
> work properly (from the mri dir)? Also, please send us the entire
> recon-all.log so we can have a look
>
> cheers
> Bruce
>
> On Fri, 4 Dec 2015,
> LIEWALD
> David wrote:
>
>>
>> Environment : Opensuse 13.2 Freesurver Version 6 (Beta)
>>
>>
>> Hi I hope you can help with this problem
>>
>>
>> I'm using the version 6 Beta due to problems with license authentication. 
>> Freesurfer runs but bails
>> out with a file not found error :
>>
>>
>>
>> Iteration 1 Fri Dec  4 09:38:57 GMT 2015
>> nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc 
>> ./tmp.mri_nu_correct.mni.24767/nu1.mnc
>> -tmpdir ./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 
>> -distance 200 -shrink 2
>>
>>
>>
>> ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist!
>> Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 
>> 2015 (ec183cc) x86_64
>> x86_64 x86_64 GNU/Linux
>>
>>
>>
>> on examination of the file structure a directory named 
>> "tmp.mri_nu_correct.mni.24767" has been
>> created under the "mri"directory and nothing has been created under the 
>> "tmp" directory  in the
>> subject root. I am guessing that this is the cause of the error.
>>
>>
>> any advice on correcting this would be extremely useful
>>
>>
>> Dave Liewald
>>
>>
>>
>
>
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Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

[UQAM]

Hi Bruce,

We were using the correct mri_cc, but our segments were numbered 251 to 262
instead of 230 to 241 in the CColorLUT.txt. With this adjustment, the
mri_cc now runs perfectly and segments in 12.

Many thanks for your support!

Best,
Genevieve



On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl 
wrote:

> Hi Genevieve
>
> are you sure you are using the correct mri_cc? I used your command line
> and got 12 segments. How many segents do you get? It should generate
> segments numbered 230-241 I think. You'll need to make your own entries in
> the ColorLUT.txt file if you want to see them in prespecified colors and
> names and such
>
> cheers
> Bruce
>
> On Fri, 27 Nov 2015, UQAM wrote:
>
> Hi Zeke,
>> We tried the new version of mri_cc and we still do not get 12 segments of
>> the corpus callosum when we open
>> the aseg.12segmentsCC.mgz in a viewer.
>>
>> Could you send us the script you launch after the recon_all to get
>> aseg.mgz files with 12 segments?
>> basically the mri_cc
>>
>> Could you also please explain how to edit the ColorLut.txt file
>>
>> Finally, what is the precise script of the mri_segstats to generate stats
>> tables.
>>
>> Thanks again,
>>
>> Cheers,
>> Genevieve
>>
>> On Tue, Nov 24, 2015 at 11:20 PM, Z K 
>> wrote:
>>   Hello Genevieve,
>>
>>   Below is a link to the newest version of mri_cc. Please copy it to
>> your FREESURFER_HOME
>>   directory and backup the original.
>>
>>
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc
>>
>>   Hope this help.
>>
>>   -Zeke
>>
>>
>>   On 11/24/2015 05:56 AM, UQAM wrote:
>> Hi Bruce,
>>
>> DELL R910
>> Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores)
>> 32 Go RAM
>> CentOS release 5.10 (Final)
>> kernel 2.6.18-371.3.1.el5
>>
>> On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl
>>  fis...@nmr.mgh.harvard.edu>> wrote:
>>
>> Hi Genevieve
>>
>> I just tracked this down and it is a bug in mri_cc. If
>> you tell Zeke
>> your hardware/software environment he can get you a new
>> version that
>> should work
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 23 Nov 2015, UQAM wrote:
>>
>> Hi Bruce,
>> Please find the two files attached.
>>
>> Genevieve
>>
>>
>>
>> On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl
>>  fis...@nmr.mgh.harvard.edu>>
>> wrote:
>>Hi Geneviève
>>
>>if you send us the $SUBJECTS_DIR/CColorLUT.txt
>> and
>> $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we
>> will take a
>>look
>>
>>cheers
>>Bruce
>>On Mon, 23 Nov 2015, UQAM wrote:
>>
>>  Hi,
>>  This a a "re-posting" of a question I've
>> raised
>> last week ; )
>>
>>  I would like to segment the corpus
>> callosum
>> into twelve even lenght segments
>>  instead of the five segments that
>> freesurfer
>> includes by default.
>>
>>  - First I ran a mri_cc on subject e0070:
>>
>>  mri_cc -aseg aseg.auto_noCCseg.mgz -o
>> aseg.12segmentsCC.mgz -d 12 e0070
>>
>>  - Then I edited the ColorLUT.txt file
>> and renamed
>> it CColorLUT.txt (see
>>  attachment, segments 251 to 262).
>>
>>  - Finally I ran a mri_segstats to
>> compute the
>> statistics on segmented
>>  volumes.
>>
>>  mri_segstats seg
>> $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab
>>  $SUBJECTS_DIR/CColorLUT.txt --nonempty
>> --excludeid
>> 0 sum
>>  --e0070_CC12.aseg.stats
>>
>>  The e0070_CC12.aseg.stats file still
>> displays only
>> five segments of the
>>  corpus callosum.
>>
>>  Any tips or clues on how I could do
>> things
>> differently to get 12 segments?
>>
>>  Thanks in advance,
>>
>>  Geneviève
>>
>>
>> ___
>>   

