There is nothing interactive. You can use mri_fdr. It will compute the
threshold, which you can then use in freeview. It will also do the
thresholding for you.
On 2/22/2021 9:25 AM, Hannah Eichhorn wrote:
External Email - Use Caution
Dear all,
I am using glmfit to analyse changes
External Email - Use Caution
Dear all,
I am using glmfit to analyse changes in cortical thickness, but I
couldn't find a description on how to perform FDR correction with
FreeSurfer.
Is there a way to perform FDR correction of the statistical maps in
Freeview, analogous to how
do you mean that nothing survived threshold? That happens sometimes.
On 12/10/18 8:03 AM, 1013364183 wrote:
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Dear Bruce??
I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected
graphs are all 0. Why is this, the instructions and the
External Email - Use Caution
Dear Bruce??
I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected
graphs are all 0. Why is this, the instructions and the running results are as
follows:
mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh
External Email - Use Caution
Dear Bruce??
I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected
graphs are all 0. Why is this, the instructions and the running results are as
follows:
mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh
High p-values (i,e close to 1) mean non-significance. I don't know how
to do a power analysis with FDR.
On 11/19/18 1:16 PM, Laura Ferrero wrote:
> External Email - Use Caution
>
> Hi,
> I performed an statistical analysis comparing autism group with control group
> using volume/area
External Email - Use Caution
Hi,
I performed an statistical analysis comparing autism group with control group
using volume/area and thickness measures. I found significant differences in
some regions but they were not significant after FDR correction. The majority
of p-values
Thank you for that clarification,Doug.
VM
On Oct 12, 2016 12:09 PM, "Douglas N Greve"
wrote:
> The sign depends on how you set up the contrast. If you are using an
> FSGD file and have two classes A and B and a contrast [+1 -1], then
> positive indicates A>B. The
The sign depends on how you set up the contrast. If you are using an
FSGD file and have two classes A and B and a contrast [+1 -1], then
positive indicates A>B. The F.mgh is the map of F values which are
unsigned. The gamma.mgh file will have the contrast values themselves
including sign. The
Thanks, Doug for the binary.
A quick follow-up: what does the sign in either mri_glmfit-sim/mri_fdr
indicate? When I open F.mgh, the values are only positive and p-values
obtained from them has sign of +/-. My understanding is + indicates where
mean_A>mean_B and vice versa.
If for example, I am
try this binary
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_fdr
On 10/07/2016 04:11 PM, neuroimage analyst wrote:
>
> Hi,
>
> I was wondering if there is a way to perform fdr correction using
> command line in freesurfer without using matlab as mri_glmfit-sim only
> does bonferroni
Hi again.
I think I can obtain fdr maps by:
mri_surfcluster --in sig.mgh --subject fsaverage --hemi lh --annot
aparc --sign pos --o fdr_005_lh_pos.mgh --fdr 0.05 --cortex --mask mask.mgh
Can anyone comment if the above command is right to generate
a clusterwise fdr corrected p<0.05?
Thanks
Hi,
I was wondering if there is a way to perform fdr correction using command
line in freesurfer without using matlab as mri_glmfit-sim only does
bonferroni ?
Thanks
Regards
MV
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Hi list,
I would like to ask you a number of questions regarding the FDR which is
performed following seed-based fcMRI using FS-FAST.1-In the previous mail you
have suggested me to use mir_fdr command line (version 6.0). Because I have
some problem with new version license (as reported in
On 01/06/2016 11:00 AM, std...@virgilio.it wrote:
> Hi list,
>
> I would like to ask you a number of questions regarding the FDR which
> is performed following seed-based fcMRI using FS-FAST.
> 1-In the previous mail you have suggested me to use mir_fdr command
> line (version 6.0). Because I
Hi
help lme_mass_FDR
and
help /lme_mass_FDR2/
For help with input and output?
Knut J
On 05/26/2014 11:24 AM, Nandita Vijayakumar wrote:
Hi FS team,
I was wondering if you could help me with FDR correction for linear
mixed models within Matlab. I have run FDR2 correction using the
Hi FS team,
I was wondering if you could help me with FDR correction for linear mixed
models within Matlab. I have run FDR2 correction using the following
command:
*dvtx = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0); *However,
dvtx was empty, so I would like to try lme_mass_FDR
Per Bruce's suggestion, I'm reposting this now. A synopsis: I'm looking for a
way to correct painted statistical maps for multiple comparisons using
Freesurfer's tools, without having segmentation or any .xfm files.
Thanks,
Clark
On Aug 23, 2012, at 10:09 AM, Clark Fisher wrote:
Hi
Hi Clark, I just made a modification to mri_binarize to make it take an
FDR as input. It computes the threshold and binarizes the input based on
the threshold. I've put a copy here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize.linux
Run it with --help to get more
Hi Clark
sorry, the end of the summer has been a period when things slip through
the cracks. I think what you want is possible without a talairach or aseg,
but it will need to wait for Doug to get back. Can you repost at the end of
next week?
