Re: [Freesurfer] Fwd: Fwd: monte-carlo error in longitudinal pipeline

[Douglas Greve]

something is wrong with the mask (the terminal output says that there 
are no voxels in the mask)



On 1/30/18 11:51 AM, miracle ozzoude wrote:


-- Forwarded message --
From: *miracle ozzoude* >

Date: Fri, Jan 26, 2018 at 7:08 PM
Subject: Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline
To: Freesurfer support list >



Hello Doug,

Thanks for the patience. Here's the output from the terminal when I 
ran mri_glmfit.


Best,
Paul

/Applications/freesurfer


START: LONGITUDINAL CORTICAL THICKNESS

1000

1000_1

1000_1.long.1000

1000_2

1000_2.long.1000

1001

1001_1

1001_1.long.1001

1001_2

1001_2.long.1001

1003

1003_1

1003_1.long.1003

1003_2

1003_2.long.1003

1005

1005_1

1005_1.long.1005

1005_2

1005_2.long.1005

1008

1008_1

1008_1.long.1008

1008_2

1008_2.long.1008

1013

1013_1

1013_1.long.1013

1013_2

1013_2.long.1013

1014

1014_1

1014_1.long.1014

1014_2

1014_2.long.1014

gdfReadHeader: reading paired_diff.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 Age 76 3.70328

Class Means of each Continuous Variable

1 ADEX76.

INFO: gd2mtx_method is doss

Reading source surface 
/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/lh.white


Number of vertices 163842

Number of faces327680

Total area 65416.648438

AvgVtxArea 0.399267

AvgVtxDist 0.721953

StdVtxDist 0.195470


$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $

cwd 
/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018


cmdline mri_glmfit --y lh.paired.diff.thickness.10.mgh --fsgd 
paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage lh 
--cortex --glmdir lh.paired.diff.glmdir


sysnameDarwin

hostname opennet-33-172.uhnres.utoronto.ca 



machinex86_64

user carm

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh

logyflag 0

usedti0

FSGD paired_diff.fsgd

labelmask/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.paired.diff.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.paired.diff.glmdir

Loading y from 
/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh


INFO: gd2mtx_method is doss

Saving design matrix to lh.paired.diff.glmdir/Xg.dat

Normalized matrix condition is 1686.7

Matrix condition is 2.46289e+06

Found 149955 points in label.

Pruning voxels by thr: 0.00

Found 0 voxels in mask

Saving mask to lh.paired.diff.glmdir/mask.mgh

Reshaping mriglm->mask...

search space = 0.00

DOF = 5

Starting fit and test

Fit completed in 8.3e-05 minutes

Computing spatial AR1 on surface

WARNING: ar1 = nan <= 0. Setting fwhm to 0.

Residual: ar1mn=nan, ar1std=nan, gstd=0.00, fwhm=0.00

Writing results

mean

maxvox sig=0F=0atindex 0 0 0seed=1517221145

age

maxvox sig=0F=0atindex 0 0 0seed=1517221145

mri_glmfit done

gdfReadHeader: reading paired_diff.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 Age 76 3.70328

Class Means of each Continuous Variable

1 ADEX76.

INFO: gd2mtx_method is doss

Reading source surface 
/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/rh.white


Number of vertices 163842

Number of faces327680

Total area 65020.765625

AvgVtxArea 0.396850

AvgVtxDist 0.717994

StdVtxDist 0.193566


$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $

cwd 
/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018


cmdline mri_glmfit --y rh.paired.diff.thickness.10.mgh --fsgd 
paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage rh 
--cortex --glmdir rh.paired.diff.glmdir


sysnameDarwin

hostname opennet-33-172.uhnres.utoronto.ca 



machinex86_64

user carm

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh

logyflag 0

usedti0

FSGD paired_diff.fsgd

labelmask/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/label/rh.cortex.label

maskinv 0

glmdir rh.paired.diff.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory rh.paired.diff.glmdir

