[Freesurfer] extract surface area for singe vertex

[Clara Kühn]

Dear Freesurfer experts,

I've run a longitudinal two stage model of 2 time points to look at the rate of 
change in surface area and whether my two groups change differently. I find a 
superior parietal cluster in the right hemisphere. So far I've already run the 
mri_glmfit-sim to get the values of rate of change in this cluster for each 
subject. Now I would like to extract the peak vertex that I get the coordinates 
of from mri_glmfit-sim for each subject from each time point.

I have tried to use mri_convert

mris_convert -c 
$SUBJECTS_DIR/WL8K_1.long.WL8K.base/surf/lh.thickness.fwhm10.81kids_template.mgh
 $SUBJECTS_DIR/001/WL8K_1.long.WL8K.base/lh.orig 
$SUBJECTS_DIR/WL8K_1.long.WL8K.base/lh.thickness.fwhm10.81kids_template.vertices.asc

however, I get this error message:

ERROR: number of vertices in 
/nobackup/etsch2/kids/prepost-61kids/WL8K_1.long.WL8K.base/surf/lh.thickness.fwhm10.81kids_template.mgh
 does not match surface (97361,109356)

I've read in other threads that I'm supposed to use mri_surf2surf to map it to 
my template (81kids_template). I thought I had already done that before the 
analysis when running long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas 
thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label 
--time years --qcache 81kids_template


Could you tell me what I need to do to extract the values of the peak vertex in 
my significant cluster for each subject and each time point?
Thank you so much!
Clara

-- 
Clara Kühn, Phd Candidate
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de



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[Freesurfer] extract surface area for singe vertex

[Clara Kühn]

Dear Freesurfer experts,

I've run a longitudinal two stage model of 2 time points to look at the rate of 
change in surface area and whether my two groups change differently. I find a 
superior parietal cluster in the right hemisphere. So far I've already run the 
mri_glmfit-sim to get the values of rate of change in this cluster for each 
subject. Now I would like to extract the peak vertex that I get the coordinates 
of from mri_glmfit-sim for each subject from each time point.

I have tried to use mri_convert

mris_convert -c 
$SUBJECTS_DIR/WL8K_1.long.WL8K.base/surf/lh.thickness.fwhm10.81kids_template.mgh
 $SUBJECTS_DIR/001/WL8K_1.long.WL8K.base/lh.orig 
$SUBJECTS_DIR/WL8K_1.long.WL8K.base/lh.thickness.fwhm10.81kids_template.vertices.asc

however, I get this error message:

ERROR: number of vertices in 
/nobackup/etsch2/kids/prepost-61kids/WL8K_1.long.WL8K.base/surf/lh.thickness.fwhm10.81kids_template.mgh
 does not match surface (97361,109356)

I've read in other threads that I'm supposed to use mri_surf2surf to map it to 
my template (81kids_template). I thought I had already done that before the 
analysis when running long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas 
thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label 
--time years --qcache 81kids_template


Could you tell me what I need to do to extract the values of the peak vertex in 
my significant cluster for each subject and each time point?
Thank you so much!
Clara

-- 
Clara Kühn, Phd Candidate
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] extract values for significant cluster

[Clara Kühn]

Dear Doug,

thank you so much. I now have a value for each of my participants. Since I work 
with rate of change from pre to post time point I should interpret these values 
as mm per year that each subjects changes in thickness in this cluster, right? 
Because I have values between -3.37363  and 2.99830. Does that mean that these 
subject would lose or gain 3 mm per year in thickness in this specific area?

Thank you for you help!
Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 27. Juli 2017 19:10:50
Betreff: Re: [Freesurfer] extract values for significant cluster

You can use mri_segstats specifying the ocn as the segmentation, the 
stack of thicknesses as the input, and --avgwf file.dat as the output. 
Make sure to add --excludeid 0 to exclude background voxels


On 07/27/2017 06:18 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> in the longitudinal 2 stage model I find a difference in rate between my two 
> groups in right intra parietal sulcus for surface area (survives MC 
> correction). I would like to look at the cortical thickness in that same 
> cluster. Is it possible to use any of the output files from the MC correction 
> as a mask or something to get the rate of change values for thickness in that 
> region? Even though this region does not show a significant difference 
> between the groups I would like to look at the individual values for rate of 
> change in that specific region (like the ones I received in the 
> cache.th30.abs.y.ocn.dat file)
>
> Could you please tell me if this is possible and how?
>
> Thank you very much!
> Clara
>

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

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

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[Freesurfer] extract values for significant cluster

[Clara Kühn]

Dear FreeSurfer experts,

in the longitudinal 2 stage model I find a difference in rate between my two 
groups in right intra parietal sulcus for surface area (survives MC 
correction). I would like to look at the cortical thickness in that same 
cluster. Is it possible to use any of the output files from the MC correction 
as a mask or something to get the rate of change values for thickness in that 
region? Even though this region does not show a significant difference between 
the groups I would like to look at the individual values for rate of change in 
that specific region (like the ones I received in the cache.th30.abs.y.ocn.dat 
file)

Could you please tell me if this is possible and how?

Thank you very much!
Clara

-- 
Clara Kühn, Phd Candidate
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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[Freesurfer] UPDATE: Matlab Problem LME

[Clara Kühn]

Dear FreeSurfer experts,

I have figured out what the problem is, however I do not know how to solve it.

Apparently the homogeneity function within the lme_mass_RgGrow function does 
not recognize the voxels as homogenous if they have zeros in all columns 
because the correlation coefficient is NaN.

How do I deal with zero columns in my input file (lh.thickness) which will be 
carried over into the Theta0 and Re?

Thank you for any suggestions!
Clara





- Weitergeleitete Mail -
Von: "ckuehn" <cku...@cbs.mpg.de>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Montag, 3. Juli 2017 18:27:46
Betreff: [Freesurfer] Matlab Problem LME

Dear FreeSurfer experts,

I am following the LME tutorial for the spatiotemporal mass-univariate model on 
Matlab 8.2. When I get to the point where the covariance estimates are 
segmented into homogeneous regions I run into a problem. Nothing really happens 
in Matlab anymore. 

This is my  command:

[lhRgs,lhRgMeans] = lme_mass_RgGrow (lhsphere, lhRe, lhTh0, lhcortex, 2, 95);

And this is what the Matlab output looks like:

connected to 12 workers.
Starting region growing algorithm
Computing seeds ...


I've tried this already last week and nothing happened for a few days. 

When I terminate the command this is the Matlab output:

Operation terminated by user during kron (after line 36)


In lme_mass_RgGrow>homogenity (line 299)
if (sum(sum(DistRgParams <= kron(ones(1,nv),thr),1) == np) >= prc*nv/100) 
&&...

In lme_mass_RgGrow>merge (line 320)
if homogenity(Re,Params,auxRgs,Rkn,nst,prc)

In lme_mass_RgGrow>split (line 269)
[Rgs,mrg] = merge(Rgs,Re,Params,mrgRgs(i),mrgRgs(j),nst,prc);

In lme_mass_RgGrow>seeds (line 208)
[Rgs,spltf(i),nnRgs] = split(Rgs,Re,Params,coord,splRgs(i),nst,prc);

In lme_mass_RgGrow>vtxwGrowing (line 77)
[Rgs1,Rgseed,Rgstd]= 
seeds(Re(:,maskvtx),Params(:,maskvtx),coord(:,maskvtx),nst,prc);

In lme_mass_RgGrow (line 62)
Regions = vtxwGrowing(Re,Theta,sphcoord,AdjM,maskvtx,nst,prc);


I have then copied the function and added a few "fprintf" (see attachment) to 
get an idea as to where matlab has problems and the output looks like this:
Starting region growing algorithm
Computing seeds ...
point5
point6
point7
point8
point7
point8
point7
point8
point7
point8
point7
point8
point7
point8
point7
point6
point7
point8
point7
point8
point7
point8
point7
point8
point7
point8
point7
[...]

If I understand that correctly, matlab gets hung up on functions 'function tf = 
homogenity(Re,Params,Rgs,Rn,nst,prc)' and 'function [Rgs,tf] = 
merge(Rgs,Re,Params,Rn1,Rn2,nst,prc)'. Does anybody have an idea what that 
means and how it can be fixed?

How long is this step supposed to take? I have 81 subjects with 1 - 3 time 
points.

Any help or suggestions would be much appreciated!
Cheers
Clara

-- 
Clara Kühn, Phd Candidate
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de
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[Freesurfer] Matlab Problem LME

[Clara Kühn]

Dear FreeSurfer experts,

I am following the LME tutorial for the spatiotemporal mass-univariate model on 
Matlab 8.2. When I get to the point where the covariance estimates are 
segmented into homogeneous regions I run into a problem. Nothing really happens 
in Matlab anymore. 

This is my  command:

[lhRgs,lhRgMeans] = lme_mass_RgGrow (lhsphere, lhRe, lhTh0, lhcortex, 2, 95);

And this is what the Matlab output looks like:

connected to 12 workers.
Starting region growing algorithm
Computing seeds ...


I've tried this already last week and nothing happened for a few days. 

When I terminate the command this is the Matlab output:

Operation terminated by user during kron (after line 36)


In lme_mass_RgGrow>homogenity (line 299)
if (sum(sum(DistRgParams <= kron(ones(1,nv),thr),1) == np) >= prc*nv/100) 
&&...

In lme_mass_RgGrow>merge (line 320)
if homogenity(Re,Params,auxRgs,Rkn,nst,prc)

In lme_mass_RgGrow>split (line 269)
[Rgs,mrg] = merge(Rgs,Re,Params,mrgRgs(i),mrgRgs(j),nst,prc);

In lme_mass_RgGrow>seeds (line 208)
[Rgs,spltf(i),nnRgs] = split(Rgs,Re,Params,coord,splRgs(i),nst,prc);

In lme_mass_RgGrow>vtxwGrowing (line 77)
[Rgs1,Rgseed,Rgstd]= 
seeds(Re(:,maskvtx),Params(:,maskvtx),coord(:,maskvtx),nst,prc);

In lme_mass_RgGrow (line 62)
Regions = vtxwGrowing(Re,Theta,sphcoord,AdjM,maskvtx,nst,prc);


I have then copied the function and added a few "fprintf" (see attachment) to 
get an idea as to where matlab has problems and the output looks like this:
Starting region growing algorithm
Computing seeds ...
point5
point6
point7
point8
point7
point8
point7
point8
point7
point8
point7
point8
point7
point8
point7
point6
point7
point8
point7
point8
point7
point8
point7
point8
point7
point8
point7
[...]

If I understand that correctly, matlab gets hung up on functions 'function tf = 
homogenity(Re,Params,Rgs,Rn,nst,prc)' and 'function [Rgs,tf] = 
merge(Rgs,Re,Params,Rn1,Rn2,nst,prc)'. Does anybody have an idea what that 
means and how it can be fixed?

How long is this step supposed to take? I have 81 subjects with 1 - 3 time 
points.

Any help or suggestions would be much appreciated!
Cheers
Clara

-- 
Clara Kühn, Phd Candidate
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.defunction [Regions,RgMeans] = lme_mass_RgGrow(SphSurf,Re,Theta,maskvtx,nst,prc)
% [Regions,RgMeans] = lme_mass_RgGrow(SphSurf,Re,Theta,maskvtx,nst,prc)
% 
% This function implements a region growing algorithm along the spherical
% surface to find homogeneous regions comprising locations with similar  
% covariance components.
%
% Input
% SphSurf: Spherical surface, which represent a spherical coordinate system
% for the surface where the analysis is to be done. It is a structure in
% fs_read_surf format. SphSurf.tri = t x 3 matrix of triangle indices,
% 1-based, t=#triangles and SphSurf.coord = 3 x nv matrix of coordinates,
% nv=#vertices.
% Re: Matrix of residual errors at each location (nmxnv, nm total # of
% maps, nv #vertices.
% Theta: Matrix whose colums are estimators of the covariance components at.
% each location.
% maskvtx: Mask's vertices (1-based). Default [] (all vertices included).
% nst: Number of standard deviations of Theta inside a region for it to
% be considered as homogeneous. Default 2.
% prc: Percent of vertices inside an homogeneous region that are allowed to
% not meet the homogenity criteria. This parameter makes the algorithm
% robust to noise and outliers. Default 95%.
%
% Output
% Regions: 1 x nv segmentation vector containing a region number assigned 
% to each vertice along the surface.
% RgMeans: Matrix assigning the mean of Theta within a region to each vertex
% belonging to that region.
%
% $Revision: 1.1.2.2 $  $Date: 2013/02/23 21:08:10 $
% Original Author: Jorge Luis Bernal Rusiel 
% CVS Revision Info:
%$Author: nicks $
%$Date: 2013/02/23 21:08:10 $
%$Revision: 1.1.2.2 $
% References: 
% Gonzalez, R.C., Woods, R.E. (2002). Digital Image Processing. 2nd Edition, 
% New Jersey: Prentice Hall, Inc.
%
tic;
if nargin < 3
error('Too few inputs');
elseif nargin < 6
prc = 95;
if nargin < 5
nst = 2;
if nargin < 4
maskvtx = [];
end
end;
end;
nv = size(Theta,2);
if isempty(maskvtx)
maskvtx = 1:nv;
end;
AdjM = AdjMtx(SphSurf,maskvtx);
display(' ');
display('Starting region growing algorithm');
[phi,theta] = sphCoord(SphSurf.coord');
sphcoord = [phi,theta]';
Regions = vtxwGrowing(Re,Theta,sphcoord,AdjM,maskvtx,nst,prc);
[RgMeans,nRg] = lme_mass_RgMean(Regions,Theta);
display(' ');
display([num2str(nRg-1) ' homogeneous regions were obtained.']);
et = toc;
display(['Elapsed time is ' num2str(et/60) ' minutes.']);
end






function Rgs = vtxwGrowing(Re,Params,

[Freesurfer] UPDATE: error in long_mris_slopes

[Clara Kühn]

Hi everyone,

it seems the error  isn't hemisphere specific after all. It shows up on 1 
subject in the left hemisphere, too (just later in the subject list). Weirdly 
the subjects that produce the error on the right hemisphere are different one 
than those producing the error when working on the left hemisphere.

I've also narrowed the problem down to server-vs-local hard drive. We have a 
server at work that I work on that emulates a hard drive which is where the 
error occurs. When I tried running the same command again on my local hard 
drive it worked fine.

Is there some bug in the program that has problems when running it remotely?

Cheers, 
Clara


- Weitergeleitete Mail -
Von: "ckuehn" <cku...@cbs.mpg.de>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Mittwoch, 24. Mai 2017 19:00:51
Betreff: [Freesurfer] error in long_mris_slopes

Dear Freesurfer experts,

I'm running into some problems when running the long_mris_slopes command 
(longitudinal 2 stage model) to get the rate of change for thickness and area 
for each hemisphere.

This is the command I ran:

for i in thickness area ; do
for j in rh ; do

long_mris_slopes --qdec $SUBJECTS_DIR/qdec/39kids-covariates-MT2-1.dat 
--meas ${i} --hemi ${j} --do-rate --do-stack --do-label --time years --qcache 
81kids_template --sd $SUBJECTS_DIR

done
done


For the left hemisphere everything works fine but for the right hemisphere it 
stops working at my second subject and I get the following error:

ERROR -6 : mris_label_calc intersect did not work?

This is the terminal output for said subject:
Subject-Template: BJ4K.base


INFO: 2 TPs in BJ4K.base , mean age: 0.041095


===
SUBJECT BJ4K.base  Intersecting Within-Subject Cortex Label

cp 
/data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K_1.long.BJ4K.base/label/rh.cortex.label
 
/data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K.base/label/rh.long.cortex.label



mris_label_calc intersect 
/data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K_2.long.BJ4K.base/label/rh.cortex.label
 
/data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K.base/label/rh.long.cortex.label
 
/data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K.base/label/rh.long.cortex.label

mris_label_calc: malloc.c:2392: sysmalloc: Assertion `(old_top == initial_top 
(av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse 
(old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed.
ERROR -6 : mris_label_calc intersect did not work?


I've googled a bit and suggestions were a memory problem but I don't think 
that's the case if it is hemisphere specific and the first subject in the list 
works fine...

I've also attached the input file.

What could be the problem and how can I fix it?
Cheers Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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[Freesurfer] error in long_mris_slopes

[Clara Kühn]

Dear Freesurfer experts,

I'm running into some problems when running the long_mris_slopes command 
(longitudinal 2 stage model) to get the rate of change for thickness and area 
for each hemisphere.

This is the command I ran:

for i in thickness area ; do
for j in rh ; do

long_mris_slopes --qdec $SUBJECTS_DIR/qdec/39kids-covariates-MT2-1.dat 
--meas ${i} --hemi ${j} --do-rate --do-stack --do-label --time years --qcache 
81kids_template --sd $SUBJECTS_DIR

done
done


For the left hemisphere everything works fine but for the right hemisphere it 
stops working at my second subject and I get the following error:

ERROR -6 : mris_label_calc intersect did not work?

This is the terminal output for said subject:
Subject-Template: BJ4K.base


INFO: 2 TPs in BJ4K.base , mean age: 0.041095


===
SUBJECT BJ4K.base  Intersecting Within-Subject Cortex Label

cp 
/data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K_1.long.BJ4K.base/label/rh.cortex.label
 
/data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K.base/label/rh.long.cortex.label



mris_label_calc intersect 
/data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K_2.long.BJ4K.base/label/rh.cortex.label
 
/data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K.base/label/rh.long.cortex.label
 
/data/p_npsy001_neurotrain/kids_data/39kids-sem-con-3goodscans/semcon-3goodscans2-1/BJ4K.base/label/rh.long.cortex.label

mris_label_calc: malloc.c:2392: sysmalloc: Assertion `(old_top == initial_top 
(av) && old_size == 0) || ((unsigned long) (old_size) >= MINSIZE && prev_inuse 
(old_top) && ((unsigned long) old_end & (pagesize - 1)) == 0)' failed.
ERROR -6 : mris_label_calc intersect did not work?


I've googled a bit and suggestions were a memory problem but I don't think 
that's the case if it is hemisphere specific and the first subject in the list 
works fine...

I've also attached the input file.

What could be the problem and how can I fix it?
Cheers Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de


39kids-covariates-MT2-1.dat
Description: Binary data
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Re: [Freesurfer] REPOST: Two stage model question

[Clara Kühn]

Hi Martin,

thanks for your reply. From your email I understand that looking at the rate of 
change between time points is more useful than spc if I want to look at only 2 
time points at a time.

I have a pre training scan, a post training scan (approximately 3 weeks apart 
with a training intervention in between scans) and a follow up scan after 3 
weeks of no intervention for either group.
Therefore I could compare the rate of change in thickness and area from pre 
scan to post scan between the training group and the control group. Similarly, 
I could check if the rates differ between the groups when looking at post scan 
and follow up. And that I could do with the longitudinal two stage model, right?

Could you explain what you mean with "node at the intervention time" with 
regards to LMEs? Also I'm not sure what you mean with piecewise. I've tried to 
follow the LME tutorial once before. Do you mean that I should only try the 
linear version of the model? How would I do this piecewise?


Thanks for your help!
Clara



- Ursprüngliche Mail -
Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Freitag, 21. April 2017 22:09:14
Betreff: Re: [Freesurfer] REPOST: Two stage model question

Hi Clara, 

the SPC (or any percent change) could be problematic, as the base value (either 
the volume at the baseline timepoint, or the average volume) will change 
depending wich interval you look at. You could check if the rate (mm/time_unit) 
or mm^3/time_unit is changing.

I am not sure how your study is setup, so I cannot really recommend anything 
here (e.g. when did the intervention happen exactly). 

Generally I would recommend a piecewise linear model with node at the 
intervention time in LME (mixed effects). 

Best, Martin

> On 21 Apr 2017, at 17:15, Clara Kühn <cku...@cbs.mpg.de> wrote:
> 
> 
> 
> Dear FreeSurfer experts,
> 
> I have a longitudinal design with 3 groups and 3 time points. For one group 
> the intervention did not work so for now I would like to look at 2 groups 
> only. Can I do this with the Longitudinal Two Stage Model by looking at the 
> spc from tp1 to tp2 and then looking at the spc from tp2 to tp3?
> 
> Are there statistical reasons that forbid this procedure of comparing the 
> change across time between groups?
> 
> Thanks for your help!
> Clara
> 
> -- 
> Clara Kühn, Phd Student
> 
> Max-Planck-Institute for Human Cognitive and Brain Science
> Department of Neuropsychology
> Stephanstrasse 1A
> 04103 Leipzig, Germany
> 
> Phone: +49 341 - 9940 2271
> Fax: +49 341 - 9940 2260
> Web: www.cbs.mpg.de
> E-Mail: cku...@cbs.mpg.de
> 
> ___
> Freesurfer mailing list
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> 
> 


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Re: [Freesurfer] REPOST: Two stage model question

[Clara Kühn]

Hi Martin,

thanks for your reply. From your email I understand that looking at the rate of 
change between time points is more useful than spc if I want to look at only 2 
time points at a time.

I have a pre training scan, a post training scan (approximately 3 weeks apart 
with a training intervention in between scans) and a follow up scan after 3 
weeks of no intervention for either group.
Therefore I could compare the rate of change in thickness and area from pre 
scan to post scan between the training group and the control group. Similarly, 
I could check if the rates differ between the groups when looking at post scan 
and follow up. And that I could do with the longitudinal two stage model, right?

Could you explain what you mean with "node at the intervention time" with 
regards to LMEs? Also I'm not sure what you mean with piecewise. I've tried to 
follow the LME tutorial once before. Do you mean that I should only try the 
linear version of the model? How would I do this piecewise?


Thanks for your help!
Clara



- Ursprüngliche Mail -
Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Freitag, 21. April 2017 22:09:14
Betreff: Re: [Freesurfer] REPOST: Two stage model question

Hi Clara, 

the SPC (or any percent change) could be problematic, as the base value (either 
the volume at the baseline timepoint, or the average volume) will change 
depending wich interval you look at. You could check if the rate (mm/time_unit) 
or mm^3/time_unit is changing.

I am not sure how your study is setup, so I cannot really recommend anything 
here (e.g. when did the intervention happen exactly). 

Generally I would recommend a piecewise linear model with node at the 
intervention time in LME (mixed effects). 

Best, Martin

> On 21 Apr 2017, at 17:15, Clara Kühn <cku...@cbs.mpg.de> wrote:
> 
> 
> 
> Dear FreeSurfer experts,
> 
> I have a longitudinal design with 3 groups and 3 time points. For one group 
> the intervention did not work so for now I would like to look at 2 groups 
> only. Can I do this with the Longitudinal Two Stage Model by looking at the 
> spc from tp1 to tp2 and then looking at the spc from tp2 to tp3?
> 
> Are there statistical reasons that forbid this procedure of comparing the 
> change across time between groups?
> 
> Thanks for your help!
> Clara
> 
> -- 
> Clara Kühn, Phd Student
> 
> Max-Planck-Institute for Human Cognitive and Brain Science
> Department of Neuropsychology
> Stephanstrasse 1A
> 04103 Leipzig, Germany
> 
> Phone: +49 341 - 9940 2271
> Fax: +49 341 - 9940 2260
> Web: www.cbs.mpg.de
> E-Mail: cku...@cbs.mpg.de
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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> 
> 


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[Freesurfer] REPOST: Two stage model question

[Clara Kühn]

Dear FreeSurfer experts,

I have a longitudinal design with 3 groups and 3 time points. For one group the 
intervention did not work so for now I would like to look at 2 groups only. Can 
I do this with the Longitudinal Two Stage Model by looking at the spc from tp1 
to tp2 and then looking at the spc from tp2 to tp3?

Are there statistical reasons that forbid this procedure of comparing the 
change across time between groups?

Thanks for your help!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Two stage model question

[Clara Kühn]

Dear FreeSurfer experts,

I have a longitudinal design with 3 groups and 3 time points. For one group the 
intervention did not work so for now I would like to look at 2 groups only. Can 
I do this with the Longitudinal Two Stage Model by looking at the spc from tp1 
to tp2 and then looking at the spc from tp2 to tp3?

Are there statistical reasons that forbid this procedure of comparing the 
change across time between groups?

Thanks for your help!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

[Clara Kühn]

I added --surf mytemplate lh to the command and now it works.

Thank you so much!!

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 11. April 2017 20:13:21
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
columns

oh, I think I see the problem now. The input is surface-based data, but 
you did not include a --surf subject hemi option, so it thinks that it 
is a volume.


