Re: [Freesurfer] group level analysis

[Zeng, Qi]

External Email - Use Caution

Now I see. Thank you very much and have a good night!

Best,
Qi

On Mon, Aug 31, 2020 at 11:12 PM Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> Let me put it this way. It's possible that your amygdala is bigger than
> mine without your brain overall being bigger than mine. But if your corpus
> callosum has higher average FA than mine, then your brain overall will have
> higher average FA than mine (assuming we don't have a reverse difference
> somewhere else). Higher average whole-brain FA doesn’t mean that the FA is
> higher *everywhere* in the brain, so it's not a global effect in the way
> that a bigger brain would be a global effect. I hope this makes sense!
> --
> *From:* Zeng, Qi 
> *Sent:* Monday, August 31, 2020 10:57 PM
> *To:* Yendiki, Anastasia 
> *Cc:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] group level analysis
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> Thank you for the clarification! As you said, if I regress out the global
> FA, I could wipe out the regional FA. But what if my question is to find
> out exactly which regional FA differentiate the two groups rather than if
> global FA is different between groups. In that case, should I control the
> global FA when running regional FA between groups?
>
> Best,
> Qi
>
> On Mon, Aug 31, 2020 at 10:41 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or
> surface area measures.
>
> In a situation where a regional FA difference is high enough to also cause
> a whole brain FA difference, regressing out the latter could wipe out the
> former. Not sure why you'd want to do that, unless there's a specific
> question you want to ask that requires it.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, August 31, 2020 10:03 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] group level analysis
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> Thank you for your reply. So for segmentation.stats, should I divide the
> regional areas by eTIV or treat it as a covariate for a group comparison?
> Is it the same with Total cerebral white matter volume for wmparc.stats.
> For Diffusion measurement, for example, FA, if a subject has lower FA in
> general in the brain, should I adjust the whole brain FA or average FA for
> that matter?
>
> Best,
> Qi
>
> On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Qi - Correcting for overall brain size is important when you are
> comparing measures of length/area/volume. As in, you want to know if a
> region specifically is bigger in population A vs. B, and not just because
> the whole brain is bigger. In that case, use eTIV (estimated total
> intracranial volume) from the freesurfer segmentation stats.
>
> FA is not measuring size of a region, so correcting for brain size is less
> of an issue there. It's a possibility perhaps that for someone with a
> substantially smaller brain there may be more partial voluming affecting
> FA, so it can't hurt to check for an effect before including it in your
> analysis.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, August 31, 2020 11:44 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] group level analysis
>
>
> External Email - Use Caution
>
> Hi,
>
> When conducting group-level analysis, for example comparing volumetric
> differences or tractography FA across subjects between groups. How we
> correct for the size of the brain when comparing volumetric differences or
> correct for the whole brain FA?
> Thank you so much!
>
> Best,
> Qi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
>
> Ph.D. candidate
> Icahn School of Medicine at Mount Sinai
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
>
> --
>
> Ph.D. candidate
> Icahn School of Medicine at Mount Sinai
>
>

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Re: [Freesurfer] group level analysis

[Yendiki, Anastasia]

Let me put it this way. It's possible that your amygdala is bigger than mine 
without your brain overall being bigger than mine. But if your corpus callosum 
has higher average FA than mine, then your brain overall will have higher 
average FA than mine (assuming we don't have a reverse difference somewhere 
else). Higher average whole-brain FA doesn’t mean that the FA is higher 
*everywhere* in the brain, so it's not a global effect in the way that a bigger 
brain would be a global effect. I hope this makes sense!

From: Zeng, Qi 
Sent: Monday, August 31, 2020 10:57 PM
To: Yendiki, Anastasia 
Cc: Freesurfer support list 
Subject: Re: [Freesurfer] group level analysis


External Email - Use Caution

Hi Anastasia,

Thank you for the clarification! As you said, if I regress out the global FA, I 
could wipe out the regional FA. But what if my question is to find out exactly 
which regional FA differentiate the two groups rather than if global FA is 
different between groups. In that case, should I control the global FA when 
running regional FA between groups?

Best,
Qi

On Mon, Aug 31, 2020 at 10:41 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or 
surface area measures.