Loading y from 
/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh


INFO: gd2mtx_method is doss

Saving design matrix to rh.paired.diff.glmdir/Xg.dat

Normalized matrix condition is 1686.7

Matrix condition is 2.46289e+06

Found 

Re: [Freesurfer] monte-carlo error in longitudinal pipeline

[Douglas Greve]

that usually means that something has gone wrong with the analysis. Do 
the maps look ok? In particular, look at the mask




On 1/20/18 1:56 PM, miracle ozzoude wrote:

Hello Doug,

I tried using the MC tables that FS distributed. However, i got an 
error about " cannot find /fwhm00/pos/th30/mc-z.csd ". I checked and 
there's no fwhm00, the table starts from fwhm01 to fwhm30. Below are 
my script and cache.mri_glmfi-sim.log files. My FreeSurfer version is 
stable version 5.3 on mac. Thank you.


Best,
Paul

mri_glmfit-sim --glmdir lh.paired.diff.glmdir --cache-dir 
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/lh/cortex --cache 3 pos 
--cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired.diff.glmdir --cache-dir 
$SUBJECTS_DIR/average/mult-comp-cor/fsaverage/rh/cortex --cache 3 pos 
--cwpvalthresh 0.05 --2spaces --overwrite


On Thu, Jan 18, 2018 at 5:23 PM, Douglas Greve 
> wrote:


Why are you doing your own MC simulation? You can just use the
tables that we distribute ...


On 1/17/18 6:12 PM, miracle ozzoude wrote:

Hello Experts,

I am running a paired t-test cortical thickness analysis based on
the instruction on the wiki page
(https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
).
However, the monte carlo files weren't not created when i
corrected for multiple comparisons. Below are my script, fsgd
files, mc-z log file, and a screenshot of contrast folder missing
mc.z maps. Please can you help me figure out why the error is
happening. Thank you.

Best,
Paul

*Script*:
pairs=pairs.fsgd paired=paired_diff.fsgd martrix1=mean.mtx
martrix2=age.mtx
#resample each subjects's left and right hemisphere data to
fsavarage.
mris_preproc --target fsaverage --hemi lh --meas thickness --out
lh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
mris_preproc --target fsaverage --hemi rh --meas thickness --out
rh.paired-diff.thickness.mgh --fsgd $pairs --paired-diff
# #smoothen the concatenated file by 5mm FWHM. --cortex means
only smooth areas in the cortex. N:B. FWHM changes based on study
type.
mri_surf2surf --hemi lh --s fsaverage --sval
lh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
lh.paired-diff.thickness.sm05.mgh
mri_surf2surf --hemi rh --s fsaverage --sval
rh.paired-diff.thickness.mgh --fwhm 5 --cortex --tval
rh.paired-diff.thickness.sm05.mgh
# #Run GLM analysis
mri_glmfit --y lh.paired-diff.thickness.sm05.mgh --fsgd $paired
--C $martrix1 --C $martrix2 --surf fsaverage lh --cortex --glmdir
lh.paired-diff.glmdirir
mri_glmfit --y rh.paired-diff.thickness.sm05.mgh --fsgd $paired
--C $martrix1 --C $martrix2 --surf fsaverage rh --cortex --glmdir
rh.paired-diff.glmdir
# # #Run Clusterwise correction for multiple comparisons using
MONTE CARLO. First create a table for of simulations
mri_glmfit-sim --glmdir lh.paired-diff.glmdir --sim mc-z 1 2
mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
mri_glmfit-sim --glmdir rh.paired-diff.glmdir --sim mc-z 1 2
mc-z.abs.2 --sim-sign abs --cwpvalthresh 0.05 --2spaces --overwrite
*Fsgd file 1:pairs.fsgd*