On 04/11/2017 12:58 PM, Clara Kühn wrote:
> Hi Doug,
>
> attached you find the rmanova directory after I ran the mri_glmfit command. I 
> hope this can shed some light on the problem...
>
> Cheers
> Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 11. April 2017 18:29:52
> Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
> columns
>
> Still a bit of a mystery. Can you tar up and send me the rmanova folder?
>
>
> On 04/11/2017 11:18 AM, Clara Kühn wrote:
>> Oh, yes, sorry:
>> command line:
>> mri_glmfit --glmdir 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ --y 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>>  --fsgd 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
>>  doss --C 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
>>
>> output:
>> gdfReadHeader: reading 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>> Continuous Variable Means (all subjects)
>> 0 pre-vs-post 0 1
>> Class Means of each Continuous Variable
>> 1 Subject1   0.
>> 2 Subject2   0.
>> 3 Subject3   0.
>> 4 Subject4   0.
>> 5 Subject5   0.
>> 6 Subject6   0.
>> 7 Subject7   0.
>> 8 Subject8   0.
>> 9 Subject9   0.
>> 10 Subject10   0.
>> 11 Subject11   0.
>> 12 Subject12   0.
>> 13 Subject13   0.
>> 14 Subject14   0.
>> 15 Subject15   0.
>> 16 Subject16   0.
>> 17 Subject17   0.
>> 18 Subject18   0.
>> 19 Subject19   0.
>> 20 Subject20   0.
>> 21 Subject21   0.
>> 22 Subject22   0.
>> 23 Subject23   0.
>> 24 Subject24   0.
>> 25 Subject25   0.
>> 26 Subject26   0.
>> 27 Subject27   0.
>> 28 Subject28   0.
>> 29 Subject29   0.
>> 30 Subject30   0.
>> 31 Subject31   0.
>> 32 Subject32   0.
>> 33 Subject33   0.
>> 34 Subject34   0.
>> 35 Subject35   0.
>> 36 Subject36   0.
>> 37 Subject37   0.
>> 38 Subject38   0.
>> 39 Subject39   0.
>> 40 Subject40   0.
>> INFO: gd2mtx_method is doss
>>
>> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>> cwd 
>> /data/p_npsy001_neurotrain/new_syntax_training/Pilot2-NachtestungPilot0/logfiles
>> cmdline mri_glmfit --glmdir 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ --y 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>>  --fsgd 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
>>  doss --C 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
>> sysname  Linux
>> hostname etsch
>> machine  x86_64
>> user ckuehn
>> FixVertexAreaFlag = 1
>> UseMaskWithSmoothing 1
>> OneSampleGroupMean 0
>> y
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>> logyflag 0
>> usedti  0
>> FSGD 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
>> glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/
>> IllCondOK 0
>> ReScaleX 1
>> DoFFx 0
>> Creating output directory 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/
>> Loading y from 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>> INFO: gd2mtx_method is doss
>> Saving design matrix to 
>> /data/p_npsy001_neurotrain/kids_data/sem

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

[Clara Kühn]

Oh, yes, sorry:
command line:
mri_glmfit --glmdir 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ --y 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
 --fsgd 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
 doss --C 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
 

output:
gdfReadHeader: reading 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 pre-vs-post 0 1
Class Means of each Continuous Variable
1 Subject1   0. 
2 Subject2   0. 
3 Subject3   0. 
4 Subject4   0. 
5 Subject5   0. 
6 Subject6   0. 
7 Subject7   0. 
8 Subject8   0. 
9 Subject9   0. 
10 Subject10   0. 
11 Subject11   0. 
12 Subject12   0. 
13 Subject13   0. 
14 Subject14   0. 
15 Subject15   0. 
16 Subject16   0. 
17 Subject17   0. 
18 Subject18   0. 
19 Subject19   0. 
20 Subject20   0. 
21 Subject21   0. 
22 Subject22   0. 
23 Subject23   0. 
24 Subject24   0. 
25 Subject25   0. 
26 Subject26   0. 
27 Subject27   0. 
28 Subject28   0. 
29 Subject29   0. 
30 Subject30   0. 
31 Subject31   0. 
32 Subject32   0. 
33 Subject33   0. 
34 Subject34   0. 
35 Subject35   0. 
36 Subject36   0. 
37 Subject37   0. 
38 Subject38   0. 
39 Subject39   0. 
40 Subject40   0. 
INFO: gd2mtx_method is doss

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd 
/data/p_npsy001_neurotrain/new_syntax_training/Pilot2-NachtestungPilot0/logfiles
cmdline mri_glmfit --glmdir 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ --y 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
 --fsgd 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
 doss --C 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
 
sysname  Linux
hostname etsch
machine  x86_64
user ckuehn
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
logyflag 0
usedti  0
FSGD 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/
Loading y from 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
INFO: gd2mtx_method is doss
Saving design matrix to 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova//Xg.dat
Normalized matrix condition is 1
Matrix condition is 40
Pruning voxels by thr: 0.00
Found 97361 voxels in mask
Saving mask to 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova//mask.mgh
search space = 97361.00
DOF = 39
Starting fit and test
Fit completed in 0.551233 minutes
Computing spatial AR1 in volume.
fMRIspatialAR1(): hit 0 voxels
WARNING: no voxels in AR1 computation
Residual: ar1mn = (-nan,-nan,-nan) fwhm = (-nan,-nan,-nan) -nan
Writing results
  C-pre-vs-post
maxvox sig=3.9739  F=18.6032  at  index 4623 0 0seed=1492398301
mri_glmfit done


Cheers, Clara



- Ursprüngliche Mail -
Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 11. April 2017 15:58:27
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
columns

sorry, that is the log file. What I want is the terminal output, ie, when you 
run it, all the stuff that is printed to the screen. 

On 4/11/17 5:07 AM, Clara Kühn wrote: 



Hi Doug
I am not conciously using a mask but I attached the glmfit.log
At the end it actually states "ResidualFWHM -nan"

How can I fix that?

Cheers, Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> An: 
freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 10. April 2017 21:41:40
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
columns

It estimates the FWHM from the residuals of the analysis (it does not 
use whatever value you smoothed it with). For some reason this estimate 
is not-a-number (NaN). Are you using a mask? Can you send the terminal 
output from running mri_glmfit?


On 03/31/2017 03:29 AM, Clara Kühn wrote: 



ah, ok. I used the proper glmdir now with this command:
  mri_glmfit-sim --glmdir 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ --cache

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

[Clara Kühn]

Hi Doug
I am not conciously using a mask but I attached the glmfit.log
At the end it actually states "ResidualFWHM -nan"

How can I fix that?

Cheers, Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Montag, 10. April 2017 21:41:40
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
columns

It estimates the FWHM from the residuals of the analysis (it does not 
use whatever value you smoothed it with). For some reason this estimate 
is not-a-number (NaN). Are you using a mask? Can you send the terminal 
output from running mri_glmfit?


On 03/31/2017 03:29 AM, Clara Kühn wrote:
> ah, ok. I used the proper glmdir now with this command:
>   mri_glmfit-sim --glmdir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ 
> --cache-dir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ 
> --cache 3.0 abs --cwp 0.05 --2spaces
>
> And this is the terminal output:
>
> cmdline mri_glmfit --glmdir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ --y 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>  --fsgd 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
>  doss --C 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
>
> WARNING: unrecognized mri_glmfit cmd option doss
>
> log file is 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova//cache.mri_glmfit-sim.log
>
> cd /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2
> /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/bin/mri_glmfit-sim
> --glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ 
> --cache-dir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ 
> --cache 3.0 abs --cwp 0.05 --2spaces
>
> $Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
> Fri Mar 31 09:17:53 CEST 2017
> Linux etsch 4.4.0-66-generic #87-Ubuntu SMP Fri Mar 3 15:29:05 UTC 2017 
> x86_64 x86_64 x86_64 GNU/Linux
> ckuehn
> setenv SUBJECTS_DIR /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/
> FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64
>
> Original mri_glmfit command line:
> cmdline mri_glmfit --glmdir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ --y 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>  --fsgd 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
>  doss --C 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
>
> DoSim = 0
> UseCache = 1
> DoPoll = 0
> DoPBSubmit = 0
> DoBackground = 0
> DiagCluster = 0
> gd2mtx = doss
> fwhm = -nan
> ERROR: cannot find 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-corcortex/fwhmNaN/abs/th30/mc-z.csd
>
>
>
> For some reason it doesn't recognize that I smoothed the data with --fwhm 10 
> during mris_surf2surf. And the other thing is, that it doesn't find the 
> correct path for the mc-z.csd. It should be in 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/81kids_template/lh/cortex/fwhm10/abs/mc-z.csd
>
> Cheers
> Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Donnerstag, 30. März 2017 19:13:43
> Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
> columns
>
> you are not giving it the proper glmdir dir. the glmdir is
>
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova
>
>
> On 03/30/2017 01:12 PM, Clara Kühn wrote:
>> I tried this command:
>>
>> mri_glmfit-sim --glmdir 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post
>>  --cache-dir 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ 
>> --cache 3.0 abs --cwp 0.05 --2spaces
>>
>> and got this error:
>> ERROR: cannot find 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post/mri_glmfit.log
>>
>> then I copied the .log file into the contrast directory C-pre-vs-post and 
>> tried the same command again and got this error:
>>
>> ERROR: could not determine file for 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post/mask
>>
>> Ususally I would run the MC

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

[Clara Kühn]

ah, ok. I used the proper glmdir now with this command:
 mri_glmfit-sim --glmdir 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ --cache-dir 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ 
--cache 3.0 abs --cwp 0.05 --2spaces

And this is the terminal output:

cmdline mri_glmfit --glmdir 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ --y 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
 --fsgd 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
 doss --C 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx

WARNING: unrecognized mri_glmfit cmd option doss

log file is 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova//cache.mri_glmfit-sim.log

cd /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2
/afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/bin/mri_glmfit-sim
--glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/ 
--cache-dir 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ 
--cache 3.0 abs --cwp 0.05 --2spaces

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Fri Mar 31 09:17:53 CEST 2017
Linux etsch 4.4.0-66-generic #87-Ubuntu SMP Fri Mar 3 15:29:05 UTC 2017 x86_64 
x86_64 x86_64 GNU/Linux
ckuehn
setenv SUBJECTS_DIR /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/
FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64

Original mri_glmfit command line:
cmdline mri_glmfit --glmdir 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ --y 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
 --fsgd 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2017.03.27-40kids-rmanova.fsgd
 doss --C 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = doss
fwhm = -nan
ERROR: cannot find 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-corcortex/fwhmNaN/abs/th30/mc-z.csd



For some reason it doesn't recognize that I smoothed the data with --fwhm 10 
during mris_surf2surf. And the other thing is, that it doesn't find the correct 
path for the mc-z.csd. It should be in 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/81kids_template/lh/cortex/fwhm10/abs/mc-z.csd

Cheers
Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 30. März 2017 19:13:43
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
columns

you are not giving it the proper glmdir dir. the glmdir is

/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova


On 03/30/2017 01:12 PM, Clara Kühn wrote:
> I tried this command:
>
> mri_glmfit-sim --glmdir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post
>  --cache-dir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ 
> --cache 3.0 abs --cwp 0.05 --2spaces
>
> and got this error:
> ERROR: cannot find 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post/mri_glmfit.log
>
> then I copied the .log file into the contrast directory C-pre-vs-post and 
> tried the same command again and got this error:
>
> ERROR: could not determine file for 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post/mask
>
> Ususally I would run the MC on the lh-Diff-1-3-Intercept-long.area-spc folder 
> but with the rmanova I get these two folders: 40kids-lh.thickness10-rmanova 
> and C-pre-vs-post
>
> Cheers
> Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Donnerstag, 30. März 2017 18:57:36
> Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
> columns
>
> what do you mean that it did not seem to work?
>
>
> On 03/30/2017 11:25 AM, Clara Kühn wrote:
>> Thank you! I completely didn't see that. It worked.
>>
>> I was wondering how to proceed next. The tutorial ends with running the 
>> glmfit command. I've tried correcting for multiple comparisons with Monte 
>> Carlo but that doesn't seem to work. How can I interpret the files that are 
>> the output from the repeated measures ANOVA?
>>
>> Cheers Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>>

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

[Clara Kühn]

I tried this command:

mri_glmfit-sim --glmdir 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post
 --cache-dir 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/ 
--cache 3.0 abs --cwp 0.05 --2spaces

and got this error:
ERROR: cannot find 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post/mri_glmfit.log

then I copied the .log file into the contrast directory C-pre-vs-post and tried 
the same command again and got this error:

ERROR: could not determine file for 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post/mask

Ususally I would run the MC on the lh-Diff-1-3-Intercept-long.area-spc folder 
but with the rmanova I get these two folders: 40kids-lh.thickness10-rmanova and 
C-pre-vs-post

Cheers
Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 30. März 2017 18:57:36
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
columns

what do you mean that it did not seem to work?


On 03/30/2017 11:25 AM, Clara Kühn wrote:
> Thank you! I completely didn't see that. It worked.
>
> I was wondering how to proceed next. The tutorial ends with running the 
> glmfit command. I've tried correcting for multiple comparisons with Monte 
> Carlo but that doesn't seem to work. How can I interpret the files that are 
> the output from the repeated measures ANOVA?
>
> Cheers Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 29. März 2017 18:15:57
> Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
> columns
>
> Since there are 40 subjects, you would only have 40+1 columns, not 80+1
>
>
> On 03/29/2017 03:42 AM, Clara Kühn wrote:
>> Hi Doug,
>>
>> I've also attached the fsgd file for you. Yes, I have 40 subjects and a 
>> contrast column. I adapted this from this tutorial: 
>> https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova where the 
>> example has 3 time points and therefore 2 contrast columns. Since I want to 
>> look at only 2 I only have one contrast column which is also my 81st column 
>> in the contrast matrix.
>>
>> Did I adapt it in a wrong way for my 2 timepoints?
>> Cheers
>> Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Dienstag, 28. März 2017 18:37:58
>> Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
>> columns
>>
>> I'm not sure what's in  your FSGD file, but you design matrix has 41
>> columns and your contrast matrix has 80. I'm guessing that  you have 40
>> subjects and that you created the contrast matrix based on DODS and not
>> DOSS (see the web page on the rmanova about creating contrasts)
>>
>>
>> On 03/28/2017 03:50 AM, Clara Kühn wrote:
>>> Sorry, I had a typo in the fsgd file. This is the correct command line and 
>>> terminal output:
>>>
>>> mri_glmfit --glmdir $SUBJECTS_DIR/qdec/rmanova/ --y 
>>> $SUBJECTS_DIR/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh 
>>> --fsgd $SUBJECTS_DIR/qdec/rmanova/2014.03.27-40kids-rmanova.fsgd doss --C 
>>> $SUBJECTS_DIR/qdec/rmanova/C-pre-vs-post.mtx
>>>
>>>
>>> gdfReadHeader: reading 
>>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
>>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>>> Continuous Variable Means (all subjects)
>>> 0 pre-vs-post 0 1
>>> Class Means of each Continuous Variable
>>> 1 Subject1   0.
>>> 2 Subject2   0.
>>> 3 Subject3   0.
>>> 4 Subject4   0.
>>> 5 Subject5   0.
>>> 6 Subject6   0.
>>> 7 Subject7   0.
>>> 8 Subject8   0.
>>> 9 Subject9   0.
>>> 10 Subject10   0.
>>> 11 Subject11   0.
>>> 12 Subject12   0.
>>> 13 Subject13   0.
>>> 14 Subject14   0.
>>> 15 Subject15   0.
>>> 16 Subject16   0.
>>> 17 Subject17   0.
>>> 18 Subject18   0.
>>> 19 Subject19   0.
>>> 20 Subject20   0.
>>> 21 Subject21   0.
>>> 22 Subject22   0.
>>> 23 Subject23   0.
>>> 24 Subject24   0.
>>> 25 Subject25   0.
>>> 26 Subject26   0.
>>>

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

[Clara Kühn]

Thank you! I completely didn't see that. It worked. 

I was wondering how to proceed next. The tutorial ends with running the glmfit 
command. I've tried correcting for multiple comparisons with Monte Carlo but 
that doesn't seem to work. How can I interpret the files that are the output 
from the repeated measures ANOVA?

Cheers Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 29. März 2017 18:15:57
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
columns

Since there are 40 subjects, you would only have 40+1 columns, not 80+1


On 03/29/2017 03:42 AM, Clara Kühn wrote:
> Hi Doug,
>
> I've also attached the fsgd file for you. Yes, I have 40 subjects and a 
> contrast column. I adapted this from this tutorial: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova where the 
> example has 3 time points and therefore 2 contrast columns. Since I want to 
> look at only 2 I only have one contrast column which is also my 81st column 
> in the contrast matrix.
>
> Did I adapt it in a wrong way for my 2 timepoints?
> Cheers
> Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 28. März 2017 18:37:58
> Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
> columns
>
> I'm not sure what's in  your FSGD file, but you design matrix has 41
> columns and your contrast matrix has 80. I'm guessing that  you have 40
> subjects and that you created the contrast matrix based on DODS and not
> DOSS (see the web page on the rmanova about creating contrasts)
>
>
> On 03/28/2017 03:50 AM, Clara Kühn wrote:
>> Sorry, I had a typo in the fsgd file. This is the correct command line and 
>> terminal output:
>>
>> mri_glmfit --glmdir $SUBJECTS_DIR/qdec/rmanova/ --y 
>> $SUBJECTS_DIR/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh 
>> --fsgd $SUBJECTS_DIR/qdec/rmanova/2014.03.27-40kids-rmanova.fsgd doss --C 
>> $SUBJECTS_DIR/qdec/rmanova/C-pre-vs-post.mtx
>>
>>
>> gdfReadHeader: reading 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>> Continuous Variable Means (all subjects)
>> 0 pre-vs-post 0 1
>> Class Means of each Continuous Variable
>> 1 Subject1   0.
>> 2 Subject2   0.
>> 3 Subject3   0.
>> 4 Subject4   0.
>> 5 Subject5   0.
>> 6 Subject6   0.
>> 7 Subject7   0.
>> 8 Subject8   0.
>> 9 Subject9   0.
>> 10 Subject10   0.
>> 11 Subject11   0.
>> 12 Subject12   0.
>> 13 Subject13   0.
>> 14 Subject14   0.
>> 15 Subject15   0.
>> 16 Subject16   0.
>> 17 Subject17   0.
>> 18 Subject18   0.
>> 19 Subject19   0.
>> 20 Subject20   0.
>> 21 Subject21   0.
>> 22 Subject22   0.
>> 23 Subject23   0.
>> 24 Subject24   0.
>> 25 Subject25   0.
>> 26 Subject26   0.
>> 27 Subject27   0.
>> 28 Subject28   0.
>> 29 Subject29   0.
>> 30 Subject30   0.
>> 31 Subject31   0.
>> 32 Subject32   0.
>> 33 Subject33   0.
>> 34 Subject34   0.
>> 35 Subject35   0.
>> 36 Subject36   0.
>> 37 Subject37   0.
>> 38 Subject38   0.
>> 39 Subject39   0.
>> 40 Subject40   0.
>> INFO: gd2mtx_method is doss
>>
>> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>> cwd /home/raid2/ckuehn
>> cmdline mri_glmfit --glmdir 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ --y 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>>  --fsgd 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
>>  doss --C 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
>> sysname  Linux
>> hostname parana
>> machine  x86_64
>> user ckuehn
>> FixVertexAreaFlag = 1
>> UseMaskWithSmoothing 1
>> OneSampleGroupMean 0
>> y
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>> logyflag 0
>> usedti  0
>> FSGD 
>> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
&

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

[Clara Kühn]

Hi Doug,

I've also attached the fsgd file for you. Yes, I have 40 subjects and a 
contrast column. I adapted this from this tutorial: 
https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova where the 
example has 3 time points and therefore 2 contrast columns. Since I want to 
look at only 2 I only have one contrast column which is also my 81st column in 
the contrast matrix.

Did I adapt it in a wrong way for my 2 timepoints?
Cheers
Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 28. März 2017 18:37:58
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
columns

I'm not sure what's in  your FSGD file, but you design matrix has 41 
columns and your contrast matrix has 80. I'm guessing that  you have 40 
subjects and that you created the contrast matrix based on DODS and not 
DOSS (see the web page on the rmanova about creating contrasts)


On 03/28/2017 03:50 AM, Clara Kühn wrote:
> Sorry, I had a typo in the fsgd file. This is the correct command line and 
> terminal output:
>
> mri_glmfit --glmdir $SUBJECTS_DIR/qdec/rmanova/ --y 
> $SUBJECTS_DIR/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh 
> --fsgd $SUBJECTS_DIR/qdec/rmanova/2014.03.27-40kids-rmanova.fsgd doss --C 
> $SUBJECTS_DIR/qdec/rmanova/C-pre-vs-post.mtx
>
>
> gdfReadHeader: reading 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 pre-vs-post 0 1
> Class Means of each Continuous Variable
> 1 Subject1   0.
> 2 Subject2   0.
> 3 Subject3   0.
> 4 Subject4   0.
> 5 Subject5   0.
> 6 Subject6   0.
> 7 Subject7   0.
> 8 Subject8   0.
> 9 Subject9   0.
> 10 Subject10   0.
> 11 Subject11   0.
> 12 Subject12   0.
> 13 Subject13   0.
> 14 Subject14   0.
> 15 Subject15   0.
> 16 Subject16   0.
> 17 Subject17   0.
> 18 Subject18   0.
> 19 Subject19   0.
> 20 Subject20   0.
> 21 Subject21   0.
> 22 Subject22   0.
> 23 Subject23   0.
> 24 Subject24   0.
> 25 Subject25   0.
> 26 Subject26   0.
> 27 Subject27   0.
> 28 Subject28   0.
> 29 Subject29   0.
> 30 Subject30   0.
> 31 Subject31   0.
> 32 Subject32   0.
> 33 Subject33   0.
> 34 Subject34   0.
> 35 Subject35   0.
> 36 Subject36   0.
> 37 Subject37   0.
> 38 Subject38   0.
> 39 Subject39   0.
> 40 Subject40   0.
> INFO: gd2mtx_method is doss
>
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd /home/raid2/ckuehn
> cmdline mri_glmfit --glmdir 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ --y 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
>  --fsgd 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
>  doss --C 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
> sysname  Linux
> hostname parana
> machine  x86_64
> user ckuehn
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
> logyflag 0
> usedti  0
> FSGD 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
> glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/
> Loading y from 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
> INFO: gd2mtx_method is doss
> Saving design matrix to 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova//Xg.dat
> Normalized matrix condition is 1
> Matrix condition is 40
> Pruning voxels by thr: 0.00
> Found 97361 voxels in mask
> Saving mask to 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova//mask.mgh
> search space = 97361.00
> ERROR: dimension mismatch between X and contrast 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
>X has 41 cols, C has 81 cols
>
>
> ----- Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: 

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

[Clara Kühn]

Sorry, I had a typo in the fsgd file. This is the correct command line and 
terminal output:

mri_glmfit --glmdir $SUBJECTS_DIR/qdec/rmanova/ --y 
$SUBJECTS_DIR/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh 
--fsgd $SUBJECTS_DIR/qdec/rmanova/2014.03.27-40kids-rmanova.fsgd doss --C 
$SUBJECTS_DIR/qdec/rmanova/C-pre-vs-post.mtx


gdfReadHeader: reading 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 pre-vs-post 0 1
Class Means of each Continuous Variable
1 Subject1   0. 
2 Subject2   0. 
3 Subject3   0. 
4 Subject4   0. 
5 Subject5   0. 
6 Subject6   0. 
7 Subject7   0. 
8 Subject8   0. 
9 Subject9   0. 
10 Subject10   0. 
11 Subject11   0. 
12 Subject12   0. 
13 Subject13   0. 
14 Subject14   0. 
15 Subject15   0. 
16 Subject16   0. 
17 Subject17   0. 
18 Subject18   0. 
19 Subject19   0. 
20 Subject20   0. 
21 Subject21   0. 
22 Subject22   0. 
23 Subject23   0. 
24 Subject24   0. 
25 Subject25   0. 
26 Subject26   0. 
27 Subject27   0. 
28 Subject28   0. 
29 Subject29   0. 
30 Subject30   0. 
31 Subject31   0. 
32 Subject32   0. 
33 Subject33   0. 
34 Subject34   0. 
35 Subject35   0. 
36 Subject36   0. 
37 Subject37   0. 
38 Subject38   0. 
39 Subject39   0. 
40 Subject40   0. 
INFO: gd2mtx_method is doss

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/raid2/ckuehn
cmdline mri_glmfit --glmdir 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ --y 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
 --fsgd 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
 doss --C 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
 
sysname  Linux
hostname parana
machine  x86_64
user ckuehn
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
logyflag 0
usedti  0
FSGD 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/
Loading y from 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
INFO: gd2mtx_method is doss
Saving design matrix to 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova//Xg.dat
Normalized matrix condition is 1
Matrix condition is 40
Pruning voxels by thr: 0.00
Found 97361 voxels in mask
Saving mask to 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova//mask.mgh
search space = 97361.00
ERROR: dimension mismatch between X and contrast 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
   X has 41 cols, C has 81 cols


- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Montag, 27. März 2017 19:49:04
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
columns