In a situation where a regional FA difference is high enough to also cause a 
whole brain FA difference, regressing out the latter could wipe out the former. 
Not sure why you'd want to do that, unless there's a specific question you want 
to ask that requires it.

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Zeng, Qi mailto:qi.z...@icahn.mssm.edu>>
Sent: Monday, August 31, 2020 10:03 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] group level analysis


External Email - Use Caution

Hi Anastasia,

Thank you for your reply. So for segmentation.stats, should I divide the 
regional areas by eTIV or treat it as a covariate for a group comparison? Is it 
the same with Total cerebral white matter volume for wmparc.stats. For 
Diffusion measurement, for example, FA, if a subject has lower FA in general in 
the brain, should I adjust the whole brain FA or average FA for that matter?

Best,
Qi

On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Qi - Correcting for overall brain size is important when you are comparing 
measures of length/area/volume. As in, you want to know if a region 
specifically is bigger in population A vs. B, and not just because the whole 
brain is bigger. In that case, use eTIV (estimated total intracranial volume) 
from the freesurfer segmentation stats.

FA is not measuring size of a region, so correcting for brain size is less of 
an issue there. It's a possibility perhaps that for someone with a 
substantially smaller brain there may be more partial voluming affecting FA, so 
it can't hurt to check for an effect before including it in your analysis.

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Zeng, Qi mailto:qi.z...@icahn.mssm.edu>>
Sent: Monday, August 31, 2020 11:44 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] group level analysis


External Email - Use Caution

Hi,

When conducting group-level analysis, for example comparing volumetric 
differences or tractography FA across subjects between groups. How we correct 
for the size of the brain when comparing volumetric differences or correct for 
the whole brain FA?
Thank you so much!

Best,
Qi


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Ph.D. candidate
Icahn School of Medicine at Mount Sinai


The information in this e-mail is intended only for the person to whom it is
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Icahn School of Medicine at Mount Sinai

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Re: [Freesurfer] group level analysis

[Zeng, Qi]

External Email - Use Caution

Hi Anastasia,

Thank you for the clarification! As you said, if I regress out the global
FA, I could wipe out the regional FA. But what if my question is to find
out exactly which regional FA differentiate the two groups rather than if
global FA is different between groups. In that case, should I control the
global FA when running regional FA between groups?

Best,
Qi

On Mon, Aug 31, 2020 at 10:41 PM Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or
> surface area measures.
>
> In a situation where a regional FA difference is high enough to also cause
> a whole brain FA difference, regressing out the latter could wipe out the
> former. Not sure why you'd want to do that, unless there's a specific
> question you want to ask that requires it.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, August 31, 2020 10:03 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] group level analysis
>
>
> External Email - Use Caution
>
> Hi Anastasia,
>
> Thank you for your reply. So for segmentation.stats, should I divide the
> regional areas by eTIV or treat it as a covariate for a group comparison?
> Is it the same with Total cerebral white matter volume for wmparc.stats.
> For Diffusion measurement, for example, FA, if a subject has lower FA in
> general in the brain, should I adjust the whole brain FA or average FA for
> that matter?
>
> Best,
> Qi
>
> On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
> Hi Qi - Correcting for overall brain size is important when you are
> comparing measures of length/area/volume. As in, you want to know if a
> region specifically is bigger in population A vs. B, and not just because
> the whole brain is bigger. In that case, use eTIV (estimated total
> intracranial volume) from the freesurfer segmentation stats.
>
> FA is not measuring size of a region, so correcting for brain size is less
> of an issue there. It's a possibility perhaps that for someone with a
> substantially smaller brain there may be more partial voluming affecting
> FA, so it can't hurt to check for an effect before including it in your
> analysis.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, August 31, 2020 11:44 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] group level analysis
>
>
> External Email - Use Caution
>
> Hi,
>
> When conducting group-level analysis, for example comparing volumetric
> differences or tractography FA across subjects between groups. How we
> correct for the size of the brain when comparing volumetric differences or
> correct for the whole brain FA?
> Thank you so much!
>
> Best,
> Qi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
>
> Ph.D. candidate
> Icahn School of Medicine at Mount Sinai
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>


-- 

Ph.D. candidate
Icahn School of Medicine at Mount Sinai
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Re: [Freesurfer] group level analysis

[Yendiki, Anastasia]

Hi Qi - Use eTIV as a covariate for any analyses on volume, thickness, or 
surface area measures.

