[Freesurfer] Extracting individual vertex values for surfaces mapped to fsaverage

[Bronwyn Overs]

Dear mailing list,

For each of the subjects in our study, we would like to extract the 
thickness values at each vertex for the surface that has been mapped to 
fsaverage (so that the number of vertices is identical for all of our 
subjects). After changing to a specific participants "surf" directory 
and starting matlab, could I use the following command and file to 
extract the data I want?:


[thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh')

Also, how do I then determine the annotation associated with each vertex 
for each subject?


--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to the 
NeuRA Magazine 


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[Freesurfer] Post-doctoral Fellowship in longitudinal image analysis at UCL

[Arman Eshaghi]

Apologies for the spam, we thought this might be of interest for Freesurfer
users.

A postdoctoral position in longitudinal image analysis is available within
the Centre for Medical Image Computing (CMIC) at UCL Department of Computer
Sciences, London, UK. We are seeking a highly motivated individual to work
within the Progression of Neurological Disease (POND) Group
cmic.cs.ucl.ac.uk/pond, led by Prof. Daniel Alexander, on
computational-statistical neurological disease progression within the
Horizon 2020 EuroPOND project: www.europond.eu.
See http://cmic.cs.ucl.ac.uk/pond/vacancies/ for more details and the
application procedure. If you have any queries regarding the vacancy or the
application process please contact Dr Neil Oxtoby n.oxt...@ucl.ac.uk.

—
Arman Eshaghi, MD
PhD Student
UCL Institute of Neurology
Queen Square Multiple Sclerosis Centre
1st Floor, Russell Square House
10-12 Russell Square
London WC1B 5EH
Tel: (+44) (0) 203 108 7420
UCL extension: 57420
arman.eshaghi...@ucl.ac.uk
Website: http://www.homepages.ucl.ac.uk/~skgtaes/
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Re: [Freesurfer] Problem with fsgd file

[chenhf_uestc]

hi, Bronwyn

You should change the position of parameter "dods" like this:

mri_glmfit --fsgd long-2stage_ConAR.fsgd  dods --glmdir 
long-2stage_ConAR.area.lh.spc.glmdir --y long-ConAR.lh.area-spc.stack.fwhm10.mgh

Hope this helps.

Best,
Feng



发件人：Bronwyn Overs 
发送时间：2015-10-14 08:11
主题：[Freesurfer] Problem with fsgd file
收件人："Freesurfer support list"
抄送：

Dear mailing list,

I am trying to run a longitudinal 2 stage model using mri_glmfit. Here is the 
command I am using:

mri_glmfit --fsgd long-2stage_ConAR.fsgd --glmdir 
long-2stage_ConAR.area.lh.spc.glmdir --y 
long-ConAR.lh.area-spc.stack.fwhm10.mgh dods --C me_age-all.mtx --C 
me_gender.mtx --C me_group.mtx --C int_ageXgroup.mtx --C int_ageXgender.mtx --C 
int_genderXgroup.mtx --C int_ageXgenderXgroup.mtx --surf fsaverage lh --label 
long-ConAR.lh.area.fsaverage.cortex.label

However, when I try to run the command it has problems reading my fsgd file. I 
have attached my file for reference and here are the errors it spits out:

gdfReadHeader: reading long-2stage_ConAR.fsgd
INFO: ignoring tag 7541001001 
INFO: ignoring tag 7541002001 
INFO: ignoring tag 7541003001 
INFO: ignoring tag 7541006001 
INFO: ignoring tag 7541009001 
INFO: ignoring tag 7541011004 
INFO: ignoring tag 7541012004 
INFO: ignoring tag 7541017001 
INFO: ignoring tag 7541018001 
INFO: ignoring tag 7541020001 
INFO: ignoring tag 7541022001 
INFO: ignoring tag 7541023001 
INFO: ignoring tag 7541024001 
INFO: ignoring tag 7541026001 
INFO: ignoring tag 7541030001 
INFO: ignoring tag 7541031001 
INFO: ignoring tag 7541036001 
INFO: ignoring tag 7541040001 
INFO: ignoring tag 7541041001 
INFO: ignoring tag 7541042001 
INFO: ignoring tag 7541044001 
INFO: ignoring tag 7541046001 
INFO: ignoring tag 7541047001 
INFO: ignoring tag 7541048004 
INFO: ignoring tag 7541049001 
INFO: ignoring tag 7541052001 
INFO: ignoring tag 7541055001 
INFO: ignoring tag 7541057001 
INFO: ignoring tag 7541058001 
INFO: ignoring tag 7541059001 
INFO: ignoring tag 7541060001 
INFO: ignoring tag 7541062001 
INFO: ignoring tag 7541070001 
INFO: ignoring tag 7541075001 
INFO: ignoring tag 7541078001 
INFO: ignoring tag 7541080001 
INFO: ignoring tag 7541084001 
INFO: ignoring tag 7541085001 
INFO: ignoring tag 7541088001 
INFO: ignoring tag 7541090001 
INFO: ignoring tag 7541093001 
INFO: ignoring tag 7541094001 
INFO: ignoring tag 7541096001 
INFO: ignoring tag 7541097004 
INFO: ignoring tag 7541099001 
INFO: ignoring tag 754111 
INFO: ignoring tag 7541101001 
INFO: ignoring tag 7541102001 
INFO: ignoring tag 7541103001 
INFO: ignoring tag 7541106001 
INFO: ignoring tag 7541108001 
INFO: ignoring tag 7541110004 
INFO: ignoring tag 7541112001 
INFO: ignoring tag 7541114001 
INFO: ignoring tag 7541116001 
INFO: ignoring tag 7541118001 
INFO: ignoring tag 7541119001 
INFO: ignoring tag 7541120001 
INFO: ignoring tag 7541124001 
INFO: ignoring tag 7541125001 
INFO: ignoring tag 7541132004 
INFO: ignoring tag 7541133001 
INFO: ignoring tag 7541139001 
INFO: ignoring tag 7541142001 
INFO: ignoring tag 7541143001 
INFO: ignoring tag 7541146001 
INFO: ignoring tag 7541149001 
INFO: ignoring tag 7541150001 
INFO: ignoring tag 7541151001 
INFO: ignoring tag 7541156001 
INFO: ignoring tag 7541161001 
INFO: ignoring tag 7541165001 
INFO: ignoring tag 7541168001 
INFO: ignoring tag 7541175001 
INFO: ignoring tag 7541177001 
INFO: ignoring tag 7541178001 
INFO: ignoring tag 7541182001 
INFO: ignoring tag 7541185001 
INFO: ignoring tag 7541188001 
INFO: ignoring tag 7541190004 
INFO: ignoring tag 7541192004 
INFO: ignoring tag 7541196001 
INFO: ignoring tag 7541198001 
INFO: ignoring tag 7541209001 
INFO: ignoring tag 7541223001 
INFO: ignoring tag 7541227001 
INFO: ignoring tag 7541334001 
INFO: ignoring tag 7541337001 
INFO: ignoring tag 7541345001 
INFO: ignoring tag 7541346001 
INFO: ignoring tag 7541353001 
INFO: ignoring tag 7541366001 
INFO: ignoring tag 7541378001 
INFO: ignoring tag 7541383001 
INFO: ignoring tag 7541388001 
INFO: ignoring tag 7541391001 
INFO: ignoring tag 7541396001 
INFO: ignoring tag 754141 
INFO: ignoring tag 7541401001 
INFO: ignoring tag 7541402001 
INFO: ignoring tag 7541409001 
INFO: ignoring tag 7541411001 
INFO: ignoring tag 7541412001 
INFO: ignoring tag 7541421001 
INFO: ignoring tag 7541442004 
INFO: ignoring tag 7541443001 
INFO: ignoring tag 7541445001 
WARNING: gdfReadV1: class genderM-groupCtl is defined but not used.
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 years -nan -nan
1 age_mc -nan -nan
Class Means of each Continuous Variable
1 genderM-groupCtl -nan -nan 
2 genderF-groupCtl -nan -nan 
3 genderM-groupAR -nan -nan 
4 genderF-groupAR -nan -nan 
INFO: gd2mtx_method is dods
ERROR: Option dods unknown

Can you tell me what is wrong?



