date:20191216

Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

2019-12-16 Thread Bronwyn Overs

External Email - Use Caution

Thank you very much Kersten! 



Kind regards, 





Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1725 


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From: "Kersten Diers, DZNE"  
To: "Freesurfer support list"  
Sent: Monday, December 16, 2019 9:20:49 PM 
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary 
file 



External Email - Use Caution 


Hi Bronwyn, 

you can just add the two betas: it's the slope for the non-case group plus the 
difference in slopes between case and non-case group, so it should give the 
slope in the case group. 

Best regards, 

Kersten 

On Mi, 2019-12-11 at 12:53 +1100, Bronwyn Overs wrote: 




External Email - Use Caution 


Hi Kersten, 

Thank you for all of your help so far. I have now located the unstandardized 
beta values in lhstats(i).Bhat. Unfortunately one of the effects I was 
interested in was the slope for years within my case group, which required the 
use of the following contrast vector: 
0 1 0 0 0 0 0 1 

Do you know how I could estimate the effect size for this contrast given that 
it corresponds to two beta values (1 and 7)? 



Kind regards, 





Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1725 


[ http://neura.edu.au/ | neura.edu.au  ] 



[ https://twitter.com/neuraustralia | Twitter ] | [ 
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ 
http://www.neura.edu.au/help-research/subscribe | Subscribe ] 




From: "Kersten Diers, DZNE"  
To: "Freesurfer support list"  
Sent: Saturday, November 30, 2019 6:50:26 AM 
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary 
file 



External Email - Use Caution 


Hi, 

please see my inline responses below. 

Best, 

Kersten 

On Fr, 2019-11-29 at 13:20 +1100, Bronwyn Overs wrote: 

BQ_BEGIN

Hi Kersten, 

Thank you this is a good suggestion. Where can I get the unstandardized beta 
values for the lme I have already run? 




They are in e.g. lhstats(i).Bhat; see the tutorial webpage for some 
explanation. 


BQ_BEGIN

Also, i'm not really sure how to interpret the unstandardized beta values for 
interaction effects like group X years, do you have any suggestions? 

BQ_END


This would model a difference in slopes, right? So the beta value should 
reflect difference between the two particular groups of this contrast per year 
(if year is the unit of time). 


BQ_BEGIN

Finally, do you know why the max vertex is listed as '-inf' for my largets 
cluster and is this a problem at all? 

BQ_END


I can only speculate here, but it's probably worth checking: A sig value of 
'Inf' would correspond to a p-value of (exactly) zero. So, one might 
investigate if any zeros are contained within the p-value arrays / maps, and if 
these zeros (if any) reflect the outcome of a statistical test (then it should 
be no problem) or if they were erroneously introduced. 


BQ_BEGIN




Kind regards, 





Bronwyn Overs 


Research Assistant 



Neuroscience Research Australia 
Margarete Ainsworth Building 
Barker Street Randwick Sydney NSW 2031 Australia 
M 0411 308 769 T +61 2 9399 1725 


[ http://neura.edu.au/ | neura.edu.au  ] 



[ https://twitter.com/neuraustralia | Twitter ] | [ 
https://www.facebook.com/NeuroscienceResearchAustralia | Facebook ] | [ 
http://www.neura.edu.au/help-research/subscribe | Subscribe ] 




From: "Kersten Diers, DZNE"  
To: "Bronwyn Overs"  
Cc: "Freesurfer support list"  
Sent: Friday, November 29, 2019 8:39:55 AM 
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary 
file 

Hello, 

and thanks for the explanation! 

Here's my first impression: 

I do not think that there is a really satisfying solution given these 
particular stats maps and the effect size measure you describe. 

I may be missing something, but I also have to admit that it is not immediately 
clear to me what motivates the choice of cohen's d (and the calculation you 
describe) in the current scenario - I've always thought of it as a measure of 
'difference in means'. 

