[Freesurfer] Difference between 2 ways to set up fsgd file and contrasts

[Lydia Chung]

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Hi FS support team,

I am going to be using mri_glmfit to test 1) main effects (which regions
show differences in cortical thickness between group 1 and group 2) and 2)
interaction effects (does the relationship between IV and DV depend on
moderator). Depending on the model, the IV is sometimes a binary
categorical variable and sometimes a continuous variable. The moderator is
always continuous. So, interaction effects are either continuous x
continuous OR categorical x continuous.

One thing I'm trying to understand is whether the two examples below are
basically two different approaches that answer the SAME question: Do people
in Group 1 differ from Group 2 on cortical thickness? Version 1 is the one
provided by FS and Version 2 is an analog of another setup I have been
provided by colleagues. Are these models answering the same or different
questions? The freesurfer link below also shows an example of how to do an
interaction (Group x Age) using Version 1 setup; for Version 2 setup of an
interaction, I know I would multiply the IV and Moderator before this step
so that I would have an additional "interaction variable" column to add as
one of the 'Variables' listed in the fsgd code.  So, I'm also curious if
the two different methods of testing an interaction (in addition to the
first question about the main effect) will get you the identical answer OR
if there is something conceptually different? Do the nuances of this setup
have to do with the difference between using DODS or DOSS?


*Main effect of Group on cortical thickness Version 1 (copied from FS
example. link here 
)*
GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
Variables Age Weight
Input subject1 Group1 30 100
Input subject2 Group2 40 120

Contrasts: 1 -1 0 0 0 0 (to test main effect of group; this feels like an
anova approach?)

*Main effect of Group on cortical thickness Version 2*
GroupDescriptorFile 1
Title OSGM
Class Subjects
Variables Group Age Weight
Input subject1 Subjects 0.5 30 100
Input subject2 Subjects -.5 40 120

contrasts: 0 1 0 0 (to test main effect of group; this feels like a linear
regression approach?)

Thank you in advance for your help!

Lydia
-- 


Lydia Wu-Chung, M.A.
Doctoral candidate
BMED Lab
Department of Psychological Sciences
Rice University
6500 Main St - MS201
Houston, TX 77030
Lab Phone: 713-348-8126
Email: lydia...@rice.edu 



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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

[Reuter, Martin,Ph.D.]

Hi Dan,

I have not worked with this code in a decade, but Kersten in my group maintains 
our  R package of it ( see https://github.com/deep-mi/fslmer ). I will bring 
this to his attention.

Basically I think you determine the joint p-threshold across hemispheres and 
convert it to FreeSurfer ( - log10 pth) and use that value as a threshold when 
plotting the original p-values. That way you only need one threshold for the 
full plot, rather than two different ones (or the more pessimistic of the two).

Also you may be interested in our whippersnappy python tool to generate nice 
looking screenshots of the surface overlay:
https://github.com/Deep-MI/whippersnappy

which is pip installable.

Best, Martin

On 2. May 2024, at 20:25, Dan Levitas  wrote:


Hi Martin,

Thanks for the response!

After my original post I went through things more carefully based on my two 
original two questions and made a follow-up post here 
(https://secure-web.cisco.com/1sMx-dupqFSyAsxsQl8ukXwR4v0-vTUkX2pc5vfwlqp166rCrDoo2bdx6p4keFMRMtTwBjqZmzCoopCuxETJGlS8kVcVUlFiUtWqouZifh-kkm5McZTXjC343IuxhPxggRZIGBfOCndTyBEfHU5yg-L0SF7Jk48ZP-_Yqg9JiZoQkXi347bobVlhhfUqU5umz6cI2eBD7bplC11HyJwUubhLdjnAYGV4QPy_JoqteaGamkmGiiirkesm6JsOmE4dUgh5w8JJfJIwHhiSus176NtxI70y9Cnc5-fIyFxbJ4NUpR41z8diD-6jjtGRt3yoMyyevPtGsNu9rgHK_-JalrQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76783.html)
 with two final questions. The gist of these is that I’m unsure how to apply my 
multiple comparisons (for both hemispheres) to the analysis and subsequent 
visualization. Do you have any guidance on how I should proceed.