Re: [Freesurfer] Path Problem

[Bruce Fischl]

HI David

can you write to that dir? For example, does

echo test >  ./tmp.mri_nu_correct.mni.24767/test.dat


work properly (from the mri dir)? Also, please send us the entire 
recon-all.log so we can have a look


cheers
Bruce

On Fri, 4 Dec 2015, 
LIEWALD 
David wrote:




Environment : Opensuse 13.2 Freesurver Version 6 (Beta)


Hi I hope you can help with this problem


I'm using the version 6 Beta due to problems with license authentication. 
Freesurfer runs but bails
out with a file not found error :



Iteration 1 Fri Dec  4 09:38:57 GMT 2015
nu_correct -clobber ./tmp.mri_nu_correct.mni.24767/nu0.mnc 
./tmp.mri_nu_correct.mni.24767/nu1.mnc
-tmpdir ./tmp.mri_nu_correct.mni.24767/0/ -iterations 1000 -stop 1e-4 -distance 
200 -shrink 2
 
 
 
ERROR: file ./tmp.mri_nu_correct.mni.24767/nu1.mnc does not exist!
Linux CCACE-PROC5 3.16.7-24-desktop #1 SMP PREEMPT Mon Aug 3 14:37:06 UTC 2015 
(ec183cc) x86_64
x86_64 x86_64 GNU/Linux



on examination of the file structure a directory named 
"tmp.mri_nu_correct.mni.24767" has been
created under the "mri"directory and nothing has been created under the "tmp" 
directory  in the
subject root. I am guessing that this is the cause of the error.


any advice on correcting this would be extremely useful


Dave Liewald


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[Freesurfer] Freesurfer V6 (beta) and MacOS 10.11 (El Capitan)

[Kevin Aquino]

Dear all,

I was wondering if many users have had freesurfer 6 (beta) working (well)
with Mac OS 10.11?

(or Freesurfer V5.3)

Thanks!


*Dr Kevin Aquino*
Research fellow,
Sir Peter Mansfield Magnetic Resonance Center, The University of
Nottingham.

Honorary Research Fellow
School of Physics, Faculty of Science, University of Sydney

*E* kevin.aqu...@nottingham.ac.uk, aqu...@physics.usyd.edu.au | *W*
www.physics.usyd.edu.au/~aquino/

--

The brain is a wonderful organ. It starts working the moment you get up and
does not stop until you get into the office.
-
Robert Frost

CRICOS 00026A
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delete it and any attachments.

Please think of our environment and only print this e-mail if necessary.
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Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

[Bruce Fischl]

Hi Genevieve

I just reran it locally and confirmed that the segments start at 230 for 
me, so I'm not sure what's going on. Still, maybe it meets your needs for 
now (but be aware that when we release V6 the segment numbering is likely 
to start at 230)


cheers
Bruce


On Fri, 4 Dec 2015, UQAM wrote:


Hi Bruce,
We were using the correct mri_cc, but our segments were numbered 251 to 262 
instead of 230 to 241
in the CColorLUT.txt. With this adjustment, the mri_cc now runs perfectly and 
segments in 12.