Kind regards,
Bronwyn Overs
Research Assistant
 
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 

[Freesurfer] Error in Monte Carlo simulation

[Baumann Philipp]

Dear Expert,

I'm using Qdec to run some correlation analysis (cortical thickness). When I 
try to apply Monte Carlo simulation, I get the following error message:

Error in Monte Carlo simulation: Error running mri_surfcluster!

I tried to use different paramers (e.g. different smoothing) which didn't 
change anything at the error message.

What's going wrong ?

Many thanks for your help,

Best regards,

Philipp
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Re: [Freesurfer] Extracting individual vertex values for surfaces mapped to fsaverage

[Bruce Fischl]

Hi Bronwyn

you can use read_annotation.m to read in the parcellation that you want and 
go from there.

cheers
Bruce


On Wed, 14 Oct 2015, Bronwyn Overs wrote:

> Dear mailing list,
>
> For each of the subjects in our study, we would like to extract the thickness 
> values at each vertex for the surface that has been mapped to fsaverage (so 
> that the number of vertices is identical for all of our subjects). After 
> changing to a specific participants "surf" directory and starting matlab, 
> could I use the following command and file to extract the data I want?:
>
> [thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh')
>
> Also, how do I then determine the annotation associated with each vertex for 
> each subject?
>
>
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Re: [Freesurfer] pial surface encircling the optical chiasm

[Bruce Fischl]

Hi Antonin

it is probably fine, but can you send us an image so that we can see?

cheers
Bruce
On 
Tue, 13 Oct 2015, Antonin Skoch wrote:

> Dear FreeSurfer experts,
> 
> during inspection of reconstructions of our data, I found that in many cases
> the pial (and sometimes also white) surface is extending out of the brain
> and encircling the optical chiasm. Does this situation has any effect to the
> results (i.e. cortex parcellation, whole-brain group thickness or local
> gyrification index analysis), i.e. is it an reconstruction error which
> should be manually corrected? Or can we safely ignore it?
> 
> Regards,
> 
> Antonin Skoch
> 
>
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Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

[pablo najt]

Dear FS experts.I have query about a relating to a previous email (below). I am 
aiming to run a LME analysis on cross-sectional data from different families 
and have variable 'family' (number of families) as my NI vector. My design has 
three groups and therefore I am not able to use qdec. I am running the matlab 
commands below and finding some difficulty would really appreciate if you could 
help out.ThanksPablo
Start analysis as follows:
1-Read your label eg.:
lhcortex = fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');
2-Read the data file eg.:
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh'); 
 %-I input the concatenated .mgh image from preproc and 
mris_surf2surf---%
3-Fit a vertex-wise lme model with random effects.:
lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex); 
Here I am getting the following problems:% If I use number 
of families as my ni get the 
following%lhstats
 = lme_mass_fit_vw(X, [1 2], lhY, 82, lhcortex);Error using lme_mass_fit (line 
108)The total number of measurements, indicated by sum(ni), mustbe the same as 
the number of rows of the designmatrix X
Error in lme_mass_fit_vw (line 73)[stats1,st1] = 
lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);
 My matrix is organised in "family", "group", Sex" and "age" columns".
  
4-Perform vertex-wise inference eg.:
CM.C = [your contrast matrix];
F_lhstats = lme_mass_F(lhstats, CM);
5-Save results eg.: 
fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig');  

Date: Thu, 10 Sep 2015 13:44:36 +
From: jbernal0...@yahoo.es
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] A mixed effect model approach in within subject 
dataset

Hi Pablo

I think you can use
LME to analyze your data by ordering the rows of your design matrix
appropriately. You can consider all subjects belonging to the same
family as if they were a single subject in a longitudinal analysis.
You can put in your design matrix all subjects belonging to family1
first, then all subjects belonging to family 2 and so on. Then the
'ni' required by lme_mass_fit_vw is a vector with the number of
subjects in each family as its entries (ordered according to your
design matrix). So the length of the 'ni'  vector is equal to the
number of different families in your data.  





Now you can go
further and additionally order the rows of your design matrix within
each family by age. This will allow you to test the effect of age
within family. 





When choosing the
random effects for your statistical model remember that a random
effect can only be the intercept term or any covariate that varies
within family. For example you can compare a model with a single
random effect for the intercept term against the same model but
considering both the intercept  term and age as random effects.




Hope that helps




Cheers
-Jorge




 De: pablo najt 
 Para: "freesurfer@nmr.mgh.harvard.edu"  
 Enviado: Jueves 10 de septiembre de 2015 8:07
 Asunto: [Freesurfer] A mixed effect model approach in within subject dataset
   






Dear Freesurfer users,I wanted to enquire if anyone had successfully been able 
to implement Bernal's Linear Mixed Effects (LME) Models in cross-section 
dataset *not longitudinal* (please see previous thread below).  I am willing to 
perform a LME (3 groups (HC, PT and Unaffected_relatives) and 3 covariates 
(sex, age, and family) with "family" variable been a within-subject factor. LME 
will allow to control for the non-independence of data contributed by patients 
and relatives from the same families.Thanks in advance!Pablo
From: michaelnot...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 19 Feb 2014 13:10:09 +0100
Subject: [Freesurfer] Analysis of structural data acquired from multiple sites 
by using a mixed effect model approach







Hi everybody,

I want to compare the surface data of 3 groups (GroupA, GroupB and Controlls) 
but have the problem that they were acquired from 4 different scanner sites. As 
I can see it, there are three ways how I could tackle this problem:

1. I could use mri_glmfit and create a qdec table / fsgd-file with 12 classes: 
Class GroupA_site1; Class GroupA_site2,... And then use the contrasts [0.25 
0.25 0.25 0.25 0 0 0 0 -0.25 -0.25 -0.25 -0.25] to compare GroupA to the 
Controlls. My Problem with this approach is, that the sites don't contribute 
the same amount of subjects to the analysis. I'm not sure if this could be 
handled by simply using a weighted contrast. Meaning, if Site1 and Site2 had 
twice as many subjects than Site3 and Site4, I could modify the contrast to 
[0.33 0.33 0.17 0.17 0 0 0 0 -0.33 -0.33 -0.17 -0.17].

2. I could create dummy variables to account for the variability between sites. 
In this case, I only need to specify 3 classes (Class GroupA; Class Grou

Re: [Freesurfer] A mixed effect model approach in within subject dataset {Disarmed}

[Martin Reuter]

Hi Pablo,

you should run something like this to get the ni:

[M,Y,ni] = sortData(M,1,Y,sID);  # (sorts the data)

see
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels

hope that helps, Martin


On 10/14/2015 10:43 AM, pablo najt wrote:

Dear FS experts.
I have query about a relating to a previous email (below). I am aiming 
to run a LME analysis on cross-sectional data from different families 
and have variable 'family' (number of families) as my NI vector.
My design has three groups and therefore I am not able to use qdec. I 
am running the matlab commands below and finding some difficulty would 
really appreciate if you could help out.

Thanks
Pablo

Start analysis as follows:

1-Read your label eg.:
lhcortex = 
fs_read_label('freesurfer/subjects/fsaverage/label/lh.cortex.label');

2-Read the data file eg.:
[lhY, lhmri] = fs_read_Y('lh.thickness.mgh');

%-I input the concatenated .mgh image from
preproc and

mris_surf2surf---%

3-Fit a vertex-wise lme model with random effects.:
lhstats = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex);

Here I am getting the following problems:

% If I use number of families as my ni get the

following%

lhstats = lme_mass_fit_vw(X, [1 2], lhY, 82, lhcortex);

Error using lme_mass_fit (line 108)

The total number of measurements, indicated by sum(ni),
mustbe the same as the number of rows of the design

matrix X

Error in lme_mass_fit_vw (line 73)

[stats1,st1] = lme_mass_fit(X,[],Xrows,Zcols,Y,ni,prs,e);

My matrix is organised in "family", "group", Sex" and "age" columns".

