Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"

[Caspar M. Schwiedrzik]

External Email - Use Caution

Hi!
I wanted to ask again whether there is a way to display the color wheel in
rtview and/or freeview. We are debugging our analyses and it would be
immensely helpful to have a legend that specifies the color assignments.
Thank you,
Caspar

On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik <
cschwie...@rockefeller.edu> wrote:

> Hi!
> I am following up on this thread trying to understand how to make the
> color wheel visible in rtview, or, if necessary, in freeview.
> Thank you! Caspar
>
>
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[Freesurfer] Morphological Features, Description & References

[Loske, Philipp]

External Email - Use Caution

Hello FreeSurfer Developers,


I have a question about references and descriptions to all the morphological 
features available in aparc.stats, extracted from structural MRI. I am using 
all the different features (SurfArea, GrayVol, ThickAvg, ThickStd, MeanCurv, 
GausCurv, FoldInd, CurvInd) for the 68 cortical regions available from the 
Desikan Kiliany atlas. I have been trying to find references to how these 
features are measured or derived, but couldn't find a proper list of references 
to each of the features. I a lot of references here 
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation, with 
detailed descriptions on surface reconstruction and how cortical thickness is 
measured, but couldn't find a detailed explanation on the other features, 
especially curvature values.

I think I have been able to find out what each of the measurements mean and how 
they are calculated in principle, through searching the internet a lot, but 
with no direct link to FreeSurfer. For instance, I know you can calculate the 
curvature values from the principle curvatures, but how does FS estimate those 
form the reconstructed Surface? And which one of the two surfaces does it use? 
White-pial or pial-csf surface? I found https://brainder.org/ really helpful, 
but it says for example that a new way of measuring cortical volume was 
implemented in FS 6.0.0, so does that mean for previous versions FS uses the 
Thickness x SurfaceArea method? Would be great if you can help me with this, or 
point me to the correct website I might just have missed during my search.


Best wishes

Philipp



The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. 
SC013683.
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[Freesurfer] (revised) mri_glmfit error

[Gwang-Won Kim]

External Email - Use CautionHi there, I tried to analysed "mri_glmfit --glmdir g1v7.wls --y ces.nii.gz --wls cesvar.nii.gz --C Main.mtx --C PDI.mtx --C Sex.mtx --C Age.mtx --C Edu.mtx --C BDI.mtx --C SBQ.mtx --C CD.mtx --fsgd g1v7.fsgd --surface fsaverage lh --cortex --fwhm 5 " There were messages for error as follows: Error: matrix is ill-conditioned or badly scaled, condno = 10649.3--- Possible problem with experimental design:Check for duplicate entries and/or lack of range ofcontinuous variables within a class.If you seek help with this problem, make sure to send:  1. Your command line:    mri_glmfit.bin --glmdir g1v7.wls --y ces.nii.gz --wls cesvar.nii.gz --C Main.mtx --C PDI.mtx --C Sex.mtx --C Age.mtx --C Edu.mtx --C BDI.mtx --C SBQ.mtx --C CD.mtx --fsgd g1v7.fsgd --surface fsaverage lh --cortex --fwhm 5   2. The FSGD file (if using one)  3. And the design matrix aboveAttempting to diagnose further SumSq: Min=8.774964 (col 3), Max=724.138794 (col 8) The scale is much different between columns 3 and 8, you may want to  normalize by subtracting the mean and dividing by the standard deviation.  What is the problem? Gwang-Won Kim













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Re: [Freesurfer] Problem with lGI

[Greve, Douglas N.,Ph.D.]

Don't know. Looks like it is some kind of internal matlab error. Did you 
recently change versions?
btw We are no longer supporting lGI at this time.

On 9/3/2019 12:11 PM, Avi Gharehgazlou wrote:

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Hi,

I have ran the lGI flag many times in the past. However, now that I am trying 
to run the flag on a new group of participants I get the below error. Will you 
please tell me how I can fix this?