Many thanks for your support!

Best, 
Genevieve 



On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl  
wrote:
  Hi Genevieve

  are you sure you are using the correct mri_cc? I used your command line 
and got 12
  segments. How many segents do you get? It should generate segments 
numbered 230-241 I
  think. You'll need to make your own entries in the ColorLUT.txt file if 
you want to see
  them in prespecified colors and names and such

  cheers
  Bruce
  On Fri, 27 Nov 2015, UQAM wrote:

Hi Zeke,
We tried the new version of mri_cc and we still do not get 12 
segments of
the corpus callosum when we open
the aseg.12segmentsCC.mgz in a viewer.

Could you send us the script you launch after the recon_all to get 
aseg.mgz
files with 12 segments?
basically the mri_cc

Could you also please explain how to edit the ColorLut.txt file

Finally, what is the precise script of the mri_segstats to generate 
stats
tables. 

Thanks again,

Cheers,
Genevieve

On Tue, Nov 24, 2015 at 11:20 PM, Z K 
 wrote:
      Hello Genevieve,

      Below is a link to the newest version of mri_cc. Please copy 
it to
your FREESURFER_HOME
      directory and backup the original.

       

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

      Hope this help.

      -Zeke


      On 11/24/2015 05:56 AM, UQAM wrote:
            Hi Bruce,

            DELL R910
            Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores)
            32 Go RAM
            CentOS release 5.10 (Final)
            kernel 2.6.18-371.3.1.el5

            On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl
            > wrote:

                Hi Genevieve

                I just tracked this down and it is a bug in mri_cc. 
If you
tell Zeke
                your hardware/software environment he can get you a 
new
version that
                should work

                cheers
                Bruce


                On Mon, 23 Nov 2015, UQAM wrote:

                    Hi Bruce,
                    Please find the two files attached.

                    Genevieve



                    On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl
                    >
                    wrote:
                           Hi Geneviève

                           if you send us the 
$SUBJECTS_DIR/CColorLUT.txt
and
                    $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz 
and we
will take a
                           look

                           cheers
                           Bruce
                           On Mon, 23 Nov 2015, UQAM wrote:

                                 Hi,
                                 This a a "re-posting" of a 
question I've
raised
                    last week ; )

                                 I would like to segment the corpus
callosum
                    into twelve even lenght segments
                                 instead of the five segments that
freesurfer
                    includes by default.

                                 - First I ran a mri_cc on subject 
e0070:

                                 mri_cc -aseg aseg.auto_noCCseg.mgz 
-o
                    aseg.12segmentsCC.mgz -d 12 e0070

                                 - Then I edited the ColorLUT.txt 
file and
renamed
                    it CColorLUT.txt (see
                                 attachment, segments 251 to 262).

                            

Re: [Freesurfer] Recon-all -bigventricles option : general use or not in Alzheimer cases ?

[Matthieu Vanhoutte]

Hi Bruce,

Exactly I want to be sure that I process my data in the same way, so not
introduce bias with partially use of -bigventricles option.

1) I tried the recon-all process on AD patient with big ventricles and
atrophy with and without the -bigventricles option. I am not pretty sure of
which process is the best in terms of segmentation according the aseg.mgz ?
(I'll send you T1 and aseg.mgz for the two process)
2) Considering cortical atrophy, a lot of gray matter hasn't been taken
account in the cortex segmentation. Is there an automatic way to improve
the cortical segmentation in case of visible atrophy ?

