Re: [Freesurfer] multiple comparisons correction

External Email - Use Caution Dear Douglas, And can I include abs to the --grf 3 command? I read this in the tutorial: "NOTE: the "abs" for GRF is only approximate. For volumes, it may give very conservative results" Is it better to include neg or pos? Thank you! Regards, Agurne

Re: [Freesurfer] multiple comparisons correction

External Email - Use Caution Dear Douglas, I have another question regarding multiple comparisons correction: Can I use --cache with volume analyses? Or should I use --grf? Thank you very much, Kind regards, Agurne El mar, 9 feb 2021 a las 18:11, Agurne Sampedro Calvete (

Re: [Freesurfer] multiple comparisons correction

You have to use --grf. I never computed the cache tables for volumes On 2/19/2021 9:58 AM, Agurne Sampedro Calvete wrote: External Email - Use Caution Dear Douglas, I have another question regarding multiple comparisons correction: Can I use --cache  with volume analyses? Or should I

Re: [Freesurfer] multiple comparisons correction

External Email - Use Caution Dear Douglas, Thank you very much ! This paper is very helpful. Regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neuro

Re: [Freesurfer] multiple comparisons correction

External Email - Use Caution Dear Douglas, So, as far as I understand you, if I use a smoothing of 15 I can use a --cache of 2 in thickness analysis, but I should use a higher --cache for volume, such as 3. Is that correct? And would you recommend me using another smoothing level?

Re: [Freesurfer] multiple comparisons correction

External Email - Use Caution Dear Douglas, I am doing both thickness and GM volume analyses. I am using a smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too low? And would a --cache of 2 be too low for both thickness and volume analyses, or would it be adeq

Re: [Freesurfer] multiple comparisons correction

Yes, cache 3 is ok for volume. BTW, you can see for your self in Fig 1 of this paper False positive rates in surface-based anatomical analysis Douglas N. Greve a, b, * , Bruce Fischl a, b On 2/9/2021 11:51 AM, Agurne Sampedro Calvete wrote: External Email - Use Caution Dear Douglas,

Re: [Freesurfer] multiple comparisons correction

That is ok for thickness, but not for volume On 2/9/2021 11:06 AM, Agurne Sampedro Calvete wrote: External Email - Use Caution Dear Douglas, I am doing both thickness and GM volume analyses. I am using a smoothing of 15. With a smoothing of 15, would a --cache of 2 be still too low?

Re: [Freesurfer] multiple comparisons correction

On 2/5/2021 9:54 AM, Agurne Sampedro Calvete wrote: External Email - Use Caution Dear Freesurfer experts, I am doing a longitudinal repeated measures ANOVA 2x2, with two groups (experimental vs control) and two time points (pre and post treatment). I have followed the group analy

Re: [Freesurfer] Multiple comparisons

My preferred method is to use permutation https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 11/14/19 12:29 PM, Juan Rivas wrote: > > External Email - Use Caution > > I would like to know how the correction is made for multiple > comparisons in the statist

Re: [Freesurfer] multiple comparisons correction for brain-behaviour correlations

I think you could get the p-valueus for the clusters and do FDR on those (or maybe the most significant of more than one cluster in a given comparison) On 9/11/19 9:26 AM, Annelies Vant Westeinde wrote: External Email - Use Caution Dear members, I have run several analyses in which we

Re: [Freesurfer] Multiple comparisons

Do you mean that you are doing an ROI analysis on the volume of the ROI? If so, then you still need to correct for multiple ROIs, probably with bonferroni or FDR. On 5/31/17 8:10 AM, Laura Ferrero Montes wrote: >Dear FS team, >I was doing a statistical analysis using metrics that are pr

Re: [Freesurfer] Multiple Comparisons Correction thresh error

Hi, We managed to avoid getting the error by typing the following in the terminal before the command: export LC_NUMERIC="en_US.UTF-8" Best,Teodora On Thursday, April 6, 2017, 5:59:05 PM GMT+2, Douglas Greve wrote: I think this is a "language" problem in that it is converting the "1.3" into "1

Re: [Freesurfer] Multiple Comparisons Correction thresh error

I think this is a "language" problem in that it is converting the "1.3" into "1,3" and then getting confused. I'm not sure how to fix it, but I think it has to do with the LOCAL setting. On 4/6/17 5:07 AM, teodora petrova wrote: Hello, I would like to correct my glm_fit results for multiple

Re: [Freesurfer] Multiple Comparisons Correction thresh error

Hello, I forgot to mention in my previous email that the system locale is in Swedish. Can this be the reason? Regards,Teodora On Thursday, April 6, 2017, 1:07:56 PM GMT+2, teodora petrova wrote:Hello, I would like to correct my glm_fit results for multiple comparisons. I am using the followi