GroupDescriptorFile 1

Class ADEX

Input 1000_1 ADEX

Input 1000_2 ADEX

Input 1001_1 ADEX

Input 1001_2 ADEX

Input 1003_1 ADEX

Input 1003_2 ADEX

Input 1005_1 ADEX

Input 1005_2 ADEX

Input 1008_1 ADEX

Input 1008_2 ADEX

Input 1013_1 ADEX

Input 1013_2 ADEX

Input 1014_1 ADEX

Input 1014_2 ADEX

*Fsgd file 2: paired_diff.fsgd*

GroupDescriptorFile 1

Class ADEX

Variables Age

Input 1000 ADEX 72

Input 1001 ADEX 76

Input 1003 ADEX 72

Input 1005 ADEX 80

Input 1008 ADEX 72

Input 1013 ADEX 80

Input 1014 ADEX 80



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Re: [Freesurfer] Issue with mri_convert on centOS 7

[Bruce Fischl]

Hi Danielle

can you post the full command line and screen output?

cheers
Bruce
On Tue, 30 Jan 2018, 
Cooke,Danielle ( BIDMC - Neurology ) wrote:




Hello,

 

I recently ran into issues using mri_convert on a CentOS 7 platform while 
having the same command work fine on CentOS 6. The
error that results is:

Segmentation fault (core dumped)

 

I've tried on multiple machines with both operating systems to confirm the 
issue. I was wondering if you might have any
insights or suggestions on how to fix this.

 

Thank you!

Danielle 

 


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[Freesurfer] Issue with mri_convert on centOS 7

[Cooke,Danielle ( BIDMC - Neurology )]

Hello,



I recently ran into issues using mri_convert on a CentOS 7 platform while 
having the same command work fine on CentOS 6. The error that results is:

Segmentation fault (core dumped)



I've tried on multiple machines with both operating systems to confirm the 
issue. I was wondering if you might have any insights or suggestions on how to 
fix this.



Thank you!

Danielle




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information is prohibited. If you have received this message in error, please 
permanently delete it and immediately notify the sender. Thank you.
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[Freesurfer] annotation to volume with custom color scheme (Yeo parcellations)

[Dorit Kliemann]

Hi,
I’m trying to use the Yeo2011 annotations to create individual volume masks in 
subject space.

I first use mri_surf2surf to map the annotations from fsaverage to individual 
subjects:

mri_surf2surf --srcsubject fsaverage --trgsubject subject --hemi rh 
--sval-annot fsaverage/label/rh.Yeo2011_7Networks_N1000.annot --tval 
$SUBJECTS_DIR/subject/label/rh.Yeo2011_7Networks_N1000

Then I use mri_apar2aseg to map the annotation from the surface to the volume 
and thought he annot-table flag would use the labels provided in the custom 
color lut file.

mri_aparc2aseg --s subject --o test.mgz --annot Yeo2011_7Networks_N1000 
--annot-table path_to/Yeo2011_7Networks_ColorLUT.txt


However the output is using different segmentation/color assignments. I can 
certainly find out which segmentation corresponds to which color and extract 
them separately (i.e. with fslmath or mri_binarize)..just wandering if I missed 
something or something changed since these posts?


https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35247.html


Thanks
Dorit






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Re: [Freesurfer] Strange Segmentation

[Antonin Skoch]

Dear Arkadiy,

I see sometimes these kind of errors. I think they are caused by local 
mis-segmentation due to WM hypointensities (enlarged perivascular spaces or 
other lesions, usually benign) located just under GM. Sometimes it is hard to 
discern where it is a hypointensity and where it is just a sulcus. I recommend 
to assess them using all 3 slice orientations. I correct them by editing wm.mgz 
(filling in voxels by value 255).

Regards,

Antonin Skoch


Dear Experts, 
This brain looks a little bit strange to us, and I was wondering if  someone 
might be able to chime in about whether this is worth editing,  based on the 
screenshots of different slices from the sagittal view.. 
Thank you for your expertise. 
-Arkadiy ___
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Re: [Freesurfer] fast_selxavg3.m error/analysis.info file

[Douglas Greve]

Does the file 
/home/vm01/local/freesurfer/Project_bold/rtopyTR2.rh/analysis.info 
exist? If so, can you run it with -debug as the first option and send 
the terminal output?



