date:20170202

Re: [Freesurfer] Multiple comparison question

2017-02-02 Thread Anderson M. Winkler

Hi VM,

They can stay all in the same .csv file. The "fwep" files will have
p-values corrected across all columns of this input.

All the best,

Anderson


On 2 February 2017 at 12:09, neuroimage analyst <
neuroimage.anal...@gmail.com> wrote:

> Thanks, Anderson. If there are several other measures such as volume,
> thickness, FA,  can I then put them in a single csv file and run the
> command or I have to create 3 csv files, one each for volume, thickness,and
> FA and also invoke -corrmod?
>
> Thanks
>
> Regards
> VM
>
> On Feb 2, 2017 1:01 AM, "Anderson M. Winkler" 
> wrote:
>
> Hi VM,
>
> Please see below:
>
>
> On 1 February 2017 at 02:38, neuroimage analyst <
> neuroimage.anal...@gmail.com> wrote:
>
>> Hi,
>>
>> We extracted volume measures from 7 ROIs in 2 groups and compared
>> a) Mean of each ROI volume between group, and compared independently such
>> as
>> i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2
>> ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2
>>  and so on
>>
>
> This means 7 comparisons, or 14 if you test both directions (tails)
> separately.
>
>
>>
>> b) Plotted the mean ROI volume for 2 independent measures and compared
>> whether the slope between and within group is significantly different. such
>> as
>> i) Slope of ROI1 is positively associated with MoCA , age (grp1) ?
>> ii) Slope of ROI1 is negatively associated with MoCA, age (grp2) ?
>> iii) Slope of ROI1 vs MoCA (grp1) is significantly different
>> than slope of ROI1 vs MoCA (grp2) ?
>> iv) Slope of ROI1 vs MoCA (grp2) is significantly different than slope of
>> ROI2 vs MoCA (grp2) ?
>>
>
> These sound tests for main effects and interaction, with various
> combinations possible.
>
>
>>
>> Q1) Do we have to perform multiple comparisons for (a) and (b)?
>>
>
> Yes.
>
>
>
>> Q2) If yes, do we correct across 7 measurements for (a) and 2
>> measurements for (b) or 7 measurements for both (a) and (b)?
>>
>
> You could put the values for the 7 ROIs in a table in .csv format, with
> one column per ROI and one row per subject. This would be the input data.
> Create a design matrix as:
>
> EV1: 0 or 1 coding for group 1
> EV2: 0 or 1 coding for group 2
> EV3: MoCA group 1
> EV4: MoCA group 2
> EV5: Age group 1
> EV6: Age group 2
> etc
>
> Then define a set of contrasts such as:
>
> C1: [1 -1 0 0 0 0 ...] - This tests if mean for group 1 > mean for group 2
> C2: [-1 1 0 0 0 0 ...] - This tests if mean for group 1 < mean for group 2
> C3: [0 0 1 -1 0 0 ...] - This tests if the slope for MoCA for group 1 >
> slope for MoCA for group 2
> C4: [0 0 -1 1 0 0 ...] - This tests if the slope for MoCA for group 1 <
> slope for MoCA for group 2
> C5: [0 0 1 0 0 0 ...] - This tests if slope for MoCA for group 1 > 0
> C6: [0 0 -1 0 0 0 ...] - This tests if slope for MoCA for group 1 < 0
> etc
>
> You'd run this analysis in PALM with something as:
>
> *palm -i input.csv -d design.mat -t design.con -corrcon -o myresults -logp*
>
>
> Hope this helps!
>
> All the best,
>
> Anderson
>
>
>
>> There is evidence to both performing and nonperforming multiple
>> comparisons In the literature.
>>
>> Any response (hopefully pointing to a literature) will be greatly
>> appreciated.
>>
>> Thanks
>>
>> Regards
>>
>> --VM
>>
>> ___
>> 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
>
>
> 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
>
>
> 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
>

Re: [Freesurfer] Error: if: Expression Syntax.

2017-02-02 Thread Douglas Greve

Why are you passing a dicom file as the registration file? The reg file 
is a FS-specific text file used to store the registration matrix.



On 2/2/17 6:35 PM, Anderson Napolitano wrote:


Hello Experts!



I am having trouble running the following command:


tkregisterfv --mov 
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm 
--reg 
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm 
--surfs


as it outputs the following error:

if: Expression Syntax.

I've attached below the full output with the debug flag on. Any help 
would be greatly appreciated.


Thank you in advance.

Regards,
Anderson


___
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] CUDA in FS6?

2017-02-02 Thread Chris Adamson

I have tested a recon-all -all CPU and GPU with and without the -hires option 
and everything seems to run fine. So at the moment they seem to be compatible 
or at least the GPU version doesn't crash. So that is ok.

Thanks for your time.

Dr Chris Adamson
Research Officer, Developmental Imaging, Murdoch Childrens Research Institute
Murdoch Childrens Research Institute
Royal Children’s Hospital
Flemington Road, Parkville, Victoria  3052, Australia
www.mcri.edu.au
E   chris.adam...@mcri.edu.au
T   03 9936 6780

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of R Edgar 
[freesurfer@gmail.com]
Sent: Friday, 3 February 2017 1:32 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] CUDA in FS6?

On 1 February 2017 at 22:07, Chris Adamson  wrote:

> I understand they are not a priority. But are they compatible with the CPU 
> versions? Should we be using the CUDA versions if they aren't guaranteed to 
> be up-to-date?

I haven't run any comparisons against the CPU binaries recently. And
if any extra pipeline stages were added to the CPU versions, I haven't
ported those to CUDA either.

Richard
___
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.

__
This email has been scanned by the Symantec Email Security.cloud service.
For more information please visit http://www.symanteccloud.com

If you have any questions, please contact MCRI IT Servicedesk for further 
assistance.
__

__
This email has been scanned by the Symantec Email Security.cloud service.
For more information please visit http://www.symanteccloud.com
__

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

Re: [Freesurfer] CUDA in FS6?

2017-02-02 Thread R Edgar

On 1 February 2017 at 22:07, Chris Adamson  wrote:

> I understand they are not a priority. But are they compatible with the CPU 
> versions? Should we be using the CUDA versions if they aren't guaranteed to 
> be up-to-date?

I haven't run any comparisons against the CPU binaries recently. And
if any extra pipeline stages were added to the CPU versions, I haven't
ported those to CUDA either.

Richard
___
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] license file not working

2017-02-02 Thread Matt Glasser

Strange, that fixed things right up for me.  You might make sure you know
where you are calling FreeSurfer from and that there are no old license
files lying around.

Peace,

Matt.

From:   on behalf of Anthony Dick

Reply-To:  Freesurfer support list 
Date:  Thursday, February 2, 2017 at 5:46 PM
To:  
Subject:  Re: [Freesurfer] license file not working


 

Thanks Matt. I already tried it with a new registration, but it doesn't hurt
to try it again. That may be where the issue is. I'll post if that turns out
to be the problem. Thanks!
 

