This is the kind of thing that happens with clusterwise corrections. It
is hard to predict what happens. When you raise the threshold, you lose
some of the activation in your real map (ie, clusters become smaller).
But in the Null map, clusters also become smaller. So, at the lower
threshold,
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assuming that all preprocessing steps, fsgd file and contrasts are correct,
the choice between doss and dods could explain some of the variability
you're seeing in your results. Consider running both models and possibly
additional validation to see
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Hi all,
I took the freesurfer course in the recent past, and I am now beginning to run
some glm thickness analyses!
Currently I am doing a thickness analysis looking at the difference between two
groups while controlling for age, and two continuous
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which part do you want to fix? the command not found or the lack of
clusters?
On 6/28/2023 6:25 PM, jordan wagner wrote:
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Hello,
My name is Jordan and I am working on cluster correction between two
groups. I
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Hello,
My name is Jordan and I am working on cluster correction between two
groups. I ran the step before: "freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=sig.mgh". I was able to
find many significant values of p<0.05. However, when I
You can, but you need to give mri_glmfit the specific label to use as a
mask (eg, --label or --mask). You can extract labels from an annot with
mri_annotation2label. Then mri_glmfit-sim will automatically restrict
the correction to that label
On 4/6/2023 10:05 AM, John Anderson wrote:
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Dear Dr Greve,
Apologize for not providing a clear explanation earlier. The file
lh.all.suvr.sm05.proj0.5.nii.gz is the result of combining all SUVR maps,
using mri_concat, after projecting them onto the brain surface with
mri_vol2surf.
I would like to
What is h.all.suvr.sm05.proj0.5.nii.gz? Where did it come from? The name
looks like it might be a voxel-wise map, but you say something about
ROIs. mri_glmfit does not correct for multiple comparisons. For
ROI-based analyses, you can use bonferroni or FDR. For maps you can use
mri_glmfit-sim.
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Hello Freesurfer,
Currently, I am using the Petsurfer manual, which is easily understandable
and clear. Nonetheless, I have a question regarding the "mri_glmfit" step.
As far as I know, this command is used to correct data for multiple
comparisons
The scale is much different between columns 1 and 8, you may want to
normalize by subtracting the mean and dividing by the standard deviation.
On 3/21/2023 1:53 PM, miracle ozzoude wrote:
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Hello,
Any idea how to solve this problem? I have tried the
.mgh.harvard.edu
on behalf of mariangela
asimina
*Sent:* Monday, March 20, 2023 8:13 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] mri_glmfit-sim error
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Hello FreeSurfer developers and experts,
I am trying to do cluster correction with mri_
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Hello,
Any idea how to solve this problem? I have tried the suggested solutions on
the archive, that's Demean and Rescale but to no avail.
I have attached the necessary files in the email below.
Many thanks,
Miracle
mri_glmfit command: mri_glmfit
: Monday, March 20, 2023 8:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_glmfit-sim error
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Hello FreeSurfer developers and experts,
I am trying to do cluster correction with mri_glmfit-sim after running
mri_glmfit.
The command I ran
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Hello FreeSurfer developers and experts,
I am trying to do cluster correction with mri_glmfit-sim after running
mri_glmfit.
The command I ran:
mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 3.0 abs
--cwp 0.05 --2spaces
It is probably a scaling problem with using age^2. Try normalizing the
age^2 column (ie, remove the mean and divide by the sum of the squares)
On 3/9/2023 3:30 PM, Triebswetter, Curtis wrote:
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Hello Freesurfer experts,
I am attempting to run the command
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Hello Freesurfer experts,
I am attempting to run the command
mri_glmfit --y lh.RBS_ADRC_N0_control.10.mgh --fsgd RBS_ADRC_APOE_age22.fsgd
dods --C APOE_ageINT.mtx --surf fsaverage lh --cortex --glmdir
lh.RBS_ADRC_N0.glmdir
On this .fsgd file:
?
They are annot files. You can use mri_annotation2label to break them
into label files.