Thanks so much,

Avi




New invocation of recon-all



Fri Aug 30 16:47:49 EDT 2019
/d/mjt/9/users/avideh/data/recon/MR160-114-0370_01
/usr/local/freesurfer/bin/recon-all
-s MR160-114-0370_01 -localGI -openmp 2
subjid MR160-114-0370_01
setenv SUBJECTS_DIR /d/mjt/9/users/avideh/data/recon
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux apollo.sickkids.ca 4.15.0-50-generic 
#54-Ubuntu SMP Mon May 6 18:46:08 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 16384 kbytes
maxproc  321903
maxlocks unlimited
maxsignal321903
maxmessage   819200
maxnice  0
maxrtprio0
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   824734641899414026581924  3746363689740062364472
Swap:   8388604 1922560 6466044


program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info
ProgramName: mri_convert.bin  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2019/08/30-20:47:49-GMT  BuildTimeStamp: Jan 18 
2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp 
$  User: avideh  Machine: apollo.sickkids.ca  
Platform: Linux  PlatformVersion: 4.15.0-50-generic  CompilerName: GCC  
CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version
stable6
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2019/08/30-20:47:49-GMT  BuildTimeStamp: Jan 18 
2017 16:38:58  CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve 
Exp $  User: avideh  Machine: apollo.sickkids.ca  
Platform: Linux  PlatformVersion: 4.15.0-50-generic  CompilerName: GCC  
CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier 
(x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2019/08/30-20:47:49-GMT  BuildTimeStamp: Jan 18 
2017 16:38:58  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ 
 User: avideh  Machine: apollo.sickkids.ca  
Platform: Linux  PlatformVersion: 4.15.0-50-generic  CompilerName: GCC  
CompilerVersion: 40400
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2019/08/30-20:47:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  
CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $  User: 
avideh  Machine: apollo.sickkids.ca  Platform: Linux 
 PlatformVersion: 4.15.0-50-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/08/30-20:47:49-GMT  BuildTimeStamp: Jan 18 2017 
16:38:58  CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp 
$  User: avideh  Machine: apollo.sickkids.ca  
Platform: Linux  PlatformVersion: 4.15.0-50-generic  CompilerName: GCC  
CompilerVersion: 40400
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/08/30-20:47:49-GMT  BuildTimeStamp: Jan 18 2017 
16:38:58  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: 
avideh  Machine: apollo.sickkids.ca  Platform: Linux 
 PlatformVersion: 4.15.0-50-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2019/08/30-20:47:49-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  
CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $  User: 
avideh  Machine: apollo.sickkids.ca  Platform: Linux 
 PlatformVersion: 4.15.0-50-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2019/08/30-20:47:50-GMT  BuildTimeS

Re: [Freesurfer] Morphological Features, Description & References

[Bruce Fischl]

Hi Philipp

I'll leave the volume question to Doug. The curvatures are estimated by 
fitting a second order polynomial to the local height function in the 
tangent bundle then computing the Hessian using the white (gray/white 
boundary) surface. We also have some discrete measures of curvature that 
uses the Gauss-Bonnet theorem, but those aren't run by default.


cheers
Bruce


On Fri, 6 Sep 2019, Loske, Philipp wrote:



External Email - Use Caution

Hello FreeSurfer Developers,


I have a question about references and descriptions to all the morphological
features available in aparc.stats, extracted from structural MRI. I am using
all the different features (SurfArea, GrayVol, ThickAvg, ThickStd, MeanCurv,
GausCurv, FoldInd, CurvInd) for the 68 cortical regions available from the
Desikan Kiliany atlas. I have been trying to find references to how these
features are measured or derived, but couldn't find a proper list of
references to each of the features. I a lot of references
here https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation,
with detailed descriptions on surface reconstruction and how cortical
thickness is measured, but couldn't find a detailed explanation on the other
features, especially curvature values.

