Re: [Freesurfer] GLM Using 2 Surfaces - Thickness and Area

On 4/18/2024 1:59 PM, Tejaswi D. Sudhakar wrote: External Email - Use Caution Hello Freesurfer team, I am interested in doing one glm analysis using both the thickness and cortical surface area. My question is two-fold: First, is it possible to provide both the thickness and

[Freesurfer] GLM Using 2 Surfaces - Thickness and Area

External Email - Use Caution Hello Freesurfer team, I am interested in doing one glm analysis using both the thickness and cortical surface area. My question is two-fold: First, is it possible to provide both the thickness and area files to mris_preproc and mri_surf2surf

Re: [Freesurfer] GLM with multiple nuisance variables

External Email - Use Caution Have you looked at this page

[Freesurfer] GLM with multiple nuisance variables

External Email - Use Caution Dear Freesurfer experts, I want to run a GLM to analyze the correlation between a continuous variable Y and a morphometric measure (eg. Cortical thickness). I want to control for some nuisance variables: sex, scan site, age, age squared, age * sex

Re: [Freesurfer] GLM error: matrix is ill-conditioned or badly scale

__ 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 代表 Douglas N. Greve 发送时间: Monday, September 12, 2022 10:10:45 PM 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Re: [Freesurfer] GLM error: matrix is ill-conditioned or badly scale HCs always have 0 medicationload so it is not possible to measure a load

Re: [Freesurfer] GLM error: matrix is ill-conditioned or badly scale

HCs always have 0 medicationload so it is not possible to measure a load slope for them. Is it the case that a BD with load=0 is the same as HC? If so, then just have one class. If not, do you expect the age, edu, and tiv slopes to differ between the groups? If not, then use DOSS (default was

[Freesurfer] GLM error: matrix is ill-conditioned or badly scale

External Email - Use Caution Dear experts, I would like to run mri_glmfit in a group analysis. However, I met the following error when I added the medicationload as variable in my fsgd file. Since I have 305 subjects and only 75 of these have medication load, it seems to this

Re: [Freesurfer] GLM analysis - volume and surface area

External Email - Use Caution Ok! Thanks so much for the answer! Best, Laura. De: Douglas N. Greve Enviado: segunda-feira, 28 de março de 2022 00:29 Para: Laura Willers de Souza Cc: freesurfer@nmr.mgh.harvard.edu Assunto: Re: [Freesurfer] GLM

Re: [Freesurfer] GLM analysis - volume and surface area

Hi, sorry for the late response. No, there is nothing else you have to do. Using perm is a really good idea with volume and area, so glad to hear that is what you are doing. best doug On 3/10/2022 8:21 AM, Laura Willers de Souza wrote: External Email - Use Caution Of course! To do

Re: [Freesurfer] GLM analysis - volume and surface area

External Email - Use Caution Of course! To do GLM for volume and surface area analysis, is there any change in commands in relation to cortical thickness analysis? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies

Re: [Freesurfer] GLM analysis - volume and surface area

Can you just ask the question again so I don't have to sort it out myself? On 3/2/2022 3:30 PM, Laura Willers de Souza wrote: External Email - Use Caution Sorry about that! I'm resending with previous emails. The first message below is the one you didn't know how to respond to

Re: [Freesurfer] GLM analysis - volume and surface area

External Email - Use Caution Sorry about that! I'm resending with previous emails. The first message below is the one you didn't know how to respond to because you didn't have the previous e-mails.

Re: [Freesurfer] GLM analysis - volume and surface area

! De: Douglas N. Greve Enviado: terça-feira, 22 de fevereiro de 2022 20:01 Para: Laura Willers de Souza Cc: freesurfer@nmr.mgh.harvard.edu Assunto: Re: [Freesurfer] GLM analysis - volume and surface area Sorry, your previous emails were cut off so I'm not sure what command

Re: [Freesurfer] GLM analysis - volume and surface area

External Email - Use Caution Thanks so much for the explanation! There is something different in the analysis of volume and surface area in relation to the analysis of cortical thickness? Like some more command, or some other detail that must be changed (besides, of course, the

Re: [Freesurfer] GLM analysis - volume and surface area

Yes, it is. It is confusing when you talk about area and volume since these are not point measures like thickness (ie, what is the volume or area of a vertex?). The area of a vertex is computed as the mean of the adjacent triangles of the vertex. The volume is the mean of the neighboring

