[Freesurfer] Optseq2 timing outputs

[Ruthie Shaffer]

Hi all,

I sent a message previously and just wanted to check in one more time about 
this question (apologies for the repeat message!).

I’m using Optseq2 to generate stimulus / jitter schedules and, depending on the 
TR I use, in the output files I see onset times like 124.4001 (instead of 
124.4) or 124.7999 (instead of 124.8).  

This is the command I’m using:
optseq2 --ntp 75 --tr 3.2 --psdwin 0 22.4 3.2 --ev wordPair 3.2 45 --nkeep 6 
--o CRtiming.2017 --nsearch 10 --tnullmin 0 --tnullmax 6.4

Should I be concerned about the outputs (does it mean that I’ve specified 
something incorrectly in the above command), or is it correct to assume that 
something like 124.4001 just means 124.4?

Anyway, thank you so much for your help on this!

Best wishes,

Ruth Shaffer  ___
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[Freesurfer] VBM

[Shane S]

Hello Experts, 

Can we do VBM in MNI template using the outputs from recon all? Which file 
should I be using? And how do I smooth the volumes? 

Thank you for the tips!

-- 
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Re: [Freesurfer] multi-frame input error with PAR/SEC origin file

[Bruce Fischl]

Hi Idil
you have to figure out what the input volume has more than 1 frame (that 
is, why is it 4d). It could be because you saved phase and mag, or because 
there are multiple echoes, but until you understand what the additional 
frames are we can't process it. YOu can start by bringing the orig.mgz up 
in freeview and looking at it and seeing what the different frames look 
like. If one of them looks like the T1-weighted image and the other doesn't 
(maybe it's a phase map?) you would run:


cd  /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/
mv 001.mgz 001.multiframe.mgz
mri_convert -nth 0 001.multiframe.mgz 001.mgz


assuming that the 0th (first) frame is the T1 weighted. If it was the next 
one you would do -nth 1 instead


cheers
Bruce


On Tue, 8 Aug 2017, Yagmur Ozdemir 19 wrote:


Hello FreeSurfer experts,

I am trying to run recon-all on a nifti file converted from PAR/SEC using
dcm2niix, and this error came up pretty soon after the script started to
run;

>> mri_convert.bin
/home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz
/home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from
/home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (-0, 0.916013, -0.401149)
k_ras = (0, 0.401149, 0.916013)
writing to
/home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz...
#
#@# MotionCor Tue Aug  8 17:42:13 EDT 2017
Found 1 runs
/home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!

I am pretty inexperienced with FreeSurfer, but does this error mean I need
to slice my file? I would really appreciate if someone could give me some
ideas for commands to use.

Thank you all!
Best,
Idil



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[Freesurfer] multi-frame input error with PAR/SEC origin file

[Yagmur Ozdemir 19]

Hello FreeSurfer experts,

I am trying to run recon-all on a nifti file converted from PAR/SEC using 
dcm2niix, and this error came up pretty soon after the script started to run;

>> mri_convert.bin 
>> /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz 
>> /home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /home/lab/Desktop/freesurfer/subjects/sub-06_run-01_T1w.nii.gz...
TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (-0, 0.916013, -0.401149)
k_ras = (0, 0.401149, 0.916013)
writing to 
/home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz...
#
#@# MotionCor Tue Aug  8 17:42:13 EDT 2017
Found 1 runs
/home/lab/Desktop/freesurfer/subjects/sub-06-error/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!

I am pretty inexperienced with FreeSurfer, but does this error mean I need to 
slice my file? I would really appreciate if someone could give me some ideas 
for commands to use.

Thank you all!
Best,
Idil


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Re: [Freesurfer] Generating Surfaces from Labels

[Bruce Fischl]

Hi Zach

I think if you cut and flatten the cortical part of the surfaces, convert 
tha .annot files to separate label files, you can then use label2flat on 
each label to generate a flattened patch that is just taht label. I haven't 
used it in years (decades?), but I think it should work


cheers
Bruce
 On Tue, 8 Aug 2017, 
Zach Humphrey wrote:



Hello All, 
I have been attempting to convert Label files generated using
mri_annotation2label into surface files for use in external programs. In
order to do this I first need to convert the label files into freesurfer
binary. I have attempted to use the mri_label2vol function to generate an
mgz file which could then be converted into freesurfer binary but this has
resulted in mgz files which depict a solid cube rather than any brain
structure. Any ideas as to why this could be? 