I think I have been able to find out what each of the measurements mean and
how they are calculated in principle, through searching the internet a lot,
but with no direct link to FreeSurfer. For instance, I know you can calculate
the curvature values from the principle curvatures, but how does FS estimate
those form the reconstructed Surface? And which one of the two surfaces does
it use? White-pial or pial-csf surface? I found https://brainder.org/ really
helpful, but it says for example that a new way of measuring cortical volume
was implemented in FS 6.0.0, so does that mean for previous versions FS uses
the Thickness x SurfaceArea method? Would be great if you can help me with
this, or point me to the correct website I might just have missed during my
search.


Best wishes

Philipp




The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir.
SC013683.
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Re: [Freesurfer] qdec contrast and data extraction

[Greve, Douglas N.,Ph.D.]

Look  in the *.y.ocn.dat file.

 From mri_glmfit-sim --help

csdbase.y.ocn.dat - this is a summary of the input (y) over each
cluster. It has a column for each cluster. Each row is a subject. The
value is the average of the input (y) in each cluster. This is a
simple text file.



On 9/3/2019 5:16 PM, Maximo, Jose Omar wrote:
>  External Email - Use Caution
>
> Hi,
>
> Which specific file should I load? I see cluster.mgh, cluster.summary, 
> sign.ocn.annot, sig.ocn.mgh, sig.vertex.mgh, and pdf.dat.
>
> How can I extract the values from fsaverage space?
>
> Basically, what is the correct way to extract values from these significant 
> clusters?
>
> Many thanks,
> Omar
>
>  Date: Tue, 3 Sep 2019 15:15:02 +
>  From: "Greve, Douglas N.,Ph.D." 
>  Subject: Re: [Freesurfer] qdec contrast and data extraction
>  To: "freesurfer@nmr.mgh.harvard.edu" 
>  Message-ID: <2286f9bf-37a4-1be9-2252-0bccc833a...@mgh.harvard.edu>
>  Content-Type: text/plain; charset="utf-8"
>  
>  You might have done something wrong along the way. When you run the 
> montecarlo correction, it will create a file with the thickness values in it 
> for each cluster. the first thing to do is to load that and see if you see 
> the expected differences. The other thing is to not go back into native space 
> to extract the numbers. There are several operations that happen as it moves 
> into fsaverage space and in preparation for group analysis (interpolation, 
> and smoothing); sometimes these make a big difference. if the ROI is small, 
> it may not map accurately back into the native space (and you should not need 
> to draw it in the first place)
>  
>  On 8/30/2019 11:36 AM, Maximo, Jose Omar wrote:
>  
>  External Email - Use Caution
>  Hi,
>  
>  I have a question:
>  
>  My design is 2 groups (HC and Patients in that respective order) and 2 
> nuisance factors (age and eTIV). When I look at the average volume difference 
> between the 2 groups, I get blue and red clusters. I presume the color coding 
> is where each group is greater than the other (Blue = Patients > HC and Red = 
> HC > Patients).
>  
>  Then, I processed to extract individual values from each cluster in 
> order to plot them. When I extract data from the blue clusters and plot them, 
> the two groups show no difference in thickness at all, whereas when I look at 
> volume, HC show more than patients in blue clusters (see attached figure). I 
> would assume that both figures would show patients > HC based on the negative 
> statistic.
>  
>  Am I interpreting the colors wrong? Or am I doing something wrong?
>  
>  These are my steps 1) After applying montecarlo correction, I drew my 
> ROIs to extract the data from; 2) map it onto every single subject; and then 
> 3) used mris_anatomical_stats to extract the data from each subject.
>  
>  Any suggestions are welcome.
>  
>  Best,
>  Omar
>  
>  Jose O. Maximo, Ph.D. | Postdoctoral Fellow
>  Department of Psychiatry & Behavioral Neurobiology
>  UAB School of Medicine
>  University of Alabama at Birmingham
>  Cell Phone: (619) 252-3492
>  Email: jomax...@uabmc.edu
>  
>  
>
>
> ___
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Re: [Freesurfer] issue with lesions

[Greve, Douglas N.,Ph.D.]