Best regards,
Matthieu

2015-12-03 18:03 GMT+01:00 Bruce Fischl :

> Hi Matthie
>
> do you find that it doesn't work well without bigventricles? You just
> want to be sure that you process your data in the same way so there is no
> bias in the results. We have found that most early AD cases work fine
> without needing special flags. It's more for late stage AD or hydrocephalus
> and such.
>
> cheers
> Bruce
>
>
>
> On Thu, 3 Dec 2015, Matthieu
> Vanhoutte wrote:
>
> > Dear FreeSurfer experts,
> >
> > My question is in the title. I'm working on Alzheimer case where most of
> the cases have large
> > ventricles. Is it better in general use to apply -bigventricles option
> on all subjects (for
> > homogeneous calculus or something like that...) or to distinct subtle
> cases of patients with not so
> > big ventricles ?
> >
> > Thanks in advance for helping !
> >
> > Best regards,
> >
> > Matthie
> >
> >
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Re: [Freesurfer] bring volumes to fsaverage space

[Andrew Bock]

Hi all,

It turns out this error was due to a lack of memory, increasing to ~15GB of
memory solved the problem.

Andrew

On Wed, Nov 25, 2015 at 2:50 PM, Andrew Bock  wrote:

> Hi all,
>
> I am receiving the same error, using the same version of Freesurfer (
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0).
>
> Was a solution found?
>
> Andrew
>
> On Mon, Nov 2, 2015 at 3:31 AM, Shani Ben Amitay 
> wrote:
>
>> Dear Lilla and freesurfers,
>>
>> I hvae tried to rub the mri_CVS_register and got the following error:
>> VolumeMorph load - failed to open input stream.
>> I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>> Any idea how to fix this>
>> Log file atttached
>> Thanks!
>>
>> Shani
>>
>> On Fri, Oct 30, 2015 at 11:17 PM, Lilla Zollei <
>> lzol...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Shani,
>>>
>>> Sure. You can do
>>>
>>> mri_cvs_register --help
>>>
>>> and that should give you lots of information.
>>>
>>> Alternatively you can also go to
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register
>>>
>>> and read through the presentation that we give at the FS course:
>>> http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt
>>>
>>> Best, Lilla
>>>
>>>
>>> On Fri, 30 Oct 2015, Shani Ben Amitay wrote:
>>>
>>>
 Hello
 Can you please direct me to more information about the CVS.
 Thanks!
 Shani

 בתאריך 30 באוק' 2015 14:39, "Bruce Fischl" 
 כתב:
   Hi Shani

   you can use mri_vol2vol with the talairach.m3z. Alternatively,
 you can run CVS which will give you more accurate cortical matching and use
 the transform that it produces.

   cheers
   Bruce
   On Fri, 30 Oct 2015, Shani Ben Amitay wrote:

 Dear freesurfers,
 I would like to know what will be the best way to bring
 volumes in the
 individual subject's space  to the fsaverage space.

 Thanks,
 Shani


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>>> ___
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>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
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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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>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
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>>
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>> addressed. If you believe this e-mail was sent to you in error and the
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>>
>
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Re: [Freesurfer] Left and right white matter intensity ratio

[Sabrina Yu]

Absolutely, sorry for the confusion. I am looking at decreased ipsilesional 
myelination signal intensity in patients with unilateral strokes. The goal is 
to run the T1 scans through FreeSurfer, then determine the ratio of signal 
intensity - contralesional: ipsilesional.

Thanks,
Sabrina



On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve" 
> wrote:

I guess I'm not sure what you are trying to do. Can you elaborate?

On 12/3/15 6:24 PM, Sabrina Yu wrote:
> Hi Doug,
>
> Thanks for the quick reply. Is Xhemi only for measuring volumes for both 
> hemispheres?
>
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
> You mentioned editing pctsurfcon to set white matter and gray matter in this 
> email thread here. Can this be used to measure of white matter intensity for 
> lh only, and then rh only? This email thread sounded promising for what I 
> need, but am also unsure of how to input set wm and gm commands.
>
> Thanks,
> Sabrina
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Thursday, December 3, 2015 2:31 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Left and right white matter intensity ratio
>
> see if this tool is what you need. It allows you to map to the homolgous
> vertex on the contralateral hemisphere
> http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
>
> On 12/03/2015 05:25 PM, Sabrina Yu wrote:
>> Hi there,
>>
>>
>> Would it be possible to use pctsurfcon to calculate the ratio of white
>> matter signal intensity between left and right hemispheres?
>>
>> Thank you
>> Sabrina
>>
>>
>> ___
>> 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
>
>