On 1/30/18 8:51 AM, Yagmur Ozdemir 19 wrote:



Hello FreeSurfer experts,

I am getting this strange error when running selxavg3-sess. (in 
selxavg3 command I am calling the analysis file with: -a rtopyTR2.rh) 
When the system enters fast_selxavg3, it cannot read analysis.info, 
thus produces the following output:


#@# Sess05 ###
/home/vm01/local/freesurfer/Project_bold/Sess05
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /home/vm01/local/freesurfer/Project_bold
Extension format = nii.gz
ERROR: could not open rtopyTR2.rh/analysis.info
else
else
echo "--" | tee -a $LF
echo --
tee -a 
/home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log

--
rm $MLF
rm /tmp/selxavg3-sess-10173.m
if ( ! -e $okfile ) then
if ( ! -e /tmp/selxavg3-sess-10173.ok ) then
echo "ERROR: fast_selxavg3() failed\n" ;
echo ERROR: fast_selxavg3() failed\n
ERROR: fast_selxavg3() failed\n
exit 1 ;
exit 1

The analysis folder it is referring to( rtopyTR2.rh) is in the 
directory from which I am calling selxavg3-sess. It has the 
analysis.info file in which doesn't have any restrictions. To 
troubleshoot, I moved the folder to inside the session's functional 
directory and inside the session folder and these didn't create any 
changes. I looked at the script and tried to debug there but didn't 
give any results. It gave a similar error when trying to open the 
config file of contrast in mkcontrast-sess. (I also don't have root 
access)Any help is appreciated!


Best,
Idil




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[Freesurfer] A question about FS6 hippocampal subfield segmentation output file

[Darko Komnenić]

Dear FreeSurfer experts,
in the txt files [lr]h.hippoSfVolumes-T1.v10.txt we can see the
volumes of individual hippocampal subfields - I was wondering what are
the units in which volume is given? Millimeters cubic, voxels, or
something else?
Thanks in advance!
Best,
Darko
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Re: [Freesurfer] To Yendiki, Anastasia on TRACULA (Yendiki, Anastasia)

[Yendiki, Anastasia]

See tutorial: 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula#Settingupaconfigurationfile


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Renew Andrade 

Sent: Tuesday, January 30, 2018 12:35:24 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] To Yendiki, Anastasia on TRACULA (Yendiki, Anastasia)

What is the configuration file or where can I find it?
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Re: [Freesurfer] To Yendiki, Anastasia on TRACULA (Yendiki, Anastasia)

[Renew Andrade]

What is the configuration file or where can I find it?
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[Freesurfer] Fwd: Fwd: monte-carlo error in longitudinal pipeline

[miracle ozzoude]

-- Forwarded message --
From: miracle ozzoude 
Date: Fri, Jan 26, 2018 at 7:08 PM
Subject: Re: [Freesurfer] Fwd: monte-carlo error in longitudinal pipeline
To: Freesurfer support list 


Hello Doug,

Thanks for the patience. Here's the output from the terminal when I ran
mri_glmfit.

Best,
Paul

/Applications/freesurfer


 START: LONGITUDINAL CORTICAL THICKNESS

1000

1000_1

1000_1.long.1000

1000_2

1000_2.long.1000

1001

1001_1

1001_1.long.1001

1001_2

1001_2.long.1001

1003

1003_1

1003_1.long.1003

1003_2

1003_2.long.1003

1005

1005_1

1005_1.long.1005

1005_2

1005_2.long.1005

1008

1008_1

1008_1.long.1008

1008_2

1008_2.long.1008

1013

1013_1

1013_1.long.1013

1013_2

1013_2.long.1013

1014

1014_1

1014_1.long.1014

1014_2

1014_2.long.1014

gdfReadHeader: reading paired_diff.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 Age 76 3.70328