Need command line and terminal output


On 03/27/2017 09:08 AM, Clara Kühn wrote:
> Dear Freesurfer experts,
>
> I'm trying to run a repeated measures anova as described here: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
>
> I have 40 subjects with 2 time points each, so it's quite a large matrix.
> When running the mri_glmfit command I get the following error:
>
> ERROR: dimension mismatch between X and contrast 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
>X has 41 cols, C has 81 cols
>
> I'm not sure what to do as the matrix and the contrast (see attachments) 
> actually have the same amount of columns...
>
> Any help would be much appreciated, thank you!
> Clara
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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Fre

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

[Clara Kühn]

commandline:
mri_glmfit --glmdir $SUBJECTS_DIR/qdec/rmanova/ --y 
$SUBJECTS_DIR/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh 
--fsgd $SUBJECTS_DIR/qdec/rmanova/2014.03.27-40kids-rmanova.fsgd doss --C 
$SUBJECTS_DIR/qdec/rmanova/C-pre-vs-post.mtx 

terminal output:
gdfReadHeader: reading 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 pre-vs-post 0 1
Class Means of each Continuous Variable
1 Subject1   0. 
2 Subject2   0. 
3 Subject3   0. 
4 Subject4   0. 
5 Subject5   0. 
6 Subject6   0. 
7 Subject7   0. 
8 Subject8   0. 
9 Subject9   0. 
10 Subject10   0. 
11 Subject11   0. 
12 Subject12   0. 
13 Subject13   0. 
14 Subject14   0. 
15 Subject15   0. 
16 Subject16   0. 
17 Subject17   0. 
18 Subject18   0. 
19 Subject19   0. 
20 Subject20   0. 
21 Subject21   0. 
22 Subject22  -1. 
23 Subject23   0. 
24 Subject24   0. 
25 Subject25   0. 
26 Subject26   0. 
27 Subject27   0. 
28 Subject28   0. 
29 Subject29   0. 
30 Subject30   0. 
31 Subject31   0. 
32 Subject32   0. 
33 Subject33   0. 
34 Subject34   0. 
35 Subject35   0. 
36 Subject36   0. 
37 Subject37   0. 
38 Subject38   0. 
39 Subject39   0. 
40 Subject40   0. 
INFO: gd2mtx_method is doss

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/raid2/ckuehn
cmdline mri_glmfit --glmdir 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/ --y 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
 --fsgd 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
 doss --C 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
 
sysname  Linux
hostname parana
machine  x86_64
user ckuehn
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
logyflag 0
usedti  0
FSGD 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/2014.03.27-40kids-rmanova.fsgd
glmdir /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/
Loading y from 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/81kids_template/GLMprep/40kids-lh.thickness-rmanova.sm10.mgh
INFO: gd2mtx_method is doss
Saving design matrix to 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova//Xg.dat
Normalized matrix condition is 1.29647
Matrix condition is 81.058
Pruning voxels by thr: 0.00
Found 97361 voxels in mask
Saving mask to 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova//mask.mgh
search space = 97361.00
ERROR: dimension mismatch between X and contrast 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
   X has 41 cols, C has 81 cols

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Montag, 27. März 2017 19:49:04
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of 
columns

Need command line and terminal output


On 03/27/2017 09:08 AM, Clara Kühn wrote:
> Dear Freesurfer experts,
>
> I'm trying to run a repeated measures anova as described here: 
> https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
>
> I have 40 subjects with 2 time points each, so it's quite a large matrix.
> When running the mri_glmfit command I get the following error:
>
> ERROR: dimension mismatch between X and contrast 
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
>X has 41 cols, C has 81 cols
>
> I'm not sure what to do as the matrix and the contrast (see attachments) 
> actually have the same amount of columns...
>
> Any help would be much appreciated, thank you!
> Clara
>
>
>
> ___
> 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.h

[Freesurfer] glmfit mismatch between X and C with same no of columns

[Clara Kühn]

Dear Freesurfer experts,

I'm trying to run a repeated measures anova as described here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova

I have 40 subjects with 2 time points each, so it's quite a large matrix. 
When running the mri_glmfit command I get the following error:

ERROR: dimension mismatch between X and contrast 
/data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post.mtx
   X has 41 cols, C has 81 cols

I'm not sure what to do as the matrix and the contrast (see attachments) 
actually have the same amount of columns...

Any help would be much appreciated, thank you!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de


Xg.dat
Description: Binary data


C-pre-vs-post.mtx
Description: Binary data
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Re: [Freesurfer] cluster as ROI

[Clara Kühn]

that doesn't change the values. I've attached the file for you.

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 18:56:17
Betreff: Re: [Freesurfer] cluster as ROI

That will be the average value over the vertices in the ROI, which is 
not what you want for surface area. Add --accumulate to the mri_segstats 
command line to get the total area


On 02/21/2017 12:43 PM, Clara Kühn wrote:
> I have one last question about the whole thing.
>
> What is the measurement in the output file? My subjects have values between 
> 0.6 and 1.5. As the measure is surface area I was expecting different 
> numbers. Do I have to multiply by some constant to get to mm²?
>
> Thank you
> Clara
>
> - Ursprüngliche Mail -
> Von: "ckuehn" <cku...@cbs.mpg.de>
> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Gesendet: Dienstag, 21. Februar 2017 18:28:25
> Betreff: Re: [Freesurfer] cluster as ROI
>
> ah! Perfect, thank you! I'll give that a try.
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 21. Februar 2017 18:23:48
> Betreff: Re: [Freesurfer] cluster as ROI
>
> then that is the "ocn" file to use with mri_segstats
>
>
> On 02/21/2017 12:18 PM, Clara Kühn wrote:
>> yes!
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Dienstag, 21. Februar 2017 17:58:37
>> Betreff: Re: [Freesurfer] cluster as ROI
>>
>> Does this file exist?
>>
>> /nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
>>
>>
>> On 02/21/2017 11:54 AM, Clara Kühn wrote:
>>> I've attached it for you as a .txt file
>>>
>>> - Ursprüngliche Mail -
>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Dienstag, 21. Februar 2017 17:47:23
>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>
>>> Can you send the terminal output?
>>>
>>>
>>> On 02/21/2017 11:44 AM, Clara Kühn wrote:
>>>> Hm. I already did that. In none of my glmdirs are files like the 
>>>> csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran:
>>>>
>>>> mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir 
>>>> $SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces
>>>>
>>>> Cheers Clara
>>>>
>>>> - Ursprüngliche Mail -
>>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>> Gesendet: Dienstag, 21. Februar 2017 17:24:02
>>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>>
>>>> You will have to run mri_glmfit-sim
>>>>
>>>>
>>>> On 02/21/2017 04:07 AM, Clara Kühn wrote:
>>>>> Hi Doug,
>>>>>
>>>>> I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ 
>>>>> and I also have a contrasts.sig.mgh file in the gmldir.
>>>>>
>>>>> Could either of these be used instead of csdbase.sig.ocn.mgh? Or how 
>>>>> could I retrieve this file?
>>>>>
>>>>> Thanks for your help!
>>>>> Clara
>>>>>
>>>>> - Ursprüngliche Mail -
>>>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>>> Gesendet: Donnerstag, 16. Februar 2017 19:22:01
>>>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>>>
>>>>> On 02/16/2017 04:24 AM, Clara Kühn wrote:
>>>>>> Hi Doug,
>>>>>>
>>>>>> thanks for your input. Could you specify some of the flags for me?
>>>>>>
>>>>>> --i tp1.stack.mgh - is this supposed to be the cluster or file in my 
>>>>>> /template/surf/ folder that I get from mris_preproc and mris_surf2surf?
>>>>> input from preproc/surf2surf
>>>>>> --seg glmdir/contrast/csdbase.sig.ocn.mgh - I don't seem to have this 
>>>>>> file. The only files I have in the contrast folder are 2 .mat fil

Re: [Freesurfer] cluster as ROI

[Clara Kühn]

I have one last question about the whole thing.

What is the measurement in the output file? My subjects have values between 0.6 
and 1.5. As the measure is surface area I was expecting different numbers. Do I 
have to multiply by some constant to get to mm²?

Thank you
Clara

- Ursprüngliche Mail -
Von: "ckuehn" <cku...@cbs.mpg.de>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Dienstag, 21. Februar 2017 18:28:25
Betreff: Re: [Freesurfer] cluster as ROI

ah! Perfect, thank you! I'll give that a try.

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 18:23:48
Betreff: Re: [Freesurfer] cluster as ROI

then that is the "ocn" file to use with mri_segstats


On 02/21/2017 12:18 PM, Clara Kühn wrote:
> yes!
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 21. Februar 2017 17:58:37
> Betreff: Re: [Freesurfer] cluster as ROI
>
> Does this file exist?
>
> /nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
>
>
> On 02/21/2017 11:54 AM, Clara Kühn wrote:
>> I've attached it for you as a .txt file
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Dienstag, 21. Februar 2017 17:47:23
>> Betreff: Re: [Freesurfer] cluster as ROI
>>
>> Can you send the terminal output?
>>
>>
>> On 02/21/2017 11:44 AM, Clara Kühn wrote:
>>> Hm. I already did that. In none of my glmdirs are files like the 
>>> csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran:
>>>
>>> mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir 
>>> $SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces
>>>
>>> Cheers Clara
>>>
>>> - Ursprüngliche Mail -
>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Dienstag, 21. Februar 2017 17:24:02
>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>
>>> You will have to run mri_glmfit-sim
>>>
>>>
>>> On 02/21/2017 04:07 AM, Clara Kühn wrote:
>>>> Hi Doug,
>>>>
>>>> I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and 
>>>> I also have a contrasts.sig.mgh file in the gmldir.
>>>>
>>>> Could either of these be used instead of csdbase.sig.ocn.mgh? Or how could 
>>>> I retrieve this file?
>>>>
>>>> Thanks for your help!
>>>> Clara
>>>>
>>>> - Ursprüngliche Mail -
>>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>> Gesendet: Donnerstag, 16. Februar 2017 19:22:01
>>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>>
>>>> On 02/16/2017 04:24 AM, Clara Kühn wrote:
>>>>> Hi Doug,
>>>>>
>>>>> thanks for your input. Could you specify some of the flags for me?
>>>>>
>>>>> --i tp1.stack.mgh - is this supposed to be the cluster or file in my 
>>>>> /template/surf/ folder that I get from mris_preproc and mris_surf2surf?
>>>> input from preproc/surf2surf
>>>>> --seg glmdir/contrast/csdbase.sig.ocn.mgh - I don't seem to have this 
>>>>> file. The only files I have in the contrast folder are 2 .mat files
>>>> there should be a bunch of output there from mri_glmfit and
>>>> mri_glmfit-sim. Actually, if you ran qdec, then the glmfit-sim output
>>>> may not be there. you'll have to run it separately. But there should be,
>>>> eg, gamma.mgh there
>>>>> Cheers
>>>>> Clara
>>>>>
>>>>> - Ursprüngliche Mail -
>>>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>>> Gesendet: Mittwoch, 15. Februar 2017 23:35:54
>>>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>>>
>>>>> Use something like this
>>>>>
>>>>> mri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh
>>>>> --exc

Re: [Freesurfer] cluster as ROI

[Clara Kühn]

ah! Perfect, thank you! I'll give that a try.

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 18:23:48
Betreff: Re: [Freesurfer] cluster as ROI

then that is the "ocn" file to use with mri_segstats


On 02/21/2017 12:18 PM, Clara Kühn wrote:
> yes!
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 21. Februar 2017 17:58:37
> Betreff: Re: [Freesurfer] cluster as ROI
>
> Does this file exist?
>
> /nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
>
>
> On 02/21/2017 11:54 AM, Clara Kühn wrote:
>> I've attached it for you as a .txt file
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Dienstag, 21. Februar 2017 17:47:23
>> Betreff: Re: [Freesurfer] cluster as ROI
>>
>> Can you send the terminal output?
>>
>>
>> On 02/21/2017 11:44 AM, Clara Kühn wrote:
>>> Hm. I already did that. In none of my glmdirs are files like the 
>>> csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran:
>>>
>>> mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir 
>>> $SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces
>>>
>>> Cheers Clara
>>>
>>> - Ursprüngliche Mail -
>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Dienstag, 21. Februar 2017 17:24:02
>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>
>>> You will have to run mri_glmfit-sim
>>>
>>>
>>> On 02/21/2017 04:07 AM, Clara Kühn wrote:
>>>> Hi Doug,
>>>>
>>>> I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and 
>>>> I also have a contrasts.sig.mgh file in the gmldir.
>>>>
>>>> Could either of these be used instead of csdbase.sig.ocn.mgh? Or how could 
>>>> I retrieve this file?
>>>>
>>>> Thanks for your help!
>>>> Clara
>>>>
>>>> - Ursprüngliche Mail -
>>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>> Gesendet: Donnerstag, 16. Februar 2017 19:22:01
>>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>>
>>>> On 02/16/2017 04:24 AM, Clara Kühn wrote:
>>>>> Hi Doug,
>>>>>
>>>>> thanks for your input. Could you specify some of the flags for me?
>>>>>
>>>>> --i tp1.stack.mgh - is this supposed to be the cluster or file in my 
>>>>> /template/surf/ folder that I get from mris_preproc and mris_surf2surf?
>>>> input from preproc/surf2surf
>>>>> --seg glmdir/contrast/csdbase.sig.ocn.mgh - I don't seem to have this 
>>>>> file. The only files I have in the contrast folder are 2 .mat files
>>>> there should be a bunch of output there from mri_glmfit and
>>>> mri_glmfit-sim. Actually, if you ran qdec, then the glmfit-sim output
>>>> may not be there. you'll have to run it separately. But there should be,
>>>> eg, gamma.mgh there
>>>>> Cheers
>>>>> Clara
>>>>>
>>>>> - Ursprüngliche Mail -
>>>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>>> Gesendet: Mittwoch, 15. Februar 2017 23:35:54
>>>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>>>
>>>>> Use something like this
>>>>>
>>>>> mri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh
>>>>> --excludeid 0 --avgwf tp1.clustermean.dat
>>>>>
>>>>> The output tp1.clustermean.dat will be a matrix with nsubjects rows and
>>>>> nclusters columns where the value represents the mean for that subject
>>>>> in that cluster.
>>>>>
>>>>>
>>>>>
>>>>> On 02/14/2017 11:47 AM, Clara Kühn wrote:
>>>>>> Dear FreeSurfer Experts,
>>>>>>
>>>>>> I compared 2 groups in QDEC i

Re: [Freesurfer] cluster as ROI

[Clara Kühn]

yes!

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 17:58:37
Betreff: Re: [Freesurfer] cluster as ROI

Does this file exist?

/nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh


On 02/21/2017 11:54 AM, Clara Kühn wrote:
> I've attached it for you as a .txt file
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 21. Februar 2017 17:47:23
> Betreff: Re: [Freesurfer] cluster as ROI
>
> Can you send the terminal output?
>
>
> On 02/21/2017 11:44 AM, Clara Kühn wrote:
>> Hm. I already did that. In none of my glmdirs are files like the 
>> csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran:
>>
>> mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir 
>> $SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces
>>
>> Cheers Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Dienstag, 21. Februar 2017 17:24:02
>> Betreff: Re: [Freesurfer] cluster as ROI
>>
>> You will have to run mri_glmfit-sim
>>
>>
>> On 02/21/2017 04:07 AM, Clara Kühn wrote:
>>> Hi Doug,
>>>
>>> I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and 
>>> I also have a contrasts.sig.mgh file in the gmldir.
>>>
>>> Could either of these be used instead of csdbase.sig.ocn.mgh? Or how could 
>>> I retrieve this file?
>>>
>>> Thanks for your help!
>>> Clara
>>>
>>> - Ursprüngliche Mail -
>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Donnerstag, 16. Februar 2017 19:22:01
>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>
>>> On 02/16/2017 04:24 AM, Clara Kühn wrote:
>>>> Hi Doug,
>>>>
>>>> thanks for your input. Could you specify some of the flags for me?
>>>>
>>>> --i tp1.stack.mgh - is this supposed to be the cluster or file in my 
>>>> /template/surf/ folder that I get from mris_preproc and mris_surf2surf?
>>> input from preproc/surf2surf
>>>> --seg glmdir/contrast/csdbase.sig.ocn.mgh - I don't seem to have this 
>>>> file. The only files I have in the contrast folder are 2 .mat files
>>> there should be a bunch of output there from mri_glmfit and
>>> mri_glmfit-sim. Actually, if you ran qdec, then the glmfit-sim output
>>> may not be there. you'll have to run it separately. But there should be,
>>> eg, gamma.mgh there
>>>> Cheers
>>>> Clara
>>>>
>>>> - Ursprüngliche Mail -
>>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>> Gesendet: Mittwoch, 15. Februar 2017 23:35:54
>>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>>
>>>> Use something like this
>>>>
>>>> mri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh
>>>> --excludeid 0 --avgwf tp1.clustermean.dat
>>>>
>>>> The output tp1.clustermean.dat will be a matrix with nsubjects rows and
>>>> nclusters columns where the value represents the mean for that subject
>>>> in that cluster.
>>>>
>>>>
>>>>
>>>> On 02/14/2017 11:47 AM, Clara Kühn wrote:
>>>>> Dear FreeSurfer Experts,
>>>>>
>>>>> I compared 2 groups in QDEC in spc (from pre to post) and found a cluster 
>>>>> that survives Monte Carlo correction. Now I would like to extract the 
>>>>> data for each participant and each time point from that cluster so that I 
>>>>> can plot the change.
>>>>>
>>>>> How could I do this? I tried this so far:
>>>>> aparcstats2table --qdec-long $SUBJECTS 
>>>>> DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile 
>>>>> $SUBJECTS 
>>>>> DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt 
>>>>> --parc $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area 
>>>>> again/rh-Diff-1-3-Intercept-long.area-sp

Re: [Freesurfer] cluster as ROI

[Clara Kühn]

I've attached it for you as a .txt file

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 17:47:23
Betreff: Re: [Freesurfer] cluster as ROI

Can you send the terminal output?


On 02/21/2017 11:44 AM, Clara Kühn wrote:
> Hm. I already did that. In none of my glmdirs are files like the 
> csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran:
>
> mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir 
> $SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces
>
> Cheers Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 21. Februar 2017 17:24:02
> Betreff: Re: [Freesurfer] cluster as ROI
>
> You will have to run mri_glmfit-sim
>
>
> On 02/21/2017 04:07 AM, Clara Kühn wrote:
>> Hi Doug,
>>
>> I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and I 
>> also have a contrasts.sig.mgh file in the gmldir.
>>
>> Could either of these be used instead of csdbase.sig.ocn.mgh? Or how could I 
>> retrieve this file?
>>
>> Thanks for your help!
>> Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Donnerstag, 16. Februar 2017 19:22:01
>> Betreff: Re: [Freesurfer] cluster as ROI
>>
>> On 02/16/2017 04:24 AM, Clara Kühn wrote:
>>> Hi Doug,
>>>
>>> thanks for your input. Could you specify some of the flags for me?
>>>
>>> --i tp1.stack.mgh - is this supposed to be the cluster or file in my 
>>> /template/surf/ folder that I get from mris_preproc and mris_surf2surf?
>> input from preproc/surf2surf
>>> --seg glmdir/contrast/csdbase.sig.ocn.mgh - I don't seem to have this file. 
>>> The only files I have in the contrast folder are 2 .mat files
>> there should be a bunch of output there from mri_glmfit and
>> mri_glmfit-sim. Actually, if you ran qdec, then the glmfit-sim output
>> may not be there. you'll have to run it separately. But there should be,
>> eg, gamma.mgh there
>>> Cheers
>>> Clara
>>>
>>> - Ursprüngliche Mail -
>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Mittwoch, 15. Februar 2017 23:35:54
>>> Betreff: Re: [Freesurfer] cluster as ROI
>>>
>>> Use something like this
>>>
>>> mri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh
>>> --excludeid 0 --avgwf tp1.clustermean.dat
>>>
>>> The output tp1.clustermean.dat will be a matrix with nsubjects rows and
>>> nclusters columns where the value represents the mean for that subject
>>> in that cluster.
>>>
>>>
>>>
>>> On 02/14/2017 11:47 AM, Clara Kühn wrote:
>>>> Dear FreeSurfer Experts,
>>>>
>>>> I compared 2 groups in QDEC in spc (from pre to post) and found a cluster 
>>>> that survives Monte Carlo correction. Now I would like to extract the data 
>>>> for each participant and each time point from that cluster so that I can 
>>>> plot the change.
>>>>
>>>> How could I do this? I tried this so far:
>>>> aparcstats2table --qdec-long $SUBJECTS 
>>>> DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile 
>>>> $SUBJECTS 
>>>> DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt --parc 
>>>> $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area 
>>>> again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
>>>>
>>>> But I get this error:
>>>> ERROR: The stats file 
>>>> /nobackup/etsch2/kids/prepost-61kids/AL3K_1.long.AL3K.base/stats/rh./nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh.stats
>>>>  is not found or is too small to be a valid statsfile
>>>> Use --skip flag to automatically skip bad stats files
>>>>
>>>>
>>>> Do I have to define my cluster as a ROI and then warp it onto the single 
>>>> time points? How would I do that?
>>>>
>>>> Any help is much appreciated!
>>>> Thank you
>>>>
>>>> Clara

-- 
Douglas N

Re: [Freesurfer] cluster as ROI

[Clara Kühn]

Hm. I already did that. In none of my glmdirs are files like the 
csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran:

mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir 
$SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces

Cheers Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 17:24:02
Betreff: Re: [Freesurfer] cluster as ROI

You will have to run mri_glmfit-sim


On 02/21/2017 04:07 AM, Clara Kühn wrote:
> Hi Doug,
>
> I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and I 
> also have a contrasts.sig.mgh file in the gmldir.
>
> Could either of these be used instead of csdbase.sig.ocn.mgh? Or how could I 
> retrieve this file?
>
> Thanks for your help!
> Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Donnerstag, 16. Februar 2017 19:22:01
> Betreff: Re: [Freesurfer] cluster as ROI
>
> On 02/16/2017 04:24 AM, Clara Kühn wrote:
>> Hi Doug,
>>
>> thanks for your input. Could you specify some of the flags for me?
>>
>> --i tp1.stack.mgh - is this supposed to be the cluster or file in my 
>> /template/surf/ folder that I get from mris_preproc and mris_surf2surf?
> input from preproc/surf2surf
>> --seg glmdir/contrast/csdbase.sig.ocn.mgh - I don't seem to have this file. 
>> The only files I have in the contrast folder are 2 .mat files
> there should be a bunch of output there from mri_glmfit and
> mri_glmfit-sim. Actually, if you ran qdec, then the glmfit-sim output
> may not be there. you'll have to run it separately. But there should be,
> eg, gamma.mgh there
>> Cheers
>> Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Mittwoch, 15. Februar 2017 23:35:54
>> Betreff: Re: [Freesurfer] cluster as ROI
>>
>> Use something like this
>>
>> mri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh
>> --excludeid 0 --avgwf tp1.clustermean.dat
>>
>> The output tp1.clustermean.dat will be a matrix with nsubjects rows and
>> nclusters columns where the value represents the mean for that subject
>> in that cluster.
>>
>>
>>
>> On 02/14/2017 11:47 AM, Clara Kühn wrote:
>>> Dear FreeSurfer Experts,
>>>
>>> I compared 2 groups in QDEC in spc (from pre to post) and found a cluster 
>>> that survives Monte Carlo correction. Now I would like to extract the data 
>>> for each participant and each time point from that cluster so that I can 
>>> plot the change.
>>>
>>> How could I do this? I tried this so far:
>>> aparcstats2table --qdec-long $SUBJECTS 
>>> DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile 
>>> $SUBJECTS 
>>> DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt --parc 
>>> $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area 
>>> again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
>>>
>>> But I get this error:
>>> ERROR: The stats file 
>>> /nobackup/etsch2/kids/prepost-61kids/AL3K_1.long.AL3K.base/stats/rh./nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh.stats
>>>  is not found or is too small to be a valid statsfile
>>> Use --skip flag to automatically skip bad stats files
>>>
>>>
>>> Do I have to define my cluster as a ROI and then warp it onto the single 
>>> time points? How would I do that?
>>>
>>> Any help is much appreciated!
>>> Thank you
>>>
>>> Clara

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

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

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Re: [Freesurfer] cluster as ROI

[Clara Kühn]

Hi Doug,

I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and I 
also have a contrasts.sig.mgh file in the gmldir.

Could either of these be used instead of csdbase.sig.ocn.mgh? Or how could I 
retrieve this file?