[Freesurfer] GLM analysis - volume and surface area

External Email - Use Caution Hello FreeSurfer Developers, I would like to know if it is correct to perform volume and surface area analysis using freesurfer's GLM!? In several mailing list questions I have already seen instructions for performing these types of analysis. But I

Re: [Freesurfer] GLM DOSS questions

On 2/21/2020 4:01 AM, Ferraro, Pilar wrote: External Email - Use Caution Dear Freesurfer experts, I’ve just completed a GLM analysis in Freesurfer and I’d like to be sure that all the steps I’ve performed are the right ones. My analysis is looking at age related changes in

[Freesurfer] GLM DOSS questions

External Email - Use Caution Dear Freesurfer experts, I’ve just completed a GLM analysis in Freesurfer and I’d like to be sure that all the steps I’ve performed are the right ones. My analysis is looking at age related changes in cortical thickness in one group of patients,

[Freesurfer] GLM DOSS question

External Email - Use Caution Dear Freesurfer experts, I’ve just completed a GLM analysis in Freesurfer and I’d like to be sure that all the steps I’ve performed are the right ones. My analysis is looking at age related changes in cortical thickness in one group of patients,

Re: [Freesurfer] GLM analysis question

On 9/23/2019 10:54 AM, Ferraro, Pilar wrote: > External Email - Use Caution > > To the kind attention of the FreeSurfer team, > > I have some questions concerning a GLM analysis I’m running and any help > would be greatly appreciated! > I’m interested in identifying cortical regions

[Freesurfer] GLM analysis question

External Email - Use Caution To the kind attention of the FreeSurfer team, I have some questions concerning a GLM analysis I’m running and any help would be greatly appreciated! I’m interested in identifying cortical regions where older age is associated with greater atrophy.

[Freesurfer] GLM twin design

External Email - Use Caution Dear FS List, I wanted to check if my GLM design for a surface based analysis is sound. I am new to FS so please don’t skip over details. I have 3 groups of monozygotic twins: low-risk, high-risk, ill. Twin pairs may be present in the same group (e.g

[Freesurfer] Glm for volume

External Email - Use Caution Hello developer, I am glad to tell you that after 3 hours, something did print more on terminal. when I was doing the GLM follow the tutorial, it only provided the example of the cortical thickness. And I did not know how to transfer it into volume.

Re: [Freesurfer] GLM - correction for multiple comparisons

on behalf of Greve, Douglas N.,Ph.D. Sent: Thursday, February 14, 2019 12:14:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM - correction for multiple comparisons It is certainly possible. Are some of the clusters in abs negative? Also, I would strongly recommend using

Re: [Freesurfer] GLM - correction for multiple comparisons

It is certainly possible. Are some of the clusters in abs negative? Also, I would strongly recommend using permutation if you are using such a low clusterwise threshold. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm The monte carlo simulation is not valid

Re: [Freesurfer] GLM multiple comparison correction

That is not normal. Are you sure you are looking at the different maps that are created? Also, we are recommending that people not use MCZ (especially with such a low threshold). Permutation is more accurate. See

Re: [Freesurfer] glm analysis

That matrix will test for an effect of group regressing out the effect of age. I would first test for an interaction between group and age with 0 0 0 1 -1 0 0 0 0 1 0 -1 Assuming that there is no effect, then I would re-run with DOSS (different-offset, same-slope) with a contrast like 1 -1 0 0

Re: [Freesurfer] glm analysis

Dear Freesurfers, I am trying to run a GLM analysis with 3 groups (1)long disease duration MS, 2)short disease duration MS, 3)healthy controls) and 1 variable (age). According to the formula provided on freewiki: N classes (N of variables + 1), is this contrast matrix correct? 1 -1 0 0 0

[Freesurfer] glm analysis

Dear Freesurfers, I am trying to run a GLM analysis with 3 groups (1)long disease duration MS, 2)short disease duration MS, 3)healthy controls) and 1 variable (age). According to the formula provided on freewiki: N classes (N of variables + 1), is this contrast matrix correct? 1 -1 0 0 0

Re: [Freesurfer] GLM

Sounds like you need an F-test, eg, create a contrast like 1 1 -1 -1  0  0 0 0 0 0 0 0 1 1  0  0 -1 -1 0 0 0 0 0 0 This tests the null hypothesis that p1==p2==control On 11/07/2018 10:11 AM, 13181786167 wrote: > > External Email - Use Caution > > Thanks for your reply. Using the first

Re: [Freesurfer] GLM

Use the first one. Not sure what you mean by your multiple comparisons question On 11/01/2018 11:20 PM, 郑凤莲 wrote: > > External Email - Use Caution > > Hi experts, > > I am using FS 6.0 for analyzing the cortical thickness difference > between 3 groups: patient1, patient2 and control.