Re: [Freesurfer] Multiple comparisons

We don't have something explicitly to do this, but you can run FDR on it using either mri_fdr (use nomask for the mask) or you can load the sig.mgh file into matlab and run it there, eg, sig = MRIread('sig.mgh'); p = 10^-abs(sig.vol); fdrthresh = fast_fdrthresh(p); On 3/20/17 9:32 AM, Laura F

Re: [Freesurfer] Multiple comparisons to confirm atrophy

Hi Clare, This is something that PALM can do. It seems we're in the same Dept. Please send me an email off-list and we can try to have this sorted out. All the best, Anderson On 19 November 2015 at 08:37, Clare Loane wrote: > Dear All, > > I have

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

Mar 2015 16:56:17 +0100 Subject: Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space) Hi Antonin, please remember to send responses to the list. Thanks! I've put a new version of cluster-sess in that same location. Let me know if that works. fo

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

r dir_of_my_simulation -s session_ID > > Regards, > > Antonin > > > *From:* Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > *To:* Antonin Skoch [mailto:a...@medicon.cz] > *Sent:* Mon, 02 Mar 2015 21:07:36 +0100 > *Subject:* Re: [Freesurfer] multiple compa

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

uftrag von Douglas N Greve > Gesendet: Mittwoch, 10. Dezember 2014 17:31 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] multiple comparisons correction for individual > hemispheres (native space) > > > Are you using 1.3 or 1,3 ? > > On 12/09/20

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

1 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space) Are you using 1.3 or 1,3 ? On 12/09/2014 03:10 AM, Milde, Christopher wrote: > Dear Doug, > > I tried to run MCC with cluster-sess but unfortuna

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve > Gesendet: Montag, 24. November 2014 20:34 > An: freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] multiple comparisons correction for individual > hemispheres (native s

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

yours, Christopher -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Montag, 24. November 2014 20:34 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] multiple compar

Re: [Freesurfer] multiple comparisons correction for individual hemispheres (native space)

Hi Christopher, sorry for the delay. I had a write a new program. You can download it from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/cluster-sess Let me know how it goes doug On 11/14/2014 06:05 AM, Milde, Christopher wrote: > Dear Freesurfer experts, > > I performed fMR

Re: [Freesurfer] multiple comparisons correction

On 07/16/2012 09:30 PM, Meng Li wrote: > Dear professor, > Thanks for your reply. > You said that when drawing conclusions from both hemispheres then I > need to use .025, but I found that in qdec interface, the default > value of -cwpvalue is 0.05. So are they inconsistent? This would be consi

Re: [Freesurfer] multiple comparisons correction

Dear professor, Thanks for your reply. You said that when drawing conclusions from both hemispheres then I need to use .025, but I found that in qdec interface, the default value of -cwpvalue is 0.05. So are they inconsistent? I also want to find a solution about an ERROR. I tried to run a

Re: [Freesurfer] multiple comparisons

FDR is based on the data, so you can't really say that a voxel-wise threshold is low or high. But 1x10^04 is actually not too bad, considering that the bonferonni thresh would be about 3x10^-7. The jump you see is not entirely unexpected, but I'm going to have to refer you to the FDR lituratur

Re: [Freesurfer] multiple comparisons

When I set FDR = .05, or anything under .85, and select "set threshold using FDR" the min threshold is always set to 4.03, which is about p= .0001, correct? Would you normally require such low p-values for this type of analysis? Why would such varied FDRs result in the same min threshold? We do

Re: [Freesurfer] multiple comparisons

.05 is fairly standard I think. On Mon, 9 Jan 2006, Sasha Wolosin wrote: Is this something you apply frequently at MGH? What FDR value would you typically require? Doug Greve <[EMAIL PROTECTED]> >>> Currently, mris_glm does not attempt to correct for multiple comparisons, though this featu

Re: [Freesurfer] multiple comparisons

FDR is not a one-side-fits-all kind of thing. It's based on data, and you have to look at your data to decide what threshold you want to use. The way you interpret FDR=.05 would be to ask yourself whether you would change your conclusions if *any* 5% of the voxels you declared active where act

Re: [Freesurfer] multiple comparisons

Is this something you apply frequently at MGH? What FDR value would you typically require? >>> Doug Greve <[EMAIL PROTECTED]> >>> Currently, mris_glm does not attempt to correct for multiple comparisons, though this feature will be in the next release. In the mean time, you can correct for mu

Re: [Freesurfer] multiple comparisons

Currently, mris_glm does not attempt to correct for multiple comparisons, though this feature will be in the next release. In the mean time, you can correct for multiple comparisons using FDR in tksurfer. Sasha Wolosin wrote: Dear all, I would like to learn more about group analysis usin