Thanks for your help!
Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 16. Februar 2017 19:22:01
Betreff: Re: [Freesurfer] cluster as ROI

On 02/16/2017 04:24 AM, Clara Kühn wrote:
> Hi Doug,
>
> thanks for your input. Could you specify some of the flags for me?
>
> --i tp1.stack.mgh - is this supposed to be the cluster or file in my 
> /template/surf/ folder that I get from mris_preproc and mris_surf2surf?
input from preproc/surf2surf
> --seg glmdir/contrast/csdbase.sig.ocn.mgh - I don't seem to have this file. 
> The only files I have in the contrast folder are 2 .mat files
there should be a bunch of output there from mri_glmfit and 
mri_glmfit-sim. Actually, if you ran qdec, then the glmfit-sim output 
may not be there. you'll have to run it separately. But there should be, 
eg, gamma.mgh there
>
> Cheers
> Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 15. Februar 2017 23:35:54
> Betreff: Re: [Freesurfer] cluster as ROI
>
> Use something like this
>
> mri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh
> --excludeid 0 --avgwf tp1.clustermean.dat
>
> The output tp1.clustermean.dat will be a matrix with nsubjects rows and
> nclusters columns where the value represents the mean for that subject
> in that cluster.
>
>
>
> On 02/14/2017 11:47 AM, Clara Kühn wrote:
>> Dear FreeSurfer Experts,
>>
>> I compared 2 groups in QDEC in spc (from pre to post) and found a cluster 
>> that survives Monte Carlo correction. Now I would like to extract the data 
>> for each participant and each time point from that cluster so that I can 
>> plot the change.
>>
>> How could I do this? I tried this so far:
>> aparcstats2table --qdec-long $SUBJECTS 
>> DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile 
>> $SUBJECTS 
>> DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt --parc 
>> $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area 
>> again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
>>
>> But I get this error:
>> ERROR: The stats file 
>> /nobackup/etsch2/kids/prepost-61kids/AL3K_1.long.AL3K.base/stats/rh./nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh.stats
>>  is not found or is too small to be a valid statsfile
>> Use --skip flag to automatically skip bad stats files
>>
>>
>> Do I have to define my cluster as a ROI and then warp it onto the single 
>> time points? How would I do that?
>>
>> Any help is much appreciated!
>> Thank you
>>
>> Clara

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

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

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Re: [Freesurfer] cluster as ROI

[Clara Kühn]

Hi Doug,

thanks for your input. Could you specify some of the flags for me? 

--i tp1.stack.mgh - is this supposed to be the cluster or file in my 
/template/surf/ folder that I get from mris_preproc and mris_surf2surf? 
--seg glmdir/contrast/csdbase.sig.ocn.mgh - I don't seem to have this file. The 
only files I have in the contrast folder are 2 .mat files

Cheers
Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 15. Februar 2017 23:35:54
Betreff: Re: [Freesurfer] cluster as ROI

Use something like this

mri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh 
--excludeid 0 --avgwf tp1.clustermean.dat

The output tp1.clustermean.dat will be a matrix with nsubjects rows and 
nclusters columns where the value represents the mean for that subject 
in that cluster.



On 02/14/2017 11:47 AM, Clara Kühn wrote:
> Dear FreeSurfer Experts,
>
> I compared 2 groups in QDEC in spc (from pre to post) and found a cluster 
> that survives Monte Carlo correction. Now I would like to extract the data 
> for each participant and each time point from that cluster so that I can plot 
> the change.
>
> How could I do this? I tried this so far:
> aparcstats2table --qdec-long $SUBJECTS 
> DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile 
> $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt 
> --parc $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area 
> again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh
>
> But I get this error:
> ERROR: The stats file 
> /nobackup/etsch2/kids/prepost-61kids/AL3K_1.long.AL3K.base/stats/rh./nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh.stats
>  is not found or is too small to be a valid statsfile
> Use --skip flag to automatically skip bad stats files
>
>
> Do I have to define my cluster as a ROI and then warp it onto the single time 
> points? How would I do that?
>
> Any help is much appreciated!
> Thank you
>
> Clara

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

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

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[Freesurfer] REPOST: longitudinal QDEC cluster as ROI

[Clara Kühn]

Dear FreeSurfer Experts,

I compared 2 groups in QDEC in spc (from pre to post) and found a cluster that 
survives Monte Carlo correction. Now I would like to extract the data for each 
participant and each time point from that cluster so that I can plot the change.

How could I do this? I tried this so far:
aparcstats2table --qdec-long $SUBJECTS 
DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile 
$SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt 
--parc $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area 
again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh

But I get this error:
ERROR: The stats file 
/nobackup/etsch2/kids/prepost-61kids/AL3K_1.long.AL3K.base/stats/rh./nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh.stats
 is not found or is too small to be a valid statsfile
Use --skip flag to automatically skip bad stats files

Do I have to define my cluster as a ROI and then warp it onto the single time 
points? How would I do that?
I have tried to draw the cluster as an ROI in QDEC but that didn't work (I 
could draw only on the medial surface and around the temporal sulcus). I'm 
guessing because I'm using a study specific template and not the fsaverage.

Any help is much appreciated!
Thank you

Clara
-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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[Freesurfer] cluster as ROI

[Clara Kühn]

Dear FreeSurfer Experts,

I compared 2 groups in QDEC in spc (from pre to post) and found a cluster that 
survives Monte Carlo correction. Now I would like to extract the data for each 
participant and each time point from that cluster so that I can plot the change.

How could I do this? I tried this so far:
aparcstats2table --qdec-long $SUBJECTS 
DIR/qdec/2016.12.06-40kids-long.qdec.table2-1.dat --hemi rh - -tablefile 
$SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rharea-cluster-extracted.txt 
--parc $SUBJECTS DIR/qdec/2016.12.08-40kids-2stagemodel/rh-area 
again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh

But I get this error:
ERROR: The stats file 
/nobackup/etsch2/kids/prepost-61kids/AL3K_1.long.AL3K.base/stats/rh./nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again/rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.cluster.mgh.stats
 is not found or is too small to be a valid statsfile
Use --skip flag to automatically skip bad stats files


Do I have to define my cluster as a ROI and then warp it onto the single time 
points? How would I do that?

Any help is much appreciated!
Thank you

Clara
-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] extract area.pial stats

[Clara Kühn]

alright. Thank you so much!

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 17:45:38
Betreff: Re: [Freesurfer] extract area.pial stats

No. The program is from version 6 so it is expecting v6 naming conventions


On 02/08/2017 11:38 AM, Clara Kühn wrote:
> Thank you, I think it worked. I've attached the file again.
> There was one error message in the terminal output though:
>
> atlas_icv (eTIV) = 1287829 mm^3(det: 1.512705 )
> /nobackup/etsch2/kids/prepost-61kids//ZF1K.base/mri/aseg.presurf.mgz doesn't 
> exist, using old naming conventions
>
> Is that something to worry about?
>
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 8. Februar 2017 17:34:06
> Betreff: Re: [Freesurfer] extract area.pial stats
>
> It either has to be in your path or you need to supply the full path when 
> running it, like this
> $SUBJECTS_DIR/mris_anatomical_stats-doug
>
>
> On 02/08/2017 11:27 AM, Clara Kühn wrote:
>> I'm so sorry, I don't know anything about programming...
>> I downloaded it, copied it into my SUBJECTS_DIR as 
>> mris_anatomical_stats-doug and tried to run the whole thing again like this:
>>
>> mris_anatomical_stats-doug -mgz -cortex 
>> $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f 
>> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a 
>> $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c 
>> $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
>>
>> but then I got this error:
>>
>> bash: mris_anatomical_stats-doug: command not found
>>
>>
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Mittwoch, 8. Februar 2017 17:08:26
>> Betreff: Re: [Freesurfer] extract area.pial stats
>>
>> You don't need to open it. Just download it and put it in your path. You
>> may want to call it something slightly differnt so that you don't
>> confuse it with the v5.3 version
>>
>>
>> On 02/08/2017 10:53 AM, Clara Kühn wrote:
>>> thanks. What kind of format is it? How do I open it?
>>>
>>> Cheers
>>> Clara
>>>
>>> - Ursprüngliche Mail -
>>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Mittwoch, 8. Februar 2017 16:43:47
>>> Betreff: Re: [Freesurfer] extract area.pial stats
>>>
>>> Try this version (same as version 6)
>>>
>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
>>>
>>>
>>>
>>> On 02/08/2017 04:55 AM, Clara Kühn wrote:
>>>> Hi Doug,
>>>>
>>>> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats 
>>>> file for you to take a look at. As far as I can tell it's still reporting 
>>>> the white surface area. Or am I reading it wrong?
>>>>
>>>> Cheers Clara
>>>>
>>>> - Ursprüngliche Mail -
>>>> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>>>> An: freesurfer@nmr.mgh.harvard.edu
>>>> Gesendet: Mittwoch, 8. Februar 2017 00:15:22
>>>> Betreff: Re: [Freesurfer] extract area.pial stats
>>>>
>>>> try
>>>>
>>>> cd $SUBJECTS_DIR/subject/surf
>>>>
>>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
>>>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
>>>> ../label/aparc.annot.ctab subject lh pial
>>>>
>>>>
>>>> On 2/7/17 4:48 AM, Clara Kühn wrote:
>>>>> Dear FreeSurfer experts,
>>>>>
>>>>> I'm trying to extract a total Pial Surface Area like it is extracted for 
>>>>> White Surface Area in the ?h.aparc.stats file. I have tried this command 
>>>>> but it doesn't seem to include Pial Surface Area:
>>>>>
>>>>> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
>>>>> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
>>>>>
>>>>> How could I extract the total Pial Surface Area for each participant?
>>>>>
>>>>> Thank you for you help!
>>>>> Clara
>>>>> _

Re: [Freesurfer] extract area.pial stats

[Clara Kühn]

Thank you, I think it worked. I've attached the file again. 
There was one error message in the terminal output though:

atlas_icv (eTIV) = 1287829 mm^3(det: 1.512705 )
/nobackup/etsch2/kids/prepost-61kids//ZF1K.base/mri/aseg.presurf.mgz doesn't 
exist, using old naming conventions

Is that something to worry about?


- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 17:34:06
Betreff: Re: [Freesurfer] extract area.pial stats

It either has to be in your path or you need to supply the full path when 
running it, like this
$SUBJECTS_DIR/mris_anatomical_stats-doug


On 02/08/2017 11:27 AM, Clara Kühn wrote:
> I'm so sorry, I don't know anything about programming...
> I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug 
> and tried to run the whole thing again like this:
>
> mris_anatomical_stats-doug -mgz -cortex 
> $SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f 
> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a 
> $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c 
> $SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial
>
> but then I got this error:
>
> bash: mris_anatomical_stats-doug: command not found
>
>
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 8. Februar 2017 17:08:26
> Betreff: Re: [Freesurfer] extract area.pial stats
>
> You don't need to open it. Just download it and put it in your path. You
> may want to call it something slightly differnt so that you don't
> confuse it with the v5.3 version
>
>
> On 02/08/2017 10:53 AM, Clara Kühn wrote:
>> thanks. What kind of format is it? How do I open it?
>>
>> Cheers
>> Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Mittwoch, 8. Februar 2017 16:43:47
>> Betreff: Re: [Freesurfer] extract area.pial stats
>>
>> Try this version (same as version 6)
>>
>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
>>
>>
>>
>> On 02/08/2017 04:55 AM, Clara Kühn wrote:
>>> Hi Doug,
>>>
>>> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats 
>>> file for you to take a look at. As far as I can tell it's still reporting 
>>> the white surface area. Or am I reading it wrong?
>>>
>>> Cheers Clara
>>>
>>> - Ursprüngliche Mail -
>>> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>>> An: freesurfer@nmr.mgh.harvard.edu
>>> Gesendet: Mittwoch, 8. Februar 2017 00:15:22
>>> Betreff: Re: [Freesurfer] extract area.pial stats
>>>
>>> try
>>>
>>> cd $SUBJECTS_DIR/subject/surf
>>>
>>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
>>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
>>> ../label/aparc.annot.ctab subject lh pial
>>>
>>>
>>> On 2/7/17 4:48 AM, Clara Kühn wrote:
>>>> Dear FreeSurfer experts,
>>>>
>>>> I'm trying to extract a total Pial Surface Area like it is extracted for 
>>>> White Surface Area in the ?h.aparc.stats file. I have tried this command 
>>>> but it doesn't seem to include Pial Surface Area:
>>>>
>>>> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
>>>> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
>>>>
>>>> How could I extract the total Pial Surface Area for each participant?
>>>>
>>>> Thank you for you help!
>>>> Clara
>>>> ___
>>>> 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.pa

Re: [Freesurfer] extract area.pial stats

[Clara Kühn]

I'm so sorry, I don't know anything about programming... 
I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug 
and tried to run the whole thing again like this:

mris_anatomical_stats-doug -mgz -cortex 
$SUBJECTS_DIR/ZF1K.base/label/lh.cortex.label -f 
$SUBJECTS_DIR/ZF1K.base/stats/lh.aparc.pial.stats -b -a 
$SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -c 
$SUBJECTS_DIR/ZF1K.base/label/aparc.annot.ctab ZF1K.base lh pial

but then I got this error:

bash: mris_anatomical_stats-doug: command not found



- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 17:08:26
Betreff: Re: [Freesurfer] extract area.pial stats

You don't need to open it. Just download it and put it in your path. You 
may want to call it something slightly differnt so that you don't 
confuse it with the v5.3 version


On 02/08/2017 10:53 AM, Clara Kühn wrote:
> thanks. What kind of format is it? How do I open it?
>
> Cheers
> Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 8. Februar 2017 16:43:47
> Betreff: Re: [Freesurfer] extract area.pial stats
>
> Try this version (same as version 6)
>
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
>
>
>
> On 02/08/2017 04:55 AM, Clara Kühn wrote:
>> Hi Doug,
>>
>> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats 
>> file for you to take a look at. As far as I can tell it's still reporting 
>> the white surface area. Or am I reading it wrong?
>>
>> Cheers Clara
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Mittwoch, 8. Februar 2017 00:15:22
>> Betreff: Re: [Freesurfer] extract area.pial stats
>>
>> try
>>
>> cd $SUBJECTS_DIR/subject/surf
>>
>> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
>> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
>> ../label/aparc.annot.ctab subject lh pial
>>
>>
>> On 2/7/17 4:48 AM, Clara Kühn wrote:
>>> Dear FreeSurfer experts,
>>>
>>> I'm trying to extract a total Pial Surface Area like it is extracted for 
>>> White Surface Area in the ?h.aparc.stats file. I have tried this command 
>>> but it doesn't seem to include Pial Surface Area:
>>>
>>> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
>>> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
>>>
>>> How could I extract the total Pial Surface Area for each participant?
>>>
>>> Thank you for you help!
>>> Clara
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
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-- 
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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
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Re: [Freesurfer] extract area.pial stats

[Clara Kühn]

thanks. What kind of format is it? How do I open it?

Cheers 
Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 16:43:47
Betreff: Re: [Freesurfer] extract area.pial stats

Try this version (same as version 6)

https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats



On 02/08/2017 04:55 AM, Clara Kühn wrote:
> Hi Doug,
>
> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats 
> file for you to take a look at. As far as I can tell it's still reporting the 
> white surface area. Or am I reading it wrong?
>
> Cheers Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 8. Februar 2017 00:15:22
> Betreff: Re: [Freesurfer] extract area.pial stats
>
> try
>
> cd $SUBJECTS_DIR/subject/surf
>
> mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
> ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
> ../label/aparc.annot.ctab subject lh pial
>
>
> On 2/7/17 4:48 AM, Clara Kühn wrote:
>> Dear FreeSurfer experts,
>>
>> I'm trying to extract a total Pial Surface Area like it is extracted for 
>> White Surface Area in the ?h.aparc.stats file. I have tried this command but 
>> it doesn't seem to include Pial Surface Area:
>>
>> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
>> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
>>
>> How could I extract the total Pial Surface Area for each participant?
>>
>> Thank you for you help!
>> Clara
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> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
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-- 
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
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Re: [Freesurfer] extract area.pial stats

[Clara Kühn]

Hi Doug,

thanks for your reply. I tried it out and attached the lh.aparc.pial.stats file 
for you to take a look at. As far as I can tell it's still reporting the white 
surface area. Or am I reading it wrong?

Cheers Clara

- Ursprüngliche Mail -
Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 8. Februar 2017 00:15:22
Betreff: Re: [Freesurfer] extract area.pial stats

try

cd $SUBJECTS_DIR/subject/surf

mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f 
../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c 
../label/aparc.annot.ctab subject lh pial


On 2/7/17 4:48 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I'm trying to extract a total Pial Surface Area like it is extracted for 
> White Surface Area in the ?h.aparc.stats file. I have tried this command but 
> it doesn't seem to include Pial Surface Area:
>
> mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
> $SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial
>
> How could I extract the total Pial Surface Area for each participant?
>
> Thank you for you help!
> Clara
> ___
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>
>

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lh.aparc.pial.stats
Description: Binary data
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[Freesurfer] extract area.pial stats

[Clara Kühn]

Dear FreeSurfer experts,

I'm trying to extract a total Pial Surface Area like it is extracted for White 
Surface Area in the ?h.aparc.stats file. I have tried this command but it 
doesn't seem to include Pial Surface Area:

mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f 
$SUBJECTS_DIR/ZF1K.base/stats/lh.aparc-areapial.stats -b ZF1K.base lh pial

How could I extract the total Pial Surface Area for each participant?

Thank you for you help!
Clara
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Re: [Freesurfer] extract values uncorrected clusters

[Clara Kühn]

Hi Doug,

thanks for your reply. I'm trying it out but I get this error message: 
ERROR: srcsubjid must be supplied

I have 40 subjects in 2 groups. What exactly do I enter as --subject ?

Thanks for your help!
Clara


- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 1. Februar 2017 19:18:55
Betreff: Re: [Freesurfer] extract values uncorrected clusters

You can run mri_surfcluster using the sig.mgh as the input and 
specifying a --minarea and --thmin .001. --minarea takes a surface area 
in mm2, not number of vertices, so you'll have to compute what the 
approx area is of 150 vertices. Include a --ocn output and --sum 
sumfile, then use mri_segstats with --seg ocn.mgh --excludeid 0 --i 
y.mgh --avgwf y.sum.dat

The output y.sum.dat will be a matrix of number of subjects by number of 
clusters. Look in the sumfile for the cluster identity


On 02/01/2017 11:41 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I did a group analysis in QDEC for the symmetric percent change from pre to 
> post and have a couple of clusters that don't survive the Monte Carlo 
> correction. I want to extract the values for each time point per subject for 
> those clusters that are bigger than 150 vertices to look at individual 
> trends. How could I achieve this?
>
> Thank you for your help.
> Clara
>
>
> -
> Clara Kühn, Phd Student
>   
> Max-Planck-Institute for Human Cognitive and Brain Science
> Department of Neuropsychology
> Stephanstrasse 1A
> 04103 Leipzig, Germany
>
> Phone: +49 341 - 9940 2271
> Fax: +49 341 - 9940 2260
> Web: www.cbs.mpg.de
> E-Mail: cku...@cbs.mpg.de
>
> ___
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>
>

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

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

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[Freesurfer] extract values uncorrected clusters

[Clara Kühn]

Dear FreeSurfer experts,

I did a group analysis in QDEC for the symmetric percent change from pre to 
post and have a couple of clusters that don't survive the Monte Carlo 
correction. I want to extract the values for each time point per subject for 
those clusters that are bigger than 150 vertices to look at individual trends. 
How could I achieve this? 

Thank you for your help.
Clara


- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] vertex-wise ROI analysis

[Clara Kühn]

thank you! I will give that a try.

- Ursprüngliche Mail -
Von: "Joost Janssen" <joost.jansse...@gmail.com>
An: "ckuehn" <cku...@cbs.mpg.de>, "freesurfer" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Mittwoch, 11. Januar 2017 15:07:36
Betreff: Re: [Freesurfer] vertex-wise ROI analysis

You can do a vertex-wise analysis in any region you like (e.g. cortex,
superior temporal cortex, etc.)

check the  "--label" option of mri_glmfit. see also:

https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo

-joost
<http://www.cibersam.es/grupos/grupo-de-investigacion/ficha-personal?id=14486>



On Wed, Jan 11, 2017 at 2:51 PM, Clara Kühn <cku...@cbs.mpg.de> wrote:

> Dear FreeSurfer experts,
>
> is it possible to do a vertex-wise analysis on ROIs? When I extract the
> values per subject for (e.g.) the superior temporal gyrus grom the aparc
> file it is a pretty big region to get only one value. I would like to
> analyze it on a vertex level so I can see where exactly the effects are.
>
> I'd be really happy for any suggestions!
> Thank you
> Clara
>
> --
> Clara Kühn, Phd Student
>
> Max-Planck-Institute for Human Cognitive and Brain Science
> Department of Neuropsychology
> Stephanstrasse 1A
> 04103 Leipzig, Germany
>
> Phone: +49 341 - 9940 2271
> Fax: +49 341 - 9940 2260
> Web: www.cbs.mpg.de
> E-Mail: cku...@cbs.mpg.de
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>

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[Freesurfer] vertex-wise ROI analysis

[Clara Kühn]

Dear FreeSurfer experts,

is it possible to do a vertex-wise analysis on ROIs? When I extract the values 
per subject for (e.g.) the superior temporal gyrus grom the aparc file it is a 
pretty big region to get only one value. I would like to analyze it on a vertex 
level so I can see where exactly the effects are.

I'd be really happy for any suggestions!
Thank you
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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[Freesurfer] extract thickness values from clusters

[Clara Kühn]

Dear Freesurfer Experts,

I did a longitudinal 2 stage model and now I would like to extract the 
thickness and area values from significant clusters that survived the Monte 
Carlo correction.

As I understood from the various e-mails in the archives expressing the same 
request there is a file "something.y.ocn.dat" where those thickness values are 
supposedly stored for each cluster and each subject. However, this file 
included "the average value of each subject in each cluster" (as it states in 
the group comparison tutorial), meaning the -log10(pvalue).

I would like to show that the significant difference between two groups is 
driven by a certain group and to do that I want to display the thickness and 
area values of each cluster in bar graphs.

What could I do to receive these values?

Cheers, Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] white matter errors due to inhomogeneities (bright spots) in cortex

[Clara Kühn]

Hello Ben,

I am no expert, I can only talk from my experience. 
I've had similar images in my data. Those might be blood vessels or dura that 
were included in the surface. If they are included in the surface on more than 
5 slices and pretty well visible you could delete those voxels from the 
brainmask. From the looks of the attached screenshots however I wouldn't worry 
about the brainmask but rather remove a few voxels from the wm.mgz. Then you 
rerun the subject with the -wm flag and check again. If it is only on one or 
two slices, though, I wouldn't edit it at all. The surfaces are just not going 
to be perfect.

Hope I could help.
Clara


- Ursprüngliche Mail -
Von: "Benjamin Baird" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 1. September 2016 21:56:58
Betreff: [Freesurfer] white matter errors due to inhomogeneities (bright
spots) in cortex

Dear Freesurfer experts, 

We are currently working with some scans that were collected on a GE 3T 
scanner. The goal is to analyze cortical thickness. The scans seem to be 
relatively high quality with the exception that there are what appear to be 
inhomogeneities in the intensity of the gray matter (appears too bright in 
places), which is causing the WM to extend/jump into cortex (see attached 
image). We're wondering if there are any parameter adjustments to recon that 
might help with this as the errors occur frequently enough that fixing them all 
manually will be fairly cumbersome. This type of error doesn’t seem to be 
discussed very much in the available information on freesurfer quality control 
as far as we’ve seen. 
Thanks in advance for any advice you might be able to offer. 

Best regards, 
Ben 




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Re: [Freesurfer] REPOST: problem with Qdecrc file

[Clara Kühn]

Hi Doug,

I did that. I followed the tutorial and am now stuck at qdec where the .Qdecrc 
file doesn't do the trick and I can't choose the spc or anyother measure that I 
specified in that file. I opened qdec in the folder where I store the .Qdecrc 
and table files.

Any other ideas?
Cheers
Clara

- Ursprüngliche Mail -
Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 31. August 2016 15:57:25
Betreff: Re: [Freesurfer] REPOST: problem with Qdecrc file

Try long_mris_slopes


On 8/31/16 8:34 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I still don't seem to be able to choose spc and rate etc from the dropdown 
> menu in QDEC. Is there an option to perform the longitudinal 2 stage model in 
> the command line instead of QDEC?
>
> Thank you!
> Clara
>
> - Ursprüngliche Mail -
> Von: "ckuehn" <cku...@cbs.mpg.de>
> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Gesendet: Mittwoch, 17. August 2016 13:37:00
> Betreff: Re: [Freesurfer] REPOST: problem with Qdecrc file
>
> Hi Martin,
>
> I tried both. Neither of the options worked, though.
> I have created a subdirectory SUBJECTS_DIR/qdec2stage/ where I have my dat 
> file, the .Qdecrc, the level files etc. But when I start qdec in that folder, 
> load the data table and prepare everything I still can't choose spc (for 
> example) from the measures drop down menu.
>
> Is there any other way (e.g. through glmfit) to look at spc or does that only 
> work with qdec?
>
> Best, Clara
>
> - Ursprüngliche Mail -
> Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Gesendet: Freitag, 12. August 2016 17:28:52
> Betreff: Re: [Freesurfer] REPOST: problem with Qdecrc file
>
> Hi Clara,
> Try to start qdec in the same directory. If that fails create a qdec sub 
> directory underneath the subjects _dir and put the files there.
> Best Martin
>
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Re: [Freesurfer] REPOST: problem with Qdecrc file

[Clara Kühn]

Dear FreeSurfer experts,

I still don't seem to be able to choose spc and rate etc from the dropdown menu 
in QDEC. Is there an option to perform the longitudinal 2 stage model in the 
command line instead of QDEC?