4-Perform vertex-wise inference eg.: CM.C = [your contrast matrix]; 
F_lhstats = lme_mass_F(lhstats, CM); 5-Save results eg.: 
fs_write_fstats(F_lhstats, lhmri,' sig.mgh', 'sig');



Date: Thu, 10 Sep 2015 13:44:36 + From: jbernal0...@yahoo.es To: 
freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] A mixed 
effect model approach in within subject dataset

Hi Pablo
I think you can use LME to analyze your data by ordering the rows of 
your design matrix appropriately. You can consider all subjects 
belonging to the same family as if they were a single subject in a 
longitudinal analysis. You can put in your design matrix all subjects 
belonging to family1 first, then all subjects belonging to family 2 
and so on. Then the 'ni' required by lme_mass_fit_vw is a vector with 
the number of subjects in each family as its entries (ordered 
according to your design matrix). So the length of the 'ni' vector is 
equal to the number of different families in your data.
Now you can go further and additionally order the rows of your design 
matrix within each family by age. This will allow you to test the 
effect of age within family.
When choosing the random effects for your statistical model remember 
that a random effect can only be the intercept term or any covariate 
that varies within family. For example you can compare a model with a 
single random effect for the intercept term against the same model but 
considering both the intercept term and age as random effects.

Hope that helps
Cheers
-Jorge


*De:* pablo najt  *Para:*
"freesurfer@nmr.mgh.harvard.edu" 
*Enviado:* Jueves 10 de septiembre de 2015 8:07 *Asunto:*
[Freesurfer] A mixed effect model approach in within subject dataset
Dear Freesurfer users,
I wanted to enquire if anyone had successfully been able to
implement Bernal's Linear Mixed Effects (LME) Models in
cross-section dataset *not longitudinal* (please see previous
thread below). I am willing to perform a LME (3 groups (HC, PT and
Unaffected_relatives) and 3 covariates (sex, age, and family) with
"family" variable been a within-subject factor. LME will allow to
control for the non-independence of data contributed by patients
and relatives from the same families.
Thanks in advance!
Pablo
From: michaelnot...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 19 Feb 2014 13:10:09 +0100 Subject: [Freesurfer]
Analysis of structural data acquired from multiple sites by using
a mixed effect model approach
Hi everybody, I want to compare the surface data of 3 groups
(GroupA, GroupB and Controlls) but have the problem that they were
acquired from 4 different scanner sites. As I can see it, there
are three ways how I could tackle this problem: 1. I could use
mri_glmfit and create a qdec table / fsgd-file with 12 classes:
Class GroupA_site1; Class GroupA_site2,... And then use the
contrasts [0.25 0.25 0.25 0.25 

[Freesurfer] Segmentation fault using mri_label2vol

[Syeda Maryam]

Hello Freesurfer experts,
I'm getting a segmentation fault when I use the mri_label2vol command to push 
aseg labels from freesurfer space to my subject's original T1 space (using the 
example given on the freesurfer website). I'm not sure why this is 
happening...I've tried changing the parameters countless times but nothing has 
worked. I also checked my "aseg.mgz" to make sure it's not corrupted but that 
isn't the issue either. Any help would be highly appreciated!! Thanks in advance

mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg 
/tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp 
/scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o 
/tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Number of labels: 0
Annot File:  (null)
Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   (null)
ProjTypeId: 0
ProjStart:  0
ProjStop:   0
ProjDelta:  0.1
Subject:  (null)
Hemi: (null)
UseNewASeg2Vol:  1
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
-0.000  -0.000  -0.985   128.000;
-0.000   0.833  -0.000   98.000;
 0.000   0.000   0.000   1.000;
Template Voxel Volume: 1.23773
nHits Thresh: 0
Computing registration based on header
RegMat: 
 1.000   0.000   0.000  -0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
Label RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
 0.000   0.000  -0.985   128.000;
 0.000   0.833   0.000   98.000;
 0.000   0.000   0.000   1.000;
ASeg2Vol: Building LUT
Segmentation fault

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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] Segmentation fault using mri_label2vol

[Syeda Wajiha Maryam]

Hello Freesurfer experts,

I'm getting a segmentation fault when I use the mri_label2vol command to
push aseg labels from freesurfer space to my subject's original T1 space
(using the example given on the freesurfer website). I'm not sure why this
is happening...I've tried changing the parameters countless times but
nothing has worked. I also checked my "aseg.mgz" to make sure it's not
corrupted but that isn't the issue either. Any help would be highly
appreciated!! Thanks in advance

mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
--seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
/scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
/tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Number of labels: 0
Annot File:  (null)
Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   (null)
ProjTypeId: 0
ProjStart:  0
ProjStop:   0
ProjDelta:  0.1
Subject:  (null)
Hemi: (null)
UseNewASeg2Vol:  1
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
-0.000  -0.000  -0.985   128.000;
-0.000   0.833  -0.000   98.000;
 0.000   0.000   0.000   1.000;
Template Voxel Volume: 1.23773
nHits Thresh: 0
Computing registration based on header
RegMat: 
 1.000   0.000   0.000  -0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
Label RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
 0.000   0.000  -0.985   128.000;
 0.000   0.833   0.000   98.000;
 0.000   0.000   0.000   1.000;
ASeg2Vol: Building LUT
Segmentation fault
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Segmentation fault using mri_label2vol

[Bruce Fischl]

Hi Syeda

that commnand doesn't segfault when I try it on another subject here. If 
you email me the aseg.mgz and the rawavg.mgz I'll take a look


cheers
Bruce

On Wed, 14 Oct 2015, Syeda 
Maryam wrote:



Hello Freesurfer experts,

I'm getting a segmentation fault when I use the mri_label2vol command to push 
aseg labels from freesurfer space to my
subject's original T1 space (using the example given on the freesurfer 
website). I'm not sure why this is
happening...I've tried changing the parameters countless times but nothing has worked. I 
also checked my "aseg.mgz" to
make sure it's not corrupted but that isn't the issue either. Any help would be 
highly appreciated!! Thanks in advance

mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg 
/tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
/scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o 
/tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Number of labels: 0
Annot File:  (null)
Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol:  1
ProjType:   (null)
ProjTypeId: 0
ProjStart:  0
ProjStop:   0
ProjDelta:  0.1
Subject:  (null)
Hemi: (null)
UseNewASeg2Vol:  1
DoLabelStatVol  0
LabelCodeOffset  0
setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
$Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
Template RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
-0.000  -0.000  -0.985   128.000;
-0.000   0.833  -0.000   98.000;
 0.000   0.000   0.000   1.000;
Template Voxel Volume: 1.23773
nHits Thresh: 0
Computing registration based on header
RegMat: 
 1.000   0.000   0.000  -0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;
Label RAS-to-Vox: 
-0.985   0.000   0.000   128.000;
 0.000   0.000  -0.985   128.000;
 0.000   0.833   0.000   98.000;
 0.000   0.000   0.000   1.000;
ASeg2Vol: Building LUT
Segmentation fault


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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Segmentation fault using mri_label2vol

[Syeda Maryam]

So for some reason my mail with the attachments won't get delivered...the 
message size exceeds the limits. I was wondering if the segmentation fault 
error I'm getting might be do to some problem in the freesurfer version I'm 
running?
Thanks,Syeda
 


 On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam  
wrote:
   

 I'm not sure if my last message got delivered or not so I'll resend it.
Thanks very much for looking into this so quickly. Sure thing! I've 
attached the images here. The aseg file opens up with freeview, and the 
mri_label2vol command works fine on my local machine but when I try to 
implement it on our server using nipype, it gives me the error I mentioned. 

Best,Syeda 


 On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam  
wrote:
   

 Thanks very much for looking into this so quickly. Sure thing! I've attached 
the images here. The aseg file opens up with freeview, and the mri_label2vol 
command works fine on my local machine but when I try to implement it on our 
server using nipype, it gives me the error I mentioned. 

Best,Syeda
 


 On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl 
 wrote:
   

 Hi Syeda

that commnand doesn't segfault when I try it on another subject here. If 
you email me the aseg.mgz and the rawavg.mgz I'll take a look

cheers
Bruce

On Wed, 14 Oct 2015, Syeda 
Maryam wrote:

> Hello Freesurfer experts,
> 
> I'm getting a segmentation fault when I use the mri_label2vol command to push 
> aseg labels from freesurfer space to my
> subject's original T1 space (using the example given on the freesurfer 
> website). I'm not sure why this is
> happening...I've tried changing the parameters countless times but nothing 
> has worked. I also checked my "aseg.mgz" to
> make sure it's not corrupted but that isn't the issue either. Any help would 
> be highly appreciated!! Thanks in advance
> 
> mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz --seg 
> /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o 
> /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> Number of labels: 0
> Annot File:  (null)
> Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> Registration File: (null)
> Fill Threshold: 0
> Label Vox Vol:  1
> ProjType:   (null)
> ProjTypeId: 0
> ProjStart:  0
> ProjStop:   0
> ProjDelta:  0.1
> Subject:  (null)
> Hemi: (null)
> UseNewASeg2Vol:  1
> DoLabelStatVol  0
> LabelCodeOffset  0
> setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> Template RAS-to-Vox: 
> -0.985   0.000   0.000   128.000;
> -0.000  -0.000  -0.985   128.000;
> -0.000   0.833  -0.000   98.000;
>  0.000   0.000   0.000   1.000;
> Template Voxel Volume: 1.23773
> nHits Thresh: 0
> Computing registration based on header
> RegMat: 
>  1.000   0.000   0.000  -0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> Label RAS-to-Vox: 
> -0.985   0.000   0.000   128.000;
>  0.000   0.000  -0.985   128.000;
>  0.000   0.833   0.000   98.000;
>  0.000   0.000   0.000   1.000;
> ASeg2Vol: Building LUT
> Segmentation fault
> 
> 
>


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.


