Re: [Freesurfer] FDR correction for statistical maps in Freeview?

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 in

[Freesurfer] FDR correction for statistical maps in Freeview?

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

Re: [Freesurfer] fdr correction problem

do you mean that nothing survived threshold? That happens sometimes. On 12/10/18 8:03 AM, 1013364183 wrote: 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 run

[Freesurfer] fdr correction problem

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 lh2.gender

[Freesurfer] fdr correction problem

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 lh2.gender

Re: [Freesurfer] FDR correction

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 an

[Freesurfer] FDR correction

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 a

Re: [Freesurfer] Fdr correction using command line

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 F.mgh is the map of F values wh

Re: [Freesurfer] Fdr correction using command line

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 s

Re: [Freesurfer] Fdr correction using command line

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

Re: [Freesurfer] Fdr correction using command line

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 ?

Re: [Freesurfer] Fdr correction using command line

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 Rega

[Freesurfer] Fdr correction using command line

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 https://mail.nmr.

Re: [Freesurfer] FDR correction

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 h

[Freesurfer] FDR correction

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 previo

Re: [Freesurfer] FDR correction in Matlab

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 follo

[Freesurfer] FDR correction in Matlab

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 ins

Re: [Freesurfer] FDR Correction of NHP Surface Data

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 Freesurf

Re: [Freesurfer] FDR Correction of NHP Surface Data

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

Re: [Freesurfer] FDR Correction of NHP Surface Data

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

Re: [Freesurfer] FDR Correction of NHP Surface Data

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:

Re: [Freesurfer] FDR Correction of NHP Surface Data

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 k

Re: [Freesurfer] FDR Correction of NHP Surface Data

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 (docs /source

Re: [Freesurfer] FDR Correction of NHP Surface Data

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 automat

Re: [Freesurfer] FDR Correction of NHP Surface Data

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

Re: [Freesurfer] FDR Correction of NHP Surface Data

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 recog

Re: [Freesurfer] FDR Correction of NHP Surface Data

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 some

Re: [Freesurfer] FDR Correction of NHP Surface Data

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

Re: [Freesurfer] FDR Correction of NHP Surface Data

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

[Freesurfer] FDR Correction of NHP Surface Data

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 monk

Re: [Freesurfer] FDR correction in Qdec

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 > That is strange. Can you change the FDR to something ridiculous like .5 and > see if that changes things? > > Xiaojing Long wrote: > >> H

Re: [Freesurfer] FDR correction in Qdec

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 > That is strange. Can you change the FDR to something ridiculous like .5 and > see if that changes things? > > Xiaojing Long wrote: > >> Hi

Re: [Freesurfer] FDR correction in Qdec

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 followi

[Freesurfer] FDR correction in Qdec

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 dis

Re: [Freesurfer] FDR correction in FS vs. SPM

Hi Jürgen, 2010/5/27 Jürgen Hänggi : > 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 > NeuroImage). Sorry could you elabor

[Freesurfer] FDR correction in FS vs. SPM

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 framewor

Re: [Freesurfer] FDR correction (fwd)

te: >>> >>>> Here's Tom Nichols explanation. He points out that you use the maximum >>>> i, not the minimum, so you don't have to get past i=1. Thanks Tom! >>>> >>>> >>>> -- Forwarded message -- >>&

Re: [Freesurfer] FDR correction (fwd)

, not the minimum, so you don't have to get past i=1. Thanks Tom! >>> >>> >>> -- Forwarded message -- >>> Date: Fri, 16 Oct 2009 23:11:09 +0100 >>> From: Thomas Nichols >>> To: Doug Greve >>> Cc: Donna Dierker >>

Re: [Freesurfer] FDR correction (fwd)

not the minimum, so you don't have to get past i=1. Thanks Tom! >> >> >> -- Forwarded message -- >> Date: Fri, 16 Oct 2009 23:11:09 +0100 >> From: Thomas Nichols >> To: Doug Greve >> Cc: Donna Dierker >> Subject: Re: [Freesurfer]

Re: [Freesurfer] FDR correction (fwd)

> To: Doug Greve > Cc: Donna Dierker > 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

Re: [Freesurfer] FDR correction (fwd)

ubject: 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 for the ordered P-values P(1)<=P(2)<=...<=P(V) and desir

Re: [Freesurfer] FDR correction

Dear all, The B&H 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 p

Re: [Freesurfer] FDR correction

I would be interested in this as well. -Derin On Oct 16, 2009, at 11:40 AM, Doug Greve wrote: > > 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-de

Re: [Freesurfer] FDR correction

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 o

Re: [Freesurfer] FDR correction

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

Re: [Freesurfer] FDR correction

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 a

Re: [Freesurfer] FDR correction

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 "margi

Re: [Freesurfer] FDR correction

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

[Freesurfer] FDR correction

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 p<0.005), we obtained several regions of decreas

Re: [Freesurfer] FDR correction

s across the surface (or brain volume), but how do you > deal with a series of such analyses? Of course, if you use a different > method of correction you avoid this problem but that's not the point. > > > LMR > > > -- > Date: Tue, 24 M

Re: [Freesurfer] FDR correction

od of correction you avoid this problem but that's not the point. LMR 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

RE: [Freesurfer] FDR correction

LMR 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

Re: [Freesurfer] FDR correction

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 ---

[Freesurfer] FDR correction

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 treshol

Re: [Freesurfer] FDR correction

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

[Freesurfer] FDR correction

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 before