Thank you!
Clara

- Ursprüngliche Mail -
Von: "ckuehn" 
An: "Freesurfer support list" 
Gesendet: Mittwoch, 17. August 2016 13:37:00
Betreff: Re: [Freesurfer] REPOST: problem with Qdecrc file

Hi Martin,

I tried both. Neither of the options worked, though.
I have created a subdirectory SUBJECTS_DIR/qdec2stage/ where I have my dat 
file, the .Qdecrc, the level files etc. But when I start qdec in that folder, 
load the data table and prepare everything I still can't choose spc (for 
example) from the measures drop down menu.

Is there any other way (e.g. through glmfit) to look at spc or does that only 
work with qdec?

Best, Clara

- Ursprüngliche Mail -
Von: "mreuter" 
An: "Freesurfer support list" 
Gesendet: Freitag, 12. August 2016 17:28:52
Betreff: Re: [Freesurfer] REPOST: problem with Qdecrc file

Hi Clara, 
Try to start qdec in the same directory. If that fails create a qdec sub 
directory underneath the subjects _dir and put the files there. 
Best Martin 

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Re: [Freesurfer] REPOST: problem with Qdecrc file

[Clara Kühn]

Hi Martin,

I tried both. Neither of the options worked, though.
I have created a subdirectory SUBJECTS_DIR/qdec2stage/ where I have my dat 
file, the .Qdecrc, the level files etc. But when I start qdec in that folder, 
load the data table and prepare everything I still can't choose spc (for 
example) from the measures drop down menu.

Is there any other way (e.g. through glmfit) to look at spc or does that only 
work with qdec?

Best, Clara

- Ursprüngliche Mail -
Von: "mreuter" 
An: "Freesurfer support list" 
Gesendet: Freitag, 12. August 2016 17:28:52
Betreff: Re: [Freesurfer] REPOST: problem with Qdecrc file

Hi Clara, 
Try to start qdec in the same directory. If that fails create a qdec sub 
directory underneath the subjects _dir and put the files there. 
Best Martin 

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[Freesurfer] REPOST: problem with Qdecrc file

[Clara Kühn]

Dear FreeSurfer experts,

I'm trying to run a 2stage Model in QDEC but I have troubles with incorporating 
the .Qdecrc file. Sadly the option of spc etc doesn't show up the Design tab 
when I want to chose a measure.

the file is in the same directory the table.dat file is in. What might be the 
problem?

Thank you for your help!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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[Freesurfer] problem with Qdecrc file

[Clara Kühn]

Dear FreeSurfer experts,

I'm trying to run a 2stage Model in QDEC but I have troubles with incorporating 
the .Qdecrc file. Sadly the option of spc etc doesn't show up the Design tab 
when I want to chose a measure.

the file is in the same directory the table.dat file is in. What might be the 
problem?

Thank you for your help!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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[Freesurfer] LME for surface area

[Clara Kühn]

Dear FreeSurfer Experts,

I'm following the LME tutorial to analyze my data. The example that is given in 
the tutorial is for a left hemispheric cortical thickness analysis. I would 
also like to look at surface area. Would I follow the same steps? At the point 
in the tutorial that uses the lme_mass_fit_Rgw command I have to specify a 
Distance type (euc or surf). How would I do that regarding surface area? Would 
I have to skip this step or is there a similar command or does it just work 
with different arguments? Unfortunately, surface area isn't mentioned in LME 
tutorial.

Thanks for your help!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] DeMean Flag

[Clara Kühn]

if I start a mris_glmfit via the command line the terminal outputs a line that 
it couldn't detect the DeMeanFlag and therefore will not do any demeaning.

Cheers 
Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Montag, 18. Juli 2016 23:46:20
Betreff: Re: [Freesurfer] DeMean Flag

The DeMeanFlag in what tool?

On 07/08/2016 05:16 AM, Clara Kühn wrote:
> Dear Freesurfer experts,
>
> is there an explanation somewhere for the DeMeanFlag? I can't find it in the 
> wiki but I would like to use it to demean my covariates for the GLM and LME.
>
> Cheers
> Clara
>

-- 
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
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[Freesurfer] LME contrasts

[Clara Kühn]

Dear FreeSurfer experts,

I am following the mass-univariate (spatiotemporal) model in the LME tutorial. 
My design matrix X has the following columns:
intercept, time, time², group1, group1*time, group1*time², group2, group2*time, 
group2*time², sex, age, mean_thickness

I actually have 3 groups but group1 and group2 in X are dummy coded.

I would like to check whether there are group differences in the quadratic term 
but I don't understand what this command expresses and how the contrast was 
formed:

CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)];

Could you please explain it on the example design matrix so I can adapt it to 
mine?

Thank you!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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[Freesurfer] DeMean Flag

[Clara Kühn]

Dear Freesurfer experts,

is there an explanation somewhere for the DeMeanFlag? I can't find it in the 
wiki but I would like to use it to demean my covariates for the GLM and LME.

Cheers
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] controlling for total gray matter volume

[Clara Kühn]

Do you know, if there are any publications concerning this matter? So far I've 
found only this 
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148852 that 
controls for tGM only for area and not CT.

Cheers Clara

- Ursprüngliche Mail -
Von: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Montag, 4. Juli 2016 15:37:57
Betreff: Re: [Freesurfer] controlling for total gray matter volume

sounds right to me
Bruce
On Mon, 4 Jul 2016, Clara Kühn wrote:

> I have decided now to not control for ICV or total gray matter volume when 
> looking at cortical thickness but to control for total gray matter volume 
> when looking at surface area. Does that sound about right?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Arkadiy Maksimovskiy" <arkad...@bu.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Samstag, 2. Juli 2016 18:36:51
> Betreff: Re: [Freesurfer] controlling for total gray matter volume
>
> Hi Clara,
>
> If I am understanding your question correctly, you don't need to control for 
> brain volume when looking at thickness analyses.
>
> See quote below from this link:
>
> http://www.freesurfer.net/fswiki/eTIV
>
> "Note that this correction is only useful in situations where the structure 
> scales with head size. Outside of this, correction just adds noise, or 
> provides inaccurate data. In the case of the measures from Freesurfer, one 
> would apply correction to the volume measures and not thickness measures. 
> This is because volume scales with head size which is mostly due to changes 
> in surface area, whereas thickness alone scales to a much less degree."
>
> Best,
> Arkadiy
>
> On Sat, Jul 2, 2016 at 12:00 PM, < freesurfer-requ...@nmr.mgh.harvard.edu > 
> wrote:
>
>
> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
> 1. controlling for total gray matter volume (Clara K?hn)
> 2. cotrolling for total gray matter volume (Clara K?hn)
>
>
> --
>
> Message: 1
> Date: Thu, 30 Jun 2016 15:19:43 +0200 (CEST)
> From: Clara K?hn < cku...@cbs.mpg.de >
> Subject: [Freesurfer] controlling for total gray matter volume
> To: Freesurfer support list < freesurfer@nmr.mgh.harvard.edu >
> Message-ID:
> < 600644700.119350.1467292783757.javamail.zim...@cbs.mpg.de >
> Content-Type: text/plain; charset=utf-8
>
> Dear FreeSurfer experts,
>
> I would like to look at longitudinal thickness data and want to control for 
> total gray matter volume. Should I use that information from the CROSS before 
> anything has been registered and smoothed or from the LONG after they have 
> been registered to the BASE?
> Also I was wondering if it is useful to control for total gray matter volume 
> when looking at surface area?
>
> Thanks for your help!
> Clara
>
>
> --
>
> Message: 2
> Date: Thu, 30 Jun 2016 15:01:06 +0200 (CEST)
> From: Clara K?hn < cku...@cbs.mpg.de >
> Subject: [Freesurfer] cotrolling for total gray matter volume
> To: Freesurfer support list < freesurfer@nmr.mgh.harvard.edu >
> Message-ID:
> < 1473114832.117985.1467291666701.javamail.zim...@cbs.mpg.de >
> Content-Type: text/plain; charset=utf-8
>
> Dear FreeSurfer experts,
>
> I would like to look at longitudinal thickness data and want to control for 
> total gray matter volume. Should I use that information from the CROSS before 
> anything has been registered and smoothed or from the LONG after they have 
> been registered to the BASE?
> Also I was wondering if it is useful to control for total gray matter volume 
> when looking at surface area?
>
> Thanks for your help!
> Clara
>
>
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Re: [Freesurfer] controlling for total gray matter volume

[Clara Kühn]

Ok, thanks!

- Ursprüngliche Mail -
Von: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Montag, 4. Juli 2016 15:37:57
Betreff: Re: [Freesurfer] controlling for total gray matter volume

sounds right to me
Bruce
On Mon, 4 Jul 2016, Clara Kühn wrote:

> I have decided now to not control for ICV or total gray matter volume when 
> looking at cotrical thickness but to control for total gray matter volume 
> when looking at surface area. Does that sound about right?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Arkadiy Maksimovskiy" <arkad...@bu.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Samstag, 2. Juli 2016 18:36:51
> Betreff: Re: [Freesurfer] controlling for total gray matter volume
>
> Hi Clara,
>
> If I am understanding your question correctly, you don't need to control for 
> brain volume when looking at thickness analyses.
>
> See quote below from this link:
>
> http://www.freesurfer.net/fswiki/eTIV
>
> "Note that this correction is only useful in situations where the structure 
> scales with head size. Outside of this, correction just adds noise, or 
> provides inaccurate data. In the case of the measures from Freesurfer, one 
> would apply correction to the volume measures and not thickness measures. 
> This is because volume scales with head size which is mostly due to changes 
> in surface area, whereas thickness alone scales to a much less degree."
>
> Best,
> Arkadiy
>
> On Sat, Jul 2, 2016 at 12:00 PM, < freesurfer-requ...@nmr.mgh.harvard.edu > 
> wrote:
>
>
> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
> Today's Topics:
>
> 1. controlling for total gray matter volume (Clara K?hn)
> 2. cotrolling for total gray matter volume (Clara K?hn)
>
>
> --
>
> Message: 1
> Date: Thu, 30 Jun 2016 15:19:43 +0200 (CEST)
> From: Clara K?hn < cku...@cbs.mpg.de >
> Subject: [Freesurfer] controlling for total gray matter volume
> To: Freesurfer support list < freesurfer@nmr.mgh.harvard.edu >
> Message-ID:
> < 600644700.119350.1467292783757.javamail.zim...@cbs.mpg.de >
> Content-Type: text/plain; charset=utf-8
>
> Dear FreeSurfer experts,
>
> I would like to look at longitudinal thickness data and want to control for 
> total gray matter volume. Should I use that information from the CROSS before 
> anything has been registered and smoothed or from the LONG after they have 
> been registered to the BASE?
> Also I was wondering if it is useful to control for total gray matter volume 
> when looking at surface area?
>
> Thanks for your help!
> Clara
>
>
> --
>
> Message: 2
> Date: Thu, 30 Jun 2016 15:01:06 +0200 (CEST)
> From: Clara K?hn < cku...@cbs.mpg.de >
> Subject: [Freesurfer] cotrolling for total gray matter volume
> To: Freesurfer support list < freesurfer@nmr.mgh.harvard.edu >
> Message-ID:
> < 1473114832.117985.1467291666701.javamail.zim...@cbs.mpg.de >
> Content-Type: text/plain; charset=utf-8
>
> Dear FreeSurfer experts,
>
> I would like to look at longitudinal thickness data and want to control for 
> total gray matter volume. Should I use that information from the CROSS before 
> anything has been registered and smoothed or from the LONG after they have 
> been registered to the BASE?
> Also I was wondering if it is useful to control for total gray matter volume 
> when looking at surface area?
>
> Thanks for your help!
> Clara
>
>
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Re: [Freesurfer] controlling for total gray matter volume

[Clara Kühn]

I have decided now to not control for ICV or total gray matter volume when 
looking at cotrical thickness but to control for total gray matter volume when 
looking at surface area. Does that sound about right?

Cheers, Clara

- Ursprüngliche Mail -
Von: "Arkadiy Maksimovskiy" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Samstag, 2. Juli 2016 18:36:51
Betreff: Re: [Freesurfer] controlling for total gray matter volume

Hi Clara, 

If I am understanding your question correctly, you don't need to control for 
brain volume when looking at thickness analyses. 

See quote below from this link: 

http://www.freesurfer.net/fswiki/eTIV 

"Note that this correction is only useful in situations where the structure 
scales with head size. Outside of this, correction just adds noise, or provides 
inaccurate data. In the case of the measures from Freesurfer, one would apply 
correction to the volume measures and not thickness measures. This is because 
volume scales with head size which is mostly due to changes in surface area, 
whereas thickness alone scales to a much less degree." 

Best, 
Arkadiy 

On Sat, Jul 2, 2016 at 12:00 PM, < freesurfer-requ...@nmr.mgh.harvard.edu > 
wrote: 


Send Freesurfer mailing list submissions to 
freesurfer@nmr.mgh.harvard.edu 

To subscribe or unsubscribe via the World Wide Web, visit 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
or, via email, send a message with subject or body 'help' to 
freesurfer-requ...@nmr.mgh.harvard.edu 

You can reach the person managing the list at 
freesurfer-ow...@nmr.mgh.harvard.edu 

When replying, please edit your Subject line so it is more specific 
than "Re: Contents of Freesurfer digest..." 


Today's Topics: 

1. controlling for total gray matter volume (Clara K?hn) 
2. cotrolling for total gray matter volume (Clara K?hn) 


-- 

Message: 1 
Date: Thu, 30 Jun 2016 15:19:43 +0200 (CEST) 
From: Clara K?hn < cku...@cbs.mpg.de > 
Subject: [Freesurfer] controlling for total gray matter volume 
To: Freesurfer support list < freesurfer@nmr.mgh.harvard.edu > 
Message-ID: 
< 600644700.119350.1467292783757.javamail.zim...@cbs.mpg.de > 
Content-Type: text/plain; charset=utf-8 

Dear FreeSurfer experts, 

I would like to look at longitudinal thickness data and want to control for 
total gray matter volume. Should I use that information from the CROSS before 
anything has been registered and smoothed or from the LONG after they have been 
registered to the BASE? 
Also I was wondering if it is useful to control for total gray matter volume 
when looking at surface area? 

Thanks for your help! 
Clara 


-- 

Message: 2 
Date: Thu, 30 Jun 2016 15:01:06 +0200 (CEST) 
From: Clara K?hn < cku...@cbs.mpg.de > 
Subject: [Freesurfer] cotrolling for total gray matter volume 
To: Freesurfer support list < freesurfer@nmr.mgh.harvard.edu > 
Message-ID: 
< 1473114832.117985.1467291666701.javamail.zim...@cbs.mpg.de > 
Content-Type: text/plain; charset=utf-8 

Dear FreeSurfer experts, 

I would like to look at longitudinal thickness data and want to control for 
total gray matter volume. Should I use that information from the CROSS before 
anything has been registered and smoothed or from the LONG after they have been 
registered to the BASE? 
Also I was wondering if it is useful to control for total gray matter volume 
when looking at surface area? 

Thanks for your help! 
Clara 

-- 
Clara K?hn, Phd Student 

Max-Planck-Institute for Human Cognitive and Brain Science 
Department of Neuropsychology 
Stephanstrasse 1A 
04103 Leipzig, Germany 

Phone: +49 341 - 9940 2271 
Fax: +49 341 - 9940 2260 
Web: www.cbs.mpg.de 
E-Mail: cku...@cbs.mpg.de 



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[Freesurfer] cotrolling for total gray matter volume

[Clara Kühn]

Dear FreeSurfer experts,

I would like to look at longitudinal thickness data and want to control for 
total gray matter volume. Should I use that information from the CROSS before 
anything has been registered and smoothed or from the LONG after they have been 
registered to the BASE? 
Also I was wondering if it is useful to control for total gray matter volume 
when looking at surface area?

Thanks for your help!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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[Freesurfer] controlling for total gray matter volume

[Clara Kühn]

Dear FreeSurfer experts,

I would like to look at longitudinal thickness data and want to control for 
total gray matter volume. Should I use that information from the CROSS before 
anything has been registered and smoothed or from the LONG after they have been 
registered to the BASE?
Also I was wondering if it is useful to control for total gray matter volume 
when looking at surface area?

Thanks for your help!
Clara
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[Freesurfer] REPOST: controlling for ICV in LME

[Clara Kühn]

Dear FreeSurfer experts,

I conducted a study with 3 groups of children (2 trainings, 1 control) and I 
want to analyze them longitudinally with LMEs. While preparing my data 2 topics 
came up that I would like to know more about.

A. controlling for ICV/mean thickness/surface area

1) I want to look at changes in cortical thickness and surface area at the 
whole brain level. Would I then have to control for mean thickness/ area, 
respectively, per parcellation? Or rather ICV?
2) Is it the same for looking at changes in thickness and area in different 
ROIs?
3) Since I have (up to) 3 scans per kid, do I include mean thickness/area/ICV 
for each scan or should I use it from baseline or a mean of all scans?

B. demeaning covariates

1) Is it necessary to demean the covariates? I have not seen any hints on the 
FS wiki pages about that yet.
2) Would I also have to demean the dependent variable (in my case whole brain 
cortical thickness/surface area)?

Thank you!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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dispose of the e-mail.

[Freesurfer] controlling for ICV in LME

[Clara Kühn]

Dear FreeSurfer experts,

I conducted a study with 3 groups of children (2 trainings, 1 control) and I 
want to analyze them longitudinally with LMEs. While preparing my data 2 topics 
came up that I would like to know more about.

A. controlling for ICV/mean thickness/surface area

1) I want to look at changes in cortical thickness and surface area at the 
whole brain level. Would I then have to control for mean thickness/ area, 
respectively, per parcellation? Or rather ICV?
2) Is it the same for looking at changes in thickness and area in different 
ROIs?
3) Since I have (up to) 3 scans per kid, do I include mean thickness/area/ICV 
for each scan or should I use it from baseline or a mean of all scans?

B. demeaning covariates

1) Is it necessary to demean the covariates? I have not seen any hints on the 
FS wiki pages about that yet.
2) Would I also have to demean the dependent variable (in my case whole brain 
cortical thickness/surface area)?

Thank you!
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] correlation with glm

[Clara Kühn]

I have and it's been very helpful. I'm not sure though where a correlation was 
specified in those examples.
If I understand it correctly, I have to set my groups to 0 and my covariate to 
1. The columns in my designamtrix look like this:

1male 1female 2male 2female 3male 3female 1male_behavior 1female_behavior 
2male_behavior 2female_behavior 3male_behavior 3female_behavior

So if I want to test the correlation between thickness and behavior across all 
groups the contrast would be this:
0 0 0 0 0 0 1 1 1 1 1 1
or would it have to be 1/3 instead of 1 because I have 3 groups? Or even 1/6 
because of my 3 groups with 2 levels each?

Thanks
Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 31. Mai 2016 19:18:40
Betreff: Re: [Freesurfer] correlation with glm

have you seen our worked-out examples?

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

On 05/31/2016 03:39 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I would like to correlate my thickness data with behavioral measures. Can I 
> do that with glmfit? If so, could you explain how to specify the contrast for 
> that?
> My fsgd file looks like this:
>
> GroupDescriptorFile 1
> Class 1male plus blue
> Class 1female plus red
> Class 2male circle blue
> Class 2female circle red
> Class 3male triangle blue
> Class 3female triangle red
> Variables age_sc1 Mottier
> Input subject1 1female 51.61 10
> Input subject2 1female 48.89 15
> ...
>
> Thank you!
> Clara
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>
>

-- 
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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
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[Freesurfer] correlation with glm

[Clara Kühn]

Dear FreeSurfer experts,

I would like to correlate my thickness data with behavioral measures. Can I do 
that with glmfit? If so, could you explain how to specify the contrast for that?
My fsgd file looks like this:

GroupDescriptorFile 1  
Class 1male plus blue
Class 1female plus red
Class 2male circle blue
Class 2female circle red
Class 3male triangle blue
Class 3female triangle red
Variables age_sc1 Mottier  
Input subject1 1female 51.61 10
Input subject2 1female 48.89 15
...

Thank you!
Clara
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Re: [Freesurfer] glmdir question

[Clara Kühn]

Dear FreeSurfer experts,

I would like to correlate my thickness data with behavioral measures. Can I do 
that with glmfit? If so, could you explain how to specify the contrast for that?
My fsgd file looks like this:

GroupDescriptorFile 1  
Class 1male plus blue
Class 1female plus red
Class 2male circle blue
Class 2female circle red
Class 3male triangle blue
Class 3female triangle red
Variables age_sc1 Mottier  
Input subject1 1female 51.61 10
Input subject2 1female 48.89 15
...

Thank you!
Clara
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Re: [Freesurfer] glmdir question

[Clara Kühn]

Hm. It either doesn't recognize the --no-y flag (no matter at which position) 
or it doesn't recognize the --mczsim flag.

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 26. Mai 2016 18:58:39
Betreff: Re: [Freesurfer] glmdir question

Try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim


On 05/26/2016 12:53 PM, Clara Kühn wrote:
> Hi Doug,
>
> I ran this command with the --no-y Flag:
>   
> mri_glmfit-sim --glmdir 
> $SUBJECTS_DIR/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir
>  --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 abs --cwp 0.05 
> --2spaces --no-y
>
> and got the following error message:
>
> ERROR: Flag --no-y unrecognized.
> --glmdir 
> /scr/etsch2/kids/ct/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir
>  --cache-dir /scr/etsch2/kids/ct/average/mult-comp-cor --cache 3.0 abs --cwp 
> 0.05 --2spaces --no-y
>
> Does the flag need to be at a certain position?
> Thanks for your help
> Clara
>
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Donnerstag, 26. Mai 2016 17:53:47
> Betreff: Re: [Freesurfer] glmdir question
>
> By default it will compute a table. The rows of the table are each
> subject. The columns are the clusters. Each cell is the mean of the
> input for that subject over that cluster. It needs the input data to do
> this.
>
> On 05/26/2016 11:18 AM, Clara Kühn wrote:
>> I thought it had to be there because when I don't copy it into the glmdir I 
>> get an error message that it can't find the mgh in said glmdir.
>> I'm gonna try running it with the flag you mentioned.
>> What does it mean, though, that it won't compute means over the clusters?
>>
>> - Ursprüngliche Mail -
>> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
>> An: freesurfer@nmr.mgh.harvard.edu
>> Gesendet: Donnerstag, 26. Mai 2016 17:15:41
>> Betreff: Re: [Freesurfer] glmdir question
>>
>> What is it doing in your glmdir? Usually you'd have it in another
>> location when running mri_glmfit (which creates the glmdir). In any
>> case, you can run it with --no-y and it will not look for the input file
>> (and will not compute means over the clusters).
>>
>> On 5/26/16 8:56 AM, Clara Kühn wrote:
>>> Dear FreeSurfer Experts,
>>>
>>> when running the Monte Carlo correction on a GLM I specify this command:
>>> mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp  0.05 
>>> --2spaces
>>>
>>> This assumes that my mgh file that I used as input for the GLM is in 
>>> lh.gender_age.glmdir. That means though, that everytime I calculate a GLM 
>>> and create a new folder for this GLM I have to copy the mgh file into the 
>>> glmdir to run the Monte Carlo correction. Is there a way to specify where 
>>> that mgh is located so that I don't have a bunch of copies of it in all my 
>>> glmdirs?
>>>
>>> Thanks for your help!
>>> Cheers
>>> Clara
>>>
>> ___
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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it is
>> addressed. If you believe this e-mail was sent to you in error and the e-mail
>> contains patient information, please contact the Partners Compliance 
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>> error
>> but does not contain patient information, please contact the sender and 
>> properly
>> dispose of the e-mail.
>>
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>>
>>

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

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

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Re: [Freesurfer] glmdir question

[Clara Kühn]

Hi Doug,

I ran this command with the --no-y Flag:
 
mri_glmfit-sim --glmdir 
$SUBJECTS_DIR/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir
 --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 abs --cwp 0.05 
--2spaces --no-y

and got the following error message:

ERROR: Flag --no-y unrecognized.
--glmdir 
/scr/etsch2/kids/ct/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir
 --cache-dir /scr/etsch2/kids/ct/average/mult-comp-cor --cache 3.0 abs --cwp 
0.05 --2spaces --no-y

Does the flag need to be at a certain position?
Thanks for your help
Clara


- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 26. Mai 2016 17:53:47
Betreff: Re: [Freesurfer] glmdir question

By default it will compute a table. The rows of the table are each 
subject. The columns are the clusters. Each cell is the mean of the 
input for that subject over that cluster. It needs the input data to do 
this.

