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 area

Re: [Freesurfer] GLM with multiple nuisance variables

External Email - Use Caution Have you looked at this page https://secure-web.cisco.com/1HEsOws5HLh6urGfIzkrMbC_7g6t-p8fMP3vYoFDRvAWBsyZmdjmLZolBdJfAp6RF5d34864rZvnTvHUKt7jf7CxseHxsyQawYywC1Un3tELJ8hFiI-ukg1_Z0nHY4xuDoLLVHSXsHlAqFW1jps0N6tuwCDRTcbG9TbM-7GH2ywV6426IyNBD7IKjtAaQwrl-1e

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 slop

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 D

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 the

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 becau

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

o me? Thanks in advance! 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

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

Sorry, your previous emails were cut off so I'm not sure what command you are referring to. On 2/22/2022 9:15 AM, Laura Willers de Souza wrote: External Email - Use Caution Thanks so much for the explanation! There is something different in the analysis of volume and surface area in

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 trunca

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 cortica

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 whe

Re: [Freesurfer] GLM - correction for multiple comparisons

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 a

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 http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm?high

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 1

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 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 o

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. In

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 a

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 dir

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 /A

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 cov

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 question.

Re: [Freesurfer] GLM question

i think you would still run into the same probem On 07/11/2017 12:15 PM, Yann Ying Chye wrote: > Thanks for your reply, > > I have a follow up on my first question - if however I was not looking > for a main effect of gender, but for the main effect of something else > (e.g. diagnosis), will it

Re: [Freesurfer] GLM question

Thanks for your reply, I have a follow up on my first question - if however I was not looking for a main effect of gender, but for the main effect of something else (e.g. diagnosis), will it then be ok to include the unbalanced group (i.e. A-male), to control for gender? Thanks! Regards Yann On

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

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 = load('Xg.dat');

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 t

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

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 mri

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: > https://surfer.n

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 you mean volumes of ROIs? Ye

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 ozzo

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 t

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. A

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 > > https://mail.nmr.mgh.harvard.edu/pipermai

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 patie

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 grou

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 really a question of whether our

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! S

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 all,

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

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. The aparc stats table is an average over all vertices in th

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

Sent: 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 powerfu

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 (e.g

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 wo

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. DO

Re: [Freesurfer] GLM analysis on CBF maps

Continue with what you have done, do not model it as a continuous variable. doug On 06/02/2015 04:03 PM, Matthieu Vanhoutte wrote: > 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

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 /Howev

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 wrote

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 tes

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

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 s

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

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 c

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 table

Re: [Freesurfer] GLM: Error Matric-Scale

mmand: cat whiplash.fsgd | sed 's/\r/\n/g' > new.whiplash.fsgd However, this makes the file unreadable for FreeSurfer. Any ideas? Thank you in advance, Robby Date: Thu, 21 Aug 2014 13:30:19 -0400 From: Douglas N Greve <mailto:gr...@nmr.mgh.harvard.edu>> Subject: Re: [Fr

Re: [Freesurfer] GLM: Error Matric-Scale

2014 13:30:19 -0400 From: Douglas N Greve 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 on a wi

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 > yo

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 this

Re: [Freesurfer] GLM error in QDEC

ICV_demean 4609.048168177.248 Number of subjects: 42 Number of factors:7 (2 discrete, 5 continuous) Number of classes:4 Number of regressors: 24 ==== Data table loading completed successfully. SUBJECTS_DIR is &#x

Re: [Freesurfer] GLM error in QDEC

> ERROR: QdecProject::VerifySubjects: Couldn't find subject '1157' in > SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number > ERROR: QdecProject::VerifySubjects: Couldn't find subject '1158' in > SUBJECTS_DIR > .sh: 1: Syntax error: Bad fd number &g

Re: [Freesurfer] GLM error in QDEC

ect::VerifySubjects: Couldn't find subject '1158' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '1163' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't f

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: Thursday, July 31, 2014 5:14 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] GLM error in QDEC

Re: [Freesurfer] GLM error in QDEC

ie.mclaugh...@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 da

Re: [Freesurfer] GLM error in QDEC

below. Thanks, Kate 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: Thursday, July 31, 2014 5:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer

Re: [Freesurfer] GLM error in QDEC

What version of FS are you using? When I load that file in 5.3 qdec, it creates several discrete classes, see below doug 40 1179 c 17.514000 0.944336 f 12.00 14.00 0.00 -7.50 0.452381 1565300.00 15300.00 41 1180 c 17.330600 0.760936 f 1.00 0.00 0.00

Re: [Freesurfer] GLM: what does "mris_preproc" do?

oh, sorry, I thought you wanted to look at the script itself. The .mgh files are binary files with pixel data. You can view them with tksurfer/freeview. You can load them with MRIread.m in matlab On 6/18/14 8:41 PM, ye tian wrote: Dear Doug, These files typically end with .mgh. I tired opening

Re: [Freesurfer] GLM: what does "mris_preproc" do?

Dear Doug, These files typically end with .mgh. I tired opening them with text editors and them typically give a file of unreadable characters like: @&駺9<窣,@!礱@ ^@$圚@萗@.?@6
%@.溋@*>鳣!址@+?@!编@3岰@ 祺@€錊7]@>@ wrote: > It is just a script so you can view it with any text editor > doug > > > On

Re: [Freesurfer] GLM: What's the link?

Dear Watson, Thank you very much! Sincerely, Ye On Wed, Jun 18, 2014 at 12:36 PM, Watson, Christopher < christopher.wat...@childrens.harvard.edu> wrote: > In this case, GLM stands for "General Linear Model", and not "Generalized > Linear Model" (although the former is a subset of the latter).

Re: [Freesurfer] GLM: what does "mris_preproc" do?

It is just a script so you can view it with any text editor doug On 6/18/14 7:15 PM, ye tian wrote: Hello Freesurfers, Is there a way that I can take a look at the content of the output of "mris_preproc"? Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:33 PM, ye tian

Re: [Freesurfer] GLM: What's the link?

In this case, GLM stands for "General Linear Model", and not "Generalized Linear Model" (although the former is a subset of the latter). See e.g. http://en.wikipedia.org/wiki/Generalized_linear_model#Confusion_with_general_linear_models From: freesurfer-bo

Re: [Freesurfer] GLM: what does "mris_preproc" do?

Hello Freesurfers, Is there a way that I can take a look at the content of the output of " mris_preproc"? Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:33 PM, ye tian wrote: > Dear Doug, > > Thank you very much! > > Sincerely, > Ye > > > On Sun, Apr 6, 2014 at 5:32 PM, Douglas

Re: [Freesurfer] GLM: what does "mris_preproc" do?

Dear Doug, Thank you very much! Sincerely, Ye On Sun, Apr 6, 2014 at 5:32 PM, Douglas Greve wrote: > It resamples them to a common space (the "average" subject) but does not > average them together. The result is a "stack" which is a single file with > multiple subject it in it ready for GLM

Re: [Freesurfer] GLM: what does "mris_preproc" do?

It resamples them to a common space (the "average" subject) but does not average them together. The result is a "stack" which is a single file with multiple subject it in it ready for GLM analysis doug On 4/6/14 6:18 PM, ye tian wrote: Dear Doug, Thank you, but I am only more confused after

Re: [Freesurfer] GLM: what does "mris_preproc" do?

Dear Doug, Thank you, but I am only more confused after reading the summary. The summary basically reaffirms my understanding that "mris_preproc" gives "an average subject". How can this be an appropriate "data" for GLM, which for sure needs multiple data points? Thank you! Sincerely, Ye On Su

Re: [Freesurfer] GLM: what does "mris_preproc" do?

Hi Ye, have you looked at the mris_preproc help? You can access it with mris_preproc --help. Let me know if that does not answer your questions doug On 4/6/14 6:09 PM, ye tian wrote: Hello Freesurfers, I understand that the output of "mris_preproc" can be the input of "mris_glmfit". In mri

Re: [Freesurfer] glm specification in longitudinal analyses for one group

Hi Sandra, so you reduce the 2 thickness measures within subject to a rate of change (mm/time), then you have a single map for each subject and now your question is about your glm modeling. So the question is basically about cross sectional modeling in you GLM. Your equ 7 and 8 test if the