In a regression context, I would personally look for a measure of the 
"variance-explained" type. There seem to be at least two papers (Xu, 2003, 
Statistics in Medicine, and Selya, 2012, Frontiers) that cover these for mixed 
effects models. The calculation/implementation of these measures seems to be, 
however, not as straightforward as for classical multiple regression models; 
and as far as I can see, it would also involve fitting Null or reduced models, 
and thus

Re: [Freesurfer] (no subject)

2019-12-16 Thread Bruce Fischl


sorry, my fault. That was for someone else
On Mon, 16 Dec 2019, Boris 
Rauchmann wrote:




External Email - Use Caution

This is the log when I´m creating this file:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label
$SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
sysname  Darwin
hostname MacBook.local
machine  x86_64

setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer
mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz 


== Number of threads available to mri_ca_label for OpenMP = 1 == 
reading 1 input volumes
reading classifier array from
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
reading input volume from
/Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
reading transform from
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 4.97
Atlas used for the 3D morph was
/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 10.8   using min determinant for regularization = 11.7
0 singular and 129 ill-conditioned covariance matrices regularized
labeling volume...
0 gm and wm labels changed (%nan to gray, %nan to white out of all changed
labels)
0 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 9576 changed.
pass 2: 3286 changed.
MRItoUCHAR: min=0, max=246
MRItoUCHAR: converting to UCHAR
writing labeled volume to
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
mri_ca_label utimesec    146.184667
mri_ca_label stimesec    1.040963
mri_ca_label ru_maxrss   1436573696
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   609288
mri_ca_label ru_majflt   112
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  4
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    3
mri_ca_label ru_nivcsw   36417
auto-labeling took 2 minutes and 28 seconds.

This is what I get when I do mrs_info on the gas:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ 
mri_info/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gc
a 
reading frame -1 of gca
Volume information 
for/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gc
a
          type: GCA
    dimensions: 256 x 256 x 256 x 3
   voxel sizes: 1.00, 1.00, 1.00
          type: FLOAT (3)
           fov: 256.000
           dof: 0
        xstart: -128.0, xend: 128.0
        ystart: -128.0, yend: 128.0
        zstart: -128.0, zend: 128.0
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
       nframes: 3
       PhEncDir: UNKNOWN
       FieldStrength: 0.00
ras xform present
    xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =    
0.
              : x_a =   0., y_a =   0., z_a =   1., c_a =    
0.
              : x_s =   0., y_s =  -1., z_s =   0., c_s =    
0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.   0.   0.   128.
                0.   0.   1.  -128.
                0.  -1.   0.   128.
                0.   0.   0.     1.

voxel-to-ras determinant -1

ras to voxel transform:
               -1.  -0.  -0.   128.
               -0.  -0.  -1.   128.
               -0.   1.  -0.   128.
               -0.  -0.  -0.     1.




  Am 16.12.2019 um 21:21 schrieb Boris Rauchmann
  :

Thanks, it was created using: 
mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz

Best,
Boris


  Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D.
  :

There is something weird about that file. How was it created?
doug
ps. Please include previous correspondence in the email

On 12/16/19 1:12 PM, Boris Rauchmann wrote:

  External Email - Use Caution

  Boriss-MacBook-Pro:mri boris$ mri_info
  N_Atlas_subcotex.mgz
  mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz,
  -1): could not open file

Am 16.12.2019 um 19:08 schrieb Greve,
Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>:

mri_info N_Atlas_subcotex.mgz



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Re: [Freesurfer] (no subject)

2019-12-16 Thread Bruce Fischl


to summarize, I want a warp that:

foreach subject

   compute warp based on curvature
   apply warp to a functional overlay
   add that functional overlay to avg

return (tf.reduce_mean(tf.square(avg)))


make sense? So maximizing the mean squared average acivation

On Mon, 16 Dec 2019, Boris Rauchmann 
wrote:




External Email - Use Caution

This is the log when I´m creating this file:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label
$SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
sysname  Darwin
hostname MacBook.local
machine  x86_64

setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer
mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz 


== Number of threads available to mri_ca_label for OpenMP = 1 == 
reading 1 input volumes
reading classifier array from
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
reading input volume from
/Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
reading transform from
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 4.97
Atlas used for the 3D morph was
/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 10.8   using min determinant for regularization = 11.7
0 singular and 129 ill-conditioned covariance matrices regularized
labeling volume...
0 gm and wm labels changed (%nan to gray, %nan to white out of all changed
labels)
0 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 9576 changed.
pass 2: 3286 changed.
MRItoUCHAR: min=0, max=246
MRItoUCHAR: converting to UCHAR
writing labeled volume to
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
mri_ca_label utimesec    146.184667
mri_ca_label stimesec    1.040963
mri_ca_label ru_maxrss   1436573696
mri_ca_label ru_ixrss    0
mri_ca_label ru_idrss    0
mri_ca_label ru_isrss    0
mri_ca_label ru_minflt   609288
mri_ca_label ru_majflt   112
mri_ca_label ru_nswap    0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  4
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw    3
mri_ca_label ru_nivcsw   36417
auto-labeling took 2 minutes and 28 seconds.