Best,
Yujing
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of *James Brown
*Sent:* Thursday, January 19, 2023 7:19 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] mri_glmfit
Sent: Thursday, January 19, 2023 7:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_glmfit
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Dear FS experts,
I am working on a surface based analysis using FS 7.1.1 and I would like to run
mri_glmfit between two groups using the flag "--
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Dear FS experts,
I am working on a surface based analysis using FS 7.1.1 and I would like to
run mri_glmfit between two groups using the flag "--label" to restrict
analysis within lobes.
I ran these commands on fsaverage
mri_annotation2label
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Hello Doug,
Do you mean like this?
GroupDescriptorFile 1
Title Rivermead cluster 2
DOSS
Class PPCS_Male
Class PPCS_Female
Variables Age Sports Games Days_TBI RPQ_13
If yes, i did but still getting similar area
Best,
Paul
On Tue, Jan 3,
Oh, I see what you mean. Can you try putting the line "DOSS" (no quotes)
into your FSGD file?
On 1/3/2023 11:51 AM, miracle ozzoude wrote:
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Hello Doug,
Thanks for the quick response. I did see the error. However, I
specified doss in the mri_glmfit
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Hello Doug,
Thanks for the quick response. I did see the error. However, I specified
doss in the mri_glmfit command and my mtx looks accurate as indicated
above. Does that mean it can only work with dods? The reason I'm using 2
groups is because I
Is the error message not clear what the problem is?
On 12/30/2022 6:37 PM, miracle ozzoude wrote:
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Hello,
I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did
like to regress out the effects of groups + other variables by using
doss.
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Hello,
I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did like
to regress out the effects of groups + other variables by using doss.
However, whenever I specify doss with the mri_glmfit command, it gives me
an error message (see
Do you see where it says "ERROR: READ THIS"? And below that do you see
that it asks for four things? Can you send those four things?
On 10/5/2022 2:51 PM, fernanda rohrsetzer wrote:
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Hi,
I attempted to execute mri_glmfit on my structural data through the
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Ohh!!
I'm so sorry for my stupidity!!!
Thank you so much for your patience!!!
Em seg., 3 de out. de 2022 às 10:04, Douglas N. Greve <
dgr...@mgh.harvard.edu> escreveu:
> those are the contrast matrices. The design matrix will be in the output
>
those are the contrast matrices. The design matrix will be in the output
folder as file Xg.txt
On 9/30/2022 11:43 AM, fernanda rohrsetzer wrote:
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The design matrix (examining difference in thickness after controlling
for effects of age, sex and Average
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The design matrix (examining difference in thickness after controlling for
effects of age, sex and Average thickness)
1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx
1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx
0 1 -1 0 0 0
almost there -- you did not include the 4th ittem
On 9/30/2022 11:18 AM, fernanda rohrsetzer wrote:
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I'm so sorry...
The FSGD file is attached (called "TestCT.txt).
The design matrix (examining difference in thickness after controlling
for effects of
That terminal output asks you to send 4 things, but you only sent 2
On 9/29/2022 11:51 AM, fernanda rohrsetzer wrote:
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Hi,
I attempted to execute mri_glmfit on my structural data through the
following command -
mri_glmfit --y lh.10.teste.thickness.mgh
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Hi,
I attempted to execute mri_glmfit on my structural data through the
following command -
mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C
Contrasts/LR-HR_testcov.mtx --C Contrasts/LR-MDD_testcov.mtx --C
Contrasts/HR-MDD_testcov.mtx
: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit error: MatrixResidualForming(): X is not
invertable
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My guess is that the variable (G_cingul vol) should be normalized (remove the
mean and divide by the stddev).
On 9/6/2022 5:44 PM, Piot
My guess is that the variable (G_cingul vol) should be normalized
(remove the mean and divide by the stddev).
On 9/6/2022 5:44 PM, Piot, Alex wrote:
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Hello Freesurfer experts,
I am trying to perform a GLM, using the volume of a brain region as a
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Hello Freesurfer experts,
I am trying to perform a GLM, using the volume of a brain region as a
covariate. I am doing a two-group, one covariate design. I originally tried to
use QDEC to facilitate the process and received an error message that the
You don't have enough members in the classes to fit the model that you
have. Eg, class d has 4 members with which you are fitting an offset and
3 slopes leaving you with 0 degrees of freedom. You need to get more
subjects or change your model. btw, gender is usually modeled as a
discrete
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Hello FreeSurfer Developers,
my fsgd is this：
GroupDescriptorFile 1
Title post compane
Class d
Class m
Class h
RescaleFlag 1
DemeanFlag 1
Variables gender Age Edu
Input bd1 d 0 15 8
Input bd2 d 1 19 13
Input bd7 d 0 17 11
Input bd8 d 1 19 13
Input bd6
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Hi Dr. Greve,
Thank you very much for your solution. That solved the problem.