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[Freesurfer] gyrification and longitudinal processing

[Bernardoni, Fabio]

dear freesurfer enthusiasts,

does it makes sense to compute the local Gyrification Index (lGI) on 
longitudinally preprocessed subjects?

thanks
fabio




Dr. Fabio Bernardoni
wiss. Mitarbeiter
Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie
Tel. +49 (0)351 458-5245
Fax +49 (0)351 458-7206



Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://www.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113






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Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

[Bruce Fischl]

HI Genevieve

you'll need to send us all your command lines

cheers
Bruce

On Fri, 4 Dec 2015, UQAM 
wrote:



Hi again Bruce,
The mri_cc & mri_segstats run just fine.  
- When I open the open the new segmented .mgz files (aseg.12segmentsCC_new.mgz) 
in tkmedit I can
clearly visualize the 12 segments.
- When I open the .stats file I get volumes for each of the 12 corpus callosum 
segments. 

However, when I run the asegstats2table the result is a .txt file with the 
usual 5 segments of
the corpus callosum  (anterior, ...). 

Any clue why the asegstats2table doesn't take into account the new 12 segments?

See relevant files attached,

As usual thanks so much ; )
Genevieve




On Fri, Dec 4, 2015 at 3:07 PM, Bruce Fischl  wrote:
  Hi Genevieve

  I just reran it locally and confirmed that the segments start at 230 for 
me, so I'm not
  sure what's going on. Still, maybe it meets your needs for now (but be 
aware that when
  we release V6 the segment numbering is likely to start at 230)

  cheers
  Bruce


  On Fri, 4 Dec 2015, UQAM wrote:

Hi Bruce,
We were using the correct mri_cc, but our segments were numbered 
251 to 262
instead of 230 to 241
in the CColorLUT.txt. With this adjustment, the mri_cc now runs 
perfectly
and segments in 12.

Many thanks for your support!

Best, 
Genevieve 



On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl 

wrote:
      Hi Genevieve

      are you sure you are using the correct mri_cc? I used your 
command
line and got 12
      segments. How many segents do you get? It should generate 
segments
numbered 230-241 I
      think. You'll need to make your own entries in the 
ColorLUT.txt file
if you want to see
      them in prespecified colors and names and such

      cheers
      Bruce
      On Fri, 27 Nov 2015, UQAM wrote:

            Hi Zeke,
            We tried the new version of mri_cc and we still do not 
get 12
segments of
            the corpus callosum when we open
            the aseg.12segmentsCC.mgz in a viewer.

            Could you send us the script you launch after the 
recon_all to
get aseg.mgz
            files with 12 segments?
            basically the mri_cc

            Could you also please explain how to edit the 
ColorLut.txt file

            Finally, what is the precise script of the mri_segstats 
to
generate stats
            tables. 

            Thanks again,

            Cheers,
            Genevieve

            On Tue, Nov 24, 2015 at 11:20 PM, Z K
 wrote:
                  Hello Genevieve,

                  Below is a link to the newest version of mri_cc. 
Please
copy it to
            your FREESURFER_HOME
                  directory and backup the original.

                   
           

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

                  Hope this help.

                  -Zeke


                  On 11/24/2015 05:56 AM, UQAM wrote:
                        Hi Bruce,

                        DELL R910
                        Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 
cores)
                        32 Go RAM
                        CentOS release 5.10 (Final)
                        kernel 2.6.18-371.3.1.el5

                        On Mon, Nov 23, 2015 at 7:32 PM, Bruce 
Fischl
                        > wrote:

                            Hi Genevieve

                            I just tracked this down and it is a 
bug in
mri_cc. If you
            tell Zeke
                            your hardware/software environment he 
can get
you a new
            version that
                            should work

                            cheers
                            Bruce


                            On Mon, 23 Nov 2015, UQAM wrote:

                                Hi Bruce,
                                Please find the two files attached.