Class Means of each Continuous Variable

1 ADEX  76.

INFO: gd2mtx_method is doss

Reading source surface /Users/carm/Documents/Cas/
ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/lh.white

Number of vertices 163842

Number of faces327680

Total area 65416.648438

AvgVtxArea   0.399267

AvgVtxDist   0.721953

StdVtxDist   0.195470


$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $

cwd /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018

cmdline mri_glmfit --y lh.paired.diff.thickness.10.mgh --fsgd
paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage lh --cortex
--glmdir lh.paired.diff.glmdir

sysname  Darwin

hostname opennet-33-172.uhnres.utoronto.ca

machine  x86_64

user carm

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh

logyflag 0

usedti  0

FSGD paired_diff.fsgd

labelmask  /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.paired.diff.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.paired.diff.glmdir

Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/lh.paired.diff.thickness.10.mgh

INFO: gd2mtx_method is doss

Saving design matrix to lh.paired.diff.glmdir/Xg.dat

Normalized matrix condition is 1686.7

Matrix condition is 2.46289e+06

Found 149955 points in label.

Pruning voxels by thr: 0.00

Found 0 voxels in mask

Saving mask to lh.paired.diff.glmdir/mask.mgh

Reshaping mriglm->mask...

search space = 0.00

DOF = 5

Starting fit and test

Fit completed in 8.3e-05 minutes

Computing spatial AR1 on surface

WARNING: ar1 = nan <= 0. Setting fwhm to 0.

Residual: ar1mn=nan, ar1std=nan, gstd=0.00, fwhm=0.00

Writing results

  mean

maxvox sig=0  F=0  at  index 0 0 0seed=1517221145

  age

maxvox sig=0  F=0  at  index 0 0 0seed=1517221145

mri_glmfit done

gdfReadHeader: reading paired_diff.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 Age 76 3.70328

Class Means of each Continuous Variable

1 ADEX  76.

INFO: gd2mtx_method is doss

Reading source surface /Users/carm/Documents/Cas/
ADEX/freesurfer/Preliminary_Analysis_Jan9_2018/fsaverage/surf/rh.white

Number of vertices 163842

Number of faces327680

Total area 65020.765625

AvgVtxArea   0.396850

AvgVtxDist   0.717994

StdVtxDist   0.193566


$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $

cwd /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_Analysis_Jan9_2018

cmdline mri_glmfit --y rh.paired.diff.thickness.10.mgh --fsgd
paired_diff.fsgd doss --C mean.mtx --C age.mtx --surf fsaverage rh --cortex
--glmdir rh.paired.diff.glmdir

sysname  Darwin

hostname opennet-33-172.uhnres.utoronto.ca

machine  x86_64

user carm

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y/Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh

logyflag 0

usedti  0

FSGD paired_diff.fsgd

labelmask  /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/fsaverage/label/rh.cortex.label

maskinv 0

glmdir rh.paired.diff.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory rh.paired.diff.glmdir

Loading y from /Users/carm/Documents/Cas/ADEX/freesurfer/Preliminary_
Analysis_Jan9_2018/rh.paired.diff.thickness.10.mgh

INFO: gd2mtx_method is doss

Saving design matrix to rh.paired.diff.glmdir/Xg.dat

Normalized matrix condition is 1686.7

Matrix condition is 2.46289e+06

Found 149926 points in label.