Re: [Freesurfer] GLM p value display

The cluster p-value is the significance corrected for multiple comparisons. It is possible for a cluster to be large and yet made up of voxels whose individual significances are low. The p-value for such a cluster may be significant, whereas a small cluster made of individual highly significan

Re: [Freesurfer] GLM p value display

Oh so we don't report the significance itself? because for example if we have a small cluster but highly significant, does the cluster-wise correction p value take it into account? (compared to a large cluster but with lower significance). I may not have completely got this. Thanks Doug Celine > H

Re: [Freesurfer] GLM p value display

Hi Celine, you should report the clusterwise p-value (which is neither of those). doug On 12/17/2013 12:11 PM, Celine Louapre wrote: > Hi all > I am wondering what is the best to present GLM results in a table on top > of the visual display. > For the significant clusters after clusterwise correc

Re: [Freesurfer] GLM Analysis: ROI (--label)

Hi Rachel, I have deleted your previous msg and my response, so I don't know exactly what this is referring to. From the info below, it looks like you need a backslash ("\") after lh.oribitalfrontal.label. Note that you should not specify both --cortex and --label doug On 7/31/13 7:20 PM, Ra

Re: [Freesurfer] GLM Analysis: ROI (--label)

Hi Doug, Thanks for the response. Here is my glmfit command: mri_glmfit \ --y lh.22q_age.thickness.10.mgh \ --fsgd 22q_age.fsgd dods\ --C 22q_age_2.mtx \ --surf fsaverage lh \ --label lh.orbitofrontal.label --cortex \ --glmdir lh.22q_age_OFC.glmdir And here is the error message: gdfReadHeader:

Re: [Freesurfer] GLM Analysis: ROI (--label)

what is your command line? Also, send the terminal output. On 7/30/13 6:41 PM, Rachel Jonas wrote: Hi FreeSurfer users, I am running a GLM analysis on the command line, and would like to look specifically within an ROI. I added the flag: --label lh.orbitofrontal.label, in my case, to mri_glm

Re: [Freesurfer] GLM for volume

No, it does not change anything. Just make sure to use the new mris_preproc ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc Linda Zhang wrote: > Dear all, > > In mris_preproc, I see that there's an option to choose volume for > --meas, would this change anything in the

Re: [Freesurfer] GLM design question

Dear Doug, Michael, Thanks for thinking with me. Following the discussion, it seems to me that weighting the contrast matrix in our cohort for our question is alright. Let me describe it again: - The diseased population typically consists of 75% female. - We have three groups (HC, diseased withou

Re: [Freesurfer] GLM design question

Thanks to both Donald and Michael for catching my mistake about recommending sample-size weighting within the contrast (both responses are below). Depending upon the hypothesis being tested it is ok, but you're probably not going to be in a situation in which you will want to. doug --

Re: [Freesurfer] GLM design question

Hi Martijn, yes, that is a good thing to do! doug Martijn Steenwijk wrote: > Hi Doug, > > Thanks for your reply again. It's getting more and more clear now. > > I've however one question remaining, which is regarding the correction > for sex. What I did not tell (my fault ;-) ), is that 75% of t

Re: [Freesurfer] GLM design question

Hi Doug, Thanks for your reply again. It's getting more and more clear now. I've however one question remaining, which is regarding the correction for sex. What I did not tell (my fault ;-) ), is that 75% of the cohort is female. Comparing the sex-corrected results with male-only and female-only

Re: [Freesurfer] GLM question

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, December 23, 2011 11:20 AM To: Govindarajan, Koushik Athreya Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] GLM question Hi Koushik, it's very hard to diagnose these problems wit

Re: [Freesurfer] GLM question

Hi Koushik, it's very hard to diagnose these problems with out more detailed information (eg, the command line, the FSGD file, and the contrast). Send those along and I'll see if I can figure out what went wrong. doug Govindarajan, Koushik Athreya wrote: > Hello group, > > I am a new u

Re: [Freesurfer] GLM design question

Hi Martijn, sorry for the delay. Your contrast matrices look correct. The differences between demeaning and not demeaning is somewhat expected. When you do not demean, you are testing whether there is a difference between groups at age=0 (ie, birth). When you demean, you are testing for a dif

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