I genuinely appreciate your support!
Best,
Hyunwoo Jeong
2022년 3월 10일 (목) 오전 2:52, Douglas N. Greve 님이 작성:
> The problem is that your design matrix is badly scaled. The
The problem is that your design matrix is badly scaled. The eTIV values
are much larger than the group membership (value=1). Try subtracting the
mean of the eTIV and dividing by the stddev to normalize it.
On 2/25/2022 8:07 PM, 정현우 wrote:
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Hi Dr. Greve,
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Hi Dr. Greve,
Thank you for your response. I uploaded the .mgh, .fsgd, and .mtx files
that I used to run the mri_glmfit command. I can upload the recon-all
outputs of the individual samples as well, if needed. The files are
uploaded in google drive,
Can you upload the data to me somewhere? I'd need the input volume and
the fsgd and any contrasts
On 2/21/2022 10:24 PM, 정현우 wrote:
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Hi Dr. Greve,
Thank you for your suggestion. Unfortunately, the same problem
occurred when I ran the command with
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Hi Dr. Greve,
Thank you for your suggestion. Unfortunately, the same problem occurred
when I ran the command with --no-pcc. Folders and files with the same names
were created. and the following error message (identical to the previous
one) appeared.
of Douglas N. Greve
*Sent:* Monday, February 21, 2022 6:29 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while
regressing out cortical thickness
I just updated the code to accept PVRs. I'm not sure what I have to do
to test it; I guess I need to run
,
Asim
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
Sent: Monday, February 21, 2022 6:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out
cortical thickness
I just
External Email - Use Caution
Hi Dr. Greve,
Thank you for your suggestion. Unfortunately, the same problem occurred
when I ran the command with --no-pcc. Folders and files with the same names
were created. and the following error message (identical to the previous
one) appeared.
.
Best,
Asim
*From:* Dhungana, Asim
*Sent:* Monday, February 14, 2022 11:45 AM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while
regressing out cortical thickness
OK, I see. How
arvard.edu
on behalf of Douglas N. Greve
Sent: Sunday, February 13, 2022 5:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out
cortical thickness
Re: long run time. Sorry, permutation will not work with PVR.
Re: mean thic
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Hi Dr. Greve,
Thank you for your suggestion. Unfortunately, the same problem occurred
when I ran the command with --no-pcc. Folders and files with the same names
were created. and the following error message (identical to the previous
one) appeared.
It looks like it is failing when computing the partial correlation coef.
Try running it with --no-pcc
On 2/16/2022 10:53 AM, 정현우 wrote:
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Hi Dr. Greve,
Yes, it seems like the output folder and some output files were created.
After running the mri_glmfit,
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Hi Dr. Greve,
Yes, it seems like the output folder and some output files were created.
After running the mri_glmfit, 'three_group_comparison.area.lh.glmdir'
folder was created. In the glmdir folder, 'three_group_comparison.area'
folder was created,
Did it create the output folder and some output files? I noticed that
there is a "error: No such file or directory" error
On 2/14/2022 8:46 PM, 정현우 wrote:
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Hi Dr. Greve,
Thank you for your reply. I attached the fsgd file, mtx file and the
Xg.dat
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Hi Dr. Greve,
Thank you for your reply. I attached the fsgd file, mtx file and the Xg.dat
file below.
Hyunwoo Jeong
2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve 님이 작성:
> can you send your fsgd file and the Xg.dat file?
>
> On 2/14/2022 1:21 AM, 정현우
ebruary 13, 2022 5:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out
cortical thickness
Re: long run time. Sorry, permutation will not work with PVR.