You can get the volume from the aseg.stats file. Unfortunately, we do not 
separate the lesions into left and right. You could do something like
mri_binarize --i aseg.mgz --match 77 --o wmlesions.mgz
mri_volcluster --i wmlesions.mgz --sum lesions.sum.dat --thmin 0.5 --regheader 
subject
This will output a list of lesions clusters in lesions.sum.dat and their 
coordinates. you can see which ones are left and with ones are right.



On 9/3/2019 5:17 PM, Sam W wrote:

External Email - Use Caution

Hello,
I have run recon-all on T1 scans of patients with WM lesions. I noticed however 
that for some patients the lesion is excluded from aparc.a2009s+aseg.mgz but 
for other patients it is included (and labelled as non-lesion).
Ultimately I'd like to extract a) volume information in WM and b) volume 
information of the WM lesion. I think I can get the the WM volume from the 
wmparc.stats file. For the lesion volume I think I can take the 
WM-hypointensities from the aseg file right? However I noticed that if a lesion 
is on the right hemisphere, the Right-WM-hypointensities shows 0s in all 
columns, which cannot be right.
I have a mask of the lesion (1s where lesion occurs, 0s elsewhere) in 
anatomical space, can I use this mask somehow in FS to inform recon-all where 
the lesion occurs?
Thanks in advance!
Sam



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Re: [Freesurfer] make_average_subject error

[Greve, Douglas N.,Ph.D.]

That is the recon-all.log file. What I want is the terminal output from 
make_average_subject
You can capture it with
make_average_subject [your arguments] |& tee mas.log



On 9/4/2019 9:16 PM, Maxime Perron wrote:

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Good evening Greve,

Thanks for your quick answer.

I attached the file containing the output.

Best,
Maxime




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On Sep 4, 2019, at 6:10 PM, Greve, Douglas N.,Ph.D. 
 wrote:


Can you send the full text of the terminal output?

On 9/4/19 10:44 AM, Maxime Perron wrote:


External Email - Use Caution

Hi Greve,

The exact script is the following :


setenv SUBJECTS_DIR 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data

make_average_subject --subjects "Freesurfer_S002" "Freesurfer_S003" 
"Freesurfer_S004" "Freesurfer_S014" "Freesurfer_S018_2" "Freesurfer_S020" 
"Freesurfer_S021" "Freesurfer_S023"  "Freesurfer_S024" "Freesurfer_S027" 
"Freesurfer_S029" "Freesurfer_S035" "Freesurfer_S037" "Freesurfer_S039" 
"Freesurfer_S040" "Freesurfer_S043" "Freesurfer_S044" "Freesurfer_S046" 
"Freesurfer_S048" "Freesurfer_S053" "Freesurfer_S060" "Freesurfer_S061" 
"Freesurfer_S064" "Freesurfer_S066" "Freesurfer_S068" "Freesurfer_S070" 
"Freesurfer_S071" "Freesurfer_S078" "Freesurfer_S083" "Freesurfer_S084" 
"Freesurfer_S088" "Freesurfer_S090" "Freesurfer_S093" "Freesurfer_S095" 
"Freesurfer_S103" "Freesurfer_S105" "Freesurfer_S106" "Freesurfer_S108" 
"Freesurfer_S110" "Freesurfer_S111" "Freesurfer_S113" "Freesurfer_S114" 
"Freesurfer_S115" "Freesurfer_S117" "Freesurfer_S118" "Freesurfer_S119" 
"Freesurfer_S120" "Freesurfer_S122" "Freesurfer_S123" "Freesurfer_S125" 
"Freesurfer_S126" "Freesurfer_S129" "Freesurfer_S130" "Freesurfer_S133" 
"Freesurfer_S134" "Freesurfer_S139" "Freesurfer_S141" "Freesurfer_S142" 
"Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147" 
"Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152" 
"Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156" 
"Freesurfer_S158" "Freesurfer_S164"  --out BrainaverageN72

cd 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
mkdir ori

cd 
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72
@SUMA_Make_Spec_FS -NIFTI -sid BrainaverageN72

_

BrainaverageN72 is the output name.