Much appreciated,

Dan

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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

[Dan Levitas]

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Hi Martin,

Thanks for the response!  

After my original post I went through things more carefully based on my two 
original two questions and made a follow-up post here 
(https://secure-web.cisco.com/19ziz4OS6HL3HuOwgHLcrspNdIovd6NTUuIdpJ-mDFOvCAyWs2kPDBlUfdSjbT8fclH9nL7GIu1MIetcqQwD2s6-5_CVIvLCVZ6V0NHWw83dN7z4bxX8JjTlz4F5ySCoY2Hn-W5BAu721AwV6QhGaqXBgr32xC1Hj1I1rKrQTyQlP1eIg9Gw3g91iL5agTdIsuQfhuCLS5fDVYGvek_rQh6ZDb-tutbyEWAlZ7ea8enpBmRCBEaMTHGC1pIKz_9aNARmcDOkjf-Znc91tyjFrHT7suqi_CYkPmpMZGFa4URHOcVwpqegNeEb-sV6X4R-YqiERw6UNMAaIXGQAFjAQ4Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg76783.html)
 with two final questions. The gist of these is that I’m unsure how to apply my 
multiple comparisons (for both hemispheres) to the analysis and subsequent 
visualization. Do you have any guidance on how I should proceed.

Much appreciated,

Dan

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[Freesurfer] brain volumes normalization

[yunus soleymani]

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Thank you for the help.my next question
When I normalize the surface area to the eTV, they are in different units (mm2, 
mm3). The resulting unit will be 1/m, is that okay?

Yunus
 Soleymani
Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences
soleymani.yu...@yahoo.com+98 914 526 
9298
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Re: [Freesurfer] Lingering questions for Longitudinal spatiotemporal LME analysis

[Reuter, Martin,Ph.D.]

Hi Dan,

a) yes
b) yes

Best, Martin


On 22. Apr 2024, at 17:09, Dan Levitas  wrote:


Hello,

I've been following the FreeSurfer longitudinal LME analysis tutorial 
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels),
 which has been excellent; however I have a few lingering questions pertaining 
to my specific analysis. For reference, I am interested in assessing rates of 
longitudinal atrophy in each of my two groups (0=controls, 1=clinical). 
Regarding what I've currently done:

1). My Qdec file contains 4 columns: fsid, fsid_base, time(years), group

2). I followed the steps to create the appropriate M matrix, and since my 
preliminary analysis is simply to create a group x time linear model, my design 
matrix is X = [ones(length(M),1) M M(:,1).*M(:,2)]; and my contrast is CM = [0 
0 0 1]

3). I've followed the pipeline for the lme_mass_fit_EMinit, lme_mass_RgGrow, 
and lme_mass_fit_Rgw functions.

4). I'm skipping the model comparison steps, as I prefer my model with the two 
random effects (intercept, time).

5). Get stats (F_lhstats = lme_mass_F(lhstats, CM), applied multiple comparison 
correction ([detvtx,sided_pval,pth] = 
lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0); and saved the 
sided p-values.

My questions are:

a). Since I'm interested in both hemispheres and the tutorial only assesses the 
left, do I need to do step #3 with the right hemisphere data?

b). Would I need to do the last step in the tutorial to get a single threshold 
for both hemispheres and then perform the analysis this way?

P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ];
G = [ F_lhstats.sgn(lhcortex) F_rhstats.sgn(rhcortex) ];
[detvtx,sided_pval,pth] = lme_mass_FDR2(P,G,[],0.05,0);

pcor = -log10(pth)

Thank you for the clarification.

Dan





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Re: [Freesurfer] Infant Freesufer auto-recon failure

[Zollei, Lilla,Ph.D.]