On 05/26/2016 11:18 AM, Clara Kühn wrote:
> I thought it had to be there because when I don't copy it into the glmdir I 
> get an error message that it can't find the mgh in said glmdir.
> I'm gonna try running it with the flag you mentioned.
> What does it mean, though, that it won't compute means over the clusters?
>
> - Ursprüngliche Mail -
> Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Donnerstag, 26. Mai 2016 17:15:41
> Betreff: Re: [Freesurfer] glmdir question
>
> What is it doing in your glmdir? Usually you'd have it in another
> location when running mri_glmfit (which creates the glmdir). In any
> case, you can run it with --no-y and it will not look for the input file
> (and will not compute means over the clusters).
>
> On 5/26/16 8:56 AM, Clara Kühn wrote:
>> Dear FreeSurfer Experts,
>>
>> when running the Monte Carlo correction on a GLM I specify this command:
>> mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp  0.05 
>> --2spaces
>>
>> This assumes that my mgh file that I used as input for the GLM is in 
>> lh.gender_age.glmdir. That means though, that everytime I calculate a GLM 
>> and create a new folder for this GLM I have to copy the mgh file into the 
>> glmdir to run the Monte Carlo correction. Is there a way to specify where 
>> that mgh is located so that I don't have a bunch of copies of it in all my 
>> glmdirs?
>>
>> Thanks for your help!
>> Cheers
>> Clara
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

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Re: [Freesurfer] glmdir question

[Clara Kühn]

I thought it had to be there because when I don't copy it into the glmdir I get 
an error message that it can't find the mgh in said glmdir.
I'm gonna try running it with the flag you mentioned.
What does it mean, though, that it won't compute means over the clusters? 

- Ursprüngliche Mail -
Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 26. Mai 2016 17:15:41
Betreff: Re: [Freesurfer] glmdir question

What is it doing in your glmdir? Usually you'd have it in another 
location when running mri_glmfit (which creates the glmdir). In any 
case, you can run it with --no-y and it will not look for the input file 
(and will not compute means over the clusters).

On 5/26/16 8:56 AM, Clara Kühn wrote:
> Dear FreeSurfer Experts,
>
> when running the Monte Carlo correction on a GLM I specify this command:
> mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp  0.05 
> --2spaces
>
> This assumes that my mgh file that I used as input for the GLM is in 
> lh.gender_age.glmdir. That means though, that everytime I calculate a GLM and 
> create a new folder for this GLM I have to copy the mgh file into the glmdir 
> to run the Monte Carlo correction. Is there a way to specify where that mgh 
> is located so that I don't have a bunch of copies of it in all my glmdirs?
>
> Thanks for your help!
> Cheers
> Clara
>

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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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[Freesurfer] glmdir question

[Clara Kühn]

Dear FreeSurfer Experts,

when running the Monte Carlo correction on a GLM I specify this command:
mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp  0.05 --2spaces

This assumes that my mgh file that I used as input for the GLM is in 
lh.gender_age.glmdir. That means though, that everytime I calculate a GLM and 
create a new folder for this GLM I have to copy the mgh file into the glmdir to 
run the Monte Carlo correction. Is there a way to specify where that mgh is 
located so that I don't have a bunch of copies of it in all my glmdirs?

Thanks for your help!
Cheers
Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] correcting mri_glmfit results

[Clara Kühn]

How would I stack them? I found --do-stack only as flag during the registering 
and smoothing but not as a command itself.
Thanks, 
Clara


- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 14. April 2016 18:19:53
Betreff: Re: [Freesurfer] correcting mri_glmfit results

They are doing the same thing. If you stack the 
lh.thickness.fwhm10.87kids_template.mgh together into one file you 
should get the same thing as the output of mris_preproc. With 
mris_preproc, you have to keep track of the order of the subjects as 
specified in the --f or --fsgd options

On 04/14/2016 12:08 PM, Clara Kühn wrote:
> Hi Martin,
>
> thanks for your reply.
>
> I have two further questions on that matter:
>
> 1. I opened the stacked file (lh.thickness_sm10.mgh) in matlab but there is 
> no column for subject-id or anything to give me a hint which line is which 
> subject. Is there a way to find that out? Is it in the same order as the 
> subjects in the qdec table I gave mris_preproc as input?
>
> 2. I compared the output of mris_preproc and mris_surf2surf with the 
> recon-all --qcache. They seem to be doing different things judging by the 
> output but in the terminal it tells me that --qcache is also using preproc 
> and surf2surf. However with --qcache I get the smoothed registration for each 
> measure per subject (e.g. lh.thickness.fwhm10.87kids_template.mgh) and with 
> preproc and surf2surf I get the stacked file (i.e. lh.thickness_sm10.mgh). 
> Can you tell me what the difference between those two processes is? Are they 
> overlapping in some steps or something like that?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Gesendet: Mittwoch, 13. April 2016 16:39:18
> Betreff: Re: [Freesurfer] correcting mri_glmfit results
>
> Hi Clara,
> You need to register and smooth again for only the first time point.
> You could also open the full stack in Matlab, select the entries of your 
> first time point and write it out again.
>
> Best Martin
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] correcting mri_glmfit results

[Clara Kühn]

Awesome, thank you!
Cheers, Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 14. April 2016 18:19:53
Betreff: Re: [Freesurfer] correcting mri_glmfit results

They are doing the same thing. If you stack the 
lh.thickness.fwhm10.87kids_template.mgh together into one file you 
should get the same thing as the output of mris_preproc. With 
mris_preproc, you have to keep track of the order of the subjects as 
specified in the --f or --fsgd options

On 04/14/2016 12:08 PM, Clara Kühn wrote:
> Hi Martin,
>
> thanks for your reply.
>
> I have two further questions on that matter:
>
> 1. I opened the stacked file (lh.thickness_sm10.mgh) in matlab but there is 
> no column for subject-id or anything to give me a hint which line is which 
> subject. Is there a way to find that out? Is it in the same order as the 
> subjects in the qdec table I gave mris_preproc as input?
>
> 2. I compared the output of mris_preproc and mris_surf2surf with the 
> recon-all --qcache. They seem to be doing different things judging by the 
> output but in the terminal it tells me that --qcache is also using preproc 
> and surf2surf. However with --qcache I get the smoothed registration for each 
> measure per subject (e.g. lh.thickness.fwhm10.87kids_template.mgh) and with 
> preproc and surf2surf I get the stacked file (i.e. lh.thickness_sm10.mgh). 
> Can you tell me what the difference between those two processes is? Are they 
> overlapping in some steps or something like that?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Gesendet: Mittwoch, 13. April 2016 16:39:18
> Betreff: Re: [Freesurfer] correcting mri_glmfit results
>
> Hi Clara,
> You need to register and smooth again for only the first time point.
> You could also open the full stack in Matlab, select the entries of your 
> first time point and write it out again.
>
> Best Martin
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

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Re: [Freesurfer] correcting mri_glmfit results

[Clara Kühn]

Hi Martin,

thanks for your reply.

I have two further questions on that matter:

1. I opened the stacked file (lh.thickness_sm10.mgh) in matlab but there is no 
column for subject-id or anything to give me a hint which line is which 
subject. Is there a way to find that out? Is it in the same order as the 
subjects in the qdec table I gave mris_preproc as input?

2. I compared the output of mris_preproc and mris_surf2surf with the recon-all 
--qcache. They seem to be doing different things judging by the output but in 
the terminal it tells me that --qcache is also using preproc and surf2surf. 
However with --qcache I get the smoothed registration for each measure per 
subject (e.g. lh.thickness.fwhm10.87kids_template.mgh) and with preproc and 
surf2surf I get the stacked file (i.e. lh.thickness_sm10.mgh). Can you tell me 
what the difference between those two processes is? Are they overlapping in 
some steps or something like that?

Cheers, Clara

- Ursprüngliche Mail -
Von: "mreuter" 
An: "Freesurfer support list" 
Gesendet: Mittwoch, 13. April 2016 16:39:18
Betreff: Re: [Freesurfer] correcting mri_glmfit results

Hi Clara, 
You need to register and smooth again for only the first time point. 
You could also open the full stack in Matlab, select the entries of your first 
time point and write it out again. 

Best Martin 

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Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

[Clara Kühn]

Thank you!

- Ursprüngliche Mail -
Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 13. April 2016 16:46:19
Betreff: Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

In most neuroimaging, people use p<.01 (sig threshold > 2). It is more 
important to have a more stringent threshold when using gaussian random 
fields because the assumptions built into it. Since we use simulations 
directly, we don't have problems with those assumptions and so I think 
you can go down to p<.05 (sig>1.3). Other than that, there are not good 
guidelines.

On 4/13/16 8:36 AM, Clara Kühn wrote:
> Hi Doug,
>
> thanks for your reply. It made things a lot clearer. I totally understand 
> that you're probably receiving more than one cry for help per day.
>
> What would you say are the conventions for picking a threshold for analyses 
> on structural data?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 13. April 2016 00:15:41
> Betreff: Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC
>
> sorry, I could have sworn that I answered this one
>
> On 04/12/2016 08:57 AM, Clara Kühn wrote:
>> Dear FreeSurfer experts,
>>
>> for the analysis in QDEC I created my own Monte Carlo correction.
>> My questions relate to the threshold option.
>>
>> 1. Would I use neg if I have mostly blue clusters in the QDEC display and 
>> pos if I have mostly red clusters?
> No, you would use neg when you have an apriori assumption that your
> effect is going to be negative. Once you look at the results, it is no
> long apriori
>> 2. When do I use abs?
> If you do not have an apriori assumption about the sign of the effect
>> 3. I compared the neg option at different thresholds (1.3, 2.0 and 2.3) and 
>> I get different clusters:
>> 1.3 (=.05)
>> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow  
>>   CWPHi   NVtxs   Annot
>>  1   -2.669   76591   1148.00 -6.7   14.5   62.7  0.00880  
>> 0.00760  0.01000  1600  superiorfrontal
>>  2   -2.443   91912   2128.78-10.3   55.3  -23.5  0.00010  
>> 0.0  0.00020  2971  medialorbitofrontal
>>
>> 2.0 (=.01)
>> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow  
>>   CWPHi   NVtxs   Annot
>>  1   -3.289   92754420.03-36.5   57.0  -21.0  0.02140  
>> 0.01960  0.02330   571  parsorbitalis
>>  2   -2.669   76591428.11 -6.7   14.5   62.7  0.01940  
>> 0.01760  0.02120   604  superiorfrontal
>>
>> 2.3 (=.005)
>> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow  
>>   CWPHi   NVtxs   Annot
>>  1   -3.289   92754314.80-36.5   57.0  -21.0  0.01900  
>> 0.01730  0.02080   410  parsorbitalis
>>
>> Technically, if parsorbitalis is significant at .01 and .005, shouldn't it 
>> also be significant at .05? I've compared the clusters in freeview and the 
>> superiorfrontal is the same cluster in both 1.3 and 2.0. The parsorbitalis 
>> and the medialorbitofrontal clusters are completely different, not even 
>> closely overlapping.
> You are confusing the two types of thresholds. The voxel-wise threshold
> that you are changing defines what is and is not a cluster. As you
> change it clusters will change size. As you make it more liberal, you
> make it more likely that you see a cluster of a certain size by chance
> (ie, the p-value for the cluster gets worse). So as you make the
> threshold more liberal, there are two competing effects: (1) the cluster
> gets bigger, and (2) the p-value of a cluster of a given fixed size gets
> worse. If the cluster size does not increase enough to overcome the
> second effect, then the cluster p-value will get worse. It is just very
> complicated.
>
>> Do you have any idea why that is and what it does differently?
>> Thank you!
>> Cheers, Clara
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>

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[Freesurfer] correcting mri_glmfit results

[Clara Kühn]

Dear FreeSurfer experts,

I'm trying to run a mri_glmfit on my first time point (out of 3). I ran the glm 
with this:
mri_glmfit --table $SUBJECTS_DIR/aparcs_stats_sc1.txt --fsgd 
$SUBJECTS_DIRfsgd_sc1.txt --C $SUBJECTS_DIR/group.mtx --surf 87kids_template lh 
--cortex --glmdir $SUBJECTS_DIR/glm/lh.thick_group.glmdir

So far so good :)

Now when I try to apply the Monte Carlo correction with this:
mri_glmfit-sim --glmdir $SUBJECTS_DIR/qdec/87kids/glm/lh.thick_group.glmdir 
--cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 neg --cwp 0.05 
--2spaces

I get the error "fwhm: Undefined variable."

So I tried to run the glmfit with the --y flag and use the 
lh.thickness_sm10.mgh file but I created that when registering and smoothing 
ALL my time points to the template, so I get this error: "ERROR: dimension 
mismatch between y and X. y has 224 inputs, X has 72 rows."

I have looked at mri_glmfit-sim --help but there seems to be no flag for fwhm 
only an overwriting one.

Should I register and smooth the data again for the separate time points or is 
there another way to deal with that?
What could I do to correct my glm data?

Cheers, Clara
-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

[Clara Kühn]

Hi Doug, 

thanks for your reply. It made things a lot clearer. I totally understand that 
you're probably receiving more than one cry for help per day.

What would you say are the conventions for picking a threshold for analyses on 
structural data? 

Cheers, Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 13. April 2016 00:15:41
Betreff: Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

sorry, I could have sworn that I answered this one

On 04/12/2016 08:57 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> for the analysis in QDEC I created my own Monte Carlo correction.
> My questions relate to the threshold option.
>
> 1. Would I use neg if I have mostly blue clusters in the QDEC display and pos 
> if I have mostly red clusters?
No, you would use neg when you have an apriori assumption that your 
effect is going to be negative. Once you look at the results, it is no 
long apriori
>
> 2. When do I use abs?
If you do not have an apriori assumption about the sign of the effect
>
> 3. I compared the neg option at different thresholds (1.3, 2.0 and 2.3) and I 
> get different clusters:
> 1.3 (=.05)
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow   
>  CWPHi   NVtxs   Annot
> 1   -2.669   76591   1148.00 -6.7   14.5   62.7  0.00880  0.00760 
>  0.01000  1600  superiorfrontal
> 2   -2.443   91912   2128.78-10.3   55.3  -23.5  0.00010  0.0 
>  0.00020  2971  medialorbitofrontal
>
> 2.0 (=.01)
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow   
>  CWPHi   NVtxs   Annot
> 1   -3.289   92754420.03-36.5   57.0  -21.0  0.02140  0.01960 
>  0.02330   571  parsorbitalis
> 2   -2.669   76591428.11 -6.7   14.5   62.7  0.01940  0.01760 
>  0.02120   604  superiorfrontal
>
> 2.3 (=.005)
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow   
>  CWPHi   NVtxs   Annot
> 1   -3.289   92754314.80-36.5   57.0  -21.0  0.01900  0.01730 
>  0.02080   410  parsorbitalis
>
> Technically, if parsorbitalis is significant at .01 and .005, shouldn't it 
> also be significant at .05? I've compared the clusters in freeview and the 
> superiorfrontal is the same cluster in both 1.3 and 2.0. The parsorbitalis 
> and the medialorbitofrontal clusters are completely different, not even 
> closely overlapping.
You are confusing the two types of thresholds. The voxel-wise threshold 
that you are changing defines what is and is not a cluster. As you 
change it clusters will change size. As you make it more liberal, you 
make it more likely that you see a cluster of a certain size by chance 
(ie, the p-value for the cluster gets worse). So as you make the 
threshold more liberal, there are two competing effects: (1) the cluster 
gets bigger, and (2) the p-value of a cluster of a given fixed size gets 
worse. If the cluster size does not increase enough to overcome the 
second effect, then the cluster p-value will get worse. It is just very 
complicated.

>
> Do you have any idea why that is and what it does differently?
> Thank you!
> Cheers, Clara
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

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[Freesurfer] REPOST: Monte Carlo correction in QDEC

[Clara Kühn]

Dear FreeSurfer experts,

for the analysis in QDEC I created my own Monte Carlo correction.
My questions relate to the threshold option.

1. Would I use neg if I have mostly blue clusters in the QDEC display and pos 
if I have mostly red clusters?

2. When do I use abs?

3. I compared the neg option at different thresholds (1.3, 2.0 and 2.3) and I 
get different clusters:
1.3 (=.05)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxs   Annot
   1   -2.669   76591   1148.00 -6.7   14.5   62.7  0.00880  0.00760  
0.01000  1600  superiorfrontal
   2   -2.443   91912   2128.78-10.3   55.3  -23.5  0.00010  0.0  
0.00020  2971  medialorbitofrontal

2.0 (=.01)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxs   Annot
   1   -3.289   92754420.03-36.5   57.0  -21.0  0.02140  0.01960  
0.02330   571  parsorbitalis
   2   -2.669   76591428.11 -6.7   14.5   62.7  0.01940  0.01760  
0.02120   604  superiorfrontal

2.3 (=.005)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxs   Annot
   1   -3.289   92754314.80-36.5   57.0  -21.0  0.01900  0.01730  
0.02080   410  parsorbitalis

Technically, if parsorbitalis is significant at .01 and .005, shouldn't it also 
be significant at .05? I've compared the clusters in freeview and the 
superiorfrontal is the same cluster in both 1.3 and 2.0. The parsorbitalis and 
the medialorbitofrontal clusters are completely different, not even closely 
overlapping.

Do you have any idea why that is and what it does differently?
Thank you!
Cheers, Clara
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[Freesurfer] Monte Carlo correction in QDEC

[Clara Kühn]

Dear FreeSurfer experts,

for the analysis in QDEC I created my own Monte Carlo correction.
My questions relate to the threshold option.

1. Would I use neg if I have mostly blue clusters in the QDEC display and pos 
if I have mostly red clusters?

2. When do I use abs?

3. I compared the neg option at different thresholds (1.3, 2 and 2.3) and I get 
different clusters:
1.3 (=.05)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxs   Annot
   1   -2.669   76591   1148.00 -6.7   14.5   62.7  0.00880  0.00760  
0.01000  1600  superiorfrontal
   2   -2.443   91912   2128.78-10.3   55.3  -23.5  0.00010  0.0  
0.00020  2971  medialorbitofrontal

2.0 (=.01)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxs   Annot
   1   -3.289   92754420.03-36.5   57.0  -21.0  0.02140  0.01960  
0.02330   571  parsorbitalis
   2   -2.669   76591428.11 -6.7   14.5   62.7  0.01940  0.01760  
0.02120   604  superiorfrontal

2.3 (=.005)
# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
CWPHi   NVtxs   Annot
   1   -3.289   92754314.80-36.5   57.0  -21.0  0.01900  0.01730  
0.02080   410  parsorbitalis

Technically, if parsorbitalis is significant at .01 and .005, shouldn't it also 
be significant at .05? I've compared the clusters in freeview and the 
superiorfrontal is the same cluster in both 1.3 and 2.0. The parsorbitalis and 
the medialorbitofrontal clusters are completely different, not even closely 
overlapping.

Do you have any idea why that is and what it does differently?
Thank you!
Cheers, Clara
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Re: [Freesurfer] REPOST: QDEC analysis

[Clara Kühn]

That's what I feared. But ok, I'll try that.
Thank you!

- Ursprüngliche Mail -
Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Freitag, 8. April 2016 14:55:42
Betreff: Re: [Freesurfer] REPOST: QDEC analysis

Hi Clara,

I think the message is correct and Qdec can only do 2 levels. Qdec is 
rather limited. You need to use mri_glmfit for that.

Best, Martin

On 04/08/2016 08:14 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I am trying to analyze some single time points of my longitudinal data in 
> QDEC. I have 3 groups and created a file for the discrete factor "group" with 
> three levels (1,2 and 3). I have done the same for gender (with 2 levels). 
> The analysis with gender works just fine but when I try to use group as a 
> factor I get an error message that factor 1 must have 2 levels:
>
> SUBJECTS_DIR is '/scr/etsch2/kids/ct'
> ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
> ninputs = 72
> Checking inputs
> nframestot = 72
> Allocing output
> Done allocing
> nframes = 72
> Writing to /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh
> gdfReadHeader: reading 
> /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd
> INFO: gd2mtx_method is dods
> Reading source surface /scr/etsch2/kids/ct/87kids_template/surf/lh.white
> ERROR: no contrasts specified.
> Error in Analyze: command failed: mri_glmfit --y 
> /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh --fsgd 
> /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd dods --glmdir 
> /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1 --surf 87kids_template lh
>
> In the tutorial it doesn't state that QDEC has to have discrete factors with 
> 2 levels only.
> Am I doing something wrong or is there a work-around for that?
>
> Cheers, Clara
> ___
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> Freesurfer@nmr.mgh.harvard.edu
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>
>

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

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[Freesurfer] REPOST: QDEC analysis

[Clara Kühn]

Dear FreeSurfer experts,

I am trying to analyze some single time points of my longitudinal data in QDEC. 
I have 3 groups and created a file for the discrete factor "group" with three 
levels (1,2 and 3). I have done the same for gender (with 2 levels). The 
analysis with gender works just fine but when I try to use group as a factor I 
get an error message that factor 1 must have 2 levels:

SUBJECTS_DIR is '/scr/etsch2/kids/ct'
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
ninputs = 72
Checking inputs
nframestot = 72
Allocing output
Done allocing
nframes = 72
Writing to /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh
gdfReadHeader: reading 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd
INFO: gd2mtx_method is dods
Reading source surface /scr/etsch2/kids/ct/87kids_template/surf/lh.white
ERROR: no contrasts specified.
Error in Analyze: command failed: mri_glmfit --y 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh --fsgd 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd dods --glmdir 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1 --surf 87kids_template lh

In the tutorial it doesn't state that QDEC has to have discrete factors with 2 
levels only.
Am I doing something wrong or is there a work-around for that?

Cheers, Clara
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[Freesurfer] Fwd: QDEC analysis

[Clara Kühn]

Dear FreeSurfer experts,

I am trying to analyze some single time points of my longitudinal data in QDEC. 
I have 3 groups and created a file for the discrete factor "group" with three 
levels (1,2 and 3). I have done the same for gender (with 2 levels). The 
analysis with gender works just fine but when I try to use group as a factor I 
get an error message that factor 1 must have 2 levels:

SUBJECTS_DIR is '/scr/etsch2/kids/ct'
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
ninputs = 72
Checking inputs
nframestot = 72
Allocing output
Done allocing
nframes = 72
Writing to /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh
gdfReadHeader: reading 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd
INFO: gd2mtx_method is dods
Reading source surface /scr/etsch2/kids/ct/87kids_template/surf/lh.white
ERROR: no contrasts specified.
Error in Analyze: command failed: mri_glmfit --y 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh --fsgd 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd dods --glmdir 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1 --surf 87kids_template lh

In the tutorial it doesn't state that QDEC has to have discrete factors with 2 
levels only.
Am I doing something wrong or is there a work-around for that maybe?

Cheers, Clara
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[Freesurfer] QDEC analysis

[Clara Kühn]

Dear FreeSurfer experts,

I am trying to analyze some single time points of my longitudinal data in QDEC. 
I have 3 groups and created a file for the discrete factor "group" with three 
levels (1,2 and 3). I have done the same for gender (with 2 levels). The 
analysis with gender works just fine but when I try to use group as a factor I 
get an error message that factor 1 must have 2 levels:

SUBJECTS_DIR is '/scr/etsch2/kids/ct'
ERROR: QdecGlmDesign::GenerateContrasts: factor 1 must have 2 levels
ninputs = 72
Checking inputs
nframestot = 72
Allocing output
Done allocing
nframes = 72
Writing to /scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh
gdfReadHeader: reading 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd
INFO: gd2mtx_method is dods
Reading source surface /scr/etsch2/kids/ct/87kids_template/surf/lh.white
ERROR: no contrasts specified.
Error in Analyze: command failed: mri_glmfit --y 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/y.mgh --fsgd 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1/qdec.fsgd dods --glmdir 
/scr/etsch2/kids/ct/qdec/lh.thick10_groupdiffsc1 --surf 87kids_template lh

In the tutorial it doesn't state that QDEC has to have discrete factors with 2 
levels only.
Am I doing something wrong or is there a work-around for that maybe?

Cheers, Clara
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Re: [Freesurfer] REPOST: registering longitudinal data to template

[Clara Kühn]

So, because mris_preproc does not already try to fit the data we use that for 
LMEs because that's where different model fits are then specified.
Thanks a lot!