Bruce
On Thu, 30 Aug 2012, Clark Fisher wrote:
Hi Bruce,
Will do. Thanks again.
-Clark
On Sep 3, 2012, at 2:33 PM, Bruce Fischl wrote:
Hi Clark
sorry, the end of the summer has been a period when things slip through the
cracks. I think what you want is possible without a talairach or aseg, but it
will need to wait for Doug to get
Hi Sebastian,
I think you are right, both about tksurfer thresholding and the correct
interpretation of FDR. As you point out though, there is some value in having
maps that show how relatively well different points on the surface fit your
model.
At the very least, is there any way to
Hi Clark,
If you're loading the data into Python anyway to use with PySurfer, Nipy
seems to have some utilities to do an FDR correction
(docshttp://nipy.sourceforge.net/nipy/stable/api/generated/nipy.algorithms.statistics.empirical_pvalue.html
Thanks Michael, I'll look into Nipy's FDR tools. I actually started this
thread asking for help getting mri_surfcluster running for my situation (I have
no talraich .xfm and no segmentation for my monkeys). The silence on that
topic suggest that it might not be possible, or it's at least not
Ok, maybe I'm making this question too intricate. Here's the short version:
How can I FDR correct painted surface significance maps when I have no talraich
.xfm file and no cortical segmentation?
Thanks again,
Clark
Hi Freesurfers,
I have another monkey-specific question. I'd like to output
Hi Clark
you shouldn't need either. Load your overlays then click the button to
compute the FDR threshold in the tksurfer configure overlay interface.
cheers
Bruce
On
Tue, 28 Aug 2012, Clark Fisher wrote:
Ok, maybe I'm making this question too intricate. Here's the short version:
How can I
Hi Bruce,
Thanks. I actually have used this function of tksurfer, but am looking for a
way to save the corrected maps, so that they could be manipulated by other
tools (for instance, viewed by PySurfer). I recognize that this may not be an
officially supported functionality, but is there
I'll leave that for Doug.
Bruce
On Tue, 28 Aug 2012, Clark Fisher wrote:
Hi Bruce,
Thanks. I actually have used this function of tksurfer, but am looking for a
way to save the corrected maps, so that they could be manipulated by other
tools (for instance, viewed by PySurfer). I recognize
Hi Clark,
On Aug 28, 2012, at 11:15 AM, Clark Fisher wrote:
Hi Bruce,
Thanks. I actually have used this function of tksurfer, but am looking for a
way to save the corrected maps, so that they could be manipulated by other
tools (for instance, viewed by PySurfer).
Does it
Hi Freesurfers,
I have another monkey-specific question. I'd like to output FDR-corrected
signficance surface maps for my monkey data, or at least FDR-threshold the
maps. It seems like mri_surfcluster might be one way to go about this however:
1) I don't have any .xfm files for my
Now it works if I
enter the FDR in the text box - press Enter - click on Set Using FDR
Thank you so much.
Best,
Xiaojing
2010/7/9 Douglas N Greve gr...@nmr.mgh.harvard.edu
That is strange. Can you change the FDR to something ridiculous like .5 and
see if that changes things?
Xiaojing
Hi, all,
I have some questions about performing the FDR correction in Qdec.
I ran recon-all on all my subjects, then ran the surface group analysis
following the Qdec tutorial. There are 3 factors in the qdec.table.dat file:
age, gender and diagnosis. In the Design tab of Qdec, I selected the
That is strange. Can you change the FDR to something ridiculous like .5
and see if that changes things?
Xiaojing Long wrote:
Hi, all,
I have some questions about performing the FDR correction in Qdec.
I ran recon-all on all my subjects, then ran the surface group
analysis following
I tried that. Still no change.
And I tried running Qdec on all of my datasets. The problem occurs on all of
them.
Xiaojing
2010/7/9 Douglas N Greve gr...@nmr.mgh.harvard.edu
That is strange. Can you change the FDR to something ridiculous like .5 and
see if that changes things?
Hi Jürgen,
2010/5/27 Jürgen Hänggi j.haen...@psychologie.uzh.ch:
For SPM, it has been shown that the FDR procedure based on height threshold
(FDRp) is not appropriate in the random Gaussian field theory framework
(Chumbley et al., 2010; Chumbley and Friston, 2009, both published in
Dear FS experts
One of our reviewers would like to know whether the FDR procedures as
implemented in FS on one hand and as implemented in SPM on the other hand
are comparable.
In FS, I think FDR is based on the height threshold (FDRp) and it is outside
of the random Gaussian field theory
...@nmr.mgh.harvard.edu
Cc: Donna Dierker do...@brainvis.wustl.edu
Subject: Re: [Freesurfer] FDR correction (fwd)
Dear Doug,
Great discussion! But I think it misses the point. Can you forward the
following to the list?