Hi Rachel,

The autorecon-pial option is not yet implemented in infant freesurfer that is 
why you see the below error.

Best, Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Lemley, Rachel 

Sent: Monday, April 22, 2024 3:21 PM
To: Freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] FW: Infant Freesufer auto-recon failure


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Good afternoon,



We are attempting to run freesurfer on infant data, but are running into an 
issue with the autorecon-pial code. We corrected the pial surface on the 
brainmask.mgz in freeview, saved the brainmask.mgz edits, and are trying to run 
autorecon-pial, but we get the following error that I have attached below. It 
is looking for a file in surf labeled lh.orig.premesh, but it does not exist. 
Any suggestions on how to fix this? Am I missing a step?



Respectfully,



Rachel Lemley







The error log is attached below:

Subject Stamp: 
freesurfer-linux-centos7_x86_64-infant-dev-4a14499-20210109-4a14499

Current Stamp: 
freesurfer-linux-centos7_x86_64-infant-dev-4a14499-20210109-4a14499

INFO: SUBJECTS_DIR is /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects

Actual FREESURFER_HOME /n/sw/ncf/apps/infant-freesurfer/4a14499/centos7_x64

Linux holy7c090602.rc.fas.harvard.edu 4.18.0-425.10.1.el8_7.x86_64 #1 SMP Thu 
Jan 12 16:32:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux

'/n/sw/ncf/apps/infant-freesurfer/4a14499/centos7_x64/bin/recon-all' -> 
'/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/scripts/recon-all.local-copy'

/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri/transforms 
/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02

/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02

#

#@# Mask BFS Mon Apr 22 14:06:18 EDT 2024

/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri



mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz



threshold mask volume at 5

DoAbs = 0

Found 401939 voxels in mask (pct=  2.40)

MRImask(): AllowDiffGeom = 1

Writing masked volume to brain.finalsurfs.mgz...done.

@#@FSTIME  2024:04:22:14:06:19 mri_mask N 5 e 2.09 S 0.01 U 0.76 P 37% M 77200 
F 0 R 3233 W 0 c 64 w 51 I 768 O 768 L 2.29 1.57 1.12

@#@FSLOADPOST 2024:04:22:14:06:21 mri_mask N 5 2.29 1.57 1.12

#

#@# AutoDetGWStats lh Mon Apr 22 14:06:21 EDT 2024

cd /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri

mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i 
brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh

infant-dev-4a14499



cd /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/mri

setenv SUBJECTS_DIR /ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects

mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i 
brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh



Reading in intensity volume brain.finalsurfs.mgz

Reading in wm volume wm.mgz

Reading in surf ../surf/lh.orig.premesh

error: No such file or directory

error: MRISread(../surf/lh.orig.premesh): could not open file

Command exited with non-zero status 1

@#@FSTIME  2024:04:22:14:06:21 mris_autodet_gwstats N 8 e 0.73 S 0.00 U 0.28 P 
39% M 43208 F 0 R 1873 W 0 c 23 w 20 I 120 O 0 L 2.29 1.57 1.12

@#@FSLOADPOST 2024:04:22:14:06:22 mris_autodet_gwstats N 8 2.29 1.57 1.12

Linux holy7c090602.rc.fas.harvard.edu 4.18.0-425.10.1.el8_7.x86_64 #1 SMP Thu 
Jan 12 16:32:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux



recon-all -s KAN1_02 exited with ERRORS at Mon Apr 22 14:06:23 EDT 2024



For more details, see the log file 
/ncf/sba08/Triarchy_OA/Rachel/infantFS/subjects/KAN1_02/scripts/recon-all.log

To report a problem, see MailScanner has detected a possible fraud attempt from 
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http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Re: [Freesurfer] question about infantfreesurfer

[Zollei, Lilla,Ph.D.]

Hi Knut,

The version available on the freesurfer wiki is the one that corresponds to our 
original publication. You can use it in your publication.