- Ursprüngliche Mail -
Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Donnerstag, 24. März 2016 18:18:58
Betreff: Re: [Freesurfer] REPOST: registering longitudinal data to template

Hi Clara,

long_mris_slopes is for the 2 stage approach. It computes a linear fit 
(within each subject) across time (using the base space), then it maps 
the results to the template (fsaverage) and applies smoothing. It can 
compute rate (slope of linear fit) or some percent change measures, also 
the average across time.

mris_preproc is a tool to stack and map data to the global template 
(fsaverage) and apply smoothing etc. It does not perform any fitting.

Best, Martin

On 03/24/2016 12:44 PM, Clara Kühn wrote:
> Thank you, Martin! That clears things up a lot!
>
> Could you explain what the difference is between the commands 
> long_mris_slopes and mris_preproc? As far as I understand they give you a 
> different output. But what do they do differently in respect to mapping 
> longitudinal data?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Gesendet: Mittwoch, 23. März 2016 19:01:42
> Betreff: Re: [Freesurfer] REPOST: registering longitudinal data to template
>
> Hi Clara,
>
> 1) You'd create a different table for your time point with fsid being
> the longitudinal directories s1.long.sbase , no fsid-base column. then
> you can map and stack these using cross sectional commands (mris_preproc
> --qdec  ...)
> 2) You should use Qdec or glm_fit for cross sectional analysis
> 3) Yes, only for 2 stage model, so don't use it (for long you use LME
> anyway and for cross see 2))
> 4) that commands create a table with one entry for each subject
> (referring to the base), this is also for 2 stage model (the second
> stage works on a subject by subject basis)
> 5) the -qcache in recon all maps and smoothes surface data to the
> template, so that it is available later. You can do that even on the
> long runs, or you can just manually map ans smooth things with preproc.
> 6) A different preproc call using a fsgd file rather than a qdec table.
> see the glm_fit tutorial for these things.
>
> Best, Martin
>
> On 03/23/2016 12:28 PM, Clara Kühn wrote:
>> Dear FreeSurfer experts,
>>
>> I would like to analyze my longitudinal data also cross-sectionally at 
>> single time points. I am a little confused as to how to register my data to 
>> the template and smooth it accordingly.
>>
>> So far, I have registered my longitudinal data to my template to use in LMEs 
>> with this command:
>> mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target 30kids_template 
>> --hemi lh --meas thickness --out lh.thickness.mg
>>
>> and then smoothed it with this command:
>> mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval 
>> lh.thickness_sm10.mgh --fwhm-trg 10 --cortex  --noreshape
>>
>> (1) Do I have to do it once with a cross-sectional command and once with a 
>> longitudinal command?
>> (2) Should I do the cross-sectional analyses in QDEC or with LME?
>>
>> Now the question is what these other commands are for?
>>
>> (3) long_mris_slopes --qdec ct/qdec/long.qdec.table.dat --meas thickness 
>> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time 
>> years --qcache kids_template --sd $SUBJECTS_DIR
>> --> I understood this is only for Two-Stage-Models, is that correct?
>>
>> (4) long_qdec_table --qdec qdec/long.qdec.table.dat --cross --out 
>> qdec/cross.qdec.table.dat
>>
>> (5) recon-all -s name -qcache -target  name_of_template
>>
>> (6) mris_preproc --fsgd gender_age.fsgd --cache-in 
>> thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out 
>> lh.gender_age.thickness.10.mgh
>>
>>
>> Please help clear up my confusion :)
>> Thanks in advance,
>> Clara
>>
>>
>>

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

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Re: [Freesurfer] REPOST: registering longitudinal data to template

[Clara Kühn]

Thank you, Martin! That clears things up a lot!

Could you explain what the difference is between the commands long_mris_slopes 
and mris_preproc? As far as I understand they give you a different output. But 
what do they do differently in respect to mapping longitudinal data?

Cheers, Clara

- Ursprüngliche Mail -
Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Mittwoch, 23. März 2016 19:01:42
Betreff: Re: [Freesurfer] REPOST: registering longitudinal data to template

Hi Clara,

1) You'd create a different table for your time point with fsid being 
the longitudinal directories s1.long.sbase , no fsid-base column. then 
you can map and stack these using cross sectional commands (mris_preproc 
--qdec  ...)
2) You should use Qdec or glm_fit for cross sectional analysis
3) Yes, only for 2 stage model, so don't use it (for long you use LME 
anyway and for cross see 2))
4) that commands create a table with one entry for each subject 
(referring to the base), this is also for 2 stage model (the second 
stage works on a subject by subject basis)
5) the -qcache in recon all maps and smoothes surface data to the 
template, so that it is available later. You can do that even on the 
long runs, or you can just manually map ans smooth things with preproc.
6) A different preproc call using a fsgd file rather than a qdec table. 
see the glm_fit tutorial for these things.

Best, Martin

On 03/23/2016 12:28 PM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I would like to analyze my longitudinal data also cross-sectionally at single 
> time points. I am a little confused as to how to register my data to the 
> template and smooth it accordingly.
>
> So far, I have registered my longitudinal data to my template to use in LMEs 
> with this command:
> mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target 30kids_template 
> --hemi lh --meas thickness --out lh.thickness.mg
>
> and then smoothed it with this command:
> mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval 
> lh.thickness_sm10.mgh --fwhm-trg 10 --cortex  --noreshape
>
> (1) Do I have to do it once with a cross-sectional command and once with a 
> longitudinal command?
> (2) Should I do the cross-sectional analyses in QDEC or with LME?
>
> Now the question is what these other commands are for?
>
> (3) long_mris_slopes --qdec ct/qdec/long.qdec.table.dat --meas thickness 
> --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time 
> years --qcache kids_template --sd $SUBJECTS_DIR
> --> I understood this is only for Two-Stage-Models, is that correct?
>
> (4) long_qdec_table --qdec qdec/long.qdec.table.dat --cross --out 
> qdec/cross.qdec.table.dat
>
> (5) recon-all -s name -qcache -target  name_of_template
>
> (6) mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage 
> --target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
>
>
> Please help clear up my confusion :)
> Thanks in advance,
> Clara
>
>
>

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

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[Freesurfer] REPOST: registering longitudinal data to template

[Clara Kühn]

Dear FreeSurfer experts,

I would like to analyze my longitudinal data also cross-sectionally at single 
time points. I am a little confused as to how to register my data to the 
template and smooth it accordingly.

So far, I have registered my longitudinal data to my template to use in LMEs 
with this command:
mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target 30kids_template 
--hemi lh --meas thickness --out lh.thickness.mg 

and then smoothed it with this command:
mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval 
lh.thickness_sm10.mgh --fwhm-trg 10 --cortex  --noreshape

(1) Do I have to do it once with a cross-sectional command and once with a 
longitudinal command? 
(2) Should I do the cross-sectional analyses in QDEC or with LME?

Now the question is what these other commands are for?

(3) long_mris_slopes --qdec ct/qdec/long.qdec.table.dat --meas thickness --hemi 
lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years 
--qcache kids_template --sd $SUBJECTS_DIR 
--> I understood this is only for Two-Stage-Models, is that correct?

(4) long_qdec_table --qdec qdec/long.qdec.table.dat --cross --out 
qdec/cross.qdec.table.dat

(5) recon-all -s name -qcache -target  name_of_template

(6) mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage 
--target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh


Please help clear up my confusion :)
Thanks in advance,
Clara



-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] Matlabpool has been removed

[Clara Kühn]

Hi Kaspar,

I had the same problem. The last version that supports matlabpool is Matlab 
8.2. Maybe try it with that version.

Cheers, Clara

- Ursprüngliche Mail -
Von: "Kasper Jessen" 
An: "Freesurfer support list" 
Gesendet: Mittwoch, 23. März 2016 09:41:51
Betreff: [Freesurfer] Matlabpool has been removed

Dear FreeSurfer experts, 

Thanks again for a great FreeSurfer forum. 

I have been trying to run the linear mixed effects model on a longitudinal 
dataset. However, i get the an error in matlab: "matlabpool has been removed. 
Use PARPOOL instead". I can see in the forum that others have experienced the 
same. Unfortunately i cannot find the answer, which fixes the problem. As far 
as i understand, it may be because i am using a new version of Matlab. However, 
is there a way to fix the problem? 
Best regards, 
Kasper Jessen 
MD, PhD student 



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Re: [Freesurfer] adapt Monte Carlo correction for specific sample

[Clara Kühn]

Thanks a lot! I will do that then :)

Cheers, Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 15. März 2016 17:40:08
Betreff: Re: [Freesurfer] adapt Monte Carlo correction for specific sample

You can just store it in a different directory, then use the --cache-dir 
option when running mri_glmfit-sim to specify the new folder, eg, if you 
use --o /path/to/myspace/yoursubject/lh/cortex, then specify 
/path/to/myspace

On 03/15/2016 12:36 PM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I have a question regarding the Monte Carlo correction.
> To create a Monte Carlo correction for my specific sample (4year old kids) 
> the wiki suggests this command:
> mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/lh/cortex 
> --base mc-z --surface yoursubject lh --nreps 1
>
> I have run this command, however I get an error message that I have no rights 
> to write into the $FREESURFER_HOME directory. I work at an institute where 
> that directory is stored on a server to which many people have access but no 
> writing rights (which is definitely a good thing), so getting the rights is 
> not really an option. I was wondering now whether I could just specify a 
> different directory or whether it absolutely has to be the $FREESURFER_HOME 
> directory? If the latter is the case, would you suggest I install a local 
> copy or do you have any other suggestions?
>
> Thanks in advance!
> Clara
>
>
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-- 
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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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[Freesurfer] adapt Monte Carlo correction for specific sample

[Clara Kühn]

Dear FreeSurfer experts,

I have a question regarding the Monte Carlo correction.
To create a Monte Carlo correction for my specific sample (4year old kids) the 
wiki suggests this command:
mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/lh/cortex 
--base mc-z --surface yoursubject lh --nreps 1

I have run this command, however I get an error message that I have no rights 
to write into the $FREESURFER_HOME directory. I work at an institute where that 
directory is stored on a server to which many people have access but no writing 
rights (which is definitely a good thing), so getting the rights is not really 
an option. I was wondering now whether I could just specify a different 
directory or whether it absolutely has to be the $FREESURFER_HOME directory? If 
the latter is the case, would you suggest I install a local copy or do you have 
any other suggestions? 

Thanks in advance!
Clara___
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[Freesurfer] REPOST recon-all per hemisphere

[Clara Kühn]

Dear FreeSurfer experts,

I hava a question regarding rerunning the recon-process. I have cases where I 
do manual edits on a brain and only set a few control points on one hemisphere 
but white matter edits on the other. I would then run the -cp flag for one 
hemisphere and the -wm flag for the other. My question is, can that happen 
simultaneously, i.e. in different terminals or should I do one after the other 
because of some sort of interferences?

Also, I was wondering if it is possible to save surfaces from a BASE under a 
different name, run the recon-process again and compare the new surfaces with 
the old ones and then pick, if they are better, the old ones to go on to 
calculate the LONGs?

Thanks, 
Clara
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[Freesurfer] recon-all per hemisphere

[Clara Kühn]

Dear FreeSurfer experts,

I hava a question regarding rerunning the recon-process. I have cases where I 
do manual edits on a brain and only set a few control points on one hemisphere 
but white matter edits on the other. I would then run the -cp flag for one 
hemisphere and the -wm flag for the other. My question is, can that happen 
simultaneously, i.e. in different terminals or should I do one after the other 
because of some sort of interferences?

Thanks, 
Clara
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Re: [Freesurfer] correlations with longitudinal data

[Clara Kühn]

Hi Martin,

thanks for your reply.
It turns out that QDEC just doesn't like working on different hemispheres in 
the same instance. If I close it, restart it and do the analyses on the other 
hemisphere only, it works like a charm. Only when you try to change the 
hemisphere in the design tab, it gives out that error.

I also wanted to tell you that I'm learning to do the LMEs with Matlab and I 
run into an error with matlabpool. When I try to fit the model with 
lme_mass_fit_EMinit (which calls the function matlabpool). I get an error that 
matlabpool doesn't exist. It turns out that matlabpool is now called parpool. I 
worked with matlab 8.6. I went back to check which matlab version still uses 
matlabpool and I find that up to 8.2 matlabpool works. So maybe you could put 
that as a warning into the tutorial or something like that.

As for the qcache problem: I ended up doing exactly what you said. Good to hear 
that I did it right ;)

Thank you and Frohe Weihnachten!
Clara

- Ursprüngliche Mail -
Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Donnerstag, 17. Dezember 2015 17:40:40
Betreff: Re: [Freesurfer] correlations with longitudinal data

Hi Clara,

so are you creating the qcache files in the cross sectional directories? 
I would recommend to use the longitudinal directories, for that you can 
simply add the -qcache flag to the longitudinal recon-all like
recon-all -long-qcache -target 

I don't know why you are getting an error with the other hemisphere. 
Maybe you use a different template for qcache and then fsaverage later?

Best, Martin

On 12/11/2015 11:36 AM, Clara Kühn wrote:
> Hi Freesurfer experts,
>
> I eventually used the recon-all -s subjectname -qcache -target my_template to 
> get the smoothed surfaces to use in qdec and therefore do cross-sectional 
> analyses on the single tps of my longitudinal data.
> I did the analyses on the left hemisphere so far. Now that I tried using the 
> right hemisphere I get the error message "multiple surfaces must have the 
> same number of vertices". What does that mean? As far as I understood, the 
> recon-all -qcache created smoothed surfaces for the right and left 
> hemisphere. At least everything is in the respective folders...
>
> Cheers and thanks in advance!
> Clara
>
> - Ursprüngliche Mail -
> Von: "ckuehn" <cku...@cbs.mpg.de>
> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Gesendet: Mittwoch, 9. Dezember 2015 10:27:40
> Betreff: Re: [Freesurfer] correlations with longitudinal data
>
> Hi Martin,
>
> thanks for your reply.
> I have created a qdec file with the fsidtp1.long.fsid.base as first column 
> and specified the long directories with /path_to_data/*.long.*. And each 
> subject has a ?h.thickness file from the recon-process. However, Qdec is 
> asking for a very specific file ?h.thickness.fwhm10.nameoftemplate.mgz or 
> .mgh (even when I pick 0 smoothing).
>
> If I understand correctly, that is the file that I get when running the 
> mris_slope command. But you said I wouldn't need that. Is there a way to get 
> these files for a cross-sectional analysis of the *.long.*.base timepoints?
>
> My qdec file currently looks like this:
>
> fsid group sex age (in months) ... (behavioral measures)
> _1.long..base 1 0 52 ...
> _1.long..base 2 1 48 ...
> ...
>
> Thank you,
> Clara
>
> - Ursprüngliche Mail -
> Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 8. Dezember 2015 18:14:40
> Betreff: Re: [Freesurfer] correlations with longitudinal data
>
> Hi Clara,
>
> you would do the analysis of a single time point the same way you'd run
> a regular glm or qdec analysis on cross sectional data. You cannot use
> LME as that is for longitudinal data (more than 1 time point per
> subject, at least for most subjects). Also the two stage model, first
> reduces to multiple measures in each subject to a single measure (slope
> of the linear fit). It would not be the right tool for selecting a
> single time point.
>
> You could for example create a qdec table with the first row  fsid
> timepoint1.long.base
> for each subject and then use qdec.
>
> If you want to make use of the improved data from the longitudinal image
> processing, you need to specify the *.long.base directories, so that
> data is taken from there.
>
> Good luck, Martin
>
> On 12/08/2015 04:24 AM, Clara Kühn wrote:
>> Dear FreeSurfer experts,
>>
>> I have a subsample of my longitudinal data with 3 scans per subjects fully 
>> preprocessed and would like to start with some simple c

Re: [Freesurfer] correlations with longitudinal data

[Clara Kühn]

Hi Freesurfer experts,

I eventually used the recon-all -s subjectname -qcache -target my_template to 
get the smoothed surfaces to use in qdec and therefore do cross-sectional 
analyses on the single tps of my longitudinal data.
I did the analyses on the left hemisphere so far. Now that I tried using the 
right hemisphere I get the error message "multiple surfaces must have the same 
number of vertices". What does that mean? As far as I understood, the recon-all 
-qcache created smoothed surfaces for the right and left hemisphere. At least 
everything is in the respective folders...

Cheers and thanks in advance!
Clara

- Ursprüngliche Mail -
Von: "ckuehn" <cku...@cbs.mpg.de>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Mittwoch, 9. Dezember 2015 10:27:40
Betreff: Re: [Freesurfer] correlations with longitudinal data

Hi Martin, 

thanks for your reply.
I have created a qdec file with the fsidtp1.long.fsid.base as first column and 
specified the long directories with /path_to_data/*.long.*. And each subject 
has a ?h.thickness file from the recon-process. However, Qdec is asking for a 
very specific file ?h.thickness.fwhm10.nameoftemplate.mgz or .mgh (even when I 
pick 0 smoothing).

If I understand correctly, that is the file that I get when running the 
mris_slope command. But you said I wouldn't need that. Is there a way to get 
these files for a cross-sectional analysis of the *.long.*.base timepoints? 

My qdec file currently looks like this:

fsid group sex age (in months) ... (behavioral measures)
_1.long..base 1 0 52 ... 
_1.long..base 2 1 48 ...
...

Thank you,
Clara

- Ursprüngliche Mail -
Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 8. Dezember 2015 18:14:40
Betreff: Re: [Freesurfer] correlations with longitudinal data

Hi Clara,

you would do the analysis of a single time point the same way you'd run 
a regular glm or qdec analysis on cross sectional data. You cannot use 
LME as that is for longitudinal data (more than 1 time point per 
subject, at least for most subjects). Also the two stage model, first 
reduces to multiple measures in each subject to a single measure (slope 
of the linear fit). It would not be the right tool for selecting a 
single time point.

You could for example create a qdec table with the first row  fsid
timepoint1.long.base
for each subject and then use qdec.

If you want to make use of the improved data from the longitudinal image 
processing, you need to specify the *.long.base directories, so that 
data is taken from there.

Good luck, Martin

On 12/08/2015 04:24 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I have a subsample of my longitudinal data with 3 scans per subjects fully 
> preprocessed and would like to start with some simple correlations of 
> thickness at time 1 with behavioral measures and other factors like age.
>
> Is there a way to do that with LME (since I was planning on using that as a 
> method of choice) or is it possible to do that with QDEC? I've prepared my 
> data for both methods (LME and linear two stage model) but if I use the 
> cross.qdec.table derived from the longitudinal data, it uses the registered 
> and smoothed (with mris_slopes) surfaces from the Base, right?
> So, I would like to know how I can analyzse a single time point within my 
> longitudinal design.
>
> Cheers,
> Clara
>
>

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

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Re: [Freesurfer] correlations with longitudinal data

[Clara Kühn]

Hi Martin, 

thanks for your reply.
I have created a qdec file with the fsidtp1.long.fsid.base as first column and 
specified the long directories with /path_to_data/*.long.*. And each subject 
has a ?h.thickness file from the recon-process. However, Qdec is asking for a 
very specific file ?h.thickness.fwhm10.nameoftemplate.mgz or .mgh (even when I 
pick 0 smoothing).

If I understand correctly, that is the file that I get when running the 
mris_slope command. But you said I wouldn't need that. Is there a way to get 
these files for a cross-sectional analysis of the *.long.*.base timepoints? 

My qdec file currently looks like this:

fsid group sex age (in months) ... (behavioral measures)
_1.long..base 1 0 52 ... 
_1.long..base 2 1 48 ...
...

Thank you,
Clara

- Ursprüngliche Mail -
Von: "mreuter" <mreu...@nmr.mgh.harvard.edu>
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 8. Dezember 2015 18:14:40
Betreff: Re: [Freesurfer] correlations with longitudinal data

Hi Clara,

you would do the analysis of a single time point the same way you'd run 
a regular glm or qdec analysis on cross sectional data. You cannot use 
LME as that is for longitudinal data (more than 1 time point per 
subject, at least for most subjects). Also the two stage model, first 
reduces to multiple measures in each subject to a single measure (slope 
of the linear fit). It would not be the right tool for selecting a 
single time point.

You could for example create a qdec table with the first row  fsid
timepoint1.long.base
for each subject and then use qdec.

If you want to make use of the improved data from the longitudinal image 
processing, you need to specify the *.long.base directories, so that 
data is taken from there.

Good luck, Martin

On 12/08/2015 04:24 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I have a subsample of my longitudinal data with 3 scans per subjects fully 
> preprocessed and would like to start with some simple correlations of 
> thickness at time 1 with behavioral measures and other factors like age.
>
> Is there a way to do that with LME (since I was planning on using that as a 
> method of choice) or is it possible to do that with QDEC? I've prepared my 
> data for both methods (LME and linear two stage model) but if I use the 
> cross.qdec.table derived from the longitudinal data, it uses the registered 
> and smoothed (with mris_slopes) surfaces from the Base, right?
> So, I would like to know how I can analyzse a single time point within my 
> longitudinal design.
>
> Cheers,
> Clara
>
>

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

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[Freesurfer] correlations with longitudinal data

[Clara Kühn]

Dear FreeSurfer experts,

I have a subsample of my longitudinal data with 3 scans per subjects fully 
preprocessed and would like to start with some simple correlations of thickness 
at time 1 with behavioral measures and other factors like age.

Is there a way to do that with LME (since I was planning on using that as a 
method of choice) or is it possible to do that with QDEC? I've prepared my data 
for both methods (LME and linear two stage model) but if I use the 
cross.qdec.table derived from the longitudinal data, it uses the registered and 
smoothed (with mris_slopes) surfaces from the Base, right?
So, I would like to know how I can analyzse a single time point within my 
longitudinal design.

Cheers,
Clara


-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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[Freesurfer] obtain volumetric data with qdec

[Clara Kühn]

Dear FreeSurfer Experts,

I'm trying to follow the steps described in the univeriate LME for longitudinal 
data (https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels). 
Could you explain how you did this step:
"The qdec.table.dat file was then used to collect volumetric data for all 
subjects within the Freesurfer's Qdec interface. This resulted in a new Qdec 
table which had the previous columns plus three new columns."

I followed the instructions with mri_preproc and mri_surf2surf but when I then 
open qdec to obtain the volumetric data for (in my case) BA45 it always gives 
out the error "Error in Analyze: Coudln't open 
/path_to_subject_base/lh.thickness.fwhm0.templatename.mgz or .mgh file"
I understand that it can't find that file because it isn't there. 

Which steps do I additionally need to perfom to be able to be able to obtain 
said volumetric data. Is there an extra turorial or walkthrough for that?

Cheers, Clara

-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

[Clara Kühn]

Dear Ruopeng,

I tried different computers and on most of them it works when I test-delete a 
wm voxel and then save the wm.mgz. However, when I then go on to actually 
editing the wm.mgz Freeview crashes when I hit "save" as it's done on my 
computer. I've tried not using the button but going through the menu "save 
volume" and I tried "save as" under a different name. Still crashes. 
I've done all my editing with FS 5.3.0 and I don't think it's a good idea to 
switch versions mid-editing.

Do you have an idea whether there might be a setting or a feature or whatever 
that I can change and what this part of the error message means:
 [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range

Cheers, Clara

- Ursprüngliche Mail -
Von: "ckuehn" <cku...@cbs.mpg.de>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Mittwoch, 4. November 2015 08:07:44
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

With the FS 6 beta version the problem doesn't occur.
Cheers, Clara

- Ursprüngliche Mail -
Von: "Ruopeng Wang" <rpw...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Dienstag, 3. November 2015 18:03:52
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

Try 6.0.0beta.

On 11/03/2015 12:02 PM, Clara Kühn wrote:
> Our IT guy said it could be a software problem since he didn't have the 
> problem and the only difference between out computers was the display.
> We have these versions at the institute:
>
> 4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta
> Is the first one the dev version?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Ruopeng Wang" <rpw...@nmr.mgh.harvard.edu>
> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Gesendet: Dienstag, 3. November 2015 17:57:50
> Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
>
> There was a bug in freeview in FS 5.3.0 that may have caused the crash. 
> Clara, can you try the dev version of freeview?
>
> Ruopeng
>
> On 11/03/2015 11:50 AM, Bruce Fischl wrote:
>
>
> Hi Clara
>
> that doesn't crash for me. Are you sure you ahve write permission to the 
> file? And that the disk isn't full? Ruopeng: any other ideas?
>
> Bruce
>
> On Tue, 3 Nov 2015, Clara Kühn wrote:
>
>
>
> Hi Bruce,
>
> I attached the wm.mgz from one of my participants. It happens with any 
> participant though.
> What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and 
> then it crashes with afore mentioned error message.
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Gesendet: Dienstag, 3. November 2015 14:42:25
> Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
>
> Hi Clara
>
> can you send us the wm.mgz and tell us exactly what you did to make it
> crash?
>
> thahks
> Bruce
> On Tue, 3 Nov 2015, Clara Kühn wrote:
>
>
>
> Dear FreeSurfer experts,
>
> since last week I have the problem that FS (5.3.0) crashes when I try to save 
> changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can 
> always restore it by renaming the temporary file (wm.mgz~) but it obviously 
> doen't save any changes.
>
> I've tried different computers (same FS version) and on some it works and on 
> some the same problem occurs. I just tried it on the 6.0.0beta version and it 
> saved like a charm. I would rather, however, keep editing my data with the 
> same version.
> Here is the error message I get in the terminal:
>
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see 
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal
>  [0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on 
> Apple to find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message 
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Petsc Release Version 2.