[Freesurfer] GLM

External Email - Use Caution Hi experts, I am using FS 6.0 for analyzing the cortical thickness difference between 3 groups: patient1, patient2 and control. In DODS model, I need to creat 2 files, FSDG and mtx file. And we have 3 variables: age, gender and cortical

Re: [Freesurfer] GLM

you need to have four classes, young-female, young-male, old-female, old-male On 9/21/18 3:15 AM, 郑凤莲 wrote: External Email - Use Caution Dear experts, I am using FS 6.0 for some studies. I want to calculate the thickness difference between males and females in two group, Young group

[Freesurfer] GLM

External Email - Use Caution Dear experts, I am using FS 6.0 for some studies. I want to calculate the thickness difference between males and females in two group, Young group and Old group. In DODS model: The first step: creat a FSDG file: GroupDescriptorFile 2 Title

Re: [Freesurfer] GLM error - cannot read fsgd file for reading

y.mgh is the input file, usually the output of mris_preproc (after smoothing). See the group analysis tutorial. On 08/10/2017 11:48 AM, Nick Corriveau-Lecavalier wrote: > > Hi Freesurfer team, > > > First, sorry making a new post, I'm having trouble with my email and > I'm not able to reply

Re: [Freesurfer] GLM error - cannot read fsgd file for reading

Hi Freesurfer team, First, sorry making a new post, I'm having trouble with my email and I'm not able to reply directly on my yesterday's post. Here's my issue: I'm trying to make a group analysis with 3 groups using the mri_glmfit command. This it what the terminal says: Loading y from

Re: [Freesurfer] GLM error - cannot read fsgd file for reading

make sure you pass the full path to the fsgd, otherwise it looks in the current folder. Also make sure it is readable by you On 08/09/2017 05:12 PM, Nick Corriveau-Lecavalier wrote: > > Hi Freesurfer team, > > > I'm trying to run a GLM analysis with three groups (Controls, MCI, AD) > with 0

[Freesurfer] GLM error - cannot read fsgd file for reading

Hi Freesurfer team, I'm trying to run a GLM analysis with three groups (Controls, MCI, AD) with 0 covariables at the moment, but I would like to add two eventually. I've been following the tutorial on this link: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V, and when I write the

Re: [Freesurfer] GLM Analysis Number of vertices and Area

I'm not sure what you mean. Do you want stats for every cluster regardless of significance? If so, you can run the monte carlo correction with a clusterwise p-value (--cwp in mri_glmfit-sim) of 1.0 On 07/13/2017 11:52 AM, Aman Montazeri wrote: > Hello Friends, > > Sorry for the simple

[Freesurfer] GLM Analysis Number of vertices and Area

Hello Friends, Sorry for the simple question. I am doing GLM analysis using QDEC between two groups (one discrete variable), then I run the Monte-Carlo clustering and got the stats of my cluster. My supervisor asked me to get the Stats of blobs/clusters (area and number of vertices in each

Re: [Freesurfer] GLM question

ng the list at > freesurfer-ow...@nmr.mgh.harvard.edu > <mailto:freesurfer-ow...@nmr.mgh.harvard.edu> > > > > On 7/7/17 1:58 PM, Yann Ying Chye wrote: > > Dear FreeSurfer mailing list, > > > > I've got two questions regarding the frees

Re: [Freesurfer] GLM question

: > > Dear FreeSurfer mailing list, > > > > I've got two questions regarding the freesurfer GLM analysis. > > > > 1. I am trying to run mri_glmfit on the cortical thickness of a > > dataset that has a few interacting factors of unequal levels. > > For examp

Re: [Freesurfer] GLM question

On 7/7/17 1:58 PM, Yann Ying Chye wrote: Dear FreeSurfer mailing list, I've got two questions regarding the freesurfer GLM analysis. 1. I am trying to run mri_glmfit on the cortical thickness of a dataset that has a few interacting factors of unequal levels. For example, my dataset may have