This is what I get when I do mrs_info on the gas:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ 
mri_info/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gc
a 
reading frame -1 of gca
Volume information 
for/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gc
a
          type: GCA
    dimensions: 256 x 256 x 256 x 3
   voxel sizes: 1.00, 1.00, 1.00
          type: FLOAT (3)
           fov: 256.000
           dof: 0
        xstart: -128.0, xend: 128.0
        ystart: -128.0, yend: 128.0
        zstart: -128.0, zend: 128.0
            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
degrees
       nframes: 3
       PhEncDir: UNKNOWN
       FieldStrength: 0.00
ras xform present
    xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =    
0.
              : x_a =   0., y_a =   0., z_a =   1., c_a =    
0.
              : x_s =   0., y_s =  -1., z_s =   0., c_s =    
0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
               -1.   0.   0.   128.
                0.   0.   1.  -128.
                0.  -1.   0.   128.
                0.   0.   0.     1.

voxel-to-ras determinant -1

ras to voxel transform:
               -1.  -0.  -0.   128.
               -0.  -0.  -1.   128.
               -0.   1.  -0.   128.
               -0.  -0.  -0.     1.




  Am 16.12.2019 um 21:21 schrieb Boris Rauchmann
  :

Thanks, it was created using: 
mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz

Best,
Boris


  Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D.
  :

There is something weird about that file. How was it created?
doug
ps. Please include previous correspondence in the email

On 12/16/19 1:12 PM, Boris Rauchmann wrote:

  External Email - Use Caution

  Boriss-MacBook-Pro:mri boris$ mri_info
  N_Atlas_subcotex.mgz
  mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz,
  -1): could not open file

Am 16.12.2019 um 19:08 schrieb Greve,
Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>:

Re: [Freesurfer] (no subject)

2019-12-16 Thread Boris Rauchmann

External Email - Use Caution

This is the log when I´m creating this file:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label 
$SUBJECTS_DIR/1122/mri/brain.mgz 
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z 
$SUBJECTS_DIR/BN_Atlas_subcortex.gca 
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
sysname  Darwin
hostname MacBook.local
machine  x86_64

setenv SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
cd /Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer
mri_ca_label /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz 
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca 
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz 

== Number of threads available to mri_ca_label for OpenMP = 1 == 
reading 1 input volumes
reading classifier array from 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_subcortex.gca
reading input volume from /Users/boris/Desktop/MirLIND_test/1122/mri/brain.mgz
reading transform from 
/Users/boris/Desktop/MirLIND_test/1122/mri/transforms/talairach.m3z
setting orig areas to linear transform determinant scaled 4.97
Atlas used for the 3D morph was 
/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca
average std = 10.8   using min determinant for regularization = 11.7
0 singular and 129 ill-conditioned covariance matrices regularized
labeling volume...
0 gm and wm labels changed (%nan to gray, %nan to white out of all changed 
labels)
0 hippocampal voxels changed.
0 amygdala voxels changed.
pass 1: 9576 changed.
pass 2: 3286 changed.
MRItoUCHAR: min=0, max=246
MRItoUCHAR: converting to UCHAR
writing labeled volume to 
/Users/boris/Desktop/MirLIND_test/1122/mri/BN_Atlas_subcotex.mgz
mri_ca_label utimesec146.184667
mri_ca_label stimesec1.040963
mri_ca_label ru_maxrss   1436573696
mri_ca_label ru_ixrss0
mri_ca_label ru_idrss0
mri_ca_label ru_isrss0
mri_ca_label ru_minflt   609288
mri_ca_label ru_majflt   112
mri_ca_label ru_nswap0
mri_ca_label ru_inblock  0
mri_ca_label ru_oublock  4
mri_ca_label ru_msgsnd   0
mri_ca_label ru_msgrcv   0
mri_ca_label ru_nsignals 0
mri_ca_label ru_nvcsw3
mri_ca_label ru_nivcsw   36417
auto-labeling took 2 minutes and 28 seconds.