Pruning voxels by thr: 0.00

Found 0 voxels in mask

Saving mask to rh.paired.diff.glmdir/mask.mgh

Reshaping mriglm->mask...

search space = 0.00

DOF = 5

[Freesurfer] Programmer/Research Tech position available at Washington University in St. Louis

[Westerhaus, Elizabeth]

RESEARCH TECHNICIAN POSITION IN NEUROIMAGING
POSITION SUMMARY:  Applications are invited for a research technician at 
Washington University in St. Louis. This well-established laboratory studies 
the structural and functional organization of the human brain using multi-modal 
imaging: including magnetic resonance imaging (MRI) and positron emission 
tomography (PET). The primary focus of the lab is to understand how 
neurodegenerative diseases (especially Alzheimer’s disease) disrupt brain 
organization and mediates symptoms.
Benefits of this position include: 1) Involvement in cutting edge research 
performed by a leading neuroimaging research laboratory 2) Potential to be 
involved as an author on manuscripts 3) Potential to present results at 
national and international conferences 4) Ability to attend talks and lectures 
in the field. Funding is guaranteed for up to 2 years.
PRIMARY DUTIES AND RESPONSIBILITIES (Essential Functions): The primary 
responsibility of the research technician will be to archive/organize images 
(large multi-modal imaging datasets) and process neuroimaging data. The 
technician will study how disease affects the human brain by integrating large 
multi-modal imaging datasets and analyzing the relationship between brain 
imaging markers and clinical status. The technician will assist in various lab 
maintenance, transfer of files, database management, and organizational duties 
including tracking project progress, meet grant deadlines, and anticipate 
project needs.

Qualifications: The qualified candidate should have at least a Bachelor's 
degree in human biology, neurosciences, psychology, bioengineering, computer 
sciences, or other related fields. The qualified candidate must have computer 
skills and knowledge of computer languages (e.g. Matlab, Python, shell 
scripting in CSH or BASH). The research technician must be dependable, have 
good attention to details, be well organized, be self-motivated, and be 
comfortable working as part of a team environment. Previous experience with 
neuroimaging data analysis programs is preferred but not required. Strong 
facility with statistical analyses is also desired.

To apply, please send a letter of interest and CV to 
ban...@wustl.edu. Please arrange for three 
confidential letters of reference to be sent to the address below. Only 
applicants considered for employment will be contacted.
Contact Information:

Beau Ances MD, PhD
Department of Neurology
Washington University in Saint Louis
Box 8111
660 South Euclid Ave
Saint Louis, MO  63110


**
Elizabeth Westerhaus MA  
Clinical Research Specialist for Beau Ances MD, PhD
Washington University School of Medicine
Department of Neurology: Division of Infectious Disease
660 S. Euclid Ave.; Box 8111
St. Louis, MO  63110
Phone:  314-747-1125
Fax:  314-747-8427
>

Fed Ex or UPS Delivery:
620 S. Taylor Ave., Ste. 220
St. Louis, MO  63110



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intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
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Re: [Freesurfer] [freesurfer] Extracting values of cortical thickness in each vertex.

[Bruce Fischl]

Hi Kyung

the thickness values are stored as "curvature" file format that you can 
load into matlab with read_curv.m. Alternatively, you can convert them to 
ascii with mris_convert and do what you want with them. For each index, you 
can look up its location on the white or pial (or whatever surface). That 
is, for the 2nd thickness value (index 1), you would go find vertex #1 on 
the other surface and read its location that way


cheers
Bruce
On Tue, 30 Jan 2018, 
박경일 wrote:



Hi Bruce, I am very new for FS, so did not understand you comments completely. 
sorry..

For cortical thickness from each vertex in one subject, which scripts should follow 
"mris_convert"?
And another question is how to recognize the location of each vertex in brain 
finally.

thank you so much

Kyung
 

2017-11-13 10:06 GMT+09:00 Bruce Fischl :
  p.s. if you want the vertices to correspond, first run recon-all -qcache 
for each
  subject. That will generate a set of thickness maps in fsaverage space at 
predefined
  smoothing levels (so that the vertex numbers correspond across subjects)

  On Mon, 13 Nov 2017, 박경일 wrote:

Hi Bruce,What I want is the values of cortical thickness in each 
vertex in
each subject. Is that
possible?
Thanks so much.