Thanks,
Maxime Perron

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

 de la part de Greve, Douglas N.,Ph.D. 

Envoyé : 4 septembre 2019 10:37
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] make_average_subject error

Is BrainaverageN72 in the subjects list?

On 9/3/19 12:39 PM, Maxime Perron wrote:


External Email - Use Caution

​Dear Freesurfer Experts,


I have the following issue when running the make_average_subject command (

make_average_subject --subjects (Subjid) --out BrainaverageN72) :


Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from
/Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: ---
-1.0   0.0   0.0   128.0;
 0.0   0.0   1.0  -128.0;
 0.0  -1.0   0.0   128.0;
 0.0   0.0   0.0   1.0;
mghRead(mri/norm.mgz, -1): could not open file
-

Labeling Slice
relabeling unlikely voxels in interior of white matter
Segmentation fault
Darwin tulipe.crulrg.local 17.7.0 Darwin Kernel Version 17.7.0: Sun
Jun  2 20:31:42 PDT 2019; root:xnu-4570.71.46~1/RELEASE_X86_64 x86_64

recon-all -s BrainaverageN72 exited with ERRORS at Tue Sep  3 11:33:02
EDT 2019


I appreciate any help.

​Regards,
Maxime









​



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Re: [Freesurfer] ERROR reading //fsaverage/label/lh.BA1_exvivo.label with recon-all.log

[Greve, Douglas N.,Ph.D.]

Does this file exist 
/media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/fsaverage/label/lh.BA1_exvivo.label
and do you have read permissions to it?

On 9/5/2019 5:39 AM, liuxingze1993 wrote:

External Email - Use Caution
Hello， Dear FreeSurfer Developers,

Hi, I'm attempting to follow the steps descripted on ‘Practice Working with 
Data’ (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice) with our 
own data, but I’ve met the same problem several times when I programing the 
command ‘recon-all -all’:

SUBJECTS_DIR   /media/dell/AA32E/Data_prac/220liujiayue/20181217
FREESURFER_HOME  /usr/local/freesurfer
Loading source label
Invalid argument
ERROR reading  
/media/dell/AA32E/Data_prac/220liujieyue/20181217/fsaverage/label/lh.BA1_exvivo.label

I've searched the ‘lh.BA1_exvivo.label’ file in the related path and no such 
file here.  Maybe I need to reinstall the freesurfer?

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
2) Platform: Ubuntu14.04 LTS
3) uname -a: Linux dell 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 
UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
4) recon-all.log: see attached

Thank u for viewing, and I will be waiting here for your professional advice !















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Re: [Freesurfer] qcache after running recon-all post correction processing

[Greve, Douglas N.,Ph.D.]

You can just run recon-all again with only the -qcache flag (this is actually 
how it is intended to be run)

On 9/5/2019 2:52 PM, Swanson,Clayton wrote:

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Hi FreeSurfer folks,

I searched through the archives and was unable to find the answer I was looking 
for.  I have recently run recon-all on all our subjects (55 participants 
separated into two groups), then went through and corrected, saved and re-ran 
recon-all using the following command “recon-all -autorecon2-cp -autorecon3 
-subjid Subj_020”.

I neglected to add one additional command, the -qcache command for the second 
round of recon-all’s which I have already run for all participants.

Because I am going to be comparing the two groups and doing group analysis what 
is the most appropriate way to proceed?  Should I re-run the participants again 
although this time with the -qcache command? Or, what would be the most logical 
and efficient next step?

Thanks for the help,
Clayton

Clayton Swanson MS
Graduate Research Assistant & PhD Student
Sensorimotor Neuroimaging Laboratory
Colorado State University
Office: (970) 491-6160
clayton.swan...@colostate.edu




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Re: [Freesurfer] mri_glmfit error

[Greve, Douglas N.,Ph.D.]