[Freesurfer] GLM question

Dear FreeSurfer mailing list, I've got two questions regarding the freesurfer GLM analysis. 1. I am trying to run mri_glmfit on the cortical thickness of a dataset that has a few interacting factors of unequal levels. For example, my dataset may have groups A, B, C, and D. Within the groups

Re: [Freesurfer] glm results : opposite direction between whole-brain analysis and feature extraction in the significant clusters

In that mri_segstats command, you will get a column for everything that is not in a cluster as well as for each cluster. Make sure that you are using the correct column. The other thing you can do is to run the post hoc test in matlab, somthing like y = load('file.stats'); X =

Re: [Freesurfer] GLM fitting for the cortical volume

If you run mris_preproc, then specify --meas volume On 6/24/17 3:10 PM, Ali Radaideh wrote: Dear FS experts, I have managed to run the *glm_fit* on the cortical thickness and area on a group of MS patients. However, i am not sure how to do this on the cortical volume. which file represents

[Freesurfer] GLM fitting for the cortical volume

Dear FS experts, I have managed to run the *glm_fit* on the cortical thickness and area on a group of MS patients. However, i am not sure how to do this on the cortical volume. which file represents the cortical volume in subject's directory? Many thanks, -- *Ali M. Al-Radaideh. PhDHead

[Freesurfer] glm results : opposite direction between whole-brain analysis and feature extraction in the significant clusters

Hi, I am working on R1 maps. I ran a very simple glm on smoothed R1 maps, FWHM = 8 mm, population 1, population 2 , and age as nuisance factor. After POS MC simulation CW correction, I had two significant clusters resulting from this in the planum temporale and Heschl’s sulcus. The contrast

Re: [Freesurfer] GLM-error

The error message says that it cannot find a file. Does that file exist? Do you have fsaverage in your $SUBJECTS_DIR? On 03/07/2017 06:19 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote: > > Dear Freesurfer Experts, > > I was running qdec, and encountered an error while I was running the > analyze

[Freesurfer] GLM-error

Dear Freesurfer Experts, I was running qdec, and encountered an error while I was running the analyze button on the qdec. Subsequently, if you can help with the following error would greatly appreciate it. Continuous Variable Means (all subjects) 0 Intracranial_volume 1.53095e+06 157812 1

Re: [Freesurfer] GLM set up and correlations

That red dot is fine. I bigger question is why you are using a development version from July 2016? The development versions are often unstable. On 03/06/2017 05:27 PM, Martin Juneja wrote: > Hi Dr. Greve, > > I looked at the medial wall area in lh.MEQ_area.10.mgh and noticed a > small cluster

Re: [Freesurfer] GLM set up and correlations

Hmm, something is going wrong because medial wall areas should have been masked out. Take a look at the medial wall area in lh.MEQ_area.10.mgh file with something like tksurferfv fsaverage lh inflated -aparc -ov lh.MEQ_area.10.mgh -fminmax .001 .1 scroll through the subjects to see if you see

Re: [Freesurfer] GLM set up and correlations

Hi Dr. Greve, I am using following commands: recon-all -all -subject S01 -i T1w_S01.nii -qcache mris_preproc --fsgd MEQ.fsgd --target fsaverage --hemi lh --meas area --out lh.MEQ_area.mgh mri_surf2surf --hemi lh --s fsaverage --sval lh.MEQ_area.mgh --fwhm 10 --cortex --tval lh.MEQ_area.10.mgh

Re: [Freesurfer] GLM set up and correlations

I think you might be doing something wrong during preprocessing. Can you send your command lines? On 03/06/2017 12:11 PM, Martin Juneja wrote: > Hello experts, > > I am trying to correlate cortical surface area measure with behavioral > measures using instructions from here: >

Re: [Freesurfer] GLM on cortical and subcortical volume

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI this does not have the mri_glmfit command, but that is the same doing the voxel-wise stats with the change in --y. This does not include correction for ICV On 10/18/16 10:53 AM, miracle ozzoude wrote: hello doug, Thanks for