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

[Clara Kühn]

Our IT guy said it could be a software problem since he didn't have the problem 
and the only difference between out computers was the display.
We have these versions at the institute: 

4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta
Is the first one the dev version?

Cheers, Clara

- Ursprüngliche Mail -
Von: "Ruopeng Wang" <rpw...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Dienstag, 3. November 2015 17:57:50
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

There was a bug in freeview in FS 5.3.0 that may have caused the crash. Clara, 
can you try the dev version of freeview? 

Ruopeng 

On 11/03/2015 11:50 AM, Bruce Fischl wrote: 


Hi Clara 

that doesn't crash for me. Are you sure you ahve write permission to the file? 
And that the disk isn't full? Ruopeng: any other ideas? 

Bruce 

On Tue, 3 Nov 2015, Clara Kühn wrote: 



Hi Bruce, 

I attached the wm.mgz from one of my participants. It happens with any 
participant though. 
What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and then 
it crashes with afore mentioned error message. 

Cheers, Clara 

- Ursprüngliche Mail - 
Von: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> 
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> 
Gesendet: Dienstag, 3. November 2015 14:42:25 
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes 

Hi Clara 

can you send us the wm.mgz and tell us exactly what you did to make it 
crash? 

thahks 
Bruce 
On Tue, 3 Nov 2015, Clara Kühn wrote: 



Dear FreeSurfer experts, 

since last week I have the problem that FS (5.3.0) crashes when I try to save 
changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can 
always restore it by renaming the temporary file (wm.mgz~) but it obviously 
doen't save any changes. 

I've tried different computers (same FS version) and on some it works and on 
some the same problem occurs. I just tried it on the 6.0.0beta version and it 
saved like a charm. I would rather, however, keep editing my data with the same 
version. 
Here is the error message I get in the terminal: 

[0]PETSC ERROR: 
 
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range 
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger 
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal 
[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple 
to find memory corruption errors 
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash. 
[0]PETSC ERROR: - Error Message 
 
[0]PETSC ERROR: Signal received! 
[0]PETSC ERROR: 
 
[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 
[0]PETSC ERROR: See docs/changes/index.html for recent updates. 
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. 
[0]PETSC ERROR: See docs/index.html for manual pages. 
[0]PETSC ERROR: 
 
[0]PETSC ERROR: Unknown Name on a linux-gnu named etsch by ckuehn Fri Oct 30 
17:22:55 2015 
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
 
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 
[0]PETSC ERROR: 
 
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file 
[unset]: aborting job: 
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 
Segmentation fault (core dumped) 

Any idea what it means by Segmentation Violation and how I can fix it?? 
Cheers and thanks in advance! 
Clara Kühn 

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



___ 
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 


The information in this e-mail is intended only for the person to whom it is 
addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient inform

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

[Clara Kühn]

With the FS 6 beta version the problem doesn't occur.
Cheers, Clara

- Ursprüngliche Mail -
Von: "Ruopeng Wang" <rpw...@nmr.mgh.harvard.edu>
An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Gesendet: Dienstag, 3. November 2015 18:03:52
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

Try 6.0.0beta.

On 11/03/2015 12:02 PM, Clara Kühn wrote:
> Our IT guy said it could be a software problem since he didn't have the 
> problem and the only difference between out computers was the display.
> We have these versions at the institute:
>
> 4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1.0 ; 5.2.0 ; 5.3.0 ; 6.0.0beta
> Is the first one the dev version?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Ruopeng Wang" <rpw...@nmr.mgh.harvard.edu>
> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Gesendet: Dienstag, 3. November 2015 17:57:50
> Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
>
> There was a bug in freeview in FS 5.3.0 that may have caused the crash. 
> Clara, can you try the dev version of freeview?
>
> Ruopeng
>
> On 11/03/2015 11:50 AM, Bruce Fischl wrote:
>
>
> Hi Clara
>
> that doesn't crash for me. Are you sure you ahve write permission to the 
> file? And that the disk isn't full? Ruopeng: any other ideas?
>
> Bruce
>
> On Tue, 3 Nov 2015, Clara Kühn wrote:
>
>
>
> Hi Bruce,
>
> I attached the wm.mgz from one of my participants. It happens with any 
> participant though.
> What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and 
> then it crashes with afore mentioned error message.
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
> Gesendet: Dienstag, 3. November 2015 14:42:25
> Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
>
> Hi Clara
>
> can you send us the wm.mgz and tell us exactly what you did to make it
> crash?
>
> thahks
> Bruce
> On Tue, 3 Nov 2015, Clara Kühn wrote:
>
>
>
> Dear FreeSurfer experts,
>
> since last week I have the problem that FS (5.3.0) crashes when I try to save 
> changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can 
> always restore it by renaming the temporary file (wm.mgz~) but it obviously 
> doen't save any changes.
>
> I've tried different computers (same FS version) and on some it works and on 
> some the same problem occurs. I just tried it on the 6.0.0beta version and it 
> saved like a charm. I would rather, however, keep editing my data with the 
> same version.
> Here is the error message I get in the terminal:
>
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, 
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see 
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal
>  [0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on 
> Apple to find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message 
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR: 
> 
> [0]PETSC ERROR: Unknown Name on a linux-gnu named etsch by ckuehn Fri Oct 30 
> 17:22:55 2015
> [0]PETSC ERROR: Libraries linked from 
> /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
> [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
> --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC

[Freesurfer] Freesurfer crash upon wm.mgz changes

[Clara Kühn]

Dear FreeSurfer experts,

since last week I have the problem that FS (5.3.0) crashes when I try to save 
changes to the wm.mgz. It closes immediately and the wm.mgz is deleted. I can 
always restore it by renaming the temporary file (wm.mgz~) but it obviously 
doen't save any changes.

I've tried different computers (same FS version) and on some it works and on 
some the same problem occurs. I just tried it on the 6.0.0beta version and it 
saved like a charm. I would rather, however, keep editing my data with the same 
version. 
Here is the error message I get in the terminal:

[0]PETSC ERROR: 

[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably 
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see 
http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
 ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find 
memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: - Error Message 

[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: 

[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 
2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: 

[0]PETSC ERROR: Unknown Name on a linux-gnu named etsch by ckuehn Fri Oct 30 
17:22:55 2015
[0]PETSC ERROR: Libraries linked from 
/autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt
[0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010
[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc 
--with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 
--with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 
CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
[0]PETSC ERROR: 

[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown 
file
[unset]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
Segmentation fault (core dumped)

Any idea what it means by Segmentation Violation and how I can fix it??
Cheers and thanks in advance!
Clara Kühn

___
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] cannot find qdec file

[Clara Kühn]

Hi Doug,

this is the result it printed out in the terminal:

etsch:/scr/etsch2/kids$ mris_preproc --debug --qdec-long long.qdec.table.dat
set echo = 1 ;
set debug = 1 ;
set debug = 1
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 2 != 0 )

set flag = $argv[1] ; shift ;
set flag = --qdec-long
shift

switch ( $flag )
switch ( --qdec-long )
if ( $#argv == 0 ) goto arg1err ;
if ( 1 == 0 ) goto arg1err
set fsgdf = $argv[1] ; shift ;
set fsgdf = long.qdec.table.dat
shift
if ( ! -e $fsgdf ) then
if ( ! -e long.qdec.table.dat ) then
set sl = `cat $fsgdf | awk '{if ($1 != fsid  substr($1,0,1) != #) 
printf(%s.long.%s\n, $1, $2)}'` ;
set sl = `cat $fsgdf | awk '{if ($1 != fsid  substr($1,0,1) != #) 
printf(%s.long.%s\n, $1, $2)}'`
awk {if ($1 != fsid  substr($1,0,1) != #) printf(%s.long.%s\n, $1, $2)}
cat long.qdec.table.dat
set subjlist = ( $subjlist $sl ) ;
set subjlist = ( AL3K_1.long.AL3K.base AL3K_2.long.AL3K.base 
AL3K_3.long.AL3K.base AM1K_1.long.AM1K.base AM1K_2.long.AM1K.base 
AM1K_3.long.AM1K.base BJ4K_1.long.BJ4K.base BJ4K_2.long.BJ4K.base 
BJ4K_3.long.BJ4K.base BJ8K_1.long.BJ8K.base BJ8K_2.long.BJ8K.base 
BJ8K_3.long.BJ8K.base BN2K_1.long.BN2K.base BN2K_2.long.BN2K.base 
BN2K_3.long.BN2K.base WL3K_1.long.WL3K.base WL3K_2.long.WL3K.base 
WL3K_3.long.WL3K.base ZF1K_1.long.ZF1K.base ZF1K_2.long.ZF1K.base 
ZF1K_3.long.ZF1K.base .long. )
breaksw
breaksw

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

goto parse_args_return ;
goto parse_args_return


goto handle_fsfast ;
goto handle_fsfast

if ( $#SessFile ) then
if ( 0 ) then

goto handle_fsfast_return ;
goto handle_fsfast_return


goto check_params ;
goto check_params

if ( $#subjlistfile  $#ivplist ) then
if ( 0  0 ) then
if ( $#subjlistfile  $#fsgdf ) then
if ( 0  1 ) then
if ( $#ivplist  $#fsgdf ) then
if ( 0  1 ) then
if ( $#subjlist == 0 ) then
if ( 22 == 0 ) then
if ( $#srchemi == 0 ) then
if ( 0 == 0 ) then
echo ERROR: no source hemi specified
echo ERROR: no source hemi specified
ERROR: no source hemi specified
exit 1 ;
exit 1

Cheers, Clara

- Ursprüngliche Mail -
Von: Douglas N Greve gr...@nmr.mgh.harvard.edu
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 13. August 2015 22:10:26
Betreff: Re: [Freesurfer] cannot find qdec file

I'm not sure what to tell you. When I use the new file I don't get an 
error. When I use the old one I do. Can you run

mris_preproc --debug --qdec-long long.qdec.table.dat

and send me the result?


On 08/13/2015 01:01 PM, Clara Kühn wrote:
 do you mean the one without the blank line at the end? I've attached that for 
 you.
 Cheers, Clara

 - Ursprüngliche Mail -
 Von: Douglas N Greve gr...@nmr.mgh.harvard.edu
 An: freesurfer@nmr.mgh.harvard.edu
 Gesendet: Donnerstag, 13. August 2015 18:12:40
 Betreff: Re: [Freesurfer] cannot find qdec file

 Can you send the new qdec table file?

 On 08/05/2015 04:05 AM, Clara Kühn wrote:
 no worries!
 sadly, though, deleting the empty line wasn't the answer to the problem :(
 Cheers, Clara

 - Ursprüngliche Mail -
 Von: Douglas N Greve gr...@nmr.mgh.harvard.edu
 An: freesurfer@nmr.mgh.harvard.edu
 Gesendet: Dienstag, 4. August 2015 20:43:47
 Betreff: Re: [Freesurfer] cannot find qdec file

 oops, sorry for the delay, thanks for the reminder. The problem is that
 you have a blank line at the end of your long.qdec.table.dat file.
 Remove the line and see if it works.
 doug

 On 08/04/2015 12:42 PM, Clara Kühn wrote:
 Hi Doug,
 did the fordoug.log file give any information about why FreeSurfer can't 
 find my qdec file?

 Cheers and thanks for working on this!
 Clara

 - Ursprüngliche Mail -
 Von: Douglas Greve gr...@nmr.mgh.harvard.edu
 An: freesurfer@nmr.mgh.harvard.edu
 Gesendet: Montag, 3. August 2015 17:16:18
 Betreff: Re: [Freesurfer] cannot find qdec file

 can you run

 mris_preproc --debug --qdec-long 
 /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 
 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh 
 | tee fordoug.log

 and send me fordoug.log ?


 On 8/3/15 10:38 AM, Clara Kühn wrote:



 the command line is this:
 mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat 
 --target 7kids_template_sc1 --hemi lh --meas thickness --out 
 /scr/etsch2/kids/ct/qdec/lh.thickness.mgh

 the terminal output is this:
 nsubjects = 22
 ERROR: cannot find /scr/etsch2/kids/ct/.long.

 and the actual qdec file is attached.
 Cheers, Clara

 - Ursprüngliche Mail -
 Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: 
 freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24
 Betreff: Re: [Freesurfer] cannot find qdec file

 Can you send your command line, full terminal output, and your
 long.qdec.table.dat file?

 On 8/3/15 10:31 AM, Clara Kühn wrote:



 ok, it can only access the file if I type
 ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash)

 but if I then use that path for the mris_preproc command I get
 nsubjects = 22
 ERROR

Re: [Freesurfer] cannot find qdec file

[Clara Kühn]

do you mean the one without the blank line at the end? I've attached that for 
you.
Cheers, Clara

- Ursprüngliche Mail -
Von: Douglas N Greve gr...@nmr.mgh.harvard.edu
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 13. August 2015 18:12:40
Betreff: Re: [Freesurfer] cannot find qdec file

Can you send the new qdec table file?

On 08/05/2015 04:05 AM, Clara Kühn wrote:
 no worries!
 sadly, though, deleting the empty line wasn't the answer to the problem :(
 Cheers, Clara

 - Ursprüngliche Mail -
 Von: Douglas N Greve gr...@nmr.mgh.harvard.edu
 An: freesurfer@nmr.mgh.harvard.edu
 Gesendet: Dienstag, 4. August 2015 20:43:47
 Betreff: Re: [Freesurfer] cannot find qdec file

 oops, sorry for the delay, thanks for the reminder. The problem is that
 you have a blank line at the end of your long.qdec.table.dat file.
 Remove the line and see if it works.
 doug

 On 08/04/2015 12:42 PM, Clara Kühn wrote:
 Hi Doug,
 did the fordoug.log file give any information about why FreeSurfer can't 
 find my qdec file?

 Cheers and thanks for working on this!
 Clara

 - Ursprüngliche Mail -
 Von: Douglas Greve gr...@nmr.mgh.harvard.edu
 An: freesurfer@nmr.mgh.harvard.edu
 Gesendet: Montag, 3. August 2015 17:16:18
 Betreff: Re: [Freesurfer] cannot find qdec file

 can you run

 mris_preproc --debug --qdec-long 
 /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 
 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh 
 | tee fordoug.log

 and send me fordoug.log ?


 On 8/3/15 10:38 AM, Clara Kühn wrote:



 the command line is this:
 mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat 
 --target 7kids_template_sc1 --hemi lh --meas thickness --out 
 /scr/etsch2/kids/ct/qdec/lh.thickness.mgh

 the terminal output is this:
 nsubjects = 22
 ERROR: cannot find /scr/etsch2/kids/ct/.long.

 and the actual qdec file is attached.
 Cheers, Clara

 - Ursprüngliche Mail -
 Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: 
 freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24
 Betreff: Re: [Freesurfer] cannot find qdec file

 Can you send your command line, full terminal output, and your
 long.qdec.table.dat file?

 On 8/3/15 10:31 AM, Clara Kühn wrote:



 ok, it can only access the file if I type
 ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash)

 but if I then use that path for the mris_preproc command I get
 nsubjects = 22
 ERROR: cannot find /scr/etsch2/kids/ct/.long.



 - Ursprüngliche Mail -
 Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: 
 freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:23:48
 Betreff: Re: [Freesurfer] cannot find qdec file

 that is probably not the full path. Try typing

 ls scr/etsch2/kids/ct/qdec/long.qdec.table.dat

 If it says it cannot find the file, then it is not the full path. Maybe
 you need a forward slash (ie, /) in the beginning?

 On 8/3/15 10:18 AM, Clara Kühn wrote:



 then I get the error ERROR: cannot find 
 scr/etsch2/kids/ct/qdec/long.qdec.table.dat

 I had tried that. Sorry, no luck with that.

 - Ursprüngliche Mail -
 Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: 
 freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:16:58
 Betreff: Re: [Freesurfer] cannot find qdec file

 you have to give it the entire path to the file

 On 8/3/15 10:14 AM, Clara Kühn wrote:



 Dear FS-experts,

 I want to analyze my longitudinal data with your suggested LME models and am 
 therefore following the walkthrough by J. Bernal. I get an error though very 
 early on when using the command
 mris_preproc --qdec-long qdec/long.qdec.table.dat --target 
 7kids_template_sc1 --hemi lh --meas thickness --out qdec/lh.thickness.mgh

 It always says
 ERROR: cannot find qdec/long.qdec.table.dat

 Yes, the walkthrough asks for an input file named just qdec.table.dat, but I 
 haven't got that. So far in the longitudinal stream there are 
 long.qdec.table.dat and cross.qdec.table.dat files but no simple 
 qdec.table.dat files. So I figured I'd use the long.qdec file because FS 
 needs to get the information about the long timepoints.
 But it cannot find the file, even though I see it. I've also tried copying 
 the long.qdec file and naming it qdec.table.dat but it still doesn't find it.

 The entire path to the file is scr/etsch2/kids/ct/qdec/long.qdec.table.dat 
 and my SUBJECTS_DIR is scr/etsch2/kids/ct

 Can you help me see what I'm missing?
 Thanks a lot in advance,
 Clara
 ___
 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

Re: [Freesurfer] cannot find qdec file

[Clara Kühn]

no worries!
sadly, though, deleting the empty line wasn't the answer to the problem :(
Cheers, Clara

- Ursprüngliche Mail -
Von: Douglas N Greve gr...@nmr.mgh.harvard.edu
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 4. August 2015 20:43:47
Betreff: Re: [Freesurfer] cannot find qdec file

oops, sorry for the delay, thanks for the reminder. The problem is that 
you have a blank line at the end of your long.qdec.table.dat file. 
Remove the line and see if it works.
doug

On 08/04/2015 12:42 PM, Clara Kühn wrote:
 Hi Doug,
 did the fordoug.log file give any information about why FreeSurfer can't find 
 my qdec file?

 Cheers and thanks for working on this!
 Clara

 - Ursprüngliche Mail -
 Von: Douglas Greve gr...@nmr.mgh.harvard.edu
 An: freesurfer@nmr.mgh.harvard.edu
 Gesendet: Montag, 3. August 2015 17:16:18
 Betreff: Re: [Freesurfer] cannot find qdec file

 can you run

 mris_preproc --debug --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat 
 --target 7kids_template_sc1 --hemi lh --meas thickness --out 
 /scr/etsch2/kids/ct/qdec/lh.thickness.mgh | tee fordoug.log

 and send me fordoug.log ?


 On 8/3/15 10:38 AM, Clara Kühn wrote:



 the command line is this:
 mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat 
 --target 7kids_template_sc1 --hemi lh --meas thickness --out 
 /scr/etsch2/kids/ct/qdec/lh.thickness.mgh

 the terminal output is this:
 nsubjects = 22
 ERROR: cannot find /scr/etsch2/kids/ct/.long.

 and the actual qdec file is attached.
 Cheers, Clara

 - Ursprüngliche Mail -
 Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: 
 freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24
 Betreff: Re: [Freesurfer] cannot find qdec file

 Can you send your command line, full terminal output, and your
 long.qdec.table.dat file?

 On 8/3/15 10:31 AM, Clara Kühn wrote:



 ok, it can only access the file if I type
 ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash)

 but if I then use that path for the mris_preproc command I get
 nsubjects = 22
 ERROR: cannot find /scr/etsch2/kids/ct/.long.



 - Ursprüngliche Mail -
 Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: 
 freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:23:48
 Betreff: Re: [Freesurfer] cannot find qdec file

 that is probably not the full path. Try typing

 ls scr/etsch2/kids/ct/qdec/long.qdec.table.dat

 If it says it cannot find the file, then it is not the full path. Maybe
 you need a forward slash (ie, /) in the beginning?

 On 8/3/15 10:18 AM, Clara Kühn wrote:



 then I get the error ERROR: cannot find 
 scr/etsch2/kids/ct/qdec/long.qdec.table.dat

 I had tried that. Sorry, no luck with that.

 - Ursprüngliche Mail -
 Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: 
 freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:16:58
 Betreff: Re: [Freesurfer] cannot find qdec file

 you have to give it the entire path to the file

 On 8/3/15 10:14 AM, Clara Kühn wrote:



 Dear FS-experts,

 I want to analyze my longitudinal data with your suggested LME models and am 
 therefore following the walkthrough by J. Bernal. I get an error though very 
 early on when using the command
 mris_preproc --qdec-long qdec/long.qdec.table.dat --target 7kids_template_sc1 
 --hemi lh --meas thickness --out qdec/lh.thickness.mgh

 It always says
 ERROR: cannot find qdec/long.qdec.table.dat

 Yes, the walkthrough asks for an input file named just qdec.table.dat, but I 
 haven't got that. So far in the longitudinal stream there are 
 long.qdec.table.dat and cross.qdec.table.dat files but no simple 
 qdec.table.dat files. So I figured I'd use the long.qdec file because FS 
 needs to get the information about the long timepoints.
 But it cannot find the file, even though I see it. I've also tried copying 
 the long.qdec file and naming it qdec.table.dat but it still doesn't find it.

 The entire path to the file is scr/etsch2/kids/ct/qdec/long.qdec.table.dat 
 and my SUBJECTS_DIR is scr/etsch2/kids/ct

 Can you help me see what I'm missing?
 Thanks a lot in advance,
 Clara
 ___
 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.

 ___
 Freesurfer mailing list Freesurfer

Re: [Freesurfer] cannot find qdec file

[Clara Kühn]

Hi Doug, 
did the fordoug.log file give any information about why FreeSurfer can't find 
my qdec file?

Cheers and thanks for working on this!
Clara

- Ursprüngliche Mail -
Von: Douglas Greve gr...@nmr.mgh.harvard.edu
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Montag, 3. August 2015 17:16:18
Betreff: Re: [Freesurfer] cannot find qdec file

can you run

mris_preproc --debug --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat 
--target 7kids_template_sc1 --hemi lh --meas thickness --out 
/scr/etsch2/kids/ct/qdec/lh.thickness.mgh | tee fordoug.log

and send me fordoug.log ? 


On 8/3/15 10:38 AM, Clara Kühn wrote: 



the command line is this:
mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 
7kids_template_sc1 --hemi lh --meas thickness --out 
/scr/etsch2/kids/ct/qdec/lh.thickness.mgh

the terminal output is this:
nsubjects = 22
ERROR: cannot find /scr/etsch2/kids/ct/.long.

and the actual qdec file is attached.
Cheers, Clara

- Ursprüngliche Mail -
Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: 
freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24
Betreff: Re: [Freesurfer] cannot find qdec file

Can you send your command line, full terminal output, and your 
long.qdec.table.dat file?

On 8/3/15 10:31 AM, Clara Kühn wrote: 



ok, it can only access the file if I type
ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash)

but if I then use that path for the mris_preproc command I get
nsubjects = 22
ERROR: cannot find /scr/etsch2/kids/ct/.long.



- Ursprüngliche Mail -
Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: 
freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:23:48
Betreff: Re: [Freesurfer] cannot find qdec file

that is probably not the full path. Try typing

ls scr/etsch2/kids/ct/qdec/long.qdec.table.dat

If it says it cannot find the file, then it is not the full path. Maybe
you need a forward slash (ie, /) in the beginning?

On 8/3/15 10:18 AM, Clara Kühn wrote: 



then I get the error ERROR: cannot find 
scr/etsch2/kids/ct/qdec/long.qdec.table.dat

I had tried that. Sorry, no luck with that.

- Ursprüngliche Mail -
Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: 
freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:16:58
Betreff: Re: [Freesurfer] cannot find qdec file

you have to give it the entire path to the file

On 8/3/15 10:14 AM, Clara Kühn wrote: 



Dear FS-experts,

I want to analyze my longitudinal data with your suggested LME models and am 
therefore following the walkthrough by J. Bernal. I get an error though very 
early on when using the command
mris_preproc --qdec-long qdec/long.qdec.table.dat --target 7kids_template_sc1 
--hemi lh --meas thickness --out qdec/lh.thickness.mgh

It always says
ERROR: cannot find qdec/long.qdec.table.dat

Yes, the walkthrough asks for an input file named just qdec.table.dat, but I 
haven't got that. So far in the longitudinal stream there are 
long.qdec.table.dat and cross.qdec.table.dat files but no simple qdec.table.dat 
files. So I figured I'd use the long.qdec file because FS needs to get the 
information about the long timepoints.
But it cannot find the file, even though I see it. I've also tried copying the 
long.qdec file and naming it qdec.table.dat but it still doesn't find it.

The entire path to the file is scr/etsch2/kids/ct/qdec/long.qdec.table.dat and 
my SUBJECTS_DIR is scr/etsch2/kids/ct

Can you help me see what I'm missing?
Thanks a lot in advance,
Clara
___
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.

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