Anthony
 
 
 
On 2/2/17 6:28 PM, Matt Glasser wrote:
 
 
>   
> Like I said, they changed the format at some point and stopped accepting the
> old format with FS 6.0.  I have used FreeSurfer for a long time too and found
> that I had to get a new license file with this version.
>  
> 
>  
>  
> Peace,
>  
> 
>  
>  
> Matt.
>  
> 
>  
>   
> From:   on behalf of Anthony Dick
> 
>  Reply-To:  Freesurfer support list 
>  Date:  Thursday, February 2, 2017 at 5:18 PM
>  To:  
>  Subject:  Re: [Freesurfer] license file not working
>  
>  
> 
>  
>  
>  
>  
> 
> Hello,
>  
> 
> I have used my old file, registered under two different emails (and received
> the code and made new files each time, named both .license and license.txt).
> Restarted the computer etc. I am wondering if it is a permissions issue. It
> seems to be finding the file where I put it. Have never encountered this issue
> and have been using Freesurfer for 11 years. If history is any guide, it will
> probably turn out to be something stupid that I did :)
>  
> 
> Anthony
>  
>  
>  
> On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
>  
>  
>>  
>> The .license that it comes with is not the same as the license.txt that you
>> have to acquire. I was able to use an old license.txt from my Freesurfer 5.3
>> for 6.0. 
>> 
>>  
>>  
>> Best
>>  
>> 
>>  
>>  
>> Trisanna
>>  
>>  
>> 
>>  
>>  
>>  
>>  
>>  
>> --
>>  
>> Ph.D. Candidate 
>> McGill University
>>   
>> Integrated Program in Neuroscience
>>  
>> Psychology
>>  
>> 
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>> On Thu, Feb 2, 2017 at 3:21 PM, X K  wrote:
>>  
>>>  
>>> try to rename the file to license.txt?
>>>  
>>>  
>>>  
>>> 
>>>  
>>> On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick  wrote:
>>>  
 Hello,
  
  I have been using Freesurfer for a number of years, and just installed
  v6.0. I run into this problem:
  
  --
  ERROR: Invalid FreeSurfer license key found in license file
  /Applications/freesurfer/.license
 If you are outside the NMR-Martinos Center,
 go to http://surfer.nmr.mgh.harvard.edu/registration.html to
 get a valid license file (it's free).
 If you are inside the NMR-Martinos Center,
 make sure to source the standard environment.
  --
  
  I have a valid .license file, in the Freesurfer home directory
  
  Last login: Thu Feb  2 15:04:01 on ttys005
   freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
  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
  [38c9862eb0b0:~] adick% cd /Applications/freesurfer
  [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
  -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
  [38c9862eb0b0:/Applications/freesurfer] adick%
  
  Any ideas?
  
  Thanks!
  
  Anthony
  
  
  --
  Anthony Steven Dick, Ph.D.
  Associate Professor
  Director, Cognitive Neuroscience Program and Graduate Certificate in
 Cognitive Neuroscience
  Department of Psychology
  Florida International University Modesto A. Maidique Campus AHC4 454
  11200 S.W. 8th Street
  Miami, FL 33199
  Ph: 305-348-4202  ; Lab Ph: 305-348-9055
  ; Fx: 305-348-3879 
  Email: ad...@fiu.edu
  Webpage: http://myweb.fiu.edu/adick
  Join the Society for the Study of Human Development:
 http://www.sshdonline.org
  
  ___
  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

Re: [Freesurfer] license file not working

2017-02-02 Thread Anthony Dick

Thanks Matt. I already tried it with a new registration, but it doesn't 
hurt to try it again. That may be where the issue is. I'll post if that 
turns out to be the problem. Thanks!


Anthony


On 2/2/17 6:28 PM, Matt Glasser wrote:
Like I said, they changed the format at some point and stopped 
accepting the old format with FS 6.0.  I have used FreeSurfer for a 
long time too and found that I had to get a new license file with this 
version.


Peace,

Matt.

From: > on behalf of Anthony 
Dick >
Reply-To: Freesurfer support list >

Date: Thursday, February 2, 2017 at 5:18 PM
To: >

Subject: Re: [Freesurfer] license file not working

Hello,

I have used my old file, registered under two different emails (and 
received the code and made new files each time, named both .license 
and license.txt). Restarted the computer etc. I am wondering if it is 
a permissions issue. It seems to be finding the file where I put it. 
Have never encountered this issue and have been using Freesurfer for 
11 years. If history is any guide, it will probably turn out to be 
something stupid that I did :)


Anthony


On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
The .license that it comes with is not the same as the license.txt 
that you have to acquire. I was able to use an old license.txt from 
my Freesurfer 5.3 for 6.0.


Best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Feb 2, 2017 at 3:21 PM, X K > wrote:


try to rename the file to license.txt?

On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick > wrote:

Hello,

I have been using Freesurfer for a number of years, and just
installed
v6.0. I run into this problem:


--
ERROR: Invalid FreeSurfer license key found in license file
/Applications/freesurfer/.license
   If you are outside the NMR-Martinos Center,
   go to http://surfer.nmr.mgh.harvard.edu/registration.html
 to
   get a valid license file (it's free).
   If you are inside the NMR-Martinos Center,
   make sure to source the standard environment.

--

I have a valid .license file, in the Freesurfer home directory

Last login: Thu Feb  2 15:04:01 on ttys005
 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
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
[38c9862eb0b0:~] adick% cd /Applications/freesurfer
[38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
-rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
[38c9862eb0b0:/Applications/freesurfer] adick%

Any ideas?

Thanks!

Anthony


--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate
Certificate in Cognitive Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus
AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202 ; Lab Ph:
305-348-9055 ; Fx: 305-348-3879

Email: ad...@fiu.edu 
Webpage: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development:
http://www.sshdonline.org

___
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

[Freesurfer] Error: if: Expression Syntax.

2017-02-02 Thread Anderson Napolitano

Hello Experts!



I am having trouble running the following command:


tkregisterfv --mov 
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm
 --reg 
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm
 --surfs

as it outputs the following error:

if: Expression Syntax.

I've attached below the full output with the debug flag on. Any help would be 
greatly appreciated.

Thank you in advance.

Regards,
Anderson?
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 5 != 0 )

set flag = $argv[1] ; shift ;
set flag = --mov
shift

switch ( $flag )
switch ( --mov )
if ( $#argv < 1 ) goto arg1err ;
if ( 4 < 1 ) goto arg1err
set movvol = $argv[1] ; shift ;
set movvol = 
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm
shift
if ( ! -e $movvol ) then
if ( ! -e 
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm
 ) then
set movvol = `getfullpath $movvol`
set movvol = `getfullpath $movvol`
getfullpath 
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 3 != 0 )

set flag = $argv[1] ; shift ;
set flag = --reg
shift

switch ( $flag )
switch ( --reg )
if ( $#argv < 1 ) goto arg1err ;
if ( 2 < 1 ) goto arg1err
set reg = $argv[1] ; shift ;
set reg = 
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm
shift
set reg = `getfullpath $reg`
set reg = `getfullpath $reg`
getfullpath 
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 1 != 0 )

set flag = $argv[1] ; shift ;
set flag = --surfs
shift

switch ( $flag )
switch ( --surfs )
case "--wm-surfs":
case --wm-surfs:
set DoSurfs = 1 ;
set DoSurfs = 1
set surflist0 = ( lh.white rh.white )
set surflist0 = ( lh.white rh.white )
set surfcolor = ( yellow yellow ) ;
set surfcolor = ( yellow yellow )
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 0 != 0 )

goto parse_args_return ;
goto parse_args_return
goto check_params ;
goto check_params

if ( $#movvol == 0 ) then
if ( 1 == 0 ) then

if ( $#targ == 0 ) then
if ( 0 == 0 ) then
if ( $#subject == 0 && $#reg == 0 ) then
if ( 0 == 0 && 1 == 0 ) then
if ( $#subject == 0 ) then
if ( 0 == 0 ) then
if ( ! -e $reg ) then
if ( ! -e 
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm
 ) then
set subject = `reg2subject --r $reg`
set subject = `reg2subject --r $reg`
reg2subject --r 
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm
endif
endif
if ( ! -e $SUBJECTS_DIR/$subject ) then
if ( ! -e /usr/local/freesurfer/subjects/# transform file 
/Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm
 ) then
if: Expression Syntax.
___
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] license file not working

2017-02-02 Thread Matt Glasser

Like I said, they changed the format at some point and stopped accepting the
old format with FS 6.0.  I have used FreeSurfer for a long time too and
found that I had to get a new license file with this version.

Peace,

Matt.