Re: [Freesurfer] GLM on cortical and subcortical volume

hello doug, Thanks for the response. Please can you send me the link. Also, does GLM correct for total intracranial volume or do I need to create fsgd file with total intracranial volume as covariate? Thanks On Tue, Oct 18, 2016 at 10:48 AM, Douglas Greve wrote: > do

Re: [Freesurfer] GLM on cortical and subcortical volume

do you mean volumes of ROIs? Yes, there is a tutorial on this in our wiki, but basically you need to run aparcstats2table and/or asegstats2table to create a table of volumes for each subject and ROI. Then use mrI_glmfit with the --table option instead of --y On 10/18/16 10:18 AM, miracle

[Freesurfer] GLM on cortical and subcortical volume

Hello Expert, Is there are way to perform glm analysis on cortical and subcortical volumes. Thanks Best,. Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] GLM in groups with unequal size

It will not On 10/13/16 10:34 AM, Eelco van Duinkerken wrote: Ah sorry for the low level of info. I am aiming to do a simple group comparison, where I'm comparing thickness between controls and obese or T2DM patients, regressing out the effect of age, sex and, hypertension. So I created one

Re: [Freesurfer] GLM in groups with unequal size

It will be constrained by the group with the smaller number of subjects. There is not anything wrong with unequal group sizes, but it is less efficient than if you had split your acquisitions evenly. On 10/13/16 10:17 AM, Bruce Fischl wrote: Hi Eelco it depends on how you setup your GLM.

Re: [Freesurfer] GLM in groups with unequal size

Thank you Jurgen! That helps a lot. Good to know that the results are not driven by any difference in varience. Thanks all, Eelco 2016-10-13 12:00 GMT-03:00 Juergen Haenggi : > Dear Eelco > > years ago i posed a similar question on the FS email list > >

Re: [Freesurfer] GLM in groups with unequal size

Dear Eelco years ago i posed a similar question on the FS email list https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-November/021386.html a part of the response is below >>> The other question is how mri_glmfit estimates the variance. Because I have >>> only one subject in the

Re: [Freesurfer] GLM in groups with unequal size

Ah sorry for the low level of info. I am aiming to do a simple group comparison, where I'm comparing thickness between controls and obese or T2DM patients, regressing out the effect of age, sex and, hypertension. So I created one thickness file with fwhm 10 containing all participants of the 3

Re: [Freesurfer] GLM in groups with unequal size

Thanks for the quick reply! So if I understand correctly, the power of say the controls vs. diabetes (indeed it is type 2 diabetes) comparison is constrained by the sample size of the obese group? 2016-10-13 11:02 GMT-03:00 Bruce Fischl : > Hi Eelco > > it isn't

Re: [Freesurfer] GLM in groups with unequal size

Hi Eelco it depends on how you setup your GLM. Are you trying to regress out the effects of obesity in some way? If you give us more details I expect someone else can answer your question (Doug!) cheers Bruce On Thu, 13 Oct 2016, Eelco van Duinkerken wrote: Thanks for the quick reply!

Re: [Freesurfer] GLM in groups with unequal size

Hi Eelco it isn't really a question of whether our implementation is senstitive to this. It's that in general your power will be constrained by the size of the smaller group (I assume this is Type 2 diabetes by the way). cheers Bruce On Thu, 13 Oct 2016, Eelco van Duinkerken wrote: > Hi

[Freesurfer] GLM in groups with unequal size

Hi all, I am using FS with data from 2 different studies that were acquired on the same MRI-machine with the same T1 and FLAIR sequences. Unfortunately, the group sizes are not very balanced, with 31 controls, 16 obese and 32 diabetes patients. Is the GLM for thickness used in FS very sensitive

Re: [Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

reesurfer support list > Subject: Re: [Freesurfer] GLM surface based cortical thickness analysis vs > aparcstat table cortical thickness > > One is a map-based/voxel-wise analysis, each voxel is treated > separately. The aparc stats table is an average over all vertices in the

Re: [Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

: Wednesday, August 24, 2016 5:39 PM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness One is a map-based/voxel-wise analysis, each voxel is treated separately

Re: [Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

One is a map-based/voxel-wise analysis, each voxel is treated separately. The aparc stats table is an average over all vertices in the ROI. If you have an effect that does goes across the ROI boundary, it could be lost in the ROI analysis. On the other hand, the ROI analysis may be more

[Freesurfer] GLM surface based cortical thickness analysis vs aparcstat table cortical thickness