   

   

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Segmentation fault using mri_label2vol

[Bruce Fischl]

it's possible, or something to do with your images. You can use either 
our filedrop or ftp site to send them to me if you want
On Wed, 14 Oct 2015, 
Syeda Maryam wrote:



So for some reason my mail with the attachments won't get delivered...the
message size exceeds the limits. I was wondering if the segmentation fault
error I'm getting might be do to some problem in the freesurfer version I'm
running?

Thanks,
Syeda



On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam 
wrote:


I'm not sure if my last message got delivered or not so I'll resend it.

Thanks very much for looking into this so quickly. Sure thing! I've
attached the images here. The aseg file opens up with freeview, and the
mri_label2vol command works fine on my local machine but when I try to
implement it on our server using nipype, it gives me the error I mentioned.

Best,
Syeda



On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam 
wrote:


Thanks very much for looking into this so quickly. Sure thing! I've attached
the images here. The aseg file opens up with freeview, and the mri_label2vol
command works fine on my local machine but when I try to implement it on our
server using nipype, it gives me the error I mentioned.

Best,
Syeda



On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
 wrote:


Hi Syeda

that commnand doesn't segfault when I try it on another subject here. If
you email me the aseg.mgz and the rawavg.mgz I'll take a look

cheers
Bruce

On Wed, 14 Oct 2015, Syeda
Maryam wrote:

> Hello Freesurfer experts,
>
> I'm getting a segmentation fault when I use the mri_label2vol command to
push aseg labels from freesurfer space to my
> subject's original T1 space (using the example given on the freesurfer
website). I'm not sure why this is
> happening...I've tried changing the parameters countless times but nothing
has worked. I also checked my "aseg.mgz" to
> make sure it's not corrupted but that isn't the issue either. Any help
would be highly appreciated!! Thanks in advance
>
> mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
--seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
/tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> Number of labels: 0
> Annot File:  (null)
> Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> Registration File: (null)
> Fill Threshold: 0
> Label Vox Vol:  1
> ProjType:   (null)
> ProjTypeId: 0
> ProjStart:  0
> ProjStop:   0
> ProjDelta:  0.1
> Subject:  (null)
> Hemi: (null)
> UseNewASeg2Vol:  1
> DoLabelStatVol  0
> LabelCodeOffset  0
> setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> Template RAS-to-Vox: 
> -0.985   0.000   0.000   128.000;
> -0.000  -0.000  -0.985   128.000;
> -0.000   0.833  -0.000   98.000;
>  0.000   0.000   0.000   1.000;
> Template Voxel Volume: 1.23773
> nHits Thresh: 0
> Computing registration based on header
> RegMat: 
>  1.000   0.000   0.000  -0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> Label RAS-to-Vox: 
> -0.985   0.000   0.000   128.000;
>  0.000   0.000  -0.985   128.000;
>  0.000   0.833   0.000   98.000;
>  0.000   0.000   0.000   1.000;
> ASeg2Vol: Building LUT
> Segmentation fault

>
>
>


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.







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


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Segmentation fault using mri_label2vol

[Syeda Maryam]

Hi Bruce,I just sent you the files on filedrop! I thought it might have 
something to do with the freesurfer version since the mri_label2vol comman 
works fine on my local machine and the segmentation fault I was talking about 
only happens when I try to run it on the server our research group is using. 
But when I checked the freesurfer versions, turns out the same version is 
installed on both machines: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Needless to say, I'm well and truly stumped right now.Really appreciate your 
help in this matter!
Best,Syeda


 


 On Wednesday, October 14, 2015 12:20 PM, Bruce Fischl 
 wrote:
   

 it's possible, or something to do with your images. You can use either 
our filedrop or ftp site to send them to me if you want
On Wed, 14 Oct 2015, 
Syeda Maryam wrote:

> So for some reason my mail with the attachments won't get delivered...the
> message size exceeds the limits. I was wondering if the segmentation fault
> error I'm getting might be do to some problem in the freesurfer version I'm
> running?
> 
> Thanks,
> Syeda
> 
> 
> 
> On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam 
> wrote:
> 
> 
> I'm not sure if my last message got delivered or not so I'll resend it.
> 
> Thanks very much for looking into this so quickly. Sure thing! I've
> attached the images here. The aseg file opens up with freeview, and the
> mri_label2vol command works fine on my local machine but when I try to
> implement it on our server using nipype, it gives me the error I mentioned.
> 
> Best,
> Syeda
> 
> 
> 
> On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam 
> wrote:
> 
> 
> Thanks very much for looking into this so quickly. Sure thing! I've attached
> the images here. The aseg file opens up with freeview, and the mri_label2vol
> command works fine on my local machine but when I try to implement it on our
> server using nipype, it gives me the error I mentioned.
> 
> Best,
> Syeda
> 
> 
> 
> On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
>  wrote:
> 
> 
> Hi Syeda
> 
> that commnand doesn't segfault when I try it on another subject here. If
> you email me the aseg.mgz and the rawavg.mgz I'll take a look
> 
> cheers
> Bruce
> 
> On Wed, 14 Oct 2015, Syeda
> Maryam wrote:
> 
> > Hello Freesurfer experts,
> >
> > I'm getting a segmentation fault when I use the mri_label2vol command to
> push aseg labels from freesurfer space to my
> > subject's original T1 space (using the example given on the freesurfer
> website). I'm not sure why this is
> > happening...I've tried changing the parameters countless times but nothing
> has worked. I also checked my "aseg.mgz" to
> > make sure it's not corrupted but that isn't the issue either. Any help
> would be highly appreciated!! Thanks in advance
> >
> > mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
> --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> > /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
> /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Number of labels: 0
> > Annot File:  (null)
> > Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> > Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Registration File: (null)
> > Fill Threshold: 0
> > Label Vox Vol:  1
> > ProjType:   (null)
> > ProjTypeId: 0
> > ProjStart:  0
> > ProjStop:   0
> > ProjDelta:  0.1
> > Subject:  (null)
> > Hemi: (null)
> > UseNewASeg2Vol:  1
> > DoLabelStatVol  0
> > LabelCodeOffset  0
> > setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> > Template RAS-to-Vox: 
> > -0.985   0.000   0.000   128.000;
> > -0.000  -0.000  -0.985   128.000;
> > -0.000   0.833  -0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > Template Voxel Volume: 1.23773
> > nHits Thresh: 0
> > Computing registration based on header
> > RegMat: 
> >  1.000   0.000   0.000  -0.000;
> >  0.000   1.000   0.000   0.000;
> >  0.000   0.000   1.000   0.000;
> >  0.000   0.000   0.000   1.000;
> > Label RAS-to-Vox: 
> > -0.985   0.000   0.000   128.000;
> >  0.000   0.000  -0.985   128.000;
> >  0.000   0.833   0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > ASeg2Vol: Building LUT
> > Segmentation fault
> 
> >
> >
> >
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
> 
> 
> 
> 
> 
> 
> 
>
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The information in this e-mail is intended only 

Re: [Freesurfer] Segmentation fault using mri_label2vol

[Bruce Fischl]

Hi Syeda

it doesn't die when I run it locally. How much RAM do you have on the 
machine that it crashes on? If you want a new version we can send you one.

cheers
Bruce


On Wed, 14 Oct 2015, Syeda Maryam wrote:


Hi Bruce,
I just sent you the files on filedrop! I thought it might have something to do 
with the freesurfer version since the
mri_label2vol comman works fine on my local machine and the segmentation fault 
I was talking about only happens when I
try to run it on the server our research group is using. But when I checked the 
freesurfer versions, turns out the same
version is installed on both machines: 
freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Needless to say, I'm well and truly stumped right now.
Really appreciate your help in this matter!