From:   on behalf of Anthony Dick

Reply-To:  Freesurfer support list 
Date:  Thursday, February 2, 2017 at 5:18 PM
To:  
Subject:  Re: [Freesurfer] license file not working


 

Hello,
 

I have used my old file, registered under two different emails (and received
the code and made new files each time, named both .license and license.txt).
Restarted the computer etc. I am wondering if it is a permissions issue. It
seems to be finding the file where I put it. Have never encountered this
issue and have been using Freesurfer for 11 years. If history is any guide,
it will probably turn out to be something stupid that I did :)
 

Anthony
 
 
 
On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
 
 
>   
> The .license that it comes with is not the same as the license.txt that you
> have to acquire. I was able to use an old license.txt from my Freesurfer 5.3
> for 6.0. 
> 
>  
>  
> Best
>  
> 
>  
>  
> Trisanna
>  
>  
> 
>  
>  
>  
>  
>  
> --
>  
> Ph.D. Candidate 
> McGill University
>   
> Integrated Program in Neuroscience
>  
> Psychology
>  
> 
>  
>  
>  
>  
>  
>  
>  
>  
>  
> On Thu, Feb 2, 2017 at 3:21 PM, X K  wrote:
>  
>>  
>> try to rename the file to license.txt?
>>  
>>  
>>  
>> 
>>  
>> On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick  wrote:
>>  
>>> Hello,
>>>  
>>>  I have been using Freesurfer for a number of years, and just installed
>>>  v6.0. I run into this problem:
>>>  
>>>  --
>>>  ERROR: Invalid FreeSurfer license key found in license file
>>>  /Applications/freesurfer/.license
>>> If you are outside the NMR-Martinos Center,
>>> go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>>> get a valid license file (it's free).
>>> If you are inside the NMR-Martinos Center,
>>> make sure to source the standard environment.
>>>  --
>>>  
>>>  I have a valid .license file, in the Freesurfer home directory
>>>  
>>>  Last login: Thu Feb  2 15:04:01 on ttys005
>>>   freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>>>  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
>>>  [38c9862eb0b0:~] adick% cd /Applications/freesurfer
>>>  [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>>>  -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>>>  [38c9862eb0b0:/Applications/freesurfer] adick%
>>>  
>>>  Any ideas?
>>>  
>>>  Thanks!
>>>  
>>>  Anthony
>>>  
>>>  
>>>  --
>>>  Anthony Steven Dick, Ph.D.
>>>  Associate Professor
>>>  Director, Cognitive Neuroscience Program and Graduate Certificate in
>>> Cognitive Neuroscience
>>>  Department of Psychology
>>>  Florida International University Modesto A. Maidique Campus AHC4 454
>>>  11200 S.W. 8th Street
>>>  Miami, FL 33199
>>>  Ph: 305-348-4202  ; Lab Ph: 305-348-9055
>>>  ; Fx: 305-348-3879 
>>>  Email: ad...@fiu.edu
>>>  Webpage: http://myweb.fiu.edu/adick
>>>  Join the Society for the Study of Human Development:
>>> http://www.sshdonline.org
>>>  
>>>  ___
>>>  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.
>>>  
>>>  
>>  
>>  
>>  
>>  
>> 
>>  
>>  
>>  
>>  -- 
>>  
>>  
>> -
>> 
>>  
>> Kong Xiangzhen
>>  State Key Laboratory of Cognitive Neuroscience and Learning,
>>  Beijing Normal University,
>>  Beijing, China, 100875.
>>  
>>  
>>  ___
>>  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

Re: [Freesurfer] license file not working

2017-02-02 Thread Anthony Dick


Hello,

I have used my old file, registered under two different emails (and 
received the code and made new files each time, named both .license and 
license.txt). Restarted the computer etc. I am wondering if it is a 
permissions issue. It seems to be finding the file where I put it. Have 
never encountered this issue and have been using Freesurfer for 11 
years. If history is any guide, it will probably turn out to be 
something stupid that I did :)


Anthony


On 2/2/17 3:40 PM, Trisanna Sprung-Much wrote:
The .license that it comes with is not the same as the license.txt 
that you have to acquire. I was able to use an old license.txt from my 
Freesurfer 5.3 for 6.0.


Best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Feb 2, 2017 at 3:21 PM, X K > wrote:


try to rename the file to license.txt?

On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick > wrote:

Hello,

I have been using Freesurfer for a number of years, and just
installed
v6.0. I run into this problem:


--
ERROR: Invalid FreeSurfer license key found in license file
/Applications/freesurfer/.license
   If you are outside the NMR-Martinos Center,
   go to http://surfer.nmr.mgh.harvard.edu/registration.html
 to
   get a valid license file (it's free).
   If you are inside the NMR-Martinos Center,
   make sure to source the standard environment.

--

I have a valid .license file, in the Freesurfer home directory

Last login: Thu Feb  2 15:04:01 on ttys005
 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
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
[38c9862eb0b0:~] adick% cd /Applications/freesurfer
[38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
-rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
[38c9862eb0b0:/Applications/freesurfer] adick%

Any ideas?

Thanks!

Anthony


--
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate
Certificate in Cognitive Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus
AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202 ; Lab Ph:
305-348-9055 ; Fx: 305-348-3879

Email: ad...@fiu.edu 
Webpage: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development:
http://www.sshdonline.org

___
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.




-- 
-

Kong Xiangzhen
State Key Laboratory of Cognitive Neuroscience and Learning,
Beijing Normal University,
Beijing, China, 100875.

___
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

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6)

2017-02-02 Thread Bruce Fischl

Hi Joe

there are slight differences, and for sure we reserve the right to use 
the knowledge that it is a FLAIR scan in the algorithms, so you should 
probably rerun

cheers
Bruce
On Thu, 2 Feb 2017, Joe Necus (PGR) wrote:

> 
> Hello,
> 
> 
> I am running recon-all on the latest version of freesurfer (Version 6) and 
> would like to know whether
> there is any difference between using the -T2 -T2Pial and -Flair flags.
> 
> 
> I am currently running recon-all with a T1 and FLAIR image, but have used the 
> -T2 -T2pial flags and
> would like to know whether I need to go back and instead re-run with the 
> -FLAIR flag instead.
> 
> 
> Thanks a lot,
> 
> Joe
> 
> 
> 
> 
>
___
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] Simple question regarding -T2 and -FLAIR flags (freesurfer v6)

2017-02-02 Thread Douglas N Greve

It will behave differently as some of the parameters change depending 
upon whether it is a T2 or FLAIR. This will only affect the surface creation

On 02/02/2017 05:19 PM, Joe Necus (PGR) wrote:
>
> Hello,
>
>
> I am running recon-all on the latest version of freesurfer (Version 6) 
> and would like to know whether there is any difference between using 
> the -T2 -T2Pial and -Flair flags.
>
>
> I am currently running recon-all with a T1 and FLAIR image, but have 
> used the -T2 -T2pial flags and would like to know whether I need to go 
> back and instead re-run with the -FLAIR flag instead.
>
>
> Thanks a lot,
>
> Joe
>
>
>
>
>
> ___
> 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] Simple question regarding -T2 and -FLAIR flags (freesurfer v6)

2017-02-02 Thread Joe Necus (PGR)

Hello,


I am running recon-all on the latest version of freesurfer (Version 6) and 
would like to know whether there is any difference between using the -T2 
-T2Pial and -Flair flags.


I am currently running recon-all with a T1 and FLAIR image, but have used the 
-T2 -T2pial flags and would like to know whether I need to go back and instead 
re-run with the -FLAIR flag instead.


Thanks a lot,

Joe


___
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] design specification with 3 categorical predictors

2017-02-02 Thread Douglas N Greve

The second design is fine if there is no significant interaction between 
1 or 2 and 3. You'll have to create the design matrix yourself or you 
can create an fsgd file with 7 classes


On 02/02/2017 11:38 AM, Tim Reess wrote:
>
> Dear Freesurfer experts,
>
> I would like to set up a design matrix for a design that is not 
> QDEC-able. I have three categorical factors:
>
> 1.disease status: 2 levels
>
> 2.gender: 2 levels
>
> 3.scan site: 4 levels
>
> The first design I set up was the following (the rows are just for 
> illustration and don’t reflect the number of subjects that will enter 
> the analysis):
>
> designs4_fs_mailinglist.png
>
> However, I have my doubts as to the “efficiency” of the design (in 
> terms of number of regressors / DOF). Therefore, here is my second design:
>
> Would this design be correct for assessing the group differences for 
> disease status while regressing out gender and scanner site? My 
> understanding is, that in this design I can’t assess the effects of 
> interactions regarding scanner site. However, I think it is fair to 
> assume that the scanner site doesn’t have a differential effect on 
> either gender or disease status. Any feedback is highly appreciated. 
> Thanks a lot. Best regards,
>
> Tim
>
>
>
> ___
> 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.