                                Genevieve



                                On Mon, Nov 23, 

Re: [Freesurfer] gyrification and longitudinal processing

[Martin Reuter]

an enthusiastic "yes" from me.
Martin

On 12/04/2015 11:19 AM, Bernardoni, Fabio wrote:
> dear freesurfer enthusiasts,
>
> does it makes sense to compute the local Gyrification Index (lGI) on 
> longitudinally preprocessed subjects?
>
> thanks
> fabio
>
>
>
>
> Dr. Fabio Bernardoni
> wiss. Mitarbeiter
> Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und -psychotherapie
> Tel. +49 (0)351 458-5245
> Fax +49 (0)351 458-7206
>
>
>
> Universitätsklinikum Carl Gustav Carus
> an der Technischen Universität Dresden
> Anstalt des öffentlichen Rechts des Freistaates Sachsen
> Fetscherstraße 74, 01307 Dresden
> http://www.uniklinikum-dresden.de
> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
> Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba
> USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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[Freesurfer] including missing gray matter voxels

[Kendrick Kay]

I am trying to figure out how to manually expand the pial surface boundary 
(generated via automatic segmentation with recon-all) to include additional 
gray matter voxels which have been erroneously labeled as skull or CBF. 

i found extensive documentation on how to delete voxels (for example from white 
matter mask), but i can't seem to find relevant information advising how to 
manually include some missing gray matter voxels (on either ends of the cortex 
- i.e. white matter/gray matter boundary or gray matter/pial surface boundary).

Any help would be appreciated.



--
Kendrick Kay, PhD
Assistant Professor
Center for Magnetic Resonance Research
University of Minnesota, Twin Cities
   Web: http://cvnlab.net 
E-mail: k...@umn.edu 
  Cell: 510-206-1059
 Skype: kendrickkay

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Re: [Freesurfer] Left and right white matter intensity ratio

[Sabrina Yu]

I think averaged over an ROI is what is best. Any way to do this in FreeSurfer?

Thanks,
Sabrina



On Fri, Dec 4, 2015 at 10:16 AM -0800, "Douglas N Greve" 
> wrote:

on a voxel-by-voxel basis or averaged over an ROI?

On 12/04/2015 12:56 PM, Sabrina Yu wrote:
> Absolutely, sorry for the confusion. I am looking at decreased
> ipsilesional myelination signal intensity in patients with unilateral
> strokes. The goal is to run the T1 scans through FreeSurfer, then
> determine the ratio of signal intensity - contralesional: ipsilesional.
>
> Thanks,
> Sabrina
>
>
>
> On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve"
> > wrote:
>
> I guess I'm not sure what you are trying to do. Can you elaborate?
>
> On 12/3/15 6:24 PM, Sabrina Yu wrote:
> > Hi Doug,
> >
> > Thanks for the quick reply. Is Xhemi only for measuring volumes for
> both hemispheres?
> >
> >
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
> > You mentioned editing pctsurfcon to set white matter and gray matter
> in this email thread here. Can this be used to measure of white matter
> intensity for lh only, and then rh only? This email thread sounded
> promising for what I need, but am also unsure of how to input set wm
> and gm commands.
> >
> > Thanks,
> > Sabrina
> >
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Douglas N Greve
> 
> > Sent: Thursday, December 3, 2015 2:31 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Left and right white matter intensity ratio
> >
> > see if this tool is what you need. It allows you to map to the homolgous
> > vertex on the contralateral hemisphere
> > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
> >
> > On 12/03/2015 05:25 PM, Sabrina Yu wrote:
> >> Hi there,
> >>
> >>
> >> Would it be possible to use pctsurfcon to calculate the ratio of white
> >> matter signal intensity between left and right hemispheres?
> >>
> >> Thank you
> >> Sabrina
> >>
> >>
> >> ___
> >> 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
> >
> >
>
> ___
> 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

--
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/

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Re: [Freesurfer] Left and right white matter intensity ratio

[Douglas N Greve]

there should be a {lh,rh}.w-g.pct.stats files in 
$SUBJECTS_DIR/subject/stats. That will have the mean gray-white contrast 
for each ROI in the aparc. Does that work for you?