Lilla

From: Knut J Bjuland 
Sent: Tuesday, April 23, 2024 4:38 AM
To: freesurfer@nmr.mgh.harvard.edu ; Zollei, 
Lilla,Ph.D. 
Subject: Re: [Freesurfer] question about infantfreesurfer

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What I mean is that it's a beta version, so I just wanted to make sure that I 
can use these results in a publication.

Knut Jørgen Bjuland
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Re: [Freesurfer] brain volumes normalization

[Douglas N. Greve]

On 5/2/2024 4:03 AM, yunus soleymani wrote:


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Hello freesurfers,

I have some questions about the output variables of Freesurfer:

1. In the case of brain volume normalization, do I need to normalize 
all the volumetric results to the eTIV or just the subcortical volumes?

All volumes. And area too as you note in #4


2. Are there any formulas other than simple division in order to 
normalize the volumes?
People will sometimes use eTIV as a regressor in the GLM instead of 
dividing (make sure to normalize so that the scale does not mess up the GLM)


3. How are the .ThckStd values (like FS_R_Insula_ThckStd) calculated? 
What does the "std" mean here?

standard deviation across vertices


4. I believe that the surface area outputs are also affected by brain 
size differences in the population. Are there any reference values in 
the Freesurfer outputs to which surface areas can be normalized?

I just use eTIV


Thank you in advance for your help.

Best regards,
Yunus



*Yunus Soleymani*
**
*Ph.D. Candidate of Neuroimaging *
/*Tehran University of Medical Sciences*/
/**/
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"secure-web.cisco.com" claiming to be* *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
soleymani.yu...@yahoo.com 
/

+98 914 526 9298


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Re: [Freesurfer] Figures for publication

[Douglas N. Greve]

I would use either the ocn (cluster annotation) or the cluster-wise 
corrected map: overlay as you generally don't want to show uncorrected 
data. As for the max, it is a personal choice, just what you think looks 
good or makes your point.


On 4/22/2024 7:52 AM, Asuka Toyofuku wrote:


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Dear Freesurfer experts,

Thanks to all the help from this community, we're finally done with 
GLM analysis(mri_glimfit) and the cluster-wise correction 
(mri_glmfit_sim), and now I'm making figures for publication.


My question is

1.
Which output mgh files are commonly used for making figures for
publication? Do people use, for example,
cache.th40.abs.sig.cluster.mgh (cluster-wise corrected map:
overlay) or cache.th40.abs.sig.masked.mgh (uncorrected sig values
masked by the clusters that survive correction) or even
uncorrected ones, such as sig.mgh file in the contrast directory
before running the correction? From my impression, not many people
use e.g., cache.th40.abs.sig.cluster.mgh (which shows no colour
gradation inside the clusters)...
2.
How do you select the colour-bar cut-off and max values? Most
publications I saw use min cut-off value: -log10(p) = 2.00 and
max: -log10(p) = 5.00, but some uses min: p=0.05 and max: p=0.01.
Obviously, if you set the max value (with the configure section)
very low (e.g., 2.0), the size of the cluster gets bigger and
looks more significant. Are there any suggestions for setting the
configure/threshold for the figures?


Many thanks,
Asuka



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[Freesurfer] brain volumes normalization

[yunus soleymani]

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Hello freesurfers,
I have some questions about the output variables of Freesurfer:
1. In the case of brain volume normalization, do I need to normalize all the 
volumetric results to the eTIV or just the subcortical volumes?
2. Are there any formulas other than simple division in order to normalize the 
volumes?
3. How are the .ThckStd values (like FS_R_Insula_ThckStd) calculated? What does 
the "std" mean here?
4. I believe that the surface area outputs are also affected by brain size 
differences in the population. Are there any reference values in the Freesurfer 
outputs to which surface areas can be normalized?
Thank you in advance for your help.
Best regards,Yunus

Yunus
 Soleymani
Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences
soleymani.yu...@yahoo.com+98 914 526 
9298
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