Re: [Freesurfer] mri_glmfit-sim - Clusterwise correction for multiple comparisons.

This is the kind of thing that happens with clusterwise corrections. It is hard to predict what happens. When you raise the threshold, you lose some of the activation in your real map (ie, clusters become smaller). But in the Null map, clusters also become smaller. So, at the lower threshold,

Re: [Freesurfer] mri_glmfit-sim - Clusterwise correction for multiple comparisons.

External Email - Use Caution assuming that all preprocessing steps, fsgd file and contrasts are correct, the choice between doss and dods could explain some of the variability you're seeing in your results. Consider running both models and possibly additional validation to see

[Freesurfer] mri_glmfit-sim - Clusterwise correction for multiple comparisons.

External Email - Use Caution Hi all, I took the freesurfer course in the recent past, and I am now beginning to run some glm thickness analyses! Currently I am doing a thickness analysis looking at the difference between two groups while controlling for age, and two continuous

Re: [Freesurfer] mri_glmfit-sim cluster output issue

External Email - Use Caution which part do you want to fix? the command not found or the lack of clusters? On 6/28/2023 6:25 PM, jordan wagner wrote: External Email - Use Caution Hello, My name is Jordan and I am working on cluster correction between two groups. I

[Freesurfer] mri_glmfit-sim cluster output issue

External Email - Use Caution Hello, My name is Jordan and I am working on cluster correction between two groups. I ran the step before: "freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=sig.mgh". I was able to find many significant values of p<0.05. However, when I

Re: [Freesurfer] mri_glmfit-sim error

.mgh.harvard.edu on behalf of mariangela asimina *Sent:* Monday, March 20, 2023 8:13 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] mri_glmfit-sim error External Email - Use Caution Hello FreeSurfer developers and experts, I am trying to do cluster correction with mri_

Re: [Freesurfer] mri_glmfit-sim error

: Monday, March 20, 2023 8:13 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_glmfit-sim error External Email - Use Caution Hello FreeSurfer developers and experts, I am trying to do cluster correction with mri_glmfit-sim after running mri_glmfit. The command I ran

[Freesurfer] mri_glmfit-sim error

External Email - Use Caution Hello FreeSurfer developers and experts, I am trying to do cluster correction with mri_glmfit-sim after running mri_glmfit. The command I ran:   mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 3.0 abs --cwp 0.05 --2spaces

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

f Tarumi Takashi > > Sent: Thursday, January 20, 2022 7:59 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized > > External Email - Use Caution > > Dear Dr. Yendiki, > > Thank you so much f

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Tarumi Takashi Sent: Thursday, January 20, 2022 7:59 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized External Email - Use Caution Dear Dr

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

tak...@gmail.com> > *Sent:* Wednesday, January 12, 2022 7:04 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized > > > External Email - Use Caution > > Dear FreeSurfer Developers: > > I am attempt

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

22 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized External Email - Use Caution Dear FreeSurfer Developers: I am attempting to perform cluster-wise correction for the along-tract measures, as described on the Tract statistic

[Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

External Email - Use Caution Dear FreeSurfer Developers: I am attempting to perform cluster-wise correction for the along-tract measures, as described on the Tract statistics tutorial (

Re: [Freesurfer] mri_glmfit-sim error

This happens because the cached p-values were generated from a simulation that only went up to 30mm FWHM of smoothing. lGI has lots of internal smoothness which often pushes it over this level. You can try not using any smoothing, or, even better, try using permutation instead.

Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

Don't use --grf with surfaces On 6/15/2021 7:24 PM, Paul, Jhelum wrote: External Email - Use Caution Hello, I also have the same error. I have been looking into all the tutorials available for Freesurfer v7 and trying to search why, mri_glmfit-sim   --glmdir

Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

look at the tutorial On 6/1/2021 12:00 AM, Diógenes Bispo wrote: External Email - Use Caution I would like to know what other modification I should make to my script to run --grf (volume analysis): - mris_preproc ?? - mri_glmfit (--surf in white) - mri_glmfit-sim ?? Thanks.

Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

External Email - Use Caution I would like to know what other modification I should make to my script to run --grf (volume analysis): - mris_preproc ?? - mri_glmfit (--surf in white) - mri_glmfit-sim ?? Thanks. Diogenes Bispo diogenesdi...@gmail.com Em sáb., 29 de mai. de

Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

You can't use the --grf option with surfaces On 5/29/2021 2:14 AM, Diógenes Bispo wrote: External Email - Use Caution Hi Freesurfer team. I made the following command: #!/bin/tcsh setenv study $argv[1] foreach hemi (lh rh)   foreach smoothing (10)     foreach meas (volume)        

[Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

External Email - Use Caution Hi Freesurfer team. I made the following command: #!/bin/tcsh setenv study $argv[1] foreach hemi (lh rh) foreach smoothing (10) foreach meas (volume) mris_preproc --fsgd FSGD/{$study}.fsgd \ --cache-in

Re: [Freesurfer] mri_glmfit-sim

That can happen because the null distribution of the cluster sizes change when you change the threshold. So at a threshold of 1.3, you might have a slightly larger cluster (which improves the cluster p-value), but you pay a penalty for lowering the threshold (which hurts the cluster p-value).

Re: [Freesurfer] mri_glmfit-sim

I just wanted to add that the attached maps in the previous email, was made by the tksurfer command below. I also added the mri_glmfit command. mri_glmfit --y cespct.nii.gz --osgm --glmdir main.wls --nii.gz --mask ../mask.nii.gz --surface fsaverage ${space:(-2)} --cortex --fwhm 5 --no-prune

Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm36/pos/th40/mc-z.csd Regards, Xiaoxu From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Greve, Douglas N.,Ph.D. Sent: Wednesday, January 13, 2021 9:16 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_glmfit

Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

When you use --cache, mri_glmfit-sim will use precomputed (ie, "cached") CSD files as found in $FREESURFER_HOME/average/mult-comp-cor On 1/5/2021 4:55 PM, Na, Xiaoxu wrote: External Email - Use Caution Dear Freesurfer Experts, I’ve all the subjects successfully done recon-all, lgi

[Freesurfer] mri_glmfit-sim error with no csd files generated

External Email - Use Caution Dear Freesurfer Experts, I've all the subjects successfully done recon-all, lgi before coming to the group analysis. The following group analysis will use the 10mm smoothing as generated in previous recon-all. Mris_preproc were implemented

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

External Email - Use Caution Hi Doug, Deleting the .csd files and re-running worked. Thank you! Meaghan On Tue, Sep 15, 2020 at 11:30 AM Douglas N. Greve wrote: > *Message sent from a system outside of UConn.* > > Hmm, there should have been a lot more terminal output than

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

Hmm, there should have been a lot more terminal output than that. Try this, delete the CSD files: rm lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j*-osgm.csd Then re-run. If it fails, then send me the perm.th20.abs.j*-osgm.csd files On 9/14/2020 2:58 PM, Meaghan Perdue wrote:

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

External Email - Use Caution Hi Doug, Here is the command: mri_glmfit-sim --glmdir lh.rs6980093.thickness10.glmdir --perm 1000 2.0 abs --cwp 0.05 --2spaces --bg 4 And here is the output: mri_glmfit simulation done 4.78645 mri_glmfit simulation done 4.806 mri_glmfit

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

please send the full command line and terminal output On 9/9/2020 3:19 PM, Meaghan Perdue wrote: External Email - Use Caution Hello Freesurfer experts, We're receiving the following error message when trying to run mri_glmfit-sim: ERROR: CSDmerge: CSDs have same seed This only

Re: [Freesurfer] mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999

egards, >> Paul >> *Sent:* Wednesday, September 09, 2020 at 1:01 AM >> *From:* "Douglas N. Greve" >> *To:* freesurfer@nmr.mgh.harvard.edu >> *Subject:* Re: [Freesurfer] mri_glmfit-sim using --cwp 0.05, --cwp >> 0.1, --cwp 0.999 >> On 9/7/2020 10:52 PM,