Hello freesurfer experts,  What's the difference between GLM surface based cortical thickness analysis and the cortical thickness analysis performed when using regions extracted from aparcstat table? Best, Paul Sent from my BlackBerry 10 smartphone. ___

Re: [Freesurfer] GLM significance table

The -log10(p) is signed by the sign of the contrast, so to get back to the p value you must compute 10^-abs(sig). On 7/26/16 10:42 AM, Caroline Beelen wrote: Dear FS team, I tried to run GLM-analysis using aparc stats files. At first I created these files for a few subjects of interest

[Freesurfer] GLM significance table

Dear FS team, I tried to run GLM-analysis using aparc stats files. At first I created these files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and checked whether they looked ok, which they did (values were pretty similar). Then I used the following command (for example):

[Freesurfer] GLM significance table

Dear FS team, I tried to run GLM-analysis using aparc stats files. At first I created these files for a few subjects of interest (e.g. aparc_rh_thickness_stats.txt) and checked whether they looked ok, which they did (values were pretty similar). Then I used the following command (for example):

[Freesurfer] GLM: Define the design matrix by myself

Hello, Freesurfer experts: I want to define the design matrix by myself in GLM, I know that in FS, when we deal with the categorized factors, we treat them as classes, So basically, I want to make a design matrix like this: 1) formula_EffectOnGroupWithAgeGenderCovariates = 1 + TermGroup +

Re: [Freesurfer] GLM - covariate question

Dear Donald, Thank you very much for the explanation. I have found much trouble in modeling my data, and you are already helping a lot! I believe the "medication problem" is very hard to solve, but perhaps one or two models can be useful although reliant on a few more premisses. Without them, it

Re: [Freesurfer] GLM - covariate question

Pedro, Instead of saying that you want to include the covariate in the analysis, it's better to consider why you want to include the covariate and how it changes the interpretation. You don't necessarily want to regress out covariates, especially when the covariate is different between groups.

[Freesurfer] GLM - covariate question

Dear list, I am running a command line group analysis, and I want to include a covariate that is zero for all subjects in a group, and diverse for all subjects in the second group (medication intake, which is null for all subjects in the control group). This generates a lack of range of that

Re: [Freesurfer] GLM analysis on CBF maps

Dear Experts, I have run GLM group analyses with Freesurfer tools according DODS model, with six classes ((Male,Female) ; (Control,Left,Right)) and one age variable : /Class MaleControl Class MaleLeft Class MaleRight Class FemaleControl Class FemaleLeft Class FemaleRight Variables Age

Re: [Freesurfer] GLM analysis on CBF maps

For the intercept, you are testing for a difference in the mean CBF between the groups regressing out the effects of gender and age. For the slope, you are testing for an interaction between group and age regressing out the effects of gender. doug On 3/12/15 1:30 PM, Matthieu Vanhoutte

Re: [Freesurfer] GLM analysis on CBF maps

Hello, I have run GLM group analyses with Freesurfer tools according DODS model, with six classes ((Male,Female) ; (Control,Left,Right)) and one age variable : *Class MaleControlClass MaleLeftClass MaleRightClass FemaleControlClass FemaleLeftClass FemaleRightVariables Age * I wanted to

Re: [Freesurfer] GLM analysis on CBF maps

the sig value is actually -log10(p)*sign(gamma) where gamma is the contrast (gamma.mgh). The p-value is two-tailed, and the color indicates what tail you are on. doug On 03/10/2015 01:21 PM, Matthieu Vanhoutte wrote: Dear FreeSurfer's experts, I have launched a GLM analyses following

[Freesurfer] GLM analysis freeview error

Hello, I have encountered a silly error message I'm hoping someone can help me with. I've been following the GLM analysis tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) and have managed to go through all the steps; however I am now having issues visualizing my

Re: [Freesurfer] GLM analysis freeview error

That option is only available in the development version of freeview. You can try removing :annot_ouline=1 from the command-line and turn it on manually from the GUI. Best, Ruopeng On 01/15/2015 01:28 PM, Hirsch, Gabriella wrote: Hello, I have encountered a silly error message I'm hoping

Re: [Freesurfer] GLM contrast vector for continuous variable interaction

I think this is the contrast you need 00000000 0.50.50.50.5 - 0.5 -0.5-0.5-0.5 On 10/19/2014 06:33 PM, Bronwyn Overs wrote: Dear Freesurfer Mailing List, I am running a GLM in freesurfer 2 categorical variables (2 levels), and three