I would also prefer to avoid ever converting the label files to a volume as
converting the volume file to a surface file results in a lower quality than
if the file has been maintained as a surface file throughout. Is there any
way to use the Desikan Atlas to "divide" say the lh.pial surface file and
generate a number of .pial files each consisting of one of the regions
described by the Desikan Atlas? 

Thanks,
Zachary Humphrey

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[Freesurfer] Generating Surfaces from Labels

[Zach Humphrey]

Hello All,

I have been attempting to convert Label files generated using
mri_annotation2label into surface files for use in external programs. In
order to do this I first need to convert the label files into freesurfer
binary. I have attempted to use the mri_label2vol function to generate an
mgz file which could then be converted into freesurfer binary but this has
resulted in mgz files which depict a solid cube rather than any brain
structure. Any ideas as to why this could be?

I would also prefer to avoid ever converting the label files to a volume as
converting the volume file to a surface file results in a lower quality
than if the file has been maintained as a surface file throughout. Is there
any way to use the Desikan Atlas to "divide" say the lh.pial surface file
and generate a number of .pial files each consisting of one of the regions
described by the Desikan Atlas?

Thanks,
Zachary Humphrey
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Re: [Freesurfer] Urgent help with stats in FreeSurfer

[Douglas N Greve]

It sounds like you have reported everything correctly. The clusterwise 
p-value corresponds to a critical cluster size at the given cluster 
forming threshold (4), sign (neg), and fwhm (fwhm.dat in the glmdir). So 
the answer to the reviewer is "yes". If you want to report the critical 
size, then look in (if fwhm=10)

$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm10/neg/th40/mc-z.cdf
 


The MaxClustCDF column gives the the clusterwise p-value and the 
MaxClustBin gives the size of the cluster needed to achieve that 
p-value. Eg, a p-value of .05 would require a cluster of about 35 mm2.



On 08/08/2017 01:30 PM, Martin Juneja wrote:
> Hi,
>
> One of my papers is under review showing significant differences in 
> cortical surface area between healthy controls and patients.
>
> In this paper, regarding statistical results, for multiple comparison 
> correction, I ran Monte Carlo simulations using following command:
> mri_glmfit-sim \
>
>--cache 4 neg \
>--cwp  0.05\
> --2spaces
> In the paper, I reported that multiple comparisons were corrected at p 
> < 0.05 using Monte Carlo simulations. I also reported cluster sizes 
> (number of voxels) of all clusters which survived multiple comparison 
> correction.
>
> I checked literature and found that that's how people report cluster 
> results after running analysis in FreeSurfer.
>
> One of the reviewers asked- Did you consider any constraints on 
> findings (specifically cluster size) before considering the finding 
> significant?
>
> Could you please help me in understanding this question and how can 
> this be answered?
>
> In this paper: 
> http://onlinelibrary.wiley.com/store/10.1002/pbc.25386/asset/pbc25386.pdf?v=1=j63uanho=7c11176285c624160ccde7b1d93e759e20bc13a9,
>  
> authors reported that -
> "The data were tested against an empirical null distribution of 
> maximum cluster size across 10,000 iterations using Z Monte Carlo 
> simulations as implemented in FreeSurfer [31,32] synthesized with a 
> cluster-forming threshold of P < 0.05 (two-sided), yielding clusters 
> fully corrected for multiple comparisons across the surfaces. 
> Clusterwise corrected P < 0.05 (two-sided) was regarded significant."
>
> I assume that that's what reviewer is demanding me to report in my paper.
>
> I would really appreciate any help.
>
>
> ___
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] ASL with rcbf-prep

[Tuominen, Lauri Johannes]

Dear freesurfers, 

I have data collected here at the martinos using the Siemens ep2d_PASL 
sequence. I run the command "rcbf-prep —s subject —rcbf asl.nii —o tesfolder" 
or something like that. The resulting rcbf.nii looks good, but the values are 
negative? Is this just a matter of tag and ref images being in a wrong order 
and can I just fix it by removing the first image (after the M0)? Or is it more 
complicated?

Thanks for your help
Lauri
 

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[Freesurfer] Urgent help with stats in FreeSurfer

[Martin Juneja]

Hi,

One of my papers is under review showing significant differences in
cortical surface area between healthy controls and patients.

In this paper, regarding statistical results, for multiple comparison
correction, I ran Monte Carlo simulations using following command:

mri_glmfit-sim \

  --cache 4 neg \
  --cwp  0.05\

--2spaces
In the paper, I reported that multiple comparisons were corrected at p <
0.05 using Monte Carlo simulations. I also reported cluster sizes (number
of voxels) of all clusters which survived multiple comparison correction.