[Freesurfer] mri_glmfit-sim error CSDs have the same seed

External Email - Use Caution Hello Freesurfer experts, We're receiving the following error message when trying to run mri_glmfit-sim: ERROR: CSDmerge: CSDs have same seed This only occurs when we try to run the permutation on the LH for thickness. We've been able to run the

Re: [Freesurfer] mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999

On 9/7/2020 10:52 PM, Paul wrote: External Email - Use Caution Dear Freesurfer Experts, I have few questions regarding CWP values from mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999. Using the 3 three commands below (A, B and C): A. mri_glmfit-sim  --glmdir

[Freesurfer] mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999

External Email - Use Caution Dear Freesurfer Experts,   I have few questions regarding CWP values from mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999.   Using the 3 three commands below (A, B and C):   A. mri_glmfit-sim  --glmdir lh_status.glmdir --perm 1 1.3 abs

Re: [Freesurfer] mri_glmfit-sim running for 4 days and still not finished

Can you send your command line and terminal output? ...not all of it if it has been running for 4 days:) On 6/16/2020 8:34 AM, Mageshwar Selvakumar wrote: External Email - Use Caution Dear freesurfer community, I have been working with the freesurfer stat files for some time now

[Freesurfer] mri_glmfit-sim running for 4 days and still not finished

External Email - Use Caution Dear freesurfer community, I have been working with the freesurfer stat files for some time now but never got to explore the group analysis pipeline. I tried this mri_glmfit command to see the correlation of my anatomical data(57 subjects) with a

Re: [Freesurfer] mri_glmfit-sim FWHM error

External Email - Use Caution Hi, I did, but if this is a new version it probably co-exists with the old mri_surfcluster in my PATH (I am working on a server and am not allowed to delete files there..hmm). Why do the two flags (--sig2pmax and --bonferroni-max2) not appear in

Re: [Freesurfer] mri_glmfit-sim FWHM error

Did you down load all the files in the patch? I think the new mri_surfcluster is there On 4/8/2020 8:51 AM, s7675...@stud.uni-frankfurt.de wrote: > External Email - Use Caution > Hi again, > I already took a few more steps and set up PALM/ fspalm. It's working > fine, up to the point where it

Re: [Freesurfer] mri_glmfit-sim FWHM error

External Email - Use Caution thanks a lot! I will run both over night - if the permutation issue does not come up again, I agree that it would be the better option... Best, Doro Zitat von "Douglas N. Greve" : > On 4/6/2020 10:57 AM, s7675...@stud.uni-frankfurt.de wrote: >>

Re: [Freesurfer] mri_glmfit-sim FWHM error

On 4/6/2020 10:57 AM, s7675...@stud.uni-frankfurt.de wrote: > External Email - Use Caution > Hi Douglas, > > thanks a lot for your quick response. I wanted to use Monte Carlo sim > as all other analyses in our project include a monte carlo simulation > and I try to keep things consistent. Am

Re: [Freesurfer] mri_glmfit-sim FWHM error

The problem is that mri_glmfit-sim is looking for a entry in the table that does not exist. The table only goes up to a smoothness level of 35. LGI data tend to bed very smooth. I would strongly recommend that you use permutation instead. See

[Freesurfer] mri_glmfit-sim FWHM error

External Email - Use Caution Dear Freesurfer experts, I'm trying to run a simulation (--> mri_glmfit-sim) with cached LGI data (fwhm10), but get an error due to the estimated fwhm kernel. The folder corresponding to the fwhm value (-->37) does not exist, I guess because

Re: [Freesurfer] mri_glmfit-sim error

See this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 2/7/2020 9:52 PM, Kim, Gwang-Won wrote: Hi there, I ran “mri_glmfit-sim –glmdir g2v3.wls –2spaces –perm 1000 1.3 abs”. But, there was error message as follow: “design matrix is not orthogonal,

[Freesurfer] mri_glmfit-sim error

Hi there, I ran “mri_glmfit-sim -glmdir g2v3.wls -2spaces -perm 1000 1.3 abs”. But, there was error message as follow: “design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with -perm-force” Please let me know how to process

Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

ary 17, 2020 at 3:46 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines Hi Swati, - yes, you can treat the percent change maps (PC1) as the signal instead of the thickness and do a regular analysis (so either multiple comparisons or sim etc). - and

Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

> From: on behalf of "Greve, Douglas > N.,Ph.D." > Reply-To: Freesurfer support list > Date: Thursday, January 16, 2020 at 3:26 PM > To: "freesurfer@nmr.mgh.harvard.edu" > Subject: Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines > > S

Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

tirane/ From: on behalf of "Greve, Douglas N.,Ph.D." Reply-To: Freesurfer support list Date: Thursday, January 16, 2020 at 3:26 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines Sorry, what i

Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

lto:srle...@uw.edu> Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, January 10, 2020 at 10:06 AM To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] mri_

Re: [Freesurfer] mri_glmfit-sim for longitudinal pipelines

ect: [Freesurfer] mri_glmfit-sim for longitudinal pipelines External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare longitudinal cortical thinning rates (pc1) between 3 groups using mri_glmfit using FreeSurfer 6.0. The tutorial suggests that you could use the mult

[Freesurfer] mri_glmfit-sim for longitudinal pipelines

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compare longitudinal cortical thinning rates (pc1) between 3 groups using mri_glmfit using FreeSurfer 6.0. The tutorial suggests that you could use the multiple comparisons corrections that come with it

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

External Email - Use Caution Hi Freesurfer, I am also experiencing the same problem and everything regarding FREESURFER path looks ok just getting error that says: Reading source surface /storage/affective/ume2/confined/Amir/FS/fsaverage/surf/rh.white MRISread(): could not open

Re: [Freesurfer] mri_glmfit-sim cluster correction threshold inquiry

When you have such a low threshold, the resulting p-values are very liberal. See our paper https://www.ncbi.nlm.nih.gov/pubmed/29288131 Should be fine for exploratory On 3/7/19 7:48 PM, Arsenije Subotic wrote: > External Email - Use Caution > > Hello, > > I am planning on running a

[Freesurfer] mri_glmfit-sim cluster correction threshold inquiry

External Email - Use Caution Hello, I am planning on running a correction for multiple comparisons, and I was hoping to use a vertex wise cluster forming threshold of 1.3, however after reading more when I ran the mri_glmfit-sim —help command it recommends using the

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

On 11/27/2018 06:46 AM, C.P.E. Rollins wrote: > External Email - Use Caution > Hi Douglas, > > Thanks a lot for your answers. > > 1) For the permutations, would you recommend using this for > controlling for MC in cortical thickness analyses too? Yes > Why is it recommended to use permutation

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

External Email - Use Caution Hi Douglas, Thanks a lot for your answers. 1) For the permutations, would you recommend using this for controlling for MC in cortical thickness analyses too? Why is it recommended to use permutation simulation as opposed to Z Monte Carlo simulation

Re: [Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

On 11/23/2018 11:26 AM, C.P.E. Rollins wrote: > External Email - Use Caution > Dear Freesurfer Developers, > I have a 2-part question: > 1) I was advised to use permutation to control for multiple > comparisons in an LGI analysis, would you mind elaborating how to do > this in command line

[Freesurfer] mri_glmfit-sim error correcting for MC for LGI analysis

External Email - Use Caution Dear Freesurfer Developers, I have a 2-part question: 1) I was advised to use permutation to control for multiple comparisons in an LGI analysis, would you mind elaborating how to do this in command line (in terms of command and parameters)? 2) In

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

External Email - Use Caution Hi Douglas, Thanks for the response. Yes, I confirm that the file /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can view it in freeview. Any other possible errors? Also, would you mind elaborating how to use permutation to

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

can you verify that /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and that you have read permission to it? Eg, can you load it with freeview -f /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white On 11/20/18 8:25 AM, C.P.E. Rollins wrote: External Email - Use Caution

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

External Email - Use Caution Thanks Douglas, I've attached here the output from mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces --debug Could you clarify how to use permutation to correct for MC for LGI? (as in what to enter for command

Re: [Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

I can' tell what is going wrong there. Can you run it with --debug as the first option and send the output? BTW, the MC correction for LGI is probably not very accurate. I would recommend using permutation. See here