Re: [Freesurfer] LGI issue/Error

2017-02-02 Thread Douglas N Greve

So ismac.m is not defined in your matlab implementation? What version of 
matlab are you using? What kind of computer are you running on?


On 02/02/2017 01:48 PM, aral ahmadi wrote:
>
> Dear experts
>
> I have a question regarding Freesurfer- LGI error I got during running 
> LGI after all recon steps been ran with no problem.  you could see the 
> error below.
>
> *reading filled volume...
> *
>
> *??? undefined function or variable 'ismac'.*
> *error in -->load_mgh at 68*
> *
> *
> *if(strcmp(computer,'MAC') || strcmp(computer,'MAC') || ismac)*
> *
> *
> *error in -->MRIread at 87*
> *
> *
> *[mri, voi, M, mr_parms, volsz] = load_mgh (fspec, [], [], headeronly);*
> *
> *
> *error in --> make outer-surface at 24*
> *
> *
> *vol = MRIread(filled_volume);*
> **
> *>> ERROR:make _outer_surface did not creat output file 
> 'net/storage1/usr2/onrc/home/p2/Aahmadi/onrc/data/Aral-july/test/subject*
> *Linux compute31 2.6.32-504.12.2.e16.*86_64 #1 SMP Wed Mar11  UTC 2015 
> 86_64  86_64 GNU/Linux*
> *
> *
> *recon-all  -s  S1091RPY existed with Errors at thu jan19 2017*
> *
> *
> The error is ...Undefined function or variable 'ismac' - matlab is 
> expecting that variable to be defined (it's trying to detect the OS, 
> whether Linux, windows/ Mac), but it isn't. *
> *
>
> I appreciate if you give me your advice on this issue.
>
> Thanks,
>
> Aral
>
>
> ___
> 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.

Re: [Freesurfer] Group connectivity maps with crazy sig values

2017-02-02 Thread Douglas N Greve

I don't think there is anything really wrong. There are computation 
limits on the maximum significance. When the given voxel goes beyond 
that, I set it to this ridiculously high level. This high level just 
means that it is really significant.


On 02/02/2017 12:18 PM, Rodriguez-Thompson, Anais wrote:
> Hi freesurfer experts,
>
> I am running a group functional connectivity analysis following the steps 
> from the FsFast Functional Connectivity Walkthrough. When I visualize the 
> OSGM maps, the pattern of connectivity looks normal but there are regions of 
> ridiculously high significance values (sig= 10,000,000,000). This problem is 
> happening bilaterally for each seed. Attached are slides showing the OSGM map 
> for one of my seeds (left dlPFC) at a normal threshold, and then at a 
> threshold minimum of 100 to show the regions that have this crazy 
> significance value.
>
> After generating my .dat files using fcseed-sess and creating nuisance 
> regressors I run the following commands:
>
> $ mkanalysis-sess -analysis FC_{mask}_FS5.3_SIRP.lh -surface fsaverage lh 
> -fwhm 5 -notask -taskreg {mask}.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 
> -nuisreg global.waveform.dat 1 -mcextreg -polyfit 5 -fsd bold -rlf 
> funlist_fc_SIRP -TR 2 -per-run -force
>
> $ selxavg3-sess -sf $SUBJECTS_DIR/Subject_Files/GDD/145_GDD_FC_SerumFolate 
> -analysis FC_{mask}_FS5.3_SIRP.lh
>
> $ isxconcat-sess -sf $SUBJECTS_DIR/Subject_Files/GDD/145_GDD_FC_SerumFolate 
> -analysis FC_{mask}_FS5.3_SIRP.lh -all-contrasts -hemis -o 
> $SUBJECTS_DIR/Analyses_GDD/FC_Analyses/145_GDD_SerumFolate/bold/{mask}
>
> $ mri_glmfit --fsgd 
> /cluster/roffman/users/fsgd/GDD/145_GDD_FC_SerumFolate_OSGM.fsgd --osgm 
> --fwhm 6 --no-prune --y 
> /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/FC_Analyses/145_GDD_SerumFolate/bold/lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816/FC_lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816_FS5.3_SIRP.lh/lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816/ces.nii.gz
>  --glmdir 
> /cluster/roffman/users/Stable5_PerRun/Analyses_GDD/FC_Analyses/145_GDD_SerumFolate/bold/lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816/FC_lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816_FS5.3_SIRP.lh/lh_FPCN_DLPFC_100GDD_2vFix_osgm_peak_sm04.10e-10_121816/LH_OSGM
>  --surface fsaverage lh
>
> Am I doing something wrong in my commands that is creating these results? Is 
> there anything I can do to troubleshoot this issue?
>
> Thank you,
>
> Anais Rodriguez-Thompson
> Clinical Research Coordinator
> Brain Genomics Laboratory
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Phone: (617) 643-3215
>
>
> ___
> 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.

Re: [Freesurfer] possible atlas error to report

2017-02-02 Thread Douglas N Greve

Sorry, which labels are consistent and which are inconsistent?


On 02/02/2017 02:52 PM, Levman, Jacob wrote:
>
> Hi there,
>
>
> I've been conducting an asymmetry analysis based on FreeSurfer 
> measurements. There are regions of the brain with known left-right 
> asymmetry such as BA44 which exhibits strong leftward asymmetry (the 
> left side is bigger than the right). This is accurately reflected when 
> you compare the BA44 GrayVol measurement from lh.BA.thresh to 
> rh.BA.thresh. However, in the lh.BA and rh.BA results, the BA44 
> GrayVol measurements consistently indicate a rightward asymmetry 
> (right side larger than the left side) though this conflicts with 
> known findings in the literature for this region of the brain and is 
> the opposite pattern to that produced in lh.BA.thresh and rh.BA.thresh.
>
>
> This indicates that the lh.BA and rh.BA results may be left-right 
> inverted in BA44 and possibly in other regions as well.
>
>
> Thanks,
>
>
> Jacob
>
>
> 
>
>
>
>
> ___
> 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.

Re: [Freesurfer] license file not working

2017-02-02 Thread Trisanna Sprung-Much

The .license that it comes with is not the same as the license.txt that you
have to acquire. I was able to use an old license.txt from my Freesurfer
5.3 for 6.0.

Best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Thu, Feb 2, 2017 at 3:21 PM, X K  wrote:

> try to rename the file to license.txt?
>
> On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick  wrote:
>
>> Hello,
>>
>> I have been using Freesurfer for a number of years, and just installed
>> v6.0. I run into this problem:
>>
>> 
>> --
>> ERROR: Invalid FreeSurfer license key found in license file
>> /Applications/freesurfer/.license
>>If you are outside the NMR-Martinos Center,
>>go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>>get a valid license file (it's free).
>>If you are inside the NMR-Martinos Center,
>>make sure to source the standard environment.
>> 
>> --
>>
>> I have a valid .license file, in the Freesurfer home directory
>>
>> Last login: Thu Feb  2 15:04:01 on ttys005
>>  freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>> 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
>> [38c9862eb0b0:~] adick% cd /Applications/freesurfer
>> [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>> -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>> [38c9862eb0b0:/Applications/freesurfer] adick%
>>
>> Any ideas?
>>
>> Thanks!
>>
>> Anthony
>>
>>
>> --
>> Anthony Steven Dick, Ph.D.
>> Associate Professor
>> Director, Cognitive Neuroscience Program and Graduate Certificate in
>> Cognitive Neuroscience
>> Department of Psychology
>> Florida International University Modesto A. Maidique Campus AHC4 454
>> 11200 S.W. 8th Street
>> Miami, FL 33199
>> Ph: 305-348-4202 <(305)%20348-4202>; Lab Ph: 305-348-9055
>> <(305)%20348-9055>; Fx: 305-348-3879 <(305)%20348-3879>
>> Email: ad...@fiu.edu
>> Webpage: http://myweb.fiu.edu/adick
>> Join the Society for the Study of Human Development:
>> http://www.sshdonline.org
>>
>> ___
>> 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.
>>
>>
>
>
> --
> 
> -
> Kong Xiangzhen
> State Key Laboratory of Cognitive Neuroscience and Learning,
> Beijing Normal University,
> Beijing, China, 100875.
>
> ___
> 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


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 check recon-all finished without any error

2017-02-02 Thread Trisanna Sprung-Much

Try checking your recon all.log in your scripts folder of the subject.