Best,
Syeda





On Wednesday, October 14, 2015 12:20 PM, Bruce Fischl 
 wrote:


it's possible, or something to do with your images. You can use either
our filedrop or ftp site to send them to me if you want
On Wed, 14 Oct 2015,
Syeda Maryam wrote:

> So for some reason my mail with the attachments won't get delivered...the
> message size exceeds the limits. I was wondering if the segmentation fault
> error I'm getting might be do to some problem in the freesurfer version I'm
> running?
>
> Thanks,
> Syeda
>
>
>
> On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam 
> wrote:
>
>
> I'm not sure if my last message got delivered or not so I'll resend it.
> 
> Thanks very much for looking into this so quickly. Sure thing! I've
> attached the images here. The aseg file opens up with freeview, and the
> mri_label2vol command works fine on my local machine but when I try to
> implement it on our server using nipype, it gives me the error I mentioned.
>
> Best,
> Syeda
>
>
>
> On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam 
> wrote:
>
>
> Thanks very much for looking into this so quickly. Sure thing! I've attached
> the images here. The aseg file opens up with freeview, and the mri_label2vol
> command works fine on my local machine but when I try to implement it on our
> server using nipype, it gives me the error I mentioned.
>
> Best,
> Syeda
>
>
>
> On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
>  wrote:
>
>
> Hi Syeda
>
> that commnand doesn't segfault when I try it on another subject here. If
> you email me the aseg.mgz and the rawavg.mgz I'll take a look
>
> cheers
> Bruce
>
> On Wed, 14 Oct 2015, Syeda
> Maryam wrote:
>
> > Hello Freesurfer experts,
> >
> > I'm getting a segmentation fault when I use the mri_label2vol command to
> push aseg labels from freesurfer space to my
> > subject's original T1 space (using the example given on the freesurfer
> website). I'm not sure why this is
> > happening...I've tried changing the parameters countless times but nothing
> has worked. I also checked my "aseg.mgz" to
> > make sure it's not corrupted but that isn't the issue either. Any help
> would be highly appreciated!! Thanks in advance
> >
> > mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
> --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> > /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
> /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Number of labels: 0
> > Annot File:  (null)
> > Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> > Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > Registration File: (null)
> > Fill Threshold: 0
> > Label Vox Vol:  1
> > ProjType:   (null)
> > ProjTypeId: 0
> > ProjStart:  0
> > ProjStop:   0
> > ProjDelta:  0.1
> > Subject:  (null)
> > Hemi: (null)
> > UseNewASeg2Vol:  1
> > DoLabelStatVol  0
> > LabelCodeOffset  0
> > setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> > Template RAS-to-Vox: 
> > -0.985   0.000   0.000   128.000;
> > -0.000  -0.000  -0.985   128.000;
> > -0.000   0.833  -0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > Template Voxel Volume: 1.23773
> > nHits Thresh: 0
> > Computing registration based on header
> > RegMat: 
> >  1.000   0.000   0.000  -0.000;
> >  0.000   1.000   0.000   0.000;
> >  0.000   0.000   1.000   0.000;
> >  0.000   0.000   0.000   1.000;
> > Label RAS-to-Vox: 
> > -0.985   0.000   0.000   128.000;
> >  0.000   0.000  -0.985   128.000;
> >  0.000   0.833   0.000   98.000;
> >  0.000   0.000   0.000   1.000;
> > ASeg2Vol: Building LUT
> > Segmentation fault
>
> >
> >
> >
>
>
> 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] Segmentation fault using mri_label2vol

[Syeda Maryam]

So the strangest thing happened. Just on a hunch, I logged out of the server 
then logged back in, and now it's running! It's a mystery to me. Thanks again, 
I'll check the RAM specs and get back to you. For now though it seems to be 
working. Hope it stays that way!
Best,Syeda
 


 On Wednesday, October 14, 2015 12:48 PM, Bruce Fischl 
 wrote:
   

 Hi Syeda

it doesn't die when I run it locally. How much RAM do you have on the 
machine that it crashes on? If you want a new version we can send you one.
cheers
Bruce


On Wed, 14 Oct 2015, Syeda Maryam wrote:

> Hi Bruce,
> I just sent you the files on filedrop! I thought it might have something to 
> do with the freesurfer version since the
> mri_label2vol comman works fine on my local machine and the segmentation 
> fault I was talking about only happens when I
> try to run it on the server our research group is using. But when I checked 
> the freesurfer versions, turns out the same
> version is installed on both machines: 
> freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
> 
> Needless to say, I'm well and truly stumped right now.
> Really appreciate your help in this matter!
> 
> Best,
> Syeda
> 
> 
> 
> 
> 
> On Wednesday, October 14, 2015 12:20 PM, Bruce Fischl 
>  wrote:
> 
> 
> it's possible, or something to do with your images. You can use either
> our filedrop or ftp site to send them to me if you want
> On Wed, 14 Oct 2015,
> Syeda Maryam wrote:
> 
> > So for some reason my mail with the attachments won't get delivered...the
> > message size exceeds the limits. I was wondering if the segmentation fault
> > error I'm getting might be do to some problem in the freesurfer version I'm
> > running?
> >
> > Thanks,
> > Syeda
> >
> >
> >
> > On Wednesday, October 14, 2015 12:09 PM, Syeda Maryam 
> > wrote:
> >
> >
> > I'm not sure if my last message got delivered or not so I'll resend it.
> > 
> > Thanks very much for looking into this so quickly. Sure thing! I've
> > attached the images here. The aseg file opens up with freeview, and the
> > mri_label2vol command works fine on my local machine but when I try to
> > implement it on our server using nipype, it gives me the error I mentioned.
> >
> > Best,
> > Syeda
> >
> >
> >
> > On Wednesday, October 14, 2015 11:56 AM, Syeda Maryam 
> > wrote:
> >
> >
> > Thanks very much for looking into this so quickly. Sure thing! I've attached
> > the images here. The aseg file opens up with freeview, and the mri_label2vol
> > command works fine on my local machine but when I try to implement it on our
> > server using nipype, it gives me the error I mentioned.
> >
> > Best,
> > Syeda
> >
> >
> >
> > On Wednesday, October 14, 2015 11:50 AM, Bruce Fischl
> >  wrote:
> >
> >
> > Hi Syeda
> >
> > that commnand doesn't segfault when I try it on another subject here. If
> > you email me the aseg.mgz and the rawavg.mgz I'll take a look
> >
> > cheers
> > Bruce
> >
> > On Wed, 14 Oct 2015, Syeda
> > Maryam wrote:
> >
> > > Hello Freesurfer experts,
> > >
> > > I'm getting a segmentation fault when I use the mri_label2vol command to
> > push aseg labels from freesurfer space to my
> > > subject's original T1 space (using the example given on the freesurfer
> > website). I'm not sure why this is
> > > happening...I've tried changing the parameters countless times but nothing
> > has worked. I also checked my "aseg.mgz" to
> > > make sure it's not corrupted but that isn't the issue either. Any help
> > would be highly appreciated!! Thanks in advance
> > >
> > > mri_label2vol --regheader /scratch/o/olegm/olegm/2015/test_waj/aseg.mgz
> > --seg /tmp/tmpUj4qzA/aseg2raw/aseg.mgz --temp
> > > /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz --o
> > /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > > Number of labels: 0
> > > Annot File:  (null)
> > > Template Volume: /scratch/o/olegm/olegm/2015/test_waj/rawavg.mgz
> > > Outut Volume: /tmp/tmpUj4qzA/aseg2raw/aseg_vol.nii.gz
> > > Registration File: (null)
> > > Fill Threshold: 0
> > > Label Vox Vol:  1
> > > ProjType:   (null)
> > > ProjTypeId: 0
> > > ProjStart:  0
> > > ProjStop:   0
> > > ProjDelta:  0.1
> > > Subject:  (null)
> > > Hemi: (null)
> > > UseNewASeg2Vol:  1
> > > DoLabelStatVol  0
> > > LabelCodeOffset  0
> > > setenv SUBJECTS_DIR /scratch/o/olegm/olegm/subjects
> > > $Id: mri_label2vol.c,v 1.34.2.5 2012/06/08 17:31:03 greve Exp $
> > > Template RAS-to-Vox: 
> > > -0.985   0.000   0.000   128.000;
> > > -0.000  -0.000  -0.985   128.000;
> > > -0.000   0.833  -0.000   98.000;
> > >  0.000   0.000   0.000   1.000;
> > > Template Voxel Volume: 1.23773
> > > nHits Thresh: 0
> > > Computing registration based on header
> > > RegMat: 
> > >  1.000   0.000   0.000  -0.000;
> > >  0.000   1.000   0.000   0.000;
> > >  0.000   0.000   1.000   0.000;
> > >  0.000   0.000   0.000   1.000;
> > > Label RAS-to-Vox: 
> > > -0.985   0.000   0.000   128.000;
> > >  0.000   0.000  -0.985   128.000;
> > >  0.000  