Did you see the part where it says "If you seek help with this problem, make 
sure to send:"?

On 9/5/2019 11:00 PM, Gwang-Won Kim wrote:

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Hi there,

I tried to analysed "mri_glmfit --glmdir g1v7.wls --y ces.nii.gz --wls 
cesvar.nii.gz --C Main.mtx --C PDI.mtx --C Sex.mtx --C Age.mtx --C Edu.mtx --C 
BDI.mtx --C SBQ.mtx --C CD.mtx --fsgd g1v7.fsgd --surface fsaverage lh --cortex 
--fwhm 5 "

There were messages for error as follows: Possible problem with experimental 
design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --glmdir g1v7.wls --y ces.nii.gz --wls cesvar.nii.gz --C 
Main.mtx --C PDI.mtx --C Sex.mtx --C Age.mtx --C Edu.mtx --C BDI.mtx --C 
SBQ.mtx --C CD.mtx --fsgd g1v7.fsgd --surface fsaverage lh --cortex --fwhm 5
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=8.774964 (col 3), Max=724.138794 (col 8)
 The scale is much different between columns 3 and 8, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.


What is the problem?

Gwang-Won Kim



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Re: [Freesurfer] Morphological Features, Description & References

[Greve, Douglas N.,Ph.D.]

For cortical volume we compute  vertex-wise volume based on dividing each 
obliquely truncated   trilateral pyramid into three tetrahedra. Based on 
Anderson M. Winkler's   srf2vol matlab script.

On 9/6/2019 10:22 AM, Bruce Fischl wrote:
Hi Philipp

I'll leave the volume question to Doug. The curvatures are estimated by fitting 
a second order polynomial to the local height function in the tangent bundle 
then computing the Hessian using the white (gray/white boundary) surface. We 
also have some discrete measures of curvature that uses the Gauss-Bonnet 
theorem, but those aren't run by default.

cheers
Bruce


On Fri, 6 Sep 2019, Loske, Philipp wrote:


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Hello FreeSurfer Developers,


I have a question about references and descriptions to all the morphological
features available in aparc.stats, extracted from structural MRI. I am using
all the different features (SurfArea, GrayVol, ThickAvg, ThickStd, MeanCurv,
GausCurv, FoldInd, CurvInd) for the 68 cortical regions available from the
Desikan Kiliany atlas. I have been trying to find references to how these
features are measured or derived, but couldn't find a proper list of
references to each of the features. I a lot of references
here https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation,
with detailed descriptions on surface reconstruction and how cortical
thickness is measured, but couldn't find a detailed explanation on the other
features, especially curvature values.

I think I have been able to find out what each of the measurements mean and
how they are calculated in principle, through searching the internet a lot,
but with no direct link to FreeSurfer. For instance, I know you can calculate
the curvature values from the principle curvatures, but how does FS estimate
those form the reconstructed Surface? And which one of the two surfaces does
it use? White-pial or pial-csf surface? I found https://brainder.org/ really
helpful, but it says for example that a new way of measuring cortical volume
was implemented in FS 6.0.0, so does that mean for previous versions FS uses
the Thickness x SurfaceArea method? Would be great if you can help me with
this, or point me to the correct website I might just have missed during my
search.


Best wishes

Philipp




The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir.
SC013683.




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Re: [Freesurfer] Question about how to build .gca files from non-human atlas and images

[Greve, Douglas N.,Ph.D.]

Hi Arsene, you did not say anything wrong. What you are trying to do is a 
research project in and of itself. To support you, we would have to put huge 
amounts of time into it, which we are not willing to do.
doug


On 9/5/2019 7:56 AM, arsene ella wrote:

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Dear Douglas,
I know that you are very busy by a lot of other people to support but I don't 
understand your answer about my questions and disappointed by it...
Did I say or do something wrong?
Regards,
Arsene

Le jeu. 5 sept. 2019 à 00:12, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> a écrit :
Sorry, I think this is beyond our ability to support.