Re: [Freesurfer] GLM contrast vector for continuous variable interaction

Thanks Douglas. That is exactly what I wanted. Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

[Freesurfer] GLM contrast vector for continuous variable interaction

Dear Freesurfer Mailing List, I am running a GLM in freesurfer 2 categorical variables (2 levels), and three continuous variables (age, prs, sles). My fsgd file looks like this: GroupDescriptorFile 1 Title GLM_sles-group-gender-age Class genderMale-groupControl Class

Re: [Freesurfer] GLM: table with uncorrected clusters

Run mri_glmfit-sim with --cwp 1 This sets the clusterwise threshold to 1, meaning to keep all clusters regardless of their p-values doug On 9/1/14 9:40 AM, Robby De Pauw wrote: Dear FS-community Thx to Doug I was able to successfully run a first analysis. However, I'd like to have a

[Freesurfer] GLM: table with uncorrected clusters

Dear FS-community Thx to Doug I was able to successfully run a first analysis. However, I’d like to have a table of the uncorrected clusters. Is there any flag I can add to write these clusters to some sort of txt-file with the p-values etc.? I’m using the mri_glmfit command. Thanks, Best

Re: [Freesurfer] GLM: Error Matric-Scale

From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM: Error Matric-Scale To: freesurfer@nmr.mgh.harvard.edu Message-ID: 53f62cab.1060...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed It looks like your fsgd file may have been created

Re: [Freesurfer] GLM: Error Matric-Scale

mailto:freesurfer-requ...@nmr.mgh.harvard.edu wrote: Re: [Freesurfer] GLM: Error Matric-Scale ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center

Re: [Freesurfer] GLM: Error Matric-Scale

It looks like your fsgd file may have been created on a windows computer. Is that possible? Try reformatting it in linux or mac. doug On 08/20/2014 12:58 PM, Robby De Pauw wrote: Hi there FreeSurfer When trying the GLM-analysis I keep getting the following error. Could you help me

Re: [Freesurfer] GLM: Error Matric-Scale

One thing you can try is to run this: cat whiplash.fsgd | sed 's/\r/\n/g' new.whiplash.fsgd doug On 08/21/2014 01:30 PM, Douglas N Greve wrote: It looks like your fsgd file may have been created on a windows computer. Is that possible? Try reformatting it in linux or mac. doug On

Re: [Freesurfer] GLM error in QDEC - SOLUTION

...@nmr.mgh.harvard.edu] on behalf of McLaughlin, Katie [katie.mclaugh...@childrens.harvard.edu] Sent: Friday, August 01, 2014 5:45 PM To: Freesurfer support list Subject: Re: [Freesurfer] GLM error in QDEC Hi Doug, Same error when data table created in Linux There are a number of messages about

Re: [Freesurfer] GLM error in QDEC

...@childrens.harvard.edu] Sent: Thursday, July 31, 2014 5:20 PM To: Freesurfer support list Subject: Re: [Freesurfer] GLM error in QDEC Hi Doug, I'm using 5.3. This error was generated when I had more variables in the model, so I used the option within qdec to remove variables from the data table to see

Re: [Freesurfer] GLM error in QDEC

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, July 31, 2014 5:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM error in QDEC What version of FS are you using? When I load that file in 5.3 qdec, it creates

Re: [Freesurfer] GLM error in QDEC

From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, August 01, 2014 4:09 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM error

Re: [Freesurfer] GLM error in QDEC

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM error in QDEC So, did it generate the error when you loaded the table or when you hit analyze? List the steps and buttons that produce this error. doug On 07/31/2014 05:20 PM, McLaughlin, Katie wrote: Hi Doug, I'm using 5.3. This error was generated when

Re: [Freesurfer] GLM error in QDEC

...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, August 01, 2014 5:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM error in QDEC How did you create your qdec table? It looks like it might have been created on a windows machine. If so

[Freesurfer] GLM error in QDEC

Hi Doug et al, I'm trying to run an analysis in QDEC and continue to get an error that says that the QDEC GLM design creates 0 factors. I'm attaching my data table here as well as the output of QDEC. I've tried deleting all variables in my data file other than one and testing just that

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