Re: [Freesurfer] mris__label__calc intersect error in longitudinal qcache

[Selvaraj, Bhavani]

Hi Martin,
Thanks martin for your reply. I am also running v5.3 I am trying to run this 
command the command works fine for LH only when I run RH it fails 
long_mris_slopes --qdec $SUBJECTS_DIR/qdec/long.qdec.table.dat --meas thickness 
--hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time 
years --qcache fsaverage --sd $SUBJECTS_DIR I am sending the 3 label file 
please let me if this is the right input file you need 1.  
MPS-007_1.long.MPS-007/label/rh.cortex.label
2.  MPS-007/label/rh.long.cortex.label
3.  MPS-007/label/rh.long.cortex.label

The same command for the lh worked fine for this particular subject. I was able 
to solve the qdec error.  This one I am unable to.
Thanks ,
Bhavani

This what I get from my terminal window.
freesurfer% long_mris_slopes --qdec $SUBJECTS_DIR/qdec/long.qdec.table.dat 
--meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack 
--do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR Parsing the qdec 
table: /Applications/freesurfer/subjects/qdec/long.qdec.table.dat

Working in SUBJECTS_DIR: /Applications/freesurfer/subjects


Working on hemi: rh


Subject-Template: MPS-007


INFO: 3 TPs in MPS-007 , mean age: 3.667


===
SUBJECT MPS-007  Intersecting Within-Subject Cortex Label

cp 
/Applications/freesurfer/subjects/MPS-007_1.long.MPS-007/label/rh.cortex.label 
/Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label



mris_label_calc intersect 
/Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh.cortex.label
 /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label 
/Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label

ERROR -11 : mris_label_calc intersect did not work?
[mcradxym9290:~] freesurfer% mris_label_calc intersect 
/Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh.cortex.label
 /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label 
/Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label
Segmentation fault
[mcradxym9290:~] freesurfer% 


From: Martin Reuter [mreu...@nmr.mgh.harvard.edu]
Sent: Tuesday, October 13, 2015 3:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Selvaraj, Bhavani
Subject: Re: [Freesurfer] mris__label__calc intersect error in longitudinal 
qcache

Hi Bhavani,

when I run
  mris_label_calc intersect MPS-007_2mod.long.MPS-007\ rh.cortex.label MPS-\ 
007\ lh.cortex.label out.label

it goes through and writes the out.label file. I used fs 5.3 for that.
Can you please send me the command and input files that fail for you?


About your other questions:

qdec tables should be stored in /qdec

not sure about the other error. can you send the cross qdec table.
probably you need a level file for group?

Thanks, Martin

P.S. Please post questions to the FreeSurfer list.


On 10/13/2015 10:56 AM, Selvaraj, Bhavani wrote:
> Hi Martin,
> Thanks for the reply. Yes those files are available at these locations.
> when I run this command for LH
> 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 fsaverage --sd $SUBJECTS_DIR it runs smoothly 
> and gave me these results tksurfer MPS-007 lh pial -overlay 
> /Applications/freesurfer/subjects/MPS-007/surf/lh.long.thickness-avg.f
> whm25.mgh tksurfer MPS-005 lh pial -overlay 
> /Applications/freesurfer/subjects/MPS-005/surf/lh.long.thickness-avg.f
> whm25.mgh
>
> but for the rh only the patients MPS-007 gave me the error MPS-005 worked 
> fine.
> How do I fix that?
> I am attaching you the cortex label file I don't know how to tell if it is 
> corrupted.
>
> Also I have two more question where should I store the QDEC data table 
> Is this where I should make it?
> Applications/freesurfer/subjects/qdec/ long.qdec.table.dat
>
> also when I try to open the table in Qdec I get the following error:
> freesurfer% qdec --table ./qdec/cross.qdec.table.dat
>
> Reading /Applications/freesurfer/tktools/tkUtils.tcl
>
> Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl
>
> Loading data table ./qdec/cross.qdec.table.dat...
> Number of columns:  13
> fsid column:1
> Number of factors:  12
> Number of subjects: 2
> ERROR: QdecSubject::GetContinuousFactor failure: could not find factor 
> name: Group for subject MPS-007
>
> Thanks Martin for your help!
> bhavani
>
>
> 
> From: Martin Reuter [mreu...@nmr.mgh.harvard.edu]
> Sent: Friday, October 09, 2015 8:59 PM
> To: Selvaraj, Bhavani
> Subject: Re: [Freesurfer] mris__label__calc intersect error in longitudinal   
>   qcache
>
> Hi Bhavani,
>
> Strange, are those files available at those locations? Can you also check 
> permissions. Open the label files to see if they are corrupted.
> Best MartinOn Oct 9, 2015 11:31 AM, "Selvaraj, Bhavani" 
>  wrote:

[Freesurfer] Tracula with multi-shell data?

[Henrik Sjöström]

Hi! I have some questions regarding Tracula and multi-shell DWI.

-Is it possible to activate the multi-shell model within bedpostx when running 
it through tracula? 

-does anyone have experience on running multi-shell data through Tracula (2 or 
3 crossing fibers)?

We are planning an experiment and discussing protocols consisting of around 32 
directions with b=1000 and 64 directions at b=2500 so I'm looking for opinions 
on this with regard to Tracula processing.

Thanks!

Henrik Sjöström
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[Freesurfer] Talairach Conversion

[Ishan Patel]

Hello,

I wanted to use the function: mri_label2label to convert my label file into
talairach space.
This is the output that I am getting. On the mri_label2label information
page, it says to use 'talairach' as the target subject which is what I did,
but it cannot find  'talairach'. Does anyone have experience with this?
[image: Inline image 1]
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Re: [Freesurfer] unusually long running time in autorecon2

[Bruce Fischl]

Hi David

it works fine for me. The infinte loop happened when the brainmask was 
completely empty I believe, although we fixed it in any case. Can you check 
the brainmask? I can also send you an updated mri_cc if you want


cheers
Bruce


On Mon, 12 Oct 
2015, Slater David wrote:




Hi Bruce,

 

I’ve also run into the ‘infinite loop problem’ mentioned 
here:https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-February/027948.
html

 

30 of my 632 subject’s experienced this problem. In your post you asked for
an example file which generates this failure. I have included such a file as
an attachment along with the full job log up to the point where it hung.

 

I am running  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 and use the
simple command  recon-all -subjid  -all.

 

Cheers,

David


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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mris__label__calc intersect error in longitudinal qcache

[Martin Reuter]

Hi Bhavani,

so internally the script stops at the label intersect command:

mris_label_calc intersect 
/Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh.cortex.label
 /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label 
/Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label

The first 2 file names are the inputs, the second file is then 
overwritten with the output (3rd file name identical to 2nd).  Can you 
run this command alone? It did work for me with the files you had sent 
before.