On 9/4/19 4:44 AM, arsene ella wrote:
>
> External Email - Use Caution
>
> /Dear //Freesurfer experts,/
>
> /I’ve built an atlas of structures of a non-human average brain and now //I 
> would like to build //its//.gca files from scratch. //From the Freesurfer 
> mailing list, I saw that this is possible using 
> //*rebuild_gca_atlas.csh*//**//which trains labelled brai//ns
> (//*seg_edited.mgz*//) and their intensity volumes (it is said to use
> the //*norm.mgz*//for this purpose) from several subjects through
> //*mri_ca_train*//. //My questions are :/
> /1) How to normalize my native intensity volume to a
> //*norm.mgz*//volume without .gca and .lta files asking by
> //*mri_ca_normalize *//?/
> /Y//ou’ve suggested to give //*mri_ca_normalize*//a flag to tell it to
> use a manual segmentation instead of the gca by trying //*-seg  seg volume>*//. Then the gca name won't matter - it should ignore it…
> I tried this as followed :/
> /let : /
> /- //*Brain_Template_T1_MPR.mgz *//be my intensity native volume/
> /- //*Brain_Cortex_Atlas.mgz***//be my manual segmented volume/
> /- //*Brain_Template_T1_MPR_norm.mgz*//**//be //my
> //*norm*//output//volume/
>
> /Command lines :/
> /*mri_ca_normalize*//Brain_Template_T1_MPR.mgz
> //*-seg*//Brain_Cortex_Atlas.mgz Brain_Template_T1_MPR_norm.mgz/
> _/gave the following error message :/_
> /reading 1 input volume/
> /reading atlas from '-seg'.../
> /GCAread(-seg): could not open file/
> /No such file or directory/
> /mri_ca_normalize: could not open GCA -seg./
> /No such file or directory/
>
> /*mri_ca_normalize**-seg *//Brain_Cortex_Atlas.mgz
> Brain_Template_T1_MPR.mgz Brain_Template_T1_MPR_norm.mgz/
> _/gave the following message  and stopped:/_
> /using segmentation volume
> /home/arsene/Bureau/FS_GCA/FS_SHEEP_CGA/Brain_Cortex_Atlas.mgz to
> generate control points.../
> /usage: mri_ca_normalize []   ... 
>.../
>
> /What is wrong with theses //*mri_ca_normalize*commands ?/
>
> /2) My second question is to know how to transfert labels from mymanual 
> seg//mented//volume //(ex : //*atlas.mgz*//) to each single
> image volume (ex : vol1//*.mgz*//) ?/
> /You’ve suggested to use //*mri_label2label*//, but //I didn’t see anything 
> allowing me to do a //*volume_to_volume*//transfert //from //its 
> //*–help*//…//If I got it wrong, could you suggest a command ?/
>
> /cheers/
> /Arsene/
>
> ___
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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"

[Greve, Douglas N.,Ph.D.]

Hi Caspar, sorry for the delay. I have not used the retinotoy stream in a long, 
long time so I don't know off the top of my head. I'll have to look into it. 
tksurfer (from rtview) does have a way to display using the color wheel, but I 
don't remember how to do it.

Ruopeng, can freeview display using a color wheel?

On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:

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Hi!
I wanted to ask again whether there is a way to display the color wheel in 
rtview and/or freeview. We are debugging our analyses and it would be immensely 
helpful to have a legend that specifies the color assignments.
Thank you,
Caspar

On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik 
mailto:cschwie...@rockefeller.edu>> wrote:
Hi!
I am following up on this thread trying to understand how to make the color 
wheel visible in rtview, or, if necessary, in freeview.
Thank you! Caspar




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Re: [Freesurfer] Interruption during data processing

[Троицкий Антон Александрович]

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Bruce, could you explain how can I do that? I mean what command should I use 
and parameters?

