Dear Freesurfer experts,
I am trying to compare 3 groups (aut, sch, ges) according to thickness, area
and LGI at once (omnibus test).
I did run the following command:
mris_preproc --fsgd NSS_3_GR.fsgd \ --cache-in thickness.fwhm15.fsaverage \
--target fsaverage --hemi lh \ --out lh.NSS_3_GR.th
Many thanks!
Dusan
Date: Mon, 28 Sep 2015 11:35:50 -0400
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] 3_group_comparison
Did you include the back slashes in your command? If so, remove them
and retry.
On 9/25/15 7
Dear Freesurfer Experts,
I am trying to run a longitudinal analysis. I have done the first three steps
of the analysis. Now, I am trying to visualize my results.
However, I am having trouble doing the last step of the analysis:
https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
bas
te: Mon, 28 Sep 2015 18:33:50 -0400
> Subject: Re: [Freesurfer] 3_group_comparison
>
> I think it needs a -f before the surface
>
> On 09/28/2015 06:27 PM, Dusan Hirjak wrote:
> > Many thanks, yes, it did work well.
> >
> > But, than I ran "freeview
>
Dear Freesurfer Experts, I am trying to run a longitudinal analysis. I have
done the first three steps of the analysis. Now, I am trying to visualize my
results.
However, I am having trouble doing the last step of the analysis:
https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova
ba
ubject: Re: [Freesurfer] 3_group_comparison
Was the path of the overlay file correct? It looks like it can’t find the file.
Try providing the full path of the overlay file in the freeview command.
Best,Ruopeng
On Sep 28, 2015, at 6:46 PM, Dusan Hirjak wrote:Many
thanks!!!, yes, freeview has opened, but
Dear Freesurfer experts,
I'm using qdec to perform a statistical analysis in Freesurfer.
Could someone explain the meaning of the dependent measures (which can be used
in qdec) to me?
What does the "volume", "sulc" and "curv" etc. mean??? What kind of information
do they convey???
Dear experts,
it seems that after the new apple update "Maverick" Matlab can not get access
to Freesurfer. I already added the "recommended lines" from the homepage to
matlab startup-file, but it is still not working. Im trying to estimate the
local gyrification index. However when I type "reco
talled XQuartz, than can you please type the following on the
> command line and provide me with the output:
>
> "otool -L /opt/X11/lib/libX11.dylib"
>
> -Zeke
>
>
>
> On 01/24/2014 11:02 AM, Dusan Hirjak wrote:
> > Dear experts,
> >
> >
tem is
> supposed ouput information about that particular file. Instead you got
> the help information, which is output when you only type "otool" instead
> of ""otool -L /opt/X11/lib/libX11.dylib"
>
> Also, did you install XQuartz?
>
> -Zeke
>
>
Hi Zeke,
I have one more question: It seems that I did not copied the the "recommended
lines" from thehomepage to matlab startup-file correct. when I type "recon-all
-lgi -s G01" Im getting the following message:
ERROR: Matlab is required to run mris_compute_lgi!
When Im trying to run Qdec, the
fsmatlab;
fsfasthome = getenv('FSFAST_HOME'); fsfasttoolbox =
sprintf('%s/toolbox',fsfasthome); if (exist(fsfasttoolbox) == 7)
path(path,fsfasttoolbox); end clear fsfasthome fsfasttoolbox; Thanks!!!
Dusan Hirjak
_
an 2014 10:33:33 +0100
> CC: freesurfer@nmr.mgh.harvard.edu
> To: dusanhir...@hotmail.com
>
> Hi Dusan,
>
> (I saw your PN earlier but had no idea and hence did not reply).
> But this has more information, so I try again ;)
>
>
> On Jan 25, 2014, at 02:00 , Dusan Hirj
csh it reports tcsh; for bash
> edit ~/.bashrc, for tcsh edit ~/.cshrc. I think that the nano editor is part
> of macosx, so "nano ~/.bashrc" or "nano ~/.cshrc" should work, edit the file
> then use control-x to exit nano, it will ask whether you want to save…)
>
&g
Dear Freesurfer Experts,
I did a correlational analysis in qdec and found several significant clusters
after Monte-Carlo simulation (0.05).
Now, I would like to extract the mean cortical thickness, area and folding
values (peak maximum) of each study subject above the significant cluster.
and folding values from
> Qdec
>
> Use 1.3 not 1,3
>
> doug
> On 03/13/2014 10:12 AM, Dusan Hirjak wrote:
> > Dear Freesurfer Experts,
> >
> > I did a correlational analysis in qdec and found several significant
> > clusters after Monte-Carlo simula
ting it in quotes? If so, don't
> doug
>
> On 03/13/2014 01:46 PM, Dusan Hirjak wrote:
> > Dear Doug,
> >
> > I typed 1.3 but it is still not working.