Thanks, Martin


On 10/14/2015 01:42 PM, Selvaraj, Bhavani wrote:
> Hi Martin,
> Thanks martin for your reply. I am also running v5.3 I am trying to run this 
> command the command works fine for LH only when I run RH it fails 
> long_mris_slopes --qdec $SUBJECTS_DIR/qdec/long.qdec.table.dat --meas 
> thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack 
> --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR I am sending 
> the 3 label file please let me if this is the right input file you need 1.  
> MPS-007_1.long.MPS-007/label/rh.cortex.label
> 2.  MPS-007/label/rh.long.cortex.label
> 3.  MPS-007/label/rh.long.cortex.label
>
> The same command for the lh worked fine for this particular subject. I was 
> able to solve the qdec error.  This one I am unable to.
> Thanks ,
> Bhavani
>
> This what I get from my terminal window.
> freesurfer% long_mris_slopes --qdec $SUBJECTS_DIR/qdec/long.qdec.table.dat 
> --meas thickness --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack 
> --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR Parsing the 
> qdec table: /Applications/freesurfer/subjects/qdec/long.qdec.table.dat
>
> Working in SUBJECTS_DIR: /Applications/freesurfer/subjects
>
>
> Working on hemi: rh
>
>
> Subject-Template: MPS-007
>
>
> INFO: 3 TPs in MPS-007 , mean age: 3.667
>
>
> ===
> SUBJECT MPS-007  Intersecting Within-Subject Cortex Label
>
> cp 
> /Applications/freesurfer/subjects/MPS-007_1.long.MPS-007/label/rh.cortex.label
>  /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label
>
>
>
> mris_label_calc intersect 
> /Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh.cortex.label
>  /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label 
> /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label
>
> ERROR -11 : mris_label_calc intersect did not work?
> [mcradxym9290:~] freesurfer% mris_label_calc intersect 
> /Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh.cortex.label
>  /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label 
> /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label
> Segmentation fault
> [mcradxym9290:~] freesurfer%
>
> 
> From: Martin Reuter [mreu...@nmr.mgh.harvard.edu]
> Sent: Tuesday, October 13, 2015 3:24 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Cc: Selvaraj, Bhavani
> Subject: Re: [Freesurfer] mris__label__calc intersect error in longitudinal 
> qcache
>
> Hi Bhavani,
>
> when I run
>mris_label_calc intersect MPS-007_2mod.long.MPS-007\ rh.cortex.label MPS-\ 
> 007\ lh.cortex.label out.label
>
> it goes through and writes the out.label file. I used fs 5.3 for that.
> Can you please send me the command and input files that fail for you?
>
>
> About your other questions:
>
> qdec tables should be stored in /qdec
>
> not sure about the other error. can you send the cross qdec table.
> probably you need a level file for group?
>
> Thanks, Martin
>
> P.S. Please post questions to the FreeSurfer list.
>
>
> On 10/13/2015 10:56 AM, Selvaraj, Bhavani wrote:
>> Hi Martin,
>> Thanks for the reply. Yes those files are available at these locations.
>> when I run this command for LH
>> 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 fsaverage --sd $SUBJECTS_DIR it runs smoothly
>> and gave me these results tksurfer MPS-007 lh pial -overlay
>> /Applications/freesurfer/subjects/MPS-007/surf/lh.long.thickness-avg.f
>> whm25.mgh tksurfer MPS-005 lh pial -overlay
>> /Applications/freesurfer/subjects/MPS-005/surf/lh.long.thickness-avg.f
>> whm25.mgh
>>
>> but for the rh only the patients MPS-007 gave me the error MPS-005 worked 
>> fine.
>> How do I fix that?
>> I am attaching you the cortex label file I don't know how to tell if it is 
>> corrupted.
>>
>> Also I have two more question where should I store the QDEC data table
>> Is this where I should make it?
>> Applications/freesurfer/subjects/qdec/ long.qdec.table.dat
>>
>> also when I try to open the table in Qdec I get the following error:
>> freesurfer% qdec --table ./qdec/cross.qdec.table.dat
>>
>> Reading /Applications/freesurfer/tktools/tkUtils.tcl
>>
>> Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl
>>
>> Loadi

Re: [Freesurfer] No preprocessing on FAST

[Douglas N Greve]

This will be hard, but you might try adding
-i instem -nomc
where instem is the "stem" of the filename of the input, ie, if you 
filename is stefano.nii.gz then the stem is stephano.

doug

On 10/13/2015 09:50 AM, std...@virgilio.it wrote:
> Hi list,
> I'd like to perform FAST preprocessing for functional connectivity (seed-based
> analysis).Data have been already preprocessed by AFNI.Therefore, no smoothing,
> motion and slice timing corrections are requested.
> When I run:preproc-sess -sf sessid -nomc -fwhm 0 -surface fsaverage lhrh
> -mni305-1mm -fsd rest -per-run -nostc
>
> the analysis is stopped by an error on lacking fmcpr.nii.
> Thanks
> Best regards,
>
> Stefano
>
> Sent from Virgilio Mobile
>
>
> ___
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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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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Error in Monte Carlo simulation

[Douglas N Greve]

I'm not sure. qdec is a semi-orphaned program, meaning that no one here 
is responsible for maintaining it. It is ok for simple visualization and 
playing with the data, but the correction functionality is not easy to 
use, and it is impossible for us to track down what went wrong when we 
see something like the error you have below. You should use the 
command-line programs (ie, mris_preproc, mri_surf2surf, mri_glmfit, and 
mri_glmfit-sim).

doug

On 10/14/2015 07:56 AM, Baumann Philipp wrote:
> Dear Expert,
>
> I'm using Qdec to run some correlation analysis (cortical thickness). 
> When I try to apply Monte Carlo simulation, I get the following error 
> message:
>
> /Error in Monte Carlo simulation: Error running mri_surfcluster!
>
> /I tried to use different paramers (e.g. different smoothing) which 
> didn't change anything at the error message./
>
> /What's going wrong ?
>
> Many thanks for your help,
>
> Best regards,
>
> Philipp
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] Extracting individual vertex values for surfaces mapped to fsaverage

[Douglas N Greve]

Use

thick = MRIread('lh.thickness.fwhm10.fsaverage.mgh');
then thick.vol will be an array of the thickness at each vertex. 
Remember that matlab uses 1-based when you go to address the vertices

doug

On 10/14/2015 02:59 AM, Bronwyn Overs wrote:
> Dear mailing list,
>
> For each of the subjects in our study, we would like to extract the 
> thickness values at each vertex for the surface that has been mapped 
> to fsaverage (so that the number of vertices is identical for all of 
> our subjects). After changing to a specific participants "surf" 
> directory and starting matlab, could I use the following command and 
> file to extract the data I want?:
>
> [thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh')
>
> Also, how do I then determine the annotation associated with each 
> vertex for each subject?
>
> -- 
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
>
> Neuroscience Research Australia
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Randwick Sydney NSW 2031 Australia
> *M* 0411 308 769 *T* +61 2 9399 1883
>
> neura.edu.au 
>
> Follow @neuraustralia on twitter 
> Follow NeuRA on facebook 
> Subscribe to 
> the NeuRA Magazine 
>
>
>
> ___
> 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
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Problem with fsgd file

[Douglas N Greve]