Kyung

 

2017-11-13 0:43 GMT+09:00 Bruce Fischl :
      Hi Kyung

      you can load them into matlab or convert them to ascii if you 
want
      Bruce
      On Sun, 12 Nov 2017, 박경일 wrote:

            Dear FS experts,
            I could get QDEC image comparing two groups.
            However, is there a way to get numerical values of 
cortical
thickness in
            each vertex?

            Thank you

            Best,
            Kyung




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--

Kyung-Il Park, MD, PhD.

Professor,  

Department of Neurology, Seoul National University Hospital; Seoul 
National
University Hospital
Healthcare System Gangnam Center.

Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 

Email: kip...@snuh.org / ideo...@gmail.com



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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.




--

Kyung-Il Park, MD, PhD.

Professor,  

Department of Neurology, Seoul National University Hospital; Seoul National 
University Hospital
Healthcare System Gangnam Center.

Office: 82-2-2112-5756 / Fax: 82-2-2112-5635 

Email: kip...@snuh.org / ideo...@gmail.com


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[Freesurfer] Calculating cortex scalp distance of a region of interest

[Lucia B]

Dear Freesurfer experts,

I would like to calculate the mean distance from cortex to the scalp
in a region of interest (the area under the stimulator), to
investigate the influence of this distance on tDCS effects. A similar
question was asked in the archives, and the use of
mris_distance_transform was suggested.

I am new to freesurfer, and I wasn't able to figure out if this
approach is suitable for me and, if yes, what files I need to load in.
I checked mris_distance_transform -help, yet I am still missing some
parts. Could you point me to the right direction?

As , can I load in the ROI of the area under the scalp electrode?

I tried to run the function with lh.pial and the lh.BA45.label just to
see how it works, and I also have questions concenring the output:

mris_distance_transform surf/lh.pial label/lh.BA45_exvivo.label unsigned lh.dist
writing surface values to surf/lh.dist.w.
avg = 101.288, stdev = 50.852, min = 0.206, max = 207.610
distance transform took 0.1 minutes

How can I view the output file lh.dist.w.? And what do the values mean
(is it by any chance already the mean distance from the surface to the
label I am looking for, and if yes, what is the dimension)?

Any suggestions would be highly appreciated! Many thanks!

Lucia
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[Freesurfer] fast_selxavg3.m error/analysis.info file

[Yagmur Ozdemir 19]

Hello FreeSurfer experts,

I am getting this strange error when running selxavg3-sess. (in selxavg3 
command I am calling the analysis file with: -a rtopyTR2.rh) When the system 
enters fast_selxavg3, it cannot read analysis.info, thus produces the following 
output:

#@# Sess05 ###
/home/vm01/local/freesurfer/Project_bold/Sess05
-
$Id: fast_selxavg3b.m,v 1.4 2016/05/04 22:16:47 greve Exp $
-
outtop = /home/vm01/local/freesurfer/Project_bold
Extension format = nii.gz
ERROR: could not open rtopyTR2.rh/analysis.info
else
else
echo "--" | tee -a $LF
echo --
tee -a 
/home/vm01/local/freesurfer/Project_bold/log/selxavg3-sess-bold-rtopyTR2.rh-180130082919.log
--
rm $MLF
rm /tmp/selxavg3-sess-10173.m
if ( ! -e $okfile ) then
if ( ! -e /tmp/selxavg3-sess-10173.ok ) then
echo "ERROR: fast_selxavg3() failed\n" ;
echo ERROR: fast_selxavg3() failed\n
ERROR: fast_selxavg3() failed\n
exit 1 ;
exit 1

The analysis folder it is referring to( rtopyTR2.rh) is in the directory from 
which I am calling selxavg3-sess. It has the analysis.info file in which 
doesn't have any restrictions. To troubleshoot, I moved the folder to inside 
the session's functional directory and inside the session folder and these 
didn't create any changes. I looked at the script and tried to debug there but 
didn't give any results. It gave a similar error when trying to open the config 
file of contrast in mkcontrast-sess. (I also don't have root access)Any help is 
appreciated!

Best,
Idil


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