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology

On Thu, Feb 2, 2017 at 1:52 PM, shi yao wang 
wrote:

> Dear FS experts:
> How to check recon-all finished without any error?
> Sometime, there are showing no error message, however, when I running
> hippocampus subfield, it does not run.
>
> thanks
> Lawrence
> Emory
>
> ___
> 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

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] ROIs in midline for cortical thickness

2017-02-02 Thread Sahil Bajaj

Thanks Dr. Fischl. I will surely give a try to this.

On Wed, Feb 1, 2017 at 3:17 PM, Bruce Fischl 
wrote:

> I see. Have you run recon-all on each hemi? If so, use bbregister to
> register the surfaces to the fmri data, then use mri_vol2surf to map the
> activations on to the left and right surfaces and draw your ROIs that way.
>
> cheers
>
> Bruce
> On Wed, 1 Feb 2017, Sahil Bajaj wrote:
>
> Hi Dr. Fischl,
>> Thank you so much for your reply.
>>
>> I have this SMA activation from a fMRI task. I am interested in getting
>> cortical thickness of exactly the same area. Its showing activation in
>> both
>> hemispheres. I am also attaching here screen shot to make it more clear
>> how
>> it looks like. To do that, thats correct, I am trying to draw both left
>> and
>> right SMA thickness.
>>
>> Thanks.
>>
>> On Wed, Feb 1, 2017 at 2:46 PM, Bruce Fischl 
>> wrote:
>>   Hi Sahil
>>
>>   can you clarify what you mean. Do you have the left hemi SMA
>>   labeled in MNI space and it (incorrectly) extends into the right
>>   hemi? Or are you trying to draw both the left and the right SMA?
>>
>>   Bruce
>>   On Wed, 1 Feb 2017, Sahil Bajaj wrote:
>>
>> Hi everyone,
>> I have supplementary motor area (SMA) defined in
>> standard MNI volume space
>> and I would like to extract cortical thickness for
>> this area. I have 80% of
>> SMA in left hemisphere and 20% on right hemisphere.
>> So I am stuck at the
>> command mri_vol2surf before proceeding to
>> mri_segstats.
>>
>> In mri_vol2surf, I am not sure what should I specify
>> for --hemi i.e. whether
>> its left or right hemisphere (lh or rh). If I
>> specify e.g. lh, then would
>> not it convert left hemisphere SMA voxels to surface
>> and later on extract
>> the measure from left hemisphere only and vice-versa
>> for right hemisphere.
>>
>> I am not sure how would that work if portion of ROI
>> is on both hemispheres
>> and how can I run mri_vol2surf command?
>>
>> Thanks,
>> Sahil
>>
>>
>> ___
>> 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


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] Analysis of rates or percent changes

2017-02-02 Thread Katarina Trojacanec

Hi Martin,


I dropped --generic-time flag as you suggested in the previous e-mail and run 
the long_stats_slopes command again like this:


long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats 
aseg.stats --meas volume --sd $SUBJECTS_DIR --do-rate --do-pc1fit --do-pc1 
--do-spc --time years --stack-rate 
./qdec/long_AD_NL_TP1_2_3_4_m.aseg-rate.stack.txt --stack-pc1fit 
./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1fit.stack.txt --stack-pc1 
./qdec/long_AD_NL_TP1_2_3_4_m.aseg-pc1.stack.txt --stack-spc 
./qdec/long_AD_NL_TP1_2_3_4_m.aseg-spc.stack.txt

However, I got exactly the same results for stacked rate pc1/fit, spc (the 
files long_AD_NL_TP1_2_3_4_m.aseg-*.stack.txt) as in the case with the 
--generic-time flag. Is this reasonable?


As I read and understood, the --generic-time flag assumes that time difference 
between the time points is 1, which is not true in my case (the time difference 
between TP1 and TP2 is around six months, and between TP2 and TP3, as well as 
TP3 and TP4 is one year). This indicates that there should be some difference 
in the result.


Am I doing something wrong or misunderstood anything, or maybe there are some 
temporary files from the first running of the command that are used also in the 
second one (without --generic-time flag)?


Best, Katarina


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia


From: Katarina Trojacanec
Sent: Monday, September 12, 2016 10:01:53 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Analysis of rates or percent changes


Hi Martin,


Thanks a lot.


Best, Katarina


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Martin Reuter 

Sent: Monday, September 12, 2016 7:58:14 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Analysis of rates or percent changes


Hi Katarina,


different time spacing is OK (not optimal, but OK). This 2-stage procedure 
first fits a line in each subject, independent on how many time points the 
subject has. Of course a linear fit from 4 time points will be more reliable 
than one from just 2 time points. This is not taken into consideration and 
therefore we usually recommend the Linear Mixed Effects modeling (where it is 
considered in the model). If most of your subjects have 4 time points and the 
spacing is similar (across subjects) you should be fine.


Other things I noticed:

- you should drop the --generic-time flag. I probably should change the help 
text to be more specific, but what it does it assigns a time of 1 2 3 4 to the 
time points (this is if you do repeated measures and there is no real time). So 
don't pass it.


- you can drop some of the --do... flags. Probably you are interested in the 
rate and one of the pct change flags. The average is just the average thickness 
(across time) for each subject. Not sure you want to analyze that. The 
--do-stack is a subject-specific stack of the time points, usually only used 
for debugging.


- the -stack-avg is not needed unless you want to analyze average thickness for 
each subject, rather you may want to create a stack for the rate or the pc1 or 
whatever, to pass it into the stats tool (like mri_glmfit, or R, SPSS or 
whatever you use).


Best, Martin


On 09/12/2016 12:40 PM, Katarina Trojacanec wrote:

Hi,


I have a question about the analysis of rates or percent changes.


I use data with available scans at baseline (TP1) and the 6-month (TP2), 
12-month (TP3) and 24-month (TP4) follow-ups from ADNI dataset. An example of 
some of the data in the appropriate qdec table is given below:


fsid fsid-base years age weight diagnosis gender Glob_CDR NPI-Q_TotScr 
MMSE_TotScr FAQ_TotScr visit1_2_3_4
ADNI_sub1_sc ADNI_base1 0 81.3 y AD M x x x x sc
ADNI_sub1_m06 ADNI_base1 0.528767123 81.9 y AD M x x x x m06
ADNI_sub1_m12 ADNI_base1 1.030136986 82.4 y AD M x x x x m12
ADNI_sub1_m24 ADNI_base1 2.030136986 83.4 y AD M x x x x m24
ADNI_sub2_sc ADNI_base2 0 74 y AD F x x x x sc
ADNI_sub2_m06 ADNI_base2 0.501369863 74.5 y AD F x x x x m06
ADNI_sub2_m12 ADNI_base2 1.005479452 75 y AD F x x x x m12
ADNI_sub2_m24 ADNI_base2 2 76 y AD F x x x x m24


The base is constructed using all four time points. The time variable is given 
in years. I am using long_stats_slopes for aseg.stats as follows:


long_stats_slopes --qdec ./qdec/long_AD_NL_TP1_2_3_4.qdec.table.dat --stats 
aseg.stats --meas volume --sd $SUBJECTS_DIR --do-avg --do-rate --do-pc1fit 
--do-pc1 --do-spc --do-stack --generic-time --time years --stack-avg 
./qdec/long_AD_NL_TP1_2_3_4


(similarly for ?h.aparc.stats)


Having in mind

Re: [Freesurfer] CUDA in FS6?