You need to have "Input" as the first line to each subject, eg,

Input 7541001001  genderF-groupAR 2.489   6.77


On 10/13/2015 08:11 PM, Bronwyn Overs wrote:
> Dear mailing list,
>
> I am trying to run a longitudinal 2 stage model using mri_glmfit. Here 
> is the command I am using:
>
> mri_glmfit --fsgd long-2stage_ConAR.fsgd --glmdir 
> long-2stage_ConAR.area.lh.spc.glmdir --y 
> long-ConAR.lh.area-spc.stack.fwhm10.mgh dods --C me_age-all.mtx --C 
> me_gender.mtx --C me_group.mtx --C int_ageXgroup.mtx --C 
> int_ageXgender.mtx --C int_genderXgroup.mtx --C 
> int_ageXgenderXgroup.mtx --surf fsaverage lh --label 
> long-ConAR.lh.area.fsaverage.cortex.label
>
> However, when I try to run the command it has problems reading my fsgd 
> file. I have attached my file for reference and here are the errors it 
> spits out:
>
> gdfReadHeader: reading long-2stage_ConAR.fsgd
> INFO: ignoring tag 7541001001
> INFO: ignoring tag 7541002001
> INFO: ignoring tag 7541003001
> INFO: ignoring tag 7541006001
> INFO: ignoring tag 7541009001
> INFO: ignoring tag 7541011004
> INFO: ignoring tag 7541012004
> INFO: ignoring tag 7541017001
> INFO: ignoring tag 7541018001
> INFO: ignoring tag 7541020001
> INFO: ignoring tag 7541022001
> INFO: ignoring tag 7541023001
> INFO: ignoring tag 7541024001
> INFO: ignoring tag 7541026001
> INFO: ignoring tag 7541030001
> INFO: ignoring tag 7541031001
> INFO: ignoring tag 7541036001
> INFO: ignoring tag 7541040001
> INFO: ignoring tag 7541041001
> INFO: ignoring tag 7541042001
> INFO: ignoring tag 7541044001
> INFO: ignoring tag 7541046001
> INFO: ignoring tag 7541047001
> INFO: ignoring tag 7541048004
> INFO: ignoring tag 7541049001
> INFO: ignoring tag 7541052001
> INFO: ignoring tag 7541055001
> INFO: ignoring tag 7541057001
> INFO: ignoring tag 7541058001
> INFO: ignoring tag 7541059001
> INFO: ignoring tag 7541060001
> INFO: ignoring tag 7541062001
> INFO: ignoring tag 7541070001
> INFO: ignoring tag 7541075001
> INFO: ignoring tag 7541078001
> INFO: ignoring tag 7541080001
> INFO: ignoring tag 7541084001
> INFO: ignoring tag 7541085001
> INFO: ignoring tag 7541088001
> INFO: ignoring tag 7541090001
> INFO: ignoring tag 7541093001
> INFO: ignoring tag 7541094001
> INFO: ignoring tag 7541096001
> INFO: ignoring tag 7541097004
> INFO: ignoring tag 7541099001
> INFO: ignoring tag 754111
> INFO: ignoring tag 7541101001
> INFO: ignoring tag 7541102001
> INFO: ignoring tag 7541103001
> INFO: ignoring tag 7541106001
> INFO: ignoring tag 7541108001
> INFO: ignoring tag 7541110004
> INFO: ignoring tag 7541112001
> INFO: ignoring tag 7541114001
> INFO: ignoring tag 7541116001
> INFO: ignoring tag 7541118001
> INFO: ignoring tag 7541119001
> INFO: ignoring tag 7541120001
> INFO: ignoring tag 7541124001
> INFO: ignoring tag 7541125001
> INFO: ignoring tag 7541132004
> INFO: ignoring tag 7541133001
> INFO: ignoring tag 7541139001
> INFO: ignoring tag 7541142001
> INFO: ignoring tag 7541143001
> INFO: ignoring tag 7541146001
> INFO: ignoring tag 7541149001
> INFO: ignoring tag 7541150001
> INFO: ignoring tag 7541151001
> INFO: ignoring tag 7541156001
> INFO: ignoring tag 7541161001
> INFO: ignoring tag 7541165001
> INFO: ignoring tag 7541168001
> INFO: ignoring tag 7541175001
> INFO: ignoring tag 7541177001
> INFO: ignoring tag 7541178001
> INFO: ignoring tag 7541182001
> INFO: ignoring tag 7541185001
> INFO: ignoring tag 7541188001
> INFO: ignoring tag 7541190004
> INFO: ignoring tag 7541192004
> INFO: ignoring tag 7541196001
> INFO: ignoring tag 7541198001
> INFO: ignoring tag 7541209001
> INFO: ignoring tag 7541223001
> INFO: ignoring tag 7541227001
> INFO: ignoring tag 7541334001
> INFO: ignoring tag 7541337001
> INFO: ignoring tag 7541345001
> INFO: ignoring tag 7541346001
> INFO: ignoring tag 7541353001
> INFO: ignoring tag 7541366001
> INFO: ignoring tag 7541378001
> INFO: ignoring tag 7541383001
> INFO: ignoring tag 7541388001
> INFO: ignoring tag 7541391001
> INFO: ignoring tag 7541396001
> INFO: ignoring tag 754141
> INFO: ignoring tag 7541401001
> INFO: ignoring tag 7541402001
> INFO: ignoring tag 7541409001
> INFO: ignoring tag 7541411001
> INFO: ignoring tag 7541412001
> INFO: ignoring tag 7541421001
> INFO: ignoring tag 7541442004
> INFO: ignoring tag 7541443001
> INFO: ignoring tag 7541445001
> WARNING: gdfReadV1: class genderM-groupCtl is defined but not used.
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 years -nan -nan
> 1 age_mc -nan -nan
> Class Means of each Continuous Variable
> 1 genderM-groupCtl -nan -nan
> 2 genderF-groupCtl -nan -nan
> 3 genderM-groupAR -nan -nan
> 4 genderF-groupAR -nan -nan
> INFO: gd2mtx_method is dods
> ERROR: Option dods unknown
>
> Can you tell me what is wrong?
>
>
> Kind regards,
>
> Bronwyn Overs
> Research Assistant
>
> Neuroscience Research Australia
>
> Neuroscience Research Australia
> Margarete Ainsworth Building
> Barker Street Rand

Re: [Freesurfer] paired ttest by specifying file names

[Douglas N Greve]

yes, that is correct. It will compute condition1-condition2

On 10/09/2015 02:10 PM, Dace Apšvalka wrote:
> Hi,
>
> I am not entirely sure I am doing it right, therefore would like to 
> have a confirmation if possible.
>
> I am runing a paired ttest between two conditions by specifying file 
> names. Here is an example of 2 subjects
>
> mris_preproc \
> --target fsaverage \
> --hemi lh \
> --out /ResultsDir/lh.outfilename.mgh \
> --fsgd pairs.fsgd \
> --is /subject1/condition1.mgh \
> --is /subject1/condition2.mgh \
> --is /subject2/condition1.mgh \
> --is /subject2/condition2.mgh \
> --srcfmt curv \
> --paired-diff
>
> mri_surf2surf --s fsaverage \
> --hemi lh \
> --fwhm 5\
> --sval /ResultsDir/lh.outfilename.mgh \
> --tval /ResultsDir/lh.outfilename.sm05.mgh
>
> mri_glmfit \
> --glmdir /ResultsDir \
> --y /ResultsDir/lh.outfilename.sm05.mgh \
> --fsgd paired-diff.fsgd \
> --C mean.mtx \
> --surf fsaverage lh \
> --cortex
>
> %% my pairs.fsgd file
>
> GroupDescriptorFile 1
> Title StudyTitle
> Class Main
>
> Input subject1 Main
> Input subject1 Main
> Input subject2 Main
> Input subject2 Main
>
> %% my paired-diff.fsgd
>
> GroupDescriptorFile 1
> Title StudyTitle
> Class Main
>
> Input subject1 Main
> Input subject2 Main
>
> %% my mean.mtx file
>
> 1
>
>
> Thanks,
> Dace
>
>
>
>
> ___
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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] module BrainstemSubstructures and hippocampal subfields

[Francesca Piludu]

Hello Freesurfer experts
I am Francesca Piludu and i am interested in the use of new tools for 
segmentation of brainstem substructures and hippocampal subfields, present  in 
Freesurfer 6.0 and later.
How could I get these new functionalities for my analysis?


Best Francesca

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Re: [Freesurfer] Extracting individual vertex values for surfaces mapped to fsaverage

[Bronwyn Overs]

Hi Bruce,

Following up on your comment below, if I am using 
'lh.thickness.fwhm10.fsaverage.mgh' for my thickness values, do I read 
in the lh.aparc.annot file in the subjects directory? I tried doing this 
for one of my participants, and the vector of thickness values has 
163842 columns, while my aparc file has 116407. Or should I be reading 
in the lh.aparc.annot from fsaverage?


Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883

neura.edu.au 

Follow @neuraustralia on twitter 
Follow NeuRA on facebook 
Subscribe to the 
NeuRA Magazine 


On 14/10/2015 11:47 pm, Bruce Fischl wrote:

Hi Bronwyn

you can use read_annotation.m to read in the parcellation that you want and
go from there.

cheers
Bruce


On Wed, 14 Oct 2015, Bronwyn Overs wrote:


Dear mailing list,

For each of the subjects in our study, we would like to extract the thickness
values at each vertex for the surface that has been mapped to fsaverage (so
that the number of vertices is identical for all of our subjects). After
changing to a specific participants "surf" directory and starting matlab,
could I use the following command and file to extract the data I want?:

[thick, fnum] = read_curv('lh.thickness.fwhm10.fsaverage.mgh')

Also, how do I then determine the annotation associated with each vertex for
each subject?



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[Freesurfer] Tool for brainstem substructures and hippocampal subfields

[Francesca Piludu]

Dear freesurfer experts
I am Francesca Piludu and i am interested in the use of new tools for
segmentation of brainstem substructures and hippocampal subfields, present
in Freesurfer 6.0 and later.
How could I get these new functionalities for my analysis?

Best Francesca
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