This is what I get when I do mrs_info on the gas:

Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_info 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca 
reading frame -1 of gca
Volume information for 
/Users/boris/Desktop/MirLIND_test/BN_Atlas_freesurfer/BN_Atlas_subcortex.gca
  type: GCA
dimensions: 256 x 256 x 256 x 3
   voxel sizes: 1.00, 1.00, 1.00
  type: FLOAT (3)
   fov: 256.000
   dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
degrees
   nframes: 3
   PhEncDir: UNKNOWN
   FieldStrength: 0.00
ras xform present
xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 0.
  : x_a =   0., y_a =   0., z_a =   1., c_a = 0.
  : x_s =   0., y_s =  -1., z_s =   0., c_s = 0.
Orientation   : LIA
Primary Slice Direction: coronal

voxel to ras transform:
   -1.   0.   0.   128.
0.   0.   1.  -128.
0.  -1.   0.   128.
0.   0.   0. 1.

voxel-to-ras determinant -1

ras to voxel transform:
   -1.  -0.  -0.   128.
   -0.  -0.  -1.   128.
   -0.   1.  -0.   128.
   -0.  -0.  -0. 1.

> Am 16.12.2019 um 21:21 schrieb Boris Rauchmann :
> 
> Thanks, it was created using: 
> 
> mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
> $SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
> $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz
> 
> Best,
> Boris
> 
> 
>> Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>>:
>> 
>> There is something weird about that file. How was it created?
>> doug
>> ps. Please include previous correspondence in the email
>> 
>> On 12/16/19 1:12 PM, Boris Rauchmann wrote:
>>> 
>>> External Email - Use Caution
>>> 
>>> Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
>>> mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, 
>>> -1): could not open file
>>> 
 Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. 
 mailto:dgr...@mgh.harvard.edu> 
 >>:

 mri_info N_Atlas_subcotex.mgz
>>> 
>>> 
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu 
>>>

Re: [Freesurfer] Topological Defect

2019-12-16 Thread Kong Chuizheng

External Email - Use Caution

Hello Bruce,

Thank you again for offering helps regarding the Topological defect of one
of our subjects. we just wanted to know whether you were able to run the
SUBJECT034 file from the drive. Knowing that it takes several hours to run,
and there's also other people asking questions, we are willing to try any
suggestions and test it on our computers.

Thank you,
Kong

On Tue, Dec 10, 2019 at 1:24 PM Kong Chuizheng 
wrote:

>
> That sounds good to me! The file is about 100MB so I got a sharing link
> here.
>
> https://drive.google.com/file/d/15IfN6EzZj_wAW1y0v8USIs2tthfpdH95/view?usp=sharing
>
>
> On Tue, Dec 10, 2019 at 12:46 PM Bruce Fischl 
> wrote:
>
>> the topology fixing output should let you find the defect that is so big
>> and figure out how to fix it. If you want to tar/gzip the entire subject
>> dir and send it to us we will be happy to help
>>
>> cheers
>> Bruce
>> On Tue, 10 Dec 2019, Kong
>> Chuizheng wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Hello Bruce,
>> > We are trying to get the pial surface file for both hemisphere.
>> However, freesurfer would freeze after a
>> > while at a XL defect. Since the hemisphere without tumor also has
>> little holes, I thought this might
>> > have other reasons.
>> >
>> > Best,
>> > Chuizheng Kong
>> >
>> > On Tue, Dec 10, 2019 at 8:58 AM Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> >   Does your 3D model need to be topologically correct? What are you
>> trying
>> >   to achieve? And are the holes/handles due to the tumor? Can you
>> send us
>> >   some images?
>> >
>> >   cheers
>> >   Bruce
>> >   On Tue, 10 Dec 2019, Kong Chuizheng wrote:
>> >
>> >   >
>> >   > External Email - Use Caution
>> >   >
>> >   > Hello Freesurfer Developers,
>> >   >
>> >   >
>> >   >
>> >   > We are trying to construct a 3D cortex model of a tumour
>> subject. The recon-all.log showed
>> >   that the
>> >   > program froze at Correction of the Topology with "XL defect
>> detected." I followed the
>> >   procedure of the
>> >   > online tutorial page
>> >   (
>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
>> )
>> >   > and found that there's lots of "holes" and sharp abnormal
>> shapes in the
>> >   lh/rh.smoothwm.nofix file. It
>> >   > will be very hard to fix this by hand, and we wonder if you can
>> give us some advice.
>> >   >
>> >   >
>> >   >
>> >   > Sincerely,
>> >   >
>> >   > Chuizheng Kong
>> >   >
>> >   >
>> >   >
>> >   > Chuizheng Kong
>> >   >
>> >   >___
>> >   Freesurfer mailing list
>> >   Freesurfer@nmr.mgh.harvard.edu
>> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> >___
>> Freesurfer mailing list
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>
>
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Re: [Freesurfer] (no subject)