I checked literature and found that that's how people report cluster
results after running analysis in FreeSurfer.

One of the reviewers asked- Did you consider any constraints on findings
(specifically cluster size) before considering the finding significant?

Could you please help me in understanding this question and how can this be
answered?

In this paper:
http://onlinelibrary.wiley.com/store/10.1002/pbc.25386/asset/pbc25386.pdf?v=1=j63uanho=7c11176285c624160ccde7b1d93e759e20bc13a9,
authors reported that -
"The data were tested against an empirical null distribution of maximum
cluster size across 10,000 iterations using Z Monte Carlo simulations as
implemented in FreeSurfer [31,32] synthesized with a cluster-forming
threshold of P < 0.05 (two-sided), yielding clusters fully corrected for
multiple comparisons across the surfaces. Clusterwise corrected P < 0.05
(two-sided) was regarded significant."

I assume that that's what reviewer is demanding me to report in my paper.

I would really appreciate any help.
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[Freesurfer] question about effects of changing server and freesurfer versions IF the entire study is consistent

[STACEY M SCHAEFER]

Hello Freesurfer experts,


We have processed, hand-edited, and QA'ed over 130 subjects' scans with version 
5.3.0 on a linux sci6 box, and extracted the atlas-based ROI values for 
cortical thickness, volume, curvature, etc. The servers need upgrading but 
there are still whole brain analyses to run.  Will there be any issues if we 
have processed all subjects identically, but then run analyses on the data with 
an upgraded linux and freesurfer's latest version?

Thank you for your guidance!
Stacey


Stacey M. Schaefer, Ph.D.
Center for Healthy Minds

University of Wisconsin-Madison

625 W Washington Ave

Madison WI 53703

608-263-9321


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[Freesurfer] Sphere above a certain vetex

[Redwan Maatoug]

Hi everybody,

I have a .annot file  and I would like to display a sphere above one
certain vertex.
(I know the coordinates of the vertex)

Someone knows a way to do that ?
Thank you very much,
Redwan
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Re: [Freesurfer] Cortical thickness map for a pediatric case

[Sneha Pandya]

Thank you Bruce, sure thing :)


Regards,

Sneha


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Bruce Fischl 

Sent: Monday, August 7, 2017 6:21:57 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case

thanks Sneha

you'll probably need to wait until tomorrow for Martin to read his email :)

cheers
Bruce

On Mon, 7 Aug 2017, Sneha Pandya wrote:

>
> Hi Bruce,
>
>
> Sure, please see highlighted below part of screen output showing the error.
> Since I ran the command within a screen sesison I have saved executed screen
> session to a log file. Find attached log file with output of entire run. 
> Please
> let me know if any other files are required and if attached log file could be
> interpreted.
>
>
> Read individual LTAs
> Writing  LTA to file ped1_base_to_ped1_0.lta...
> mri_concatenate_lta successful.
>
>  mri_concatenate_lta -invert1 ped1_1_to_ped1_base.lta identity.nofile
> ped1_base_to_ped1_1.lta
>
> invert the first LTA before applying it
> Read individual LTAs
> Writing  LTA to file ped1_base_to_ped1_1.lta...
> mri_concatenate_lta successful.
>
>  mri_concatenate_lta -invert1 ped1_2_to_ped1_base.lta identity.nofile
> ped1_base_to_ped1_2.lta
>
> invert the first LTA before applying it
> Read individual LTAs
> Writing  LTA to file ped1_base_to_ped1_2.lta...
> mri_concatenate_lta successful.
>
>  mri_concatenate_lta -invert1 ped1_3_to_ped1_base.lta identity.nofile
> ped1_base_to_ped1_3.lta
>
> invert the first LTA before applying it
> Read individual LTAs
> Writing  LTA to file ped1_base_to_ped1_3.lta...
> mri_concatenate_lta successful.
>
>  mri_concatenate_lta -invert1 ped1_4_to_ped1_base.lta identity.nofile
> ped1_base_to_ped1_4.lta
>
> invert the first LTA before applying it
> Read individual LTAs
> Writing  LTA to file ped1_base_to_ped1_4.lta...
> mri_concatenate_lta successful.
> #
> #@# MotionCor Wed Jul 26 14:04:13 EDT 2017
>
>  mri_add_xform_to_header -c
> /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/talairach.xfm
> /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz
> /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz
>
> INFO: extension is mgz
> #
> #@# Talairach Wed Jul 26 14:04:14 EDT 2017
> /shared_data2/sneha/MSKCC_Processed/ped1_base/mri
>
>  mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
> orig.mgz --o orig_nu.mgz
>
> Linux gizmo 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 
> x86_64
> x86_64 x86_64 GNU/Linux
>
> recon-all -s ped1_base exited with ERRORS at Wed Jul 26 14:04:17 EDT 2017
>
> For more details, see the log file
> /shared_data2/sneha/MSKCC_Processed/ped1_base/scripts/recon-all.log
> To report a problem, see 
> https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting=DwIDbA=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=AEsux002jQ5JzIPYIcsXKAuQmrt-1dubP8ZVldIiOrE=BoRZLsXqqVT6-Qe8baTB-uaC5VkO8MylpF2Pge0ejiI=80fR0T3L4F8R5icMg6uqKyEXyWyEbcpI5AFOF2UVRzo=
>
>
> Thanks,
>
> Sneha
>
> ___
> From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> Sent: Monday, August 7, 2017 2:02:27 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case
> Hi Sneha
>
> can you include the output as text instead of an image?
>
> thanks
> Bruce
> On Mon, 7 Aug 2017,
> Sneha Pandya wrote:
>
> >
> > Hi Bruce,
> >
> >
> > Please find attached recon-all.log file and I used following command to run
> the base:
> >
> >
> > recon-all -base ped1_base -tp ped1_0 -tp ped1_1 -tp ped1_2 -tp ped1_3 -tp
> ped1_4 -all
> >
> >
> > Following is the screen shot of output showing the error:
> >
> > [IMAGE]
> >
> > Thanks,
> > Sneha
> >
> >__
> __
> 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Bruce Fischl
> 
> > Sent: Monday, August 7, 2017 1:43:01 PM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] Cortical thickness map for a pediatric case
> > Hi Sneha
> >
> > can you send us the commad you ran and the full screen output inluding
> > the error and also the recon-all.log?
> >
> > cheers
> > Bruce
> >
> > On Mon, 7
> > Aug 2017, Sneha Pandya wrote:
> >
> > >
> > > Dear team,
> > >
> > >
> > > I have completed cross-sectional pipeline on my pediatric case with a
> baseline and 4 follow up time points between 4-7 years of age. However, I was
> not able
> > to
> > > run longitudinal pipeline on it 

[Freesurfer] Matrix ill-conditioned error for dods thickness mri_glmfit analysis

[Sullivan, Danielle Renee]

Hi FreeSurfer Experts,


I am trying to run a dods cortical thickness analysis examining the interaction 
of group on a continuous variable while controlling for other variables.


Specifically, I have 6 classes (gender by three groups [zero, one, two]). I am 
interested in the group interaction with a continuous variable while 
controlling for gender (among 4 other continuous variables). I set up my fsgd 
file (see attached) and contrast file (36 dimensions- F test):

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [1 -1 0 1 -1 0]/2

0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 [1 -0 -1 1  0 -1]/2


and ran this command:


mri_glmfit --y  
lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.mgh
 --fsgd 
fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt
 dods --C 
/GLM_CONTRAST.MAT/Contrast.Male.Female.Age.PC1.PC2.PC3.GGT.RORAbySex.mtx --surf 
fsaverage lh --cortex --glmdir 
lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.glmdir


But keep getting this error:


ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08



Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

If you seek help with this problem, make sure to send:

  1. Your command line:

mri_glmfit --y 
lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.mgh
 --fsgd 
fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt
 dods --C 
/Volumes/VA_Imaging/Projects/salat/2389_TRT/dmiller/GGT_CRP/GLM_CONTRAST.MAT/Contrast.Male.Female.Age.PC1.PC2.PC3.GGT.RORAbySex.mtx
 --surf fsaverage lh --cortex --glmdir 
lh.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forfsgd.thickness.10.glmdir

  2. The FSGD file (if using one)

  3. And the design matrix above



Any idea on what I am doing wrong?