Best regards,
Anton Troitskii

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Re: [Freesurfer] Interruption during data processing

[Bruce Fischl]

Hi Anton

recon-all -sd  -s  -make all

should do the trick
cheers
Bruce
On Fri, 6 Sep 2019, 
Троицкий Антон Александрович wrote:



   External Email - Use Caution

Bruce, could you explain how can I do that? I mean what command should I use 
and parameters?

Best regards,
Anton Troitskii


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[Freesurfer] Postdoc positions in cognitive and computational neuroscience

[Ivan Alekseichuk]

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Multiple postdoc positions in cognitive neuroscience and computational
neuroscience are available in the Opitz Lab, University of Minnesota! The
lab works in the field of brain stimulation (with the focus on the
transcranial methods – TMS, tACS/tDCS) across multiple levels of
investigation. We conduct both computational research (using resources of
Minnesota Supercomputing Institute) and human experimental research (EEG,
ECoG, functional and structural MRI, psychophysics). In collaboration with
other labs at the University of Minnesota, we perform basic research in
animal models. Through the direct vicinity to the Medical School and Center
for Magnetic Resonance Research, we have several collaborators who study
brain stimulation in clinical populations.

We are looking for a postdoc to contribute to our ongoing projects:
closed-loop TMS-EEG, multiscale modeling of TMS/tACS, human research in
neurophysiology of TMS/tACS, cognitive effects of brain stimulation in
healthy humans and patients; or develop their own research agendas.
Interest and ability to integrate into a multidisciplinary team is
essential.

The ideal candidate should have Ph.D. in applied quantitative field
(Engineering, Physics, or Applied Mathematics) or life sciences
(Neuroscience, Human Biology, or Cognitive Science). Strong technical and
computational skills are preferred, but candidates with strong human
experimental background are also encouraged to apply.

The Opitz lab is committed to the career advancement of its members. We
offer a diverse and inclusive environment with numerous opportunities for
members to develop their own projects and support for fellowships and
career development awards.

Informal inquiries can be made to: aop...@umn.edu
See more on the website: http://opitzlab.umn.edu/join_us
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[Freesurfer] mris_decimate error

[roc...@netzero.net]

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When running mris_decimate on macOS High Sierra, I get this error:

dyld: Library not loaded: /usr/local/lib/libglib-2.0.0.dylib
  Referenced from: /Applications/freesurfer/bin/mris_decimate
  Reason: image not found
Abort trap: 6

Is this a library that was supposed to be installed by FreeSurfer? I did not 
make any changes to the installation so I am not sure why this error is 
occurring.

Thanks to anyone that can help. I really appreciate it.

$4.95 Natural Painkiller Working "Better Than Oxy"
worldhealthlabs.com
http://thirdpartyoffers.netzero.net/TGL3231/5d72a2fdd8cab22fd34fbst03duc

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Re: [Freesurfer] mris_decimate error

[fsbuild]

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Hello,
On the Mac, we use homebrew to provide some libraries that freesurfer binaries 
need to link against in order to run, see https://brew.sh/
Once you install homebrew you should have a “brew” command available in the 
terminal window.  Then to get libglib you could try from the terminal,
$ brew install glib
… though it may tell you it is already installed.  You could also check 
that it exists with,
$ ls /usr/local/lib/libglib-2..0.0.dylib/usr/local/lib/libglib-2.0.0.dylib@- R.

On Sep 6, 2019, at 14:17, roc...@netzero.net 
wrote:   External Email - Use Caution 
   When running mris_decimate on macOS 
High Sierra, I get this error:dyld: Library not loaded: 
/usr/local/lib/libglib-2.0.0.dylib Referenced from: 
/Applications/freesurfer/bin/mris_decimate Reason: image not foundAbort 
trap: 6Is this a library that was supposed to be installed by FreeSurfer? I did 
not make any changes to the installation so I am not sure why this error is 
occurring.Thanks to anyone that can help. I really appreciate 
it.___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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