2019-12-16 Thread Boris Rauchmann

External Email - Use Caution

Thanks, it was created using: 

mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz
$SUBJECTS_DIR/1122/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz

Best,
Boris


> Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> There is something weird about that file. How was it created?
> doug
> ps. Please include previous correspondence in the email
> 
> On 12/16/19 1:12 PM, Boris Rauchmann wrote:
>> 
>> External Email - Use Caution
>> 
>> Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
>> mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, 
>> -1): could not open file
>> 
>>> Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. 
>>> mailto:dgr...@mgh.harvard.edu>>:
>>> 
>>> mri_info N_Atlas_subcotex.mgz
>> 
>> 
>> ___
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> 
> 
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Re: [Freesurfer] (no subject)

2019-12-16 Thread Greve, Douglas N.,Ph.D.

There is something weird about that file. How was it created?
doug
ps. Please include previous correspondence in the email

On 12/16/19 1:12 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
> mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, 
> -1): could not open file
>
>> Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>>:
>>
>> mri_info N_Atlas_subcotex.mgz
>
>
> ___
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[Freesurfer] using different Freesurfer versions for cross-sectional & longitudinal processing

2019-12-16 Thread Morgan Botdorf

External Email - Use Caution

Dear Freesurfer Experts,

We have child data that was previously processed cross-sectionally using
version 5.1. We are now interested in looking at the data longitudinally.
Can the longitudinal processing stream in version 6.0 be used on data that
was processed cross-sectionally using 5.1? Or is it better that we
reprocess the data using 6.0. We appreciate any help you can provide!

Thank you,


Morgan Botdorf, M.S.

Doctoral Candidate

Neurocognitive Development Lab

University of Maryland, College Park
mbotd...@terpmail.umd.edu

Office: 301.405.5922
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Re: [Freesurfer] (no subject)

2019-12-16 Thread Boris Rauchmann

External Email - Use Caution

Boriss-MacBook-Pro:mri boris$ mri_info N_Atlas_subcotex.mgz
mghRead(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, -1): 
could not open file

> Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. 
> :
> 
> mri_info N_Atlas_subcotex.mgz

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Re: [Freesurfer] (no subject)

2019-12-16 Thread Greve, Douglas N.,Ph.D.

OK, now I'm really confused. Try this
mri_info N_Atlas_subcotex.mgz


On 12/14/19 3:04 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Here the results:
>
>
> pwd:
> /Users/boris/Desktop/MirLIND_test/1122/mri
>
> ls -l BN_Atlas_subcotex.mgz:
> -rwxrwxrwx 1 boris  staff  37013 13 Aug 23:30 BN_Atlas_subcotex.mgz
>
> Best,
> Boris
>> Am 13.12.2019 um 23:53 schrieb Greve, Douglas N.,Ph.D. 
>> mailto:dgr...@mgh.harvard.edu>>:
>>
>> pwd
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] (no subject)

2019-12-16 Thread Marina Fernández

External Email - Use Caution

Hi experts,

We are doing the segmentation of the subfields of the hippocampal and
amygdala subfields, brainstem subestructures and thalamic nuclei. When we
used segmentHA_T1.sh and segmentThalamicNuclei.sh, 'Command not found'
appears.

On the other hand, we used segmentBS.sh and we got the following message:
'Software requires 4 arguments:
segmentSFnewT1.sh matlabRuntimeDirectory FShomeDirectory subjectName
subjectDir'.
But, when we typed 'segmentSFnewT1.sh'  we got  'Command not found' again.