The Benjamini-Hochberg (BH) FDR procedure uses the inequality
P(i
. Thanks Tom!
-- Forwarded message --
Date: Fri, 16 Oct 2009 23:11:09 +0100
From: Thomas Nichols t.e.nich...@warwick.ac.uk
To: Doug Greve gr...@nmr.mgh.harvard.edu
Cc: Donna Dierker do...@brainvis.wustl.edu
Subject: Re: [Freesurfer] FDR correction (fwd)
Dear Doug,
Great
From: Thomas Nichols t.e.nich...@warwick.ac.uk
To: Doug Greve gr...@nmr.mgh.harvard.edu
Cc: Donna Dierker do...@brainvis.wustl.edu
Subject: Re: [Freesurfer] FDR correction (fwd)
Dear Doug,
Great discussion! But I think it misses the point. Can you forward
the
following to the list
--
Date: Fri, 16 Oct 2009 23:11:09 +0100
From: Thomas Nichols t.e.nich...@warwick.ac.uk
To: Doug Greve gr...@nmr.mgh.harvard.edu
Cc: Donna Dierker do...@brainvis.wustl.edu
Subject: Re: [Freesurfer] FDR correction (fwd)
Dear Doug,
Great discussion! But I think it misses the point. Can you
Dear all,
The BH procedure is dependent on the number of tests and, for
neuroimaging methods, more tests is often equivalent to higher
resolution, either in voxel-based or surface-based representations of
the brain. The question that arises is whether this would influence
sensitivity and/or
...@nmr.mgh.harvard.edu
Cc: Donna Dierker do...@brainvis.wustl.edu
Subject: Re: [Freesurfer] FDR correction (fwd)
Dear Doug,
Great discussion! But I think it misses the point. Can you forward the
following to the list?
The Benjamini-Hochberg (BH) FDR procedure uses the inequality
P(i) = i / V * q
Dear Freesurfer team,
We are currently doing a cortical thickness studies between a group of
psychiatric patients (n=60) and controls (n=30). We tested several
smoothing levels (15mm, 20mm, 25mm)
When setting an uncorrected threshold (such as p0.005), we obtained
several regions of
Your FDR analysis sounds correct. You probably have a rather small
number of marginally significant vertices, which is why none survive
FDR. You could try increasing the q value from say 0.05 to 0.1, in
which case 10% of the surviving vertices would be expected to be false
positives.
cheers,
I never heard anything on my post here, but it might just be high
surface resolution:
http://www.mail-archive.com/neuro-mult-c...@brainvis.wustl.edu/msg00026.html
On 10/16/2009 09:58 AM, Michael Harms wrote:
Your FDR analysis sounds correct. You probably have a rather small
number of
Interesting post Donna, but my understanding of FDR is that it sets the
p-value threshold based on the LARGEST p-value that satisfies the FDR
relationship.
That is, steps 3 and 4 in Genovese et al. (2002) are:
3) Let r be the largest i for which p = i/V*q (assuming c=1)
4) Threshold the image
Regardless: FDR's sensitivity appears resolution-dependent to me.
On 10/16/2009 10:39 AM, Michael Harms wrote:
Interesting post Donna, but my understanding of FDR is that it sets the
p-value threshold based on the LARGEST p-value that satisfies the FDR
relationship.
That is, steps 3 and 4
Good point (meaning that I don't know the answer). I'll see if I can
find out.
doug
On Fri, 16 Oct 2009, Donna Dierker wrote:
Regardless: FDR's sensitivity appears resolution-dependent to me.
On 10/16/2009 10:39 AM, Michael Harms wrote:
Interesting post Donna, but my understanding of
Hi,
I have done an analysis involving three groups, so there are three pairwise
comparisons across two hemispheres = 6 p-maps. I want to adjust for multiple
comparisons (across the vertices), so I use FDR. But since FDR determines
the threshold basd on the actual p-values, I get 6 different
Some links that may be helpful:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
http://surfer.nmr.mgh.harvard.edu/fswiki/MultipleComparisons
Hope it helps.
PPJ
Date: Tue, 24 Mar 2009 14:03:46 -0300
Subject: Re: [Freesurfer] FDR correction
From: p...@netfilter.com.br
To: lari...@gmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Some links that may be helpful:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecMultipleComparisons
http
Hi,
We've noticed that FDR correction produces different p-values for the
left and right hemispheres. We found that this issue was observed
previously and an email was sent to the mailing list (see below),
however, no answer was received. We wondered if anybody has noticed this
problem
Manja,
I think FDR can be different for each hemisphere since they are taken apart
during processing.
Best Regards,
Pedro Paulo Jr
2008/8/27 Manja Lehmann [EMAIL PROTECTED]
Hi,
We've noticed that FDR correction produces different p-values for the left
and right hemispheres. We found that
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