Re: mean thickness. Use the eres.mgh from you osgm analysis instead of the raw
can you send your fsgd file and the Xg.dat file?
On 2/14/2022 1:21 AM, 정현우 wrote:
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Hello FreeSurfer Developers,
I'm attempting to compare cortical surface area among three groups
while controlling for estimated total intracranial volume (eTIV), as
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to compare cortical surface area among three groups while
controlling for estimated total intracranial volume (eTIV), as described on
the Surface Based Group Analysis tutorial (
Re: long run time. Sorry, permutation will not work with PVR.
Re: mean thickness. Use the eres.mgh from you osgm analysis instead of
the raw thickness map (lh.thickness.fwhm10.mgh)
On 2/8/2022 4:12 PM, Dhungana, Asim wrote:
Dear Freesurfer experts,
I am trying to run a GLM analysis
Dear Freesurfer experts,
I am trying to run a GLM analysis comparing the difference in the cortical CBF
maps between two groups, but I would like to regress out cortical thickness. I
read through a post with a similar question
f Tarumi Takashi
>
> Sent: Thursday, January 20, 2022 7:59 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized
>
> External Email - Use Caution
>
> Dear Dr. Yendiki,
>
> Thank you so much f
.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Tarumi Takashi
Sent: Thursday, January 20, 2022 7:59 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized
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Dear Dr
tak...@gmail.com>
> *Sent:* Wednesday, January 12, 2022 7:04 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized
>
>
> External Email - Use Caution
>
> Dear FreeSurfer Developers:
>
> I am attempt
22 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized
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Dear FreeSurfer Developers:
I am attempting to perform cluster-wise correction for the along-tract
measures, as described on the Tract statistic
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Dear FreeSurfer Developers:
I am attempting to perform cluster-wise correction for the along-tract
measures, as described on the Tract statistics tutorial (
value for each input
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve
*Sent:* Wednesday, September 15, 2021 1:19 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR
Can't see the image. Can you just cut-and-pas
Subject: Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR
Can't see the image. Can you just cut-and-paste the full terminal output into
the email?
On 9/15/2021 3:02 PM, Tsiknia, Amaryllis wrote:
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Dear Freesurfer Team,
I have been struggling with an error
Can't see the image. Can you just cut-and-paste the full terminal output
into the email?
On 9/15/2021 3:02 PM, Tsiknia, Amaryllis wrote:
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Dear Freesurfer Team,
I have been struggling with an error using the mri_gmfit command. I
have been trying to run a
External Email - Use Caution
Dear Freesurfer Team,
I have been struggling with an error using the mri_gmfit command. I have been
trying to run a simple surface-based group analysis on 28 subjects testing
whether a continuous variable "OMEGA3_457" relates to various RSI measures
This happens because the cached p-values were generated from a
simulation that only went up to 30mm FWHM of smoothing. lGI has lots of
internal smoothness which often pushes it over this level. You can try
not using any smoothing, or, even better, try using permutation instead.
this especially for eTIV?
Thank you very much and
with best wishes,
Cornelius
> Date: Fri, 9 Jul 2021 14:05:31 -0400
> From: "Douglas N. Greve"
> Subject: Re: [Freesurfer] mri_glmfit DOSS
>
> You cannot use a DODS in this design as it tries to fit an offset and a
>
You cannot use a DODS in this design as it tries to fit an offset and a
slope for each class, which can't be done when the class has only one
member. Try using DOSS instead. You should probably demean and rescale
the eTIV to be between 0 and 1.
On 6/29/2021 11:19 AM, Dr. Cornelius Kronlage
f fsgdf.cpp?
Cheers,
Cornelius
Date: Tue, 29 Jun 2021 15:19:20 +
From: "Dr. Cornelius Kronlage"
Subject: [Freesurfer] mri_glmfit DOSS
To: "'freesurfer@nmr.mgh.harvard.edu'"
Message-ID: <2a173629cd4540769ec6a07d892ca...@med.uni-tuebingen.de&g
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Dear freesurfers,
for a morphometry study, I am comparing a single subject at a time to a group
of controls. I would like to include age, gender (as a continuous variable for
the sake of simplicity) and eTIV as "nuisance" regressors in the GLM.