Danielle R. Miller, Ph.D.
National Center for PTSD
VA Boston Healthcare System Jamaica Plain
Boston University School of Medicine
OFFICE: (857) 364-4022

GroupDescriptorFile 1
Title 
fsgd.age.PC1_forFSGD.PC2_forFSGD.PC3_forFSGD.GGT_forFSGD.rs8042149_A_bysex_forFSGD.152.thickness.08082017.txt
MeasurementName thickness

Class femalezero
Class femaleone
Class femaletwo
Class malezero
Class maleone
Class maletwo

Variables age PC1_forFSGD PC2_forFSGD PC3_forFSGD GGT_forFSGD

#Input TRT_0007 = 43 = = = =
#Input TRT_0015 = 38 = = = =
#Input TRT_0016 femalezero 47 0.0295 -0.1271 0.0693 =
#Input TRT_0017 maleone 29 0.0583 0.1283 -0.0139 =
#Input TRT_0019 = 43 = = = =
#Input TRT_0020 = 28 = = = =
#Input TRT_0022 malezero 23 0.0324 0.0381 0.0355 =
#Input TRT_0025 maletwo 24 -0.0619 -0.0585 -0.0010 =
#Input TRT_0026 maleone 26 0.0344 0.1225 0.0991 =
#Input TRT_0027 femaletwo 43 -0.0417 0.0989 0.0776 =
#Input TRT_0028 = 37 = = = =
#Input TRT_0030 maleone 23 0.0230 0.0637 0.0496 =
#Input TRT_0031 maleone 19 -0.0498 0.0925 -0.0851 =
#Input TRT_0032 femalezero 25 -0.0151 -0.0589 -0.0538 =
#Input TRT_0033 malezero 24 0.0675 -0.1426 0.0793 =
#Input TRT_0034 maletwo 39 -0.0826 0.0282 0.0109 =
#Input TRT_0035 maletwo 32 0.1583 -0.0853 -0.0525 =
#Input TRT_0036 maleone 49 0.1116 -0.0184 -0.0206 =
#Input TRT_0037 malezero 27 0.0836 0.0867 0.0418 =
#Input TRT_0038 = 44 = = = =
Input TRT_0042 malezero 20 0.0775 0.0252 0.0351 15
#Input TRT_0043 maleone 49 -0.0615 -0.0789 0.0855 =
#Input TRT_0045 malezero 38 -0.0078 -0.0248 -0.0194 =
#Input TRT_0047 maletwo 26 -0.0431 -0.0585 -0.0031 =
#Input TRT_0048 = 31 = = = 28
#Input TRT_0049 femaletwo 23 -0.0237 0.0189 -0.0160 =
#Input TRT_0050 = 32 = = = =
#Input TRT_0051 = 43 = = = =
#Input TRT_0052 malezero 29 -0.0980 0.0265 0.1271 =
#Input TRT_0055 malezero 33 0.1757 0.0140 -0.0469 =
Input TRT_0057 maletwo 26 0.1976 0.0419 -0.0359 32
#Input TRT_0058 = 58 = = = 10
Input TRT_0059 malezero 42 -0.0061 0.1113 -0.0729 29
#Input TRT_0060 = 37 = = = 33
Input TRT_0061 maleone 34 0.0508 -0.0194 0.0931 22
Input TRT_0062 maletwo 42 -0.1008 -0.1552 0.0298 46
#Input TRT_0063 maleone 46 -0.0077 -0.0068 0.0540 =
Input TRT_0064 maleone 47 0.0792 -0.1128 0.1746 13
Input TRT_0065 maletwo 55 -0.0489 -0.1078 0.0532 65
#Input TRT_0066 = 35 = = = 26
Input TRT_0067 maleone 40 -0.0759 0.0753 -0.0375 24
Input TRT_0068 maleone 24 -0.1071 0.0256 -0.0220 48
#Input TRT_0069 = 44 = = = 26
Input TRT_0070 maleone 47 -0.0551 0.0043 0.0556 29
Input TRT_0071 malezero 28 0.0037 -0.0156 0.0113 19
Input TRT_0072 malezero 31 0.0855 -0.0362 -0.0036 20
Input TRT_0073 malezero 21 -0.0363 0.0048 0.0014 56
Input TRT_0075 maletwo 42 -0.0713 0.0286 -0.1274 30
Input TRT_0076 malezero 33 0.0995 -0.0306 0.0634 23
Input TRT_0078 maleone 39 0.1166 -0.1302 -0.0220 19
Input TRT_0079 maletwo 33 -0.0696 0.0533 -0.0207 24
Input TRT_0082 malezero 58 0.0669 -0.0484 -0.1014 54
Input 

[Freesurfer] Linear Mixed Effects model

[Kasper Jessen]

Dear FreeSurfer,
I have a longitudinal study (patients and controls) with two time points (i.e., 
baseline and six-weeks follow-up). I would like to use the LME model as it can 
handle unequal timing and different number of time points across subjects due 
to missing data.
I would like to test if there is an effect of (a) time (b) group and (c) group 
x time interaction.
However, i am trouble with my design matrix X:
(1) How would i write X?
Thanks in advance
Best regards
Kasper___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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