On 12/04/2015 01:29 PM, Sabrina Yu wrote:
> I think averaged over an ROI is what is best. Any way to do this in 
> FreeSurfer?
>
> Thanks,
> Sabrina
>
>
>
> On Fri, Dec 4, 2015 at 10:16 AM -0800, "Douglas N Greve" 
> > wrote:
>
> on a voxel-by-voxel basis or averaged over an ROI?
>
> On 12/04/2015 12:56 PM, Sabrina Yu wrote:
> > Absolutely, sorry for the confusion. I am looking at decreased
> > ipsilesional myelination signal intensity in patients with unilateral
> > strokes. The goal is to run the T1 scans through FreeSurfer, then
> > determine the ratio of signal intensity - contralesional: ipsilesional.
> >
> > Thanks,
> > Sabrina
> >
> >
> >
> > On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve"
> > > wrote:
> >
> > I guess I'm not sure what you are trying to do. Can you elaborate?
> >
> > On 12/3/15 6:24 PM, Sabrina Yu wrote:
> > > Hi Doug,
> > >
> > > Thanks for the quick reply. Is Xhemi only for measuring volumes for
> > both hemispheres?
> > >
> > >
> > 
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
> > > You mentioned editing pctsurfcon to set white matter and gray matter
> > in this email thread here. Can this be used to measure of white matter
> > intensity for lh only, and then rh only? This email thread sounded
> > promising for what I need, but am also unsure of how to input set wm
> > and gm commands.
> > >
> > > Thanks,
> > > Sabrina
> > >
> > > 
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  on behalf of Douglas N Greve
> > 
> > > Sent: Thursday, December 3, 2015 2:31 PM
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Left and right white matter intensity ratio
> > >
> > > see if this tool is what you need. It allows you to map to the 
> homolgous
> > > vertex on the contralateral hemisphere
> > > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
> > >
> > > On 12/03/2015 05:25 PM, Sabrina Yu wrote:
> > >> Hi there,
> > >>
> > >>
> > >> Would it be possible to use pctsurfcon to calculate the ratio of 
> white
> > >> matter signal intensity between left and right hemispheres?
> > >>
> > >> Thank you
> > >> Sabrina
> > >>
> > >>
> > >> ___
> > >> 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
> > >
> > >
> >
> > ___
> > 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
>
> -- 
> 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/
>
> 

Re: [Freesurfer] Left and right white matter intensity ratio

[Douglas N Greve]

on a voxel-by-voxel basis or averaged over an ROI?

On 12/04/2015 12:56 PM, Sabrina Yu wrote:
> Absolutely, sorry for the confusion. I am looking at decreased 
> ipsilesional myelination signal intensity in patients with unilateral 
> strokes. The goal is to run the T1 scans through FreeSurfer, then 
> determine the ratio of signal intensity - contralesional: ipsilesional.
>
> Thanks,
> Sabrina
>
>
>
> On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve" 
> > wrote:
>
> I guess I'm not sure what you are trying to do. Can you elaborate?
>
> On 12/3/15 6:24 PM, Sabrina Yu wrote:
> > Hi Doug,
> >
> > Thanks for the quick reply. Is Xhemi only for measuring volumes for 
> both hemispheres?
> >
> > 
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
> > You mentioned editing pctsurfcon to set white matter and gray matter 
> in this email thread here. Can this be used to measure of white matter 
> intensity for lh only, and then rh only? This email thread sounded 
> promising for what I need, but am also unsure of how to input set wm 
> and gm commands.
> >
> > Thanks,
> > Sabrina
> >
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> > Sent: Thursday, December 3, 2015 2:31 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] Left and right white matter intensity ratio
> >
> > see if this tool is what you need. It allows you to map to the homolgous
> > vertex on the contralateral hemisphere
> > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
> >
> > On 12/03/2015 05:25 PM, Sabrina Yu wrote:
> >> Hi there,
> >>
> >>
> >> Would it be possible to use pctsurfcon to calculate the ratio of white
> >> matter signal intensity between left and right hemispheres?
> >>
> >> Thank you
> >> Sabrina
> >>
> >>
> >> ___
> >> 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
> >
> >
>
> ___
> 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

-- 
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/

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[Freesurfer] How to divide the lateral and medial vertex index of fsaverage4?