Don't use --grf with surfaces
On 6/15/2021 7:24 PM, Paul, Jhelum wrote:
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Hello,
I also have the same error. I have been looking into all the tutorials
available for Freesurfer v7 and trying to search why,
mri_glmfit-sim --glmdir
You need to include elements for the PVR regressors in your contrast. I
see that you only have four elements in the examples below and four
classes, so you will need to add more
On 6/9/2021 10:38 AM, std...@virgilio.it wrote:
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Thanks
If I have 4 groups
External Email - Use Caution
Thanks
If I have 4 groups
GroupDescriptorFile 1
Title XXX
Class G1
Class G2
Class G3
Class G4
Input subj1 G1
Input subj2 G3
Input subj3 G2
Input subj4 G2
Input subj5 G4
Are the contrasts below corrected?
G1_only_thick 1 0 0 0
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Thanks
If I have 4 groups
GroupDescriptorFile 1
Title XXX
Class G1
Class G2
Class G3
Class G4
Input subj1 G1
Input subj2 G3
Input subj3 G2
Input subj4 G2
Input subj5 G4
Are the contrasts below corrected?
G1_only_thick 1 0 0 0
look at the tutorial
On 6/1/2021 12:00 AM, Diógenes Bispo wrote:
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I would like to know what other modification I should make to my
script to run --grf (volume analysis):
- mris_preproc ??
- mri_glmfit (--surf in white)
- mri_glmfit-sim ??
Thanks.
External Email - Use Caution
I would like to know what other modification I should make to my script to
run --grf (volume analysis):
- mris_preproc ??
- mri_glmfit (--surf in white)
- mri_glmfit-sim ??
Thanks.
Diogenes Bispo
diogenesdi...@gmail.com
Em sáb., 29 de mai. de
You can't use the --grf option with surfaces
On 5/29/2021 2:14 AM, Diógenes Bispo wrote:
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Hi Freesurfer team.
I made the following command:
#!/bin/tcsh
setenv study $argv[1]
foreach hemi (lh rh)
foreach smoothing (10)
foreach meas (volume)
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Hi Freesurfer team.
I made the following command:
#!/bin/tcsh
setenv study $argv[1]
foreach hemi (lh rh)
foreach smoothing (10)
foreach meas (volume)
mris_preproc --fsgd FSGD/{$study}.fsgd \
--cache-in
Yes, exactly on both questions
On 4/22/2021 8:23 AM, Marilena Wilding wrote:
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Dear Freesurfers,
I’m currently doing 2nd level analysis on a FIR model.
I first concatenated my data with this command:
isxconcat-sess
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Dear Freesurfers,
I’m currently doing 2nd level analysis on a FIR model.
I first concatenated my data with this command:
isxconcat-sess -sf sessidlist -analysis FIR_group.lh -contrast global-v-local
-no-hrf -hemi lh -o group_analysis
I got 29
The format is not correct. It should be
Input SubjectID Class
You have SubjectID in there twice
On 4/1/2021 1:15 AM, Ishi Tandon AIB, Jaipur wrote:
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Hello FS experts,
I attempted to execute mri_glmfit on my structural data through the
following command -
External Email - Use Caution
Hello FS experts,
I attempted to execute mri_glmfit on my structural data through the
following command -
mri_glmfit --y final.lh.mTBI.volume.10.mgh --fsgd FSGD/mild.tbi.fsgd dods
-C contrats/HC-mTBI.mtx --surf fsaverage --cortex --glmdir
On 2/23/2021 11:37 PM, miracle ozzoude wrote:
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Thanks Doug. I appreciate it. I have more questions.
1) Aren't both models answering the same question regardless of which
side of the equation cortical thickness or syndromes is placed?
Similar questions,
External Email - Use Caution
Thanks Doug. I appreciate it. I have more questions.
1) Aren't both models answering the same question regardless of which side
of the equation cortical thickness or syndromes is placed?