[Freesurfer] mri_glmfit-sim MRISread(?????): could not open file

External Email - Use Caution Dear Freesurfer Developers, I'm trying to run mri_glmfit-sim to correct for multiple comparisons but am receiving the following error: cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir

[Freesurfer] mri_glmfit-sim error

External Email - Use Caution Dear Freesurfer Developers, I'm trying to run mri_glmfit-sim to correct for multiple comparisons but am receiving the following error: cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir

Re: [Freesurfer] mri_glmfit-sim error

External Email - Use Caution Hi Douglas, Yes, the file (/lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white) exists, I can view it in Freeview and have read permissions. I had recently tried downloading this patch:

Re: [Freesurfer] mri_glmfit-sim error

Can you verify that the followign file exists, that you have read permission, and that you can successfully load it into freeview? /lustre/group/p00355/REST_Beijing_SCZ/Freesurfer/fsaverage/surf/rh.white On 9/21/18 11:41 AM, C.P.E. Rollins wrote: External Email - Use Caution Hello

[Freesurfer] mri_glmfit-sim error

External Email - Use Caution Hello Freesurfer Developpers, I'm trying to use mri_glmfit-sim to make clusterwise corrections but am running into the following error: - XFM matrix (RAS2RAS) ---

Re: [Freesurfer] mri_glmfit-sim on fsaverage5

The MCZ tables were not built for fsaverage5. I think the best thing to do instead is a permutation test (since the MCZ is a little dodgy anyway:).  Instructions are here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm You should run it from the development

[Freesurfer] mri_glmfit-sim on fsaverage5

Hello freesurfers! My resting state data is in fsaverage5 space. mri_info gives dimensions of 3414 x 1 x 3 x 120 and voxelsize 1x1x1. I do the group analysis and mri_glmfit creates a sig.mgh file that is has those same dimensions and results look good. Then I say: mri_glmfit-sim --glmdir

[Freesurfer] mri_glmfit-sim and Ftest

Hi Freesurfer experts! I know we asked this question before, but maybe someone came back from holidays and know the answer! Does Hi Freesurfer experts. Does mri_glmfit-sim Monte-Carlo cluster size correction is also usable for F-test? The doc says that it synthesizes a z map (I assume from a

Re: [Freesurfer] mri_glmfit-sim over PALM

Yes, that should work, except you will need to add --perm-resid. See the --help On 09/13/2017 02:33 PM, Martin Juneja wrote: > Hi experts, > > To calculate simulations on LGI measures, I ran: > mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd > --sim-sign abs --cwpvalthresh

[Freesurfer] mri_glmfit-sim over PALM

Hi experts, To calculate simulations on LGI measures, I ran: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --sim perm 1000 3 permcsd --sim-sign abs --cwpvalthresh .05 But it gives error: ERROR: design matrix is not orthogonal, cannot be used with permutation. I came across a post where its

Re: [Freesurfer] mri_glmfit-sim annotations

it just uses the annotation of the vertex with the maximum value. You can have it use the centroid by adding --centroid On 08/18/2017 07:33 PM, Van Der Deijl, Rosanne wrote: > Dear Freesurfer team, > > I was wondering how the annotations for the clusters that came out of > mri_glmfit are

[Freesurfer] mri_glmfit-sim annotations

Dear Freesurfer team, I was wondering how the annotations for the clusters that came out of mri_glmfit are picked. I am wondering because I have a cluster which visually seems to cover mostly the insula (and with a previous set of subjects this same cluster was annotated as the insula), but it

Re: [Freesurfer] mri_glmfit-sim output

able? > > Thank you! > > Message: 8 > Date: Mon, 7 Aug 2017 15:01:46 -0400 > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mri_glmfit-sim output > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <0b5fc464-a5ed-cee5-e3fa-3603b99e8...@n

Re: [Freesurfer] mri_glmfit-sim output

Thanks for the link, I hadn't seen that one indeed! However, the variable WghtVtx is not explained on this page. What is this variable? Thank you! Message: 8 Date: Mon, 7 Aug 2017 15:01:46 -0400 From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_glmfit-sim

Re: [Freesurfer] mri_glmfit-sim output

see here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary On 08/07/2017 02:40 PM, Van Der Deijl, Rosanne wrote: > Dear Freesurfer team, > > In the mri_glmfit-sim summary output file, I get a number of output > variables, and I'm not sure what some of them are.

