t make sense since the to
> variables have inconsistent scaling (so the slopes can't be compared).
>
> On 7/30/2021 9:42 AM, Avi Gharehgazlou wrote:
>
> External Email - Use Caution
>
> Hi experts,
>
> I am using the command line stream on Freesurfer for my analyse
External Email - Use Caution
Hi,
I want to investigate lGI differences between 4 groups (n=449) while
controlling for sex, age and surface area using DODS design matrix on the
command line stream of FreeSurfer. Will you please tell me which of the
below two contrasts are correct
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Hi experts,
I am using the command line stream on Freesurfer for my analyses. Although
I have successfully designed all my contrasts, I wanted confirmation from
you regarding one contrast that I am unsure about. Will you please check if
the below
wrote:
> It looks like you are viewing the annotation. Try turning the annotation
> off and see what is underneath
>
> On 8/20/2020 2:19 PM, Avi Gharehgazlou wrote:
>
> External Email - Use Caution
> 1. You mean I should run the below command line instead?
&
I'd
really appreciate your help on how I can visualize my significant clusters
in their appropriate colours.
Thank you so much
On Fri, Jun 12, 2020 at 10:39 AM Douglas N. Greve
wrote:
>
>
> On 6/10/2020 9:54 AM, Avi Gharehgazlou wrote:
>
> External Email - Use Caution
>
External Email - Use Caution
Hi,
I want to compare mean curvature between groups on QDEC using the “curv”
measure. I've learned from the archives that FreeSurfer calculates numerous
curvature-based functions by default in the recon stream and stores them in
the “surf” directory.
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Hi experts,
I am a bit confused with visualizing my significant clusters after having
corrected my results for multiple comparisons. after running mri_glmfit, I
corrected with monte carlo and permutation as explained below, will you
please confirm my
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Thank you so much for your input, it was very helpful and I
really appreciate it.
Regarding your question with relation to my 4th question, when I run the
below command line to visualize my results after correcting for multiple
comparisons using
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Hi experts,
Upon reading your 2018 paper (cited below) and following threads on the
archives, I am aware that I should use permutation testing for lGI analyses
rather than monte carlo at p<0.05. However, I have a few questions below
that I would
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Hi experts,
I am trying to run permutation test on my lGI data using the command line
below but I get an error saying “ERROR: Flag --perm-resid unrecognized”.
I've ran my mri_glmfit command line with flag --eres-save (see below) and
have installed and
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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
?
Thanks so much,
Avi
On Tue, Aug 13, 2019 at 6:36 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Those coordinates are in mni305 space. See this page, case 8
> https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
>
>
> On 8/13/19 1:56 PM, A
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Hi,
I have a very quick question... I've ran the lGI flag (-localGI) on my
participants. However, I've then performed manual edits (i.e. control
points, etc) on some participants and re-ran recon-all and lGI flag after
my edits..
To be sure, I want
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Hi,
I am conducting a meta-analysis on papers that have looked at local
gyrification index (lGI) in Autism Spectrum Disorder (ASD) relative to
typically developing (TD) peers.
All lGI papers have used the FreeSurfer software and have reported x,y,z
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Hi,
I have a question regarding interpreting results from QDEC. I am
investigating lGI in individuals with ASD and controls (which I will refer
to as 'TD' here).
I understand from the archives that when "TD" is listed first and "ASD" is
listed second
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Hi experts,
Will you please confirm below command lines I run to examine between group
differences in LGI? I have 3 questions listed.
I can’t run the below line, it gives an error:
mris_preproc --fsgd TDvsNDDageSAsex.fsgd --cache-in
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Hi experts,
I want to examine between-group differences in LGI controlling for age, sex
and surface area (all except sex demeaned).
To do so, I ran the DODS model on QDEC selecting:
- “diagnosis” and “sex” as discrete (fixed factors)
-
Use Caution
>
> You should edit your .Qdecrc file in your SUBJECTS_DIR/qdec
> folder. Don't capitalize qdec.
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Avi Gharehgazl
pial_lgi into .Qdecrc file.
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Avi Gharehgazlou
> *Sent: *Tuesday, April 23, 2019 1:34 PM
> *To: *Freesurfer support list
> *Subject: *Re: [Freesurfer
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Avi Gharehgazlou
> *Sent: *Tuesday, April 23, 2019 12:06 PM
> *To: *Freesurfer support list
> *Subject: *[Freesurfer] LGI in QDEC menu please respond soon
>
&g
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Hi experts,
To give more detail re my previous post I have created the .Qdecrc
file in my Subjects directory and QDEC folder, which contains one line
: MEASURE1
= pial_lgi . However, LGI is still not appearing in the drop down menu on
QDEC.
When
External Email - Use Caution
To give more detail re my previous post I have created the .Qdecrc
file in my Subjects directory and QDEC folder, which contains one line
: MEASURE1
= pial_lgi . However, LGI is still not appearing in the drop down menu on
QDEC.
When I do command
External Email - Use Caution
Hi experts,
I was able to put LGI in my QDEC drop down menu in the past by following
instructions on FW wiki and archives. However, I am doing some more
analyses now and unfortunately I can't seem to bring LGI in my QDEC
repeating what I have done in
nte carlo (in general, permutation is
> better, but certainly for lGI).
>
> On 8/9/18 1:39 PM, Avi Gharehgazlou wrote:
>
> External Email - Use Caution
> Hi experts,
>
> I looked at association between LGI and a behavioural scale on QDEC. after
> the analysis, to
External Email - Use Caution
Hi experts,
I looked at association between LGI and a behavioural scale on QDEC. after
the analysis, to plot the significant clusters/ blobs, I wanted to export
LGI values for each subject from each significant blob and based on
instructions in
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Hi experts,
I have examined the relation between LGI and a behavioural continuous scale
(SCQ) on QDEC while controlling for sex, age and surface area in my model.
When I want to do another analysis, doing exactly this but also controlling
for
External Email - Use Caution
Hi experts,
I want to make plots of my results that I have from QDEC, however, I'm
having difficulty exporting values from QDEC. I examined LGI differences
between groups, and I want to export my results, so the LGI values of
significant between-group
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Hello experts,
I am using QDEC to compared LGI values between groups (typically develping
and ASD). I made a "diagnosis.levels" file, putting my 2 groups in the
following order:
Typically developing
ASD
However, when I upload my qdec.table.dat file
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