In a situation where a regional FA difference is high enough to also cause a 
whole brain FA difference, regressing out the latter could wipe out the former. 
Not sure why you'd want to do that, unless there's a specific question you want 
to ask that requires it.

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zeng, Qi 

Sent: Monday, August 31, 2020 10:03 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] group level analysis


External Email - Use Caution

Hi Anastasia,

Thank you for your reply. So for segmentation.stats, should I divide the 
regional areas by eTIV or treat it as a covariate for a group comparison? Is it 
the same with Total cerebral white matter volume for wmparc.stats. For 
Diffusion measurement, for example, FA, if a subject has lower FA in general in 
the brain, should I adjust the whole brain FA or average FA for that matter?

Best,
Qi

On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Qi - Correcting for overall brain size is important when you are comparing 
measures of length/area/volume. As in, you want to know if a region 
specifically is bigger in population A vs. B, and not just because the whole 
brain is bigger. In that case, use eTIV (estimated total intracranial volume) 
from the freesurfer segmentation stats.

FA is not measuring size of a region, so correcting for brain size is less of 
an issue there. It's a possibility perhaps that for someone with a 
substantially smaller brain there may be more partial voluming affecting FA, so 
it can't hurt to check for an effect before including it in your analysis.

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Zeng, Qi mailto:qi.z...@icahn.mssm.edu>>
Sent: Monday, August 31, 2020 11:44 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] group level analysis


External Email - Use Caution

Hi,

When conducting group-level analysis, for example comparing volumetric 
differences or tractography FA across subjects between groups. How we correct 
for the size of the brain when comparing volumetric differences or correct for 
the whole brain FA?
Thank you so much!

Best,
Qi


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--

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Icahn School of Medicine at Mount Sinai

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Re: [Freesurfer] group level analysis

[Zeng, Qi]

External Email - Use Caution

Hi Anastasia,

Thank you for your reply. So for segmentation.stats, should I divide the
regional areas by eTIV or treat it as a covariate for a group comparison?
Is it the same with Total cerebral white matter volume for wmparc.stats.
For Diffusion measurement, for example, FA, if a subject has lower FA in
general in the brain, should I adjust the whole brain FA or average FA for
that matter?

Best,
Qi

On Mon, Aug 31, 2020 at 6:53 PM Yendiki, Anastasia 
wrote:

> Hi Qi - Correcting for overall brain size is important when you are
> comparing measures of length/area/volume. As in, you want to know if a
> region specifically is bigger in population A vs. B, and not just because
> the whole brain is bigger. In that case, use eTIV (estimated total
> intracranial volume) from the freesurfer segmentation stats.
>
> FA is not measuring size of a region, so correcting for brain size is less
> of an issue there. It's a possibility perhaps that for someone with a
> substantially smaller brain there may be more partial voluming affecting
> FA, so it can't hurt to check for an effect before including it in your
> analysis.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Zeng, Qi <
> qi.z...@icahn.mssm.edu>
> *Sent:* Monday, August 31, 2020 11:44 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] group level analysis
>
>
> External Email - Use Caution
>
> Hi,
>
> When conducting group-level analysis, for example comparing volumetric
> differences or tractography FA across subjects between groups. How we
> correct for the size of the brain when comparing volumetric differences or
> correct for the whole brain FA?
> Thank you so much!
>
> Best,
> Qi
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Icahn School of Medicine at Mount Sinai
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Re: [Freesurfer] group level analysis

[Yendiki, Anastasia]

Hi Qi - Correcting for overall brain size is important when you are comparing 
measures of length/area/volume. As in, you want to know if a region 
specifically is bigger in population A vs. B, and not just because the whole 
brain is bigger. In that case, use eTIV (estimated total intracranial volume) 
from the freesurfer segmentation stats.

FA is not measuring size of a region, so correcting for brain size is less of 
an issue there. It's a possibility perhaps that for someone with a 
substantially smaller brain there may be more partial voluming affecting FA, so 
it can't hurt to check for an effect before including it in your analysis.

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zeng, Qi 

Sent: Monday, August 31, 2020 11:44 AM
To: Freesurfer support list 
Subject: [Freesurfer] group level analysis


External Email - Use Caution

Hi,

When conducting group-level analysis, for example comparing volumetric 
differences or tractography FA across subjects between groups. How we correct 
for the size of the brain when comparing volumetric differences or correct for 
the whole brain FA?
Thank you so much!