[Freesurfer] mri_glmfit-sim output

Dear Freesurfer team, In the mri_glmfit-sim summary output file, I get a number of output variables, and I'm not sure what some of them are. Could you explain the ones in bold to me? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZCWP CWPLow CWPH NVtxsWghtVtx

Re: [Freesurfer] mri_glmfit-sim --grf question

Hi Doug, it turned out to be just a viewer glitch. I can see the map now with the expected clusters. Thanks so much for your help! On Mon, Jul 24, 2017 at 4:15 PM, Douglas Greve wrote: > > > On 7/24/17 4:12 PM, Jiahe Zhang wrote: > > That makes sense. And thanks for

Re: [Freesurfer] mri_glmfit-sim --grf question

On 7/24/17 4:12 PM, Jiahe Zhang wrote: That makes sense. And thanks for the suggestion! I tried running permutation test with the following command: mri_glmfit-sim --glmdir r_PCC_glm --sim perm 1 1.3 perm.abs.1.3 --sim-sign abs The results are empty maps for all the contrasts I have,

Re: [Freesurfer] mri_glmfit-sim --grf question

That makes sense. And thanks for the suggestion! I tried running permutation test with the following command: mri_glmfit-sim --glmdir r_PCC_glm --sim perm 1 1.3 perm.abs.1.3 --sim-sign abs The results are empty maps for all the contrasts I have, which I did not expect, since some of the

Re: [Freesurfer] mri_glmfit-sim --grf question

Yes, that is expected with your command line. The issue is that you are using a positive (pos) a priori hypothesis about the sign of the effect. By default, freesurfer generates unsigned statistics (this is what you see when you just view the stats map). When you specify pos, it adjusts the

[Freesurfer] mri_glmfit-sim --grf question

Dear Freesurfer experts, I'm trying to run multiple comparisons correction using mri_glmfit-sim. Since I'm working with volume data, I used -grf instead of -cache. The resulting map has bigger clusters with higher significance values than the original sig.mgh map from mri_glmfit. Is this normal?

Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

Is this for a volume analysis? If so, then you'll need to use the --grf option instead of using the mcz simulations (those are just for surface) On 07/08/2017 01:03 PM, Aly Negreira wrote: > Hi Doug! > > Thank you for the reply! Re-ran w/ --debug as first option. Below is > the output. Not

Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

Hi Doug! Thank you for the reply! Re-ran w/ --debug as first option. Below is the output. Not sure if this is helpful, but when I cd to /Applications/freesurfer/average/mult-comp-cor/fsaverage there are only directories for lh and rh, nothing for mni. Thanks for the help! Aly

Re: [Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

Hi Aly, it is not creating the path correctly, not sure why. Can you run it again with --debug as the first option and send me the terminal output? doug On 7/1/17 1:57 PM, Aly Negreira wrote: Hi Freesurfer Community, I'm using FsFast on my dissertation data and trying to run a monte carlo

[Freesurfer] mri_glmfit-sim ERROR cannot find mc-z.csd file

Hi Freesurfer Community, I'm using FsFast on my dissertation data and trying to run a monte carlo correction on my functional data in the volume. I keep running into the below error. In attempting to troubleshoot, it looks like Yuko ran into a similiar issue (see archived email from Fri Dec 9 @

Re: [Freesurfer] mri_glmfit-sim output error

Did you name one of your contrasts "lh-Avg-thickness-Gender*Age-Inter.mtx"? If so, then remove the star ("*") as that has special meaning to the shell On 5/26/17 2:11 AM, Duy Nguyen wrote: Dear Doug After I add --debug like this: mri_glmfit-sim --debug --glmdir lh.gender_age.glmdir --cache

Re: [Freesurfer] mri_glmfit-sim output error

Dear Doug After I add --debug like this: mri_glmfit-sim --debug --glmdir lh.gender_age.glmdir --cache 3 abs --cwp .999 --2spaces The terminal output is shown in the attached file. A bit overview about my analysis: I have 148 subjects that I am interested in analyzing the gender and cortical