2) Also, I noticed in the mri_glmfit --help, it said that
Model 2 is the only one we have the ability to fit. Model 1 would need
some kind of machine learning method
On 2/23/2021 12:37 AM, miracle ozzoude wrote:
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Hello Experts,
I've a question about mri_glmfit. I want to investigate the
association between
External Email - Use Caution
Hello Experts,
I've a question about mri_glmfit. I want to investigate the association
between thickness and neuropsychiatric syndromes, controlling for age and
cognition. Which model below is mri_glmfit performing?
Model 1
neuropsych syndromes ~ age
That can happen because the null distribution of the cluster sizes
change when you change the threshold. So at a threshold of 1.3, you
might have a slightly larger cluster (which improves the cluster
p-value), but you pay a penalty for lowering the threshold (which hurts
the cluster p-value).
I just wanted to add that the attached maps in the previous email, was made by
the tksurfer command below. I also added the mri_glmfit command.
mri_glmfit --y cespct.nii.gz --osgm --glmdir main.wls --nii.gz --mask
../mask.nii.gz --surface fsaverage ${space:(-2)} --cortex --fwhm 5 --no-prune
/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm36/pos/th40/mc-z.csd
Regards,
Xiaoxu
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Greve, Douglas N.,Ph.D.
Sent: Wednesday, January 13, 2021 9:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit
When you use --cache, mri_glmfit-sim will use precomputed (ie, "cached") CSD
files as found in $FREESURFER_HOME/average/mult-comp-cor
On 1/5/2021 4:55 PM, Na, Xiaoxu wrote:
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Dear Freesurfer Experts,
I’ve all the subjects successfully done recon-all, lgi
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Dear Freesurfer Experts,
I've all the subjects successfully done recon-all, lgi before coming to the
group analysis. The following group analysis will use the 10mm smoothing as
generated in previous recon-all. Mris_preproc were implemented
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Hi Doug,
Deleting the .csd files and re-running worked.
Thank you!
Meaghan
On Tue, Sep 15, 2020 at 11:30 AM Douglas N. Greve
wrote:
> *Message sent from a system outside of UConn.*
>
> Hmm, there should have been a lot more terminal output than
Hmm, there should have been a lot more terminal output than that.
Try this, delete the CSD files:
rm lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j*-osgm.csd
Then re-run. If it fails, then send me the perm.th20.abs.j*-osgm.csd files
On 9/14/2020 2:58 PM, Meaghan Perdue wrote:
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Hi Doug,
Here is the command:
mri_glmfit-sim --glmdir lh.rs6980093.thickness10.glmdir --perm 1000 2.0 abs
--cwp 0.05 --2spaces --bg 4
And here is the output:
mri_glmfit simulation done 4.78645
mri_glmfit simulation done 4.806
mri_glmfit
please send the full command line and terminal output
On 9/9/2020 3:19 PM, Meaghan Perdue wrote:
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Hello Freesurfer experts,
We're receiving the following error message when trying to run
mri_glmfit-sim:
ERROR: CSDmerge: CSDs have same seed
This only
egards,
>> Paul
>> *Sent:* Wednesday, September 09, 2020 at 1:01 AM
>> *From:* "Douglas N. Greve"
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] mri_glmfit-sim using --cwp 0.05, --cwp
>> 0.1, --cwp 0.999
>> On 9/7/2020 10:52 PM,
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Hello Freesurfer experts,
We're receiving the following error message when trying to run
mri_glmfit-sim:
ERROR: CSDmerge: CSDs have same seed
This only occurs when we try to run the permutation on the LH for
thickness. We've been able to run the
On 9/7/2020 10:52 PM, Paul wrote:
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Dear Freesurfer Experts,
I have few questions regarding CWP values from mri_glmfit-sim using
--cwp 0.05, --cwp 0.1, --cwp 0.999.
Using the 3 three commands below (A, B and C):
A. mri_glmfit-sim --glmdir
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Dear Freesurfer Experts,
I have few questions regarding CWP values from mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999.
Using the 3 three commands below (A, B and C):
A. mri_glmfit-sim --glmdir lh_status.glmdir --perm 1 1.3 abs
you have a typo in fast_fratio. The first argument (beta) should not be
transposed
On 8/13/2020 3:40 PM, Eric Cunningham wrote:
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There's a minor bit of confusion with the code you sent.
[F p] = fast_fratio(beta,X,rvar,C); gives the error "inner error
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