[Meiling Li]

Dear Freesurfer 
Now I have two ROIs on the fsaverage4, one on the lateral and the other is the 
on the medial, how can i separate apart the two rois? Acutally, how can i 
divide the vertex index of the lateral and medial on fsaverage4 or fsaverage5?
Thanks in advance!


Meiling___
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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] How to divide the lateral and medial vertex index of fsaverage4?

[Douglas N Greve]

I don't understand what you are trying to do. Can you elaborate?

On 12/04/2015 01:56 PM, Meiling Li wrote:
> Dear Freesurfer
> Now I have two ROIs on the fsaverage4, one on the lateral and the 
> other is the on the medial, how can i separate apart the two rois? 
> Acutally, how can i divide the vertex index of the lateral and medial 
> on fsaverage4 or fsaverage5?
> Thanks in advance!
>
> Meiling
>
>
>
>
> ___
> 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/

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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] Left and right white matter intensity ratio

[Sabrina Yu]

Thanks Doug, those are calculated by pctsurfcon correct?

Is there also a way to separately measure white matter intensity, not a 
gray-white contrast?

Thanks





On Fri, Dec 4, 2015 at 10:38 AM -0800, "Douglas N Greve" 
> wrote:

there should be a {lh,rh}.w-g.pct.stats files in
$SUBJECTS_DIR/subject/stats. That will have the mean gray-white contrast
for each ROI in the aparc. Does that work for you?

On 12/04/2015 01:29 PM, Sabrina Yu wrote:
> I think averaged over an ROI is what is best. Any way to do this in
> FreeSurfer?
>
> Thanks,
> Sabrina
>
>
>
> On Fri, Dec 4, 2015 at 10:16 AM -0800, "Douglas N Greve"
> > wrote:
>
> on a voxel-by-voxel basis or averaged over an ROI?
>
> On 12/04/2015 12:56 PM, Sabrina Yu wrote:
> > Absolutely, sorry for the confusion. I am looking at decreased
> > ipsilesional myelination signal intensity in patients with unilateral
> > strokes. The goal is to run the T1 scans through FreeSurfer, then
> > determine the ratio of signal intensity - contralesional: ipsilesional.
> >
> > Thanks,
> > Sabrina
> >
> >
> >
> > On Thu, Dec 3, 2015 at 5:52 PM -0800, "Douglas Greve"
> > > wrote:
> >
> > I guess I'm not sure what you are trying to do. Can you elaborate?
> >
> > On 12/3/15 6:24 PM, Sabrina Yu wrote:
> > > Hi Doug,
> > >
> > > Thanks for the quick reply. Is Xhemi only for measuring volumes for
> > both hemispheres?
> > >
> > >
> >
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35097.html
> > > You mentioned editing pctsurfcon to set white matter and gray matter
> > in this email thread here. Can this be used to measure of white matter
> > intensity for lh only, and then rh only? This email thread sounded
> > promising for what I need, but am also unsure of how to input set wm
> > and gm commands.
> > >
> > > Thanks,
> > > Sabrina
> > >
> > > 
> > > From: freesurfer-boun...@nmr.mgh.harvard.edu
> >  on behalf of Douglas N Greve
> > 
> > > Sent: Thursday, December 3, 2015 2:31 PM
> > > To: freesurfer@nmr.mgh.harvard.edu
> > > Subject: Re: [Freesurfer] Left and right white matter intensity ratio
> > >
> > > see if this tool is what you need. It allows you to map to the
> homolgous
> > > vertex on the contralateral hemisphere
> > > http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
> > >
> > > On 12/03/2015 05:25 PM, Sabrina Yu wrote:
> > >> Hi there,
> > >>
> > >>
> > >> Would it be possible to use pctsurfcon to calculate the ratio of
> white
> > >> matter signal intensity between left and right hemispheres?
> > >>
> > >> Thank you
> > >> Sabrina
> > >>
> > >>
> > >> ___
> > >> 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
> > >
> > >
> >
> > ___
> > 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
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358