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
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 comma
External Email - Use Caution
Have you looked at this page
https://secure-web.cisco.com/1HEsOws5HLh6urGfIzkrMbC_7g6t-p8fMP3vYoFDRvAWBsyZmdjmLZolBdJfAp6RF5d34864rZvnTvHUKt7jf7CxseHxsyQawYywC1Un3tELJ8hFiI-ukg1_Z0nHY4xuDoLLVHSXsHlAqFW1jps0N6tuwCDRTcbG9TbM-7GH2ywV6426IyNBD7IKjtAaQwrl-1e
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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 in
__
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
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
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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 var
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
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
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
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
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.
-
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
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:
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Thanks so much for the explanation!
There is something different in the analysis of volume and surface
area in
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
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
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
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
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, aft
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, aft
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
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. Ho
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
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.
T
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
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
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
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
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
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
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
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
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
thickness.
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
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 Tutoria
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
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
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
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
command
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.
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 area)
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 freesurfer GLM analysis.
> >
>
ge with subject or body 'help' to
> freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
> freesurfer-ow...@nmr.mgh.harvard.edu
>
>
>
> On 7/7/17 1:58 PM, Yann Ying Chye wrote:
> > Dear FreeSurfer mailing lis
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
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 g
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');
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
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
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 bei
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
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 Gend
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
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
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
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
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
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
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
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 thi
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
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
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
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
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
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
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
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,
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 t
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
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
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
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.
___
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
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):
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):
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 + TermAg
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
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
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 contin
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
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
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
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
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
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
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
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
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
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 genderFemale-groupContro
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
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 reg
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
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
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:
>
>
>
>
>
>
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> Hi there FreeSurfer
>
> When trying the GLM-analysis I keep getting the following error. Could
> yo
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
whiplash.fsgd
Description: Binary data
group_diff.mtx
Description: Binary data
Hi there FreeSurferWhen trying the GLM-analysis I keep getting the following error. Could you help me with fixing it?ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08Pos
...@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
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
> 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
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
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