Re: [Freesurfer] mri_glmfit-sim output error

Can you add --debug as the first argument and send the terminal output? On 05/19/2017 11:48 PM, Duy Nguyen wrote: > Dear FreeSurfer experts, > > When I try to run mri_glmfit-sim, the output came out like this: > > cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd >

[Freesurfer] mri_glmfit-sim output error

Dear FreeSurfer experts, When I try to run mri_glmfit-sim, the output came out like this: cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd lh.gender-age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C lh-Avg-thickness-FemaleMale.intercept.mtx --C lh-Avg-thickness-Gender.diff.mtx

Re: [Freesurfer] mri_glmfit-sim

On 02/21/2017 02:26 PM, Shane Schofield wrote: > Hi, > > I have 3 beginner questions about the use of mri_glmfit-sim > > 1. Under what type of circumstances should I run mri_glmfit-sim with > permutation simulations? This is a little bit of an open question as there is a big debate going on

[Freesurfer] mri_glmfit-sim

Hi, I have 3 beginner questions about the use of mri_glmfit-sim 1. Under what type of circumstances should I run mri_glmfit-sim with permutation simulations?  2. The voxel threshold of 0.01 (cache 2) is used a lot. Is this too lenient in cortical thickness comparisons?  3. About the sign of

[Freesurfer] mri_glmfit-sim cannot determine file for mask after mri_glmfit --no-prune

Hello Freesurfer Experts, My apologies if this is a rather simple/obvious question. I am trying to run 3 Monte Carlos using mri_glmfit-sim with the following commands: Left hemisphere surface: mri_glmfit-sim --glmdir $SUBJECTS_DIR/.../LH_7vFix/ --sim mc-z 1 1.3 mcz1_1.3 --sim-sign abs

Re: [Freesurfer] mri_glmfit-sim

The 2nd one On 12/31/16 6:06 AM, std...@virgilio.it wrote: Hi list, which is the correct option, please? 1- mri_glmfit-sim --glmdir my-glm.wls --cache 1.3 abs --cwpvalthresh .0166 --3spaces 2- mri_glmfit-sim --glmdir my-glm.wls --cache 1.3 abs --cwpvalthresh .05 --3spaces Thanks Best

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

;>>> or is it allowed to do this instead of using tools like palm (what >>>> happens eg with the covariates when using forced permutation)? I >>>> used forced permutation and it seemed to work, results were (partly) >>>> comparable to what I found with mo

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

if you just don't do anything. > >>> > >>> > >>> On 08/29/2016 11:07 AM, maaike rive wrote: > >>>> Hi all, > >>>> > >>>> > >>>> Is using forced permutation for non-orthogonal design matrices wrong > &

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

ools like palm (what >>>> happens eg with the covariates when using forced permutation)? I >>>> used forced permutation and it seemed to work, results were (partly) >>>> comparable to what I found with monte carlo simulations. >>>> >>>> &g

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

ed permutation)? I >>> used forced permutation and it seemed to work, results were (partly) >>> comparable to what I found with monte carlo simulations. >>> >>> >>> Thanks, Maaike >>> >>> >>>--

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

o simulations. >>> >>> >>> Thanks, Maaike >>> >>> >>> >>> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu >>> <freesurfer-boun...@nmr.mgh.ha

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

- >> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu >> <freesurfer-boun...@nmr.mgh.harvard.edu> namens Harms, Michael >> <mha...@wustl.edu> >> *Verzonden:* vrijdag 26 augustus 2016 01:00:13 &g

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

arvard.edu> namens Harms, Michael > <mha...@wustl.edu> > *Verzonden:* vrijdag 26 augustus 2016 01:00:13 > *Aan:* Freesurfer support list > *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing > running after 3 days! > > Hi, > You might want to check out FSL

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

edu> > *Verzonden:* vrijdag 26 augustus 2016 01:00:13 > *Aan:* Freesurfer support list > *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing > running after 3 days! > > Hi, > You might want to check out FSL’s PALM tool, which has a bit more > sophisticate

  1   2   3   >