2017-02-02 Thread Chris Adamson

Richard,

I understand they are not a priority. But are they compatible with the CPU 
versions? Should we be using the CUDA versions if they aren't guaranteed to be 
up-to-date?

Dr Chris Adamson
Research Officer, Developmental Imaging, Murdoch Childrens Research Institute
Murdoch Childrens Research Institute
Royal Children’s Hospital
Flemington Road, Parkville, Victoria  3052, Australia
www.mcri.edu.au
E   chris.adam...@mcri.edu.au
T   03 9936 6780

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of R Edgar 
[freesurfer@gmail.com]
Sent: Thursday, 2 February 2017 12:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] CUDA in FS6?

On 1 February 2017 at 05:47, Chris Adamson  wrote:

> Are the CUDA binaries still being developed in FS6? Are they compatible with
> the CPU only versions?
> I remember asking questions about this a while ago and apparently the cuda
> binaries were no longer being developed in favour of openmp.

I try to provide what support I can, but the CUDA versions are not a priority.

Richard
___
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.

__
This email has been scanned by the Symantec Email Security.cloud service.
For more information please visit http://www.symanteccloud.com

If you have any questions, please contact MCRI IT Servicedesk for further 
assistance.
__

__
This email has been scanned by the Symantec Email Security.cloud service.
For more information please visit http://www.symanteccloud.com
__

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

[Freesurfer] Multiple comparison question

2017-02-02 Thread neuroimage analyst

Hi,

We extracted volume measures from 7 ROIs in 2 groups and compared
a) Mean of each ROI volume between group, and compared independently such
as
i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2
ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2
 and so on

b) Plotted the mean ROI volume for 2 independent measures and compared
whether the slope between and within group is significantly different. such
as
i) Slope of ROI1 is positively associated with MoCA , age (grp1) ?
ii) Slope of ROI1 is negatively associated with MoCA, age (grp2) ?
iii) Slope of ROI1 vs MoCA (grp1) is significantly different than slope of
ROI1 vs MoCA (grp2) ?
iv) Slope of ROI1 vs MoCA (grp2) is significantly different than slope of
ROI2 vs MoCA (grp2) ?

Q1) Do we have to perform multiple comparisons for (a) and (b)?
Q2) If yes, do we correct across 7 measurements for (a) and 2 measurements
for (b) or 7 measurements for both (a) and (b)?

There is evidence to both performing and nonperforming multiple comparisons
In the literature.

Any response (hopefully pointing to a literature) will be greatly
appreciated.

Thanks

Regards

--VM
___
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] Neighborhood thickness in a 10mm radius

2017-02-02 Thread Dorian P.

Hi Freesurfers,

Thank you for the help you provide through this list.

Is there a way to get, for each vertex, the identify (or thickness values)
of the surrounding vertices in a 10mm radius? The command mris_convert has
the '-v' option, but that produces only 5-6 vertices and there is no option
to query a particular radius.

I imagine this can be done manually outside Freesurfer by first identifying
the neighbors for each vertex based on the coordinates, then getting the
respective thickness value, but I wanted to check whether there is any
easier way or any advice on how to proceed.

Dorian
___
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] license file not working

2017-02-02 Thread Matt Glasser

They updated the format so you have to get another.

Peace,

Matt.

On 2/2/17, 2:13 PM, "Anthony Dick"  wrote:

>Hello,
>
>I have been using Freesurfer for a number of years, and just installed
>v6.0. I run into this problem:
>
>--
>ERROR: Invalid FreeSurfer license key found in license file
>/Applications/freesurfer/.license
>   If you are outside the NMR-Martinos Center,
>   go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
>--
>
>I have a valid .license file, in the Freesurfer home directory
>
>Last login: Thu Feb  2 15:04:01 on ttys005
> freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
>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
>[38c9862eb0b0:~] adick% cd /Applications/freesurfer
>[38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
>-rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
>[38c9862eb0b0:/Applications/freesurfer] adick%
>
>Any ideas?
>
>Thanks!
>
>Anthony
>
>
>-- 
>Anthony Steven Dick, Ph.D.
>Associate Professor
>Director, Cognitive Neuroscience Program and Graduate Certificate in
>Cognitive Neuroscience
>Department of Psychology
>Florida International University Modesto A. Maidique Campus AHC4 454
>11200 S.W. 8th Street
>Miami, FL 33199
>Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
>Email: ad...@fiu.edu
>Webpage: http://myweb.fiu.edu/adick
>Join the Society for the Study of Human Development:
>http://www.sshdonline.org
>
>___
>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

Re: [Freesurfer] license file not working

2017-02-02 Thread X K

try to rename the file to license.txt?

On Thu, Feb 2, 2017 at 9:13 PM, Anthony Dick  wrote:

> Hello,
>
> I have been using Freesurfer for a number of years, and just installed
> v6.0. I run into this problem:
>
> --
> ERROR: Invalid FreeSurfer license key found in license file
> /Applications/freesurfer/.license
>If you are outside the NMR-Martinos Center,
>go to http://surfer.nmr.mgh.harvard.edu/registration.html to
>get a valid license file (it's free).
>If you are inside the NMR-Martinos Center,
>make sure to source the standard environment.
> --
>
> I have a valid .license file, in the Freesurfer home directory
>
> Last login: Thu Feb  2 15:04:01 on ttys005
>  freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
> 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
> [38c9862eb0b0:~] adick% cd /Applications/freesurfer
> [38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
> -rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
> [38c9862eb0b0:/Applications/freesurfer] adick%
>
> Any ideas?
>
> Thanks!
>
> Anthony
>
>
> --
> Anthony Steven Dick, Ph.D.
> Associate Professor
> Director, Cognitive Neuroscience Program and Graduate Certificate in
> Cognitive Neuroscience
> Department of Psychology
> Florida International University Modesto A. Maidique Campus AHC4 454
> 11200 S.W. 8th Street
> Miami, FL 33199
> Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
> Email: ad...@fiu.edu
> Webpage: http://myweb.fiu.edu/adick
> Join the Society for the Study of Human Development:
> http://www.sshdonline.org
>
> ___
> 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.
>
>


-- 
-
Kong Xiangzhen
State Key Laboratory of Cognitive Neuroscience and Learning,
Beijing Normal University,
Beijing, China, 100875.
___
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] license file not working

2017-02-02 Thread Anthony Dick

Hello,

I have been using Freesurfer for a number of years, and just installed 
v6.0. I run into this problem:

--
ERROR: Invalid FreeSurfer license key found in license file 
/Applications/freesurfer/.license
   If you are outside the NMR-Martinos Center,
   go to http://surfer.nmr.mgh.harvard.edu/registration.html to
   get a valid license file (it's free).
   If you are inside the NMR-Martinos Center,
   make sure to source the standard environment.
--

I have a valid .license file, in the Freesurfer home directory

Last login: Thu Feb  2 15:04:01 on ttys005
 freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 
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
[38c9862eb0b0:~] adick% cd /Applications/freesurfer
[38c9862eb0b0:/Applications/freesurfer] adick% ls -al .license
-rw-r--r--  1 root  wheel  140 Feb  2 15:06 .license
[38c9862eb0b0:/Applications/freesurfer] adick%

Any ideas?

Thanks!