Best,
Qi


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[Freesurfer] mri_preproc error with FS6.0

[chelseach...@yahoo.com]

External Email - Use Caution

Hello, I am running into an error while running the LGI analyses using 
FreeSurfer 6.0 following Jove article recommendations ( 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3369773/). The error is occuring 
when I try to run the following command:
mris_preproc --fsgd FSGD.txt --target average --hemi lh --meas pial_lgi --out 
lh.lgi.mgh


Here is the error message: 
nsubjects = 57tmpdir is ./tmp.mris_preproc.174575
/data/EDresearch/AdolAN_All/enigma/output
Log file is lh.lgi.mris_preproc.log
Mon Aug 31 08:25:13 PDT 2020
setenv SUBJECTS_DIR /data/EDresearch/AdolAN_All/enigma/output
cd /data/EDresearch/AdolAN_All/enigma/output
/usr/local/freesurfer/bin/mris_preproc --fsgd FSGD.txt --target average --hemi 
lh --meas pial_lgi --out lh.lgi.mgh

Linux induction3.sdsc.edu 3.10.0-1127.el7.x86_64 #1 SMP Tue Mar 31 23:36:51 UTC 
2020 x86_64 x86_64 x86_64 GNU/Linux
$Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
tmpdir is ./tmp.mris_preproc.174575
Src lh average.sphere.reg
Trg lh sphere.reg




---
#@# 1/57 541202132011 Mon Aug 31 08:25:13 PDT 2020 --
---
mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg 
average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg sphere.reg 
--tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval 
/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi --sfmt 
curv --noreshape --cortex
MRISread(/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg):
 could not open file
Source registration surface changed to average.sphere.reg
Target registration surface changed to sphere.reg

$Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $

setenv SUBJECTS_DIR /data/EDresearch/AdolAN_All/enigma/output
cd /data/EDresearch/AdolAN_All/enigma/output
mri_surf2surf --srcsubject 541202132011 --srchemi lh --srcsurfreg 
average.sphere.reg --trgsubject average --trghemi lh --trgsurfreg sphere.reg 
--tval ./tmp.mris_preproc.174575/541202132011.1.mgh --sval 
/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi --sfmt 
curv --noreshape --cortex

sysname  Linux
hostname induction3.sdsc.edu
machine  x86_64
user     chays
srcsubject = 541202132011
srcval     = 
/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.pial_lgi
srctype    = curv
trgsubject = average
trgval     = ./tmp.mris_preproc.174575/541202132011.1.mgh
trgtype    =
srcsurfreg = average.sphere.reg
trgsurfreg = sphere.reg
srchemi    = lh
trghemi    = lh
frame      = 0
fwhm-in    = 0
fwhm-out   = 0
label-src  = lh.cortex.label
label-trg  = lh.cortex.label
OKToRevFaceOrder  = 1
UseDualHemi = 0
Reading source surface reg 
/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg
No such file or directory
mri_surf2surf: could not read surface 
/data/EDresearch/AdolAN_All/enigma/output/541202132011/surf/lh.average.sphere.reg
No such file or directory



Of note, this command works fine when substituting the fsaverage rather than 
study average template, however this is an adolescent sample so we are not able 
to use the fsaverage. Any help would be greatly appreciated! 
Best, Chelsea 


Chelsea C. Hays, Ph.D. 
Neuropsychology Postdoctoral Fellow Center of Excellence in Stress and Mental 
Health UC San Diego|VA San Diego Healthcare 
systemch...@ucsd.edu|chelsea.ha...@va.gov



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[Freesurfer] tkregister2 deprecated for FS7.1?

[Zeng, Victor (BIDMC - Keshavan - Psychiatry)]

Hi FS devs,


I am following 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview? as a 
tutorial to fix the bad talaiarch file I have. I know that tkmedit is 
deprecated, but I was wondering if tkregister2 is too. If so, I was wondering 
what software I would use (or commands, I assume using freeview) since that 
page still refers to tkregister2.


Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
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Re: [Freesurfer] VirtualBox Ubuntu Password Request

[fsbuild]

External Email - Use Caution

Hello Eileen,

I will send the password to your email shortly.
- R.