> >
> > Any other ideas???
> >
> > Thanks for your help.
> >
> > DH
>
sign neg
>
> What exactly did you type? (try separating it with lines instead of quotes)
>
> HTH,
> D
> On Mar 13, 2014, at 6:22 PM, Dusan Hirjak wrote:
>
> > Dear Doug,
> >
> > no, I did not put it in quotes. I just typed the mentioned command, but it
Dear FreeSurfer experts,
we did a FreeSurfer-Analysis of cortical thickness in schizophrenia patients
with motor abnormalities and found significant changes of cortical thickness in
many brain regions. The Qdec p-maps showed many regions with surface size
exceeding 100mm2. We used a 15mm FWHM
Dear FreeSurfer experts,
we did a FreeSurfer-Analysis of cortical thickness in schizophrenia patients
with motor abnormalities and found significant changes of cortical thickness in
many brain regions. The Qdec p-maps showed many clusters (regions) with
"surface" size exceeding 100mm2. We use
Dear Freesurfer Experts,
I am currently trying to run LGI. I have the 2017b Matlab version, Mac OS
Sierra and I already set up the freesurfer PATH in Matlab. However, I am
getting the following error after starting recon all -s localGI :
Dusans-MacBook-Pro:NSS_Analysis_01 dusan$ recon-all -s
Dear Andrew,
thank you very much! Yes, you were right! Now it works fine.
best regards
Dusan
From: Hoopes, Andrew
Sent: Tuesday, February 13, 2018 12:23 PM
To: Freesurfer support list; Dusan Hirjak
Subject: Re: [Freesurfer] Problems running LGI
Hi Dusan
Dear Freesurfer Experts,
I would like to display my results after running the LGI command on my subjects
(via Freesurfer 6.0, MacOS Sierra). Although I created the .Qdecrc (text file)
file with MEASURE1 = pial_lgi and put it in my home directory as well as in the
folder where my study subjects
External Email - Use Caution
Dear Freesurfer Experts,
I am having trouble with recon-all (Freesurfer 6.0). After running a shell
script on my subjects I get the following error:
Iteration 1 Fri Apr 20 13:22:37 CEST 2018
nu_correct -clobber ./tmp.mri_nu_correct.mni.14731/nu0.mn
External Email - Use Caution
Dear Freesurfer experts,
I have one question regarding the partial volume effects on brainstem volume
when using Freesurfer 6.0 brainstem tool: Could partial volume effects in a
comparatively small sample (n=92) have an influence on the results (grou
External Email - Use Caution
Dear Freesurfer experts,
I have one question regarding the partial volume effects on brainstem volume
when using Freesurfer 6.0 brainstem tool: Could partial volume effects in a
comparatively small sample (n=92) have an influence on the results (grou
External Email - Use Caution
Dear Freesurfer experts,
I have one question regarding the partial volume effects on brainstem volume
when using Freesurfer 6.0 brainstem tool: Could partial volume effects in a
comparatively small sample (n=92) have an influence on the results (grou
Dear Freesurfer experts,
I am a beginner in using Freesurfer.
I was wondering if ICV should be treated as a potential confounder (such as
age, education,
chlorpromazine equivalents and duration of illness) in the statistical analysis
of volumetric data/cortical thickness?
Thanks in advanc
Dear Freesurfer experts,
I created a data table with 25 subjects, 3 discrete and 6 continuous factors.
Then I tried to load my data table in qdec. However, an "error loading the data
table" occured. I received an automatic notice generated at the end of the
terminal as following, "This line (m
Dear Freesurfer experts,
I opened the table (qdec.table.dat) in a text editor and add a line at the end
of the file. Then I tried to open the data table again. However, I received an
automatic error message again:
Number of columns: 286
fsid: column: 1
Number of factors: 285
Number of subjec
Dear Freesurfer experts,
I am a beginner in using Freesurfer.
I was wondering how "straight p-values" (and not -log(10)p value) of a
correlation analysis/comparison between cortical thickeness and age, CPZ,
duration of illness etc. could be displayed on a color bar using "qdec"?
Thanks in
Dear Freesurfer experts,
I am a beginner in using Freesurfer. I did an explorative study where I
correlated cotical thickness with different neuropsychological parameters: I
found positive correlations between cortical thickness and higher scores on
different neuropsychological scales in diffe
Size in Qdec
>
> I don't think tthere is a way in qdec to define either. You can run
> mri_surfcluster externally to remove clusters under a certain size. With
> a few tricks you can remove the ones over a certain size too.
> doug
>
> Dusan Hirjak wrote:
> &g
ise threshold. You would also set --minarea to exclude clusters
> smaller than a certain size.
> doug
>
> Dusan Hirjak wrote:
> > Dear Freesurfer experts,
> >
> > after a partial correlation (cortical thickness in different brain
> > regions of 24 Subjects
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