Anthony


-- 
Anthony Steven Dick, Ph.D.
Associate Professor
Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive 
Neuroscience
Department of Psychology
Florida International University Modesto A. Maidique Campus AHC4 454
11200 S.W. 8th Street
Miami, FL 33199
Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879
Email: ad...@fiu.edu
Webpage: http://myweb.fiu.edu/adick
Join the Society for the Study of Human Development: http://www.sshdonline.org

___
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] possible atlas error to report

2017-02-02 Thread Levman, Jacob

Hi there,


I've been conducting an asymmetry analysis based on FreeSurfer measurements. 
There are regions of the brain with known left-right asymmetry such as BA44 
which exhibits strong leftward asymmetry (the left side is bigger than the 
right). This is accurately reflected when you compare the BA44 GrayVol 
measurement from lh.BA.thresh to rh.BA.thresh. However, in the lh.BA and rh.BA 
results, the BA44 GrayVol measurements consistently indicate a rightward 
asymmetry (right side larger than the left side) though this conflicts with 
known findings in the literature for this region of the brain and is the 
opposite pattern to that produced in lh.BA.thresh and rh.BA.thresh.


This indicates that the lh.BA and rh.BA results may be left-right inverted in 
BA44 and possibly in other regions as well.


Thanks,


Jacob

?

___
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] Cannot find CTF archive

2017-02-02 Thread shi yao wang

Dear FS experts:
when I running hippocampus subfield, I got error messages:" Cannot find CTF
archive".

I copied command and screen to you.

Thank you very much!

[silun.wang@node5 N01]$ *recon-all -s N01 -hippocampal-subfields-T1*
Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6
Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20160611-876a0e6
INFO: SUBJECTS_DIR is /data/home/silun.wang/silun_data
Actual FREESURFER_HOME /usr/local/freesurfer
-rw-rw-r--. 1 silun.wang silun.wang 489034 Feb  2 13:43
/data/home/silun.wang/silun_data/N01/scripts/recon-all.log
Linux node5.cluster 3.10.0-327.36.1.el7.x86_64 #1 SMP Sun Sep 18 13:04:29
UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
'/usr/local/freesurfer/bin/recon-all' ->
'/data/home/silun.wang/silun_data/N01/scripts/recon-all.local-copy'
#
#@# Hippocampal Subfields processing (T1 only) left Thu Feb  2 13:53:46 EST
2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80
/usr/local/freesurfer N01 /data/home/silun.wang/silun_data left

See log file:
/data/home/silun.wang/silun_data/N01/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
Error:Cannot find CTF archive
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf
#
#@# Hippocampal Subfields processing (T1 only) right Thu Feb  2 13:53:53
EST 2017

 /usr/local/freesurfer/bin/segmentSF_T1.sh /usr/local/freesurfer/MCRv80
/usr/local/freesurfer N01 /data/home/silun.wang/silun_data right

See log file:
/data/home/silun.wang/silun_data/N01/scripts/hippocampal-subfields-T1.log
--
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:
*Error:Cannot find CTF archive
/usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.ctf*

Started at Thu Feb 2 13:53:41 EST 2017
Ended   at Thu Feb 2 13:54:01 EST 2017
#@#%# recon-all-run-time-hours 0.006
recon-all -s N01 finished without error at Thu Feb  2 13:54:02 EST 2017
done
___
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] How to check recon-all finished without any error

2017-02-02 Thread shi yao wang

Dear FS experts:
How to check recon-all finished without any error?
Sometime, there are showing no error message, however, when I running
hippocampus subfield, it does not run.

thanks
Lawrence
Emory
___
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] LGI issue/Error

2017-02-02 Thread aral ahmadi

Dear experts

I have a question regarding Freesurfer- LGI error I got during running LGI
after all recon steps been ran with no problem.  you could see the error
below.


*reading filled volume...*
*??? undefined function or variable 'ismac'.*
*error in -->load_mgh at 68*

*if(strcmp(computer,'MAC') || strcmp(computer,'MAC') || ismac)*

*error in -->MRIread at 87*

*[mri, voi, M, mr_parms, volsz] = load_mgh (fspec, [], [], headeronly);*

*error in --> make outer-surface at 24*

*vol = MRIread(filled_volume);*

*>> ERROR:make _outer_surface did not creat output file
'net/storage1/usr2/onrc/home/p2/Aahmadi/onrc/data/Aral-july/test/subject*
*Linux compute31 2.6.32-504.12.2.e16.*86_64 #1 SMP Wed Mar11  UTC 2015
86_64  86_64 GNU/Linux*

*recon-all  -s  S1091RPY existed with Errors at thu jan19 2017*

The error is ...Undefined function or variable 'ismac' - matlab is
expecting that variable to be defined (it's trying to detect the OS,
whether Linux, windows/ Mac), but it isn't.

I appreciate if you give me your advice on this issue.

Thanks,
Aral
___
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] Freesurfer- LGI error

2017-02-02 Thread aral ahmadi

Dear experts,

I have a question regarding Freesurfer- LGI error I got during running LGI
after all recon steps been ran with no problem. Attached you could see the
error.

The error is ...Undefined function or variable 'ismac' - matlab is
expecting that variable to be defined (it's trying to detect the OS,
whether Linux, windows/ Mac), but it isn't.

I appreciate if you give me your advice on this issue.

Thanks,

Aral
___
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] design specification with 3 categorical predictors

2017-02-02 Thread Tim Reess


Dear Freesurfer experts,

I would like to set up a design matrix for a design that is not 
QDEC-able. I have three categorical factors:


1.disease status: 2 levels

2.gender: 2 levels

3.scan site: 4 levels

The first design I set up was the following (the rows are just for 
illustration and don’t reflect the number of subjects that will enter 
the analysis):


designs4_fs_mailinglist.png

However, I have my doubts as to the “efficiency” of the design (in terms 
of number of regressors / DOF). Therefore, here is my second design:


Would this design be correct for assessing the group differences for 
disease status while regressing out gender and scanner site? My 
understanding is, that in this design I can’t assess the effects of 
interactions regarding scanner site. However, I think it is fair to 
assume that the scanner site doesn’t have a differential effect on 
either gender or disease status. Any feedback is highly appreciated. 
Thanks a lot. Best regards,


Tim

___
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] Multiple comparison question

2017-02-02 Thread neuroimage analyst

Thanks, Anderson. If there are several other measures such as volume,
thickness, FA,  can I then put them in a single csv file and run the
command or I have to create 3 csv files, one each for volume, thickness,and
FA and also invoke -corrmod?

Thanks

Regards
VM

On Feb 2, 2017 1:01 AM, "Anderson M. Winkler" 
wrote:

Hi VM,

Please see below:

On 1 February 2017 at 02:38, neuroimage analyst <
neuroimage.anal...@gmail.com> wrote:

> Hi,
>
> We extracted volume measures from 7 ROIs in 2 groups and compared
> a) Mean of each ROI volume between group, and compared independently such
> as
> i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2
> ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2
>  and so on
>

This means 7 comparisons, or 14 if you test both directions (tails)
separately.

>
> b) Plotted the mean ROI volume for 2 independent measures and compared
> whether the slope between and within group is significantly different. such
> as
> i) Slope of ROI1 is positively associated with MoCA , age (grp1) ?
> ii) Slope of ROI1 is negatively associated with MoCA, age (grp2) ?
> iii) Slope of ROI1 vs MoCA (grp1) is significantly different than slope of
> ROI1 vs MoCA (grp2) ?
> iv) Slope of ROI1 vs MoCA (grp2) is significantly different than slope of
> ROI2 vs MoCA (grp2) ?
>

These sound tests for main effects and interaction, with various
combinations possible.

>
> Q1) Do we have to perform multiple comparisons for (a) and (b)?
>

Yes.