Note:  We have FS v6.0 and the runtime Matlab 2014b.

best wishes,
Marina
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Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

2019-12-16 Thread Diers, Kersten /DZNE

External Email - Use Caution

Hi Bronwyn,

you can just add the two betas: it's the slope for the non-case group plus the 
difference in slopes between case and non-case group, so it should give the 
slope in the case group.

Best regards,

Kersten

On Mi, 2019-12-11 at 12:53 +1100, Bronwyn Overs wrote:

External Email - Use Caution

Hi Kersten,

Thank you for all of your help so far. I have now located the unstandardized 
beta values in lhstats(i).Bhat. Unfortunately one of the effects I was 
interested in was the slope for years within my case group, which required the 
use of the following contrast vector:
0 1 0 0 0 0 0 1

Do you know how I could estimate the effect size for this contrast given that 
it corresponds to two beta values (1 and 7)?


Kind regards,


Bronwyn Overs

Research Assistant

[cid:1576491649.30420.8.camel@dzne.de]


Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725


neura.edu.au 


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From: "Kersten Diers, DZNE" 
To: "Freesurfer support list" 
Sent: Saturday, November 30, 2019 6:50:26 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file


External Email - Use Caution

Hi,

please see my inline responses below.

Best,

Kersten

On Fr, 2019-11-29 at 13:20 +1100, Bronwyn Overs wrote:
Hi Kersten,

Thank you this is a good suggestion. Where can I get the unstandardized beta 
values for the lme I have already run?

They are in e.g. lhstats(i).Bhat; see the tutorial webpage for some explanation.

Also, i'm not really sure how to interpret the unstandardized beta values for 
interaction effects like group X years, do you have any suggestions?

This would model a difference in slopes, right? So the beta value should 
reflect difference between the two particular groups of this contrast per year 
(if year is the unit of time).

Finally, do you know why the max vertex is listed as '-inf' for my largets 
cluster and is this a problem at all?

I can only speculate here, but it's probably worth checking: A sig value of 
'Inf' would correspond to a p-value of (exactly) zero. So, one might 
investigate if any zeros are contained within the p-value arrays / maps, and if 
these zeros (if any) reflect the outcome of a statistical test (then it should 
be no problem) or if they were erroneously introduced.



Kind regards,


Bronwyn Overs

Research Assistant


Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725


neura.edu.au 


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From: "Kersten Diers, DZNE" 
To: "Bronwyn Overs" 
Cc: "Freesurfer support list" 
Sent: Friday, November 29, 2019 8:39:55 AM
Subject: Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

Hello,

and thanks for the explanation!

Here's my first impression:

I do not think that there is a really satisfying solution given these 
particular stats maps and the effect size measure you describe.

I may be missing something, but I also have to admit that it is not immediately 
clear to me what motivates the choice of cohen's d (and the calculation you 
describe) in the  current scenario - I've always thought of it as a measure of 
'difference in means'.

In a regression context, I would personally look for a measure of the 
"variance-explained" type. There seem to be at least two papers (Xu, 2003, 
Statistics in Medicine, and Selya, 2012, Frontiers) that cover these for mixed 
effects models. The calculation/implementation of these measures seems to be, 
however, not as straightforward as for classical multiple regression models; 
and as far as I can see, it would also involve fitting Null or reduced models, 
and thus running analyses again.

By far the easiest and most straightforward way in my eyes is to report 
unstandardized effect sizes, i.e. beta estimates, as you have clearly 
interpretable main variables (group and time) with intuitive units that should 
be comparable across studies from your field. So maybe this is an argument not 
to standardize, and to state the effect size in terms of "change in thickness 
per year" etc.?

Best regards,

Kersten

On Do, 2019-11-28 at 11:29 +1100, Bronwyn Overs wrote:
Hi Kersten,

No problem at al and thank you for your reply.
While running my correction for multiple comparisons I store the df associated 
with each contrast vector using the following:

[~,~,dflh] = find(F_lhstats.df(2,:));
[~,~,dfrh] =

Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

Re: [Freesurfer] (no subject)

Re: [Freesurfer] (no subject)

Re: [Freesurfer] (no subject)

Re: [Freesurfer] Topological Defect

Re: [Freesurfer] (no subject)

Re: [Freesurfer] (no subject)

[Freesurfer] using different Freesurfer versions for cross-sectional & longitudinal processing

Re: [Freesurfer] (no subject)

Re: [Freesurfer] (no subject)

[Freesurfer] (no subject)

Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

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