> Q2) If yes, do we correct across 7 measurements for (a) and 2 measurements
> for (b) or 7 measurements for both (a) and (b)?
>

You could put the values for the 7 ROIs in a table in .csv format, with one
column per ROI and one row per subject. This would be the input data.
Create a design matrix as:

EV1: 0 or 1 coding for group 1
EV2: 0 or 1 coding for group 2
EV3: MoCA group 1
EV4: MoCA group 2
EV5: Age group 1
EV6: Age group 2
etc

Then define a set of contrasts such as:

C1: [1 -1 0 0 0 0 ...] - This tests if mean for group 1 > mean for group 2
C2: [-1 1 0 0 0 0 ...] - This tests if mean for group 1 < mean for group 2
C3: [0 0 1 -1 0 0 ...] - This tests if the slope for MoCA for group 1 >
slope for MoCA for group 2
C4: [0 0 -1 1 0 0 ...] - This tests if the slope for MoCA for group 1 <
slope for MoCA for group 2
C5: [0 0 1 0 0 0 ...] - This tests if slope for MoCA for group 1 > 0
C6: [0 0 -1 0 0 0 ...] - This tests if slope for MoCA for group 1 < 0
etc

You'd run this analysis in PALM with something as:

*palm -i input.csv -d design.mat -t design.con -corrcon -o myresults -logp*

Hope this helps!

All the best,

Anderson

> There is evidence to both performing and nonperforming multiple
> comparisons In the literature.
>
> Any response (hopefully pointing to a literature) will be greatly
> appreciated.
>
> Thanks
>
> Regards
>
> --VM
>
> ___
> 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

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

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] Multiple comparison question

2017-02-02 Thread Anderson M. Winkler

Hi VM,

Please see below:


On 1 February 2017 at 02:38, neuroimage analyst <
neuroimage.anal...@gmail.com> wrote:

> Hi,
>
> We extracted volume measures from 7 ROIs in 2 groups and compared
> a) Mean of each ROI volume between group, and compared independently such
> as
> i) whether mean of ROI 1 in group 1 is equal to mean of ROI1 in group 2
> ii)whether mean of ROI 2 in group 1 is equal to mean of ROI2 in group 2
>  and so on
>

This means 7 comparisons, or 14 if you test both directions (tails)
separately.


>
> b) Plotted the mean ROI volume for 2 independent measures and compared
> whether the slope between and within group is significantly different. such
> as
> i) Slope of ROI1 is positively associated with MoCA , age (grp1) ?
> ii) Slope of ROI1 is negatively associated with MoCA, age (grp2) ?
> iii) Slope of ROI1 vs MoCA (grp1) is significantly different than slope of
> ROI1 vs MoCA (grp2) ?
> iv) Slope of ROI1 vs MoCA (grp2) is significantly different than slope of
> ROI2 vs MoCA (grp2) ?
>

These sound tests for main effects and interaction, with various
combinations possible.


>
> Q1) Do we have to perform multiple comparisons for (a) and (b)?
>

Yes.



> Q2) If yes, do we correct across 7 measurements for (a) and 2 measurements
> for (b) or 7 measurements for both (a) and (b)?
>

You could put the values for the 7 ROIs in a table in .csv format, with one
column per ROI and one row per subject. This would be the input data.
Create a design matrix as:

EV1: 0 or 1 coding for group 1
EV2: 0 or 1 coding for group 2
EV3: MoCA group 1
EV4: MoCA group 2
EV5: Age group 1
EV6: Age group 2
etc

Then define a set of contrasts such as:

C1: [1 -1 0 0 0 0 ...] - This tests if mean for group 1 > mean for group 2
C2: [-1 1 0 0 0 0 ...] - This tests if mean for group 1 < mean for group 2
C3: [0 0 1 -1 0 0 ...] - This tests if the slope for MoCA for group 1 >
slope for MoCA for group 2
C4: [0 0 -1 1 0 0 ...] - This tests if the slope for MoCA for group 1 <
slope for MoCA for group 2
C5: [0 0 1 0 0 0 ...] - This tests if slope for MoCA for group 1 > 0
C6: [0 0 -1 0 0 0 ...] - This tests if slope for MoCA for group 1 < 0
etc

You'd run this analysis in PALM with something as:

*palm -i input.csv -d design.mat -t design.con -corrcon -o myresults -logp*


Hope this helps!

All the best,

Anderson



> There is evidence to both performing and nonperforming multiple
> comparisons In the literature.
>
> Any response (hopefully pointing to a literature) will be greatly
> appreciated.
>
> Thanks
>
> Regards
>
> --VM
>
> ___
> 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


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] longitudinal tracula error

2017-02-02 Thread Bárbara Avelar Pereira

Thanks again — it was a huge help!

On 31 Jan 2017, at 18:25, Yendiki, Anastasia 
> wrote:

Hi Barbara – Thank you for your kind words. As you’ve read, if the output files 
are generated, then you’re good to go. Bedpost does not differentiate between 
longitudinal and cross-sectional data, so it’s run separately on each time 
point’s …/dmri/ folder.

Best,
a.y

From: 
>
 on behalf of Bárbara Avelar Pereira 
>
Reply-To: Freesurfer support list 
>
Date: Monday, January 30, 2017 at 10:48 AM
To: Freesurfer support list 
>
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks again for the help! And congrats on tracula — it's a great tool, and the 
online support is really good :)

I do have a follow-up question, if that’s OK. I’m currently running bedpost, 
and it gives the following error:

(…)
53 slices processed
54 slices processed
54 slices processed
55 slices processed
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear to have successfully 
completed. Please examine your results carefully.
/usr/local/freesurfer/bin/bedpostx_mgh: line 345: kill: (21128) - No such 
process

I was not running this on a cluster, but I was running a few subjects at the 
same time so I was wondering if it could be a memory problem? Or a 
compatibility problem between FSL and freesurfer?

It seems strange that it shows the same slice more than once on the monitor. 
But from what I read, the monitor is not entirely reliable and the best way to 
check whether everything ran smoothly is to look at the output. I have all the 
files that should have been created, but I’m still suspicious that something 
might be wrong. For example, my merged_xxx files are 50 volumes (should they 
have the same number of volumes as my original nii file? Because this is not 
the case...).

I’ve also tried running it directly from the command line and the error is the 
same (however, since this is longitudinal, when running bedpost from the 
command line, can I simply run it for each timepoint separately as if it was 
cross-sectional or is there an extra step?)

Many thanks!

On 26 Jan 2017, at 14:51, Yendiki, Anastasia 
> wrote:

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need 
to dig up the beta.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu

[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!

From: 
freesurfer-boun...@nmr.mgh.harvard.edu

[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y

From: 
freesurfer-boun...@nmr.mgh.harvard.edu

[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether

Re: [Freesurfer] Multiple comparison question

Re: [Freesurfer] Error: if: Expression Syntax.

Re: [Freesurfer] CUDA in FS6?

Re: [Freesurfer] CUDA in FS6?

Re: [Freesurfer] license file not working

Re: [Freesurfer] license file not working

[Freesurfer] Error: if: Expression Syntax.

Re: [Freesurfer] license file not working

Re: [Freesurfer] license file not working

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6)

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6)

[Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6)

Re: [Freesurfer] design specification with 3 categorical predictors

Re: [Freesurfer] LGI issue/Error

Re: [Freesurfer] Group connectivity maps with crazy sig values

Re: [Freesurfer] possible atlas error to report

Re: [Freesurfer] license file not working

Re: [Freesurfer] How to check recon-all finished without any error

Re: [Freesurfer] ROIs in midline for cortical thickness

Re: [Freesurfer] Analysis of rates or percent changes

Re: [Freesurfer] CUDA in FS6?

[Freesurfer] Multiple comparison question

[Freesurfer] Neighborhood thickness in a 10mm radius

Re: [Freesurfer] license file not working

Re: [Freesurfer] license file not working

[Freesurfer] license file not working

[Freesurfer] possible atlas error to report

[Freesurfer] Cannot find CTF archive

[Freesurfer] How to check recon-all finished without any error

[Freesurfer] LGI issue/Error

[Freesurfer] Freesurfer- LGI error

[Freesurfer] design specification with 3 categorical predictors

Re: [Freesurfer] Multiple comparison question

Re: [Freesurfer] Multiple comparison question

Re: [Freesurfer] longitudinal tracula error

35 matches

Site Navigation

Mail list logo

Footer information