On Aug 31, 2020, at 11:46, XU Eileen s1659...@sms.ed.ac.uk 
wrote:External Email - Use 
CautionDear FreeSurfer 
Developers,I’m attempting to login to the Ubuntu VM disk image downloaded 
through the VirtualBox setup page, however I could not find the password for 
the “developer” account in the documentation or set up a personal account 
through the VM. I’m quite new to Linux, so apologies if this is a simple fix 
that I’ve failed to find.Many thanks,EileenThe University of 
Edinburgh is a charitable body, registered in Scotland, with registration 
number SC005336. ___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer​
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[Freesurfer] VirtualBox Ubuntu Password Request

[XU Eileen]

External Email - Use Caution

Dear FreeSurfer Developers,

I'm attempting to login to the Ubuntu VM disk image downloaded through the 
VirtualBox setup page, however I could not find the password for the 
"developer" account in the documentation or set up a personal account through 
the VM. I'm quite new to Linux, so apologies if this is a simple fix that I've 
failed to find.

Many thanks,
Eileen

The University of Edinburgh is a charitable body, registered in Scotland, with 
registration number SC005336.
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[Freesurfer] group level analysis

[Zeng, Qi]

External Email - Use Caution

Hi,

When conducting group-level analysis, for example comparing volumetric
differences or tractography FA across subjects between groups. How we
correct for the size of the brain when comparing volumetric differences or
correct for the whole brain FA?
Thank you so much!

Best,
Qi
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[Freesurfer] Asymmetry whole thalamus with native vs Iglesias method

[Chris Vriend]

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Dear freesurfer experts,



I’m currently using FreeSurfer 7.1 with the thalamus subsegmentation from
Iglesias et al (version 12) to subsegment the thalamus. Something we
noticed is that the asymmetry between the left and right whole thalamus is
reversed when comparing the native thalamus segmentation by FreeSurfer
itself and the Iglesias method. This is exemplified by the values below
where we calculated the Asymmetry Index [ (Left – right)/(left + right) *
100 ] and shows that for some subjects the left thalamus is larger when
looking at the results of the Iglesias method, but smaller with the native
method.

To allow comparison between the two methods we subtracted the LGN and MGN
volumes from the whole thalamus volume, because –  if I’m not mistaken –
 these nuclei are not segmented by the standard recon-all pipeline?

We don’t know why we observe this and not just in one dataset or one
subject but in multiple. Do you have any words of wisdom or explanation for
this phenomenon?



Your advice is much appreciated.



Kind regards,



Chris Vriend


Whole_thalamus_lh_Iglesias

whole_thalamus_rh_Iglesias

AI

Fsnative_Left-Thal

Fsnative_Right-Thal

AI

4913.391

5129.889

-2.155650345

5987.2

5764.6

1.894177913

6019.185

6235.017

-1.761289719

6793.9

6732.4

0.454669791

6374.575

6574.893

-1.546920692

7543.9

7592.1

-0.318446089

6974.051

6983.314

-0.066366395

7661.3

7624.8

0.238779021

5907.853

5798.037

0.93812602

6756.4

6485.2

2.048090865

6316.792

6382.639

-0.518503546

7191.2

6959.7

1.63593835
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[Freesurfer] Postdoc Opportunity in Montréal

[Lussier,Desiree]

External Email - Use Caution

Seeking Postdoctoral Fellow for Multiomics Investigations in Neurodegenerative 
Diseases



The Multiomics Investigation of Neurodegenerative Diseases Lab, directed by Dr. 
AmanPreet Badhwar, is looking for a postdoctoral fellow. The successful 
candidate will leverage extensive datasets (neuroimaging, molecular ‘omics’ and 
clinical/neuropsychological data)  to test hypotheses linking multiomics 
changes to age-related dementias, with an initial focus on Alzheimer’s disease 
and Vascular Cognitive Impairment and Dementia (VCID). The desired candidate is 
a motivated individual willing to work in a highly collaborative and 
multidisciplinary environment. The candidate is also expected to work closely 
with research teams with expertise in machine learning and AI, and she/he will 
have opportunities to build on, and/or develop these skills.



Education and experience requirements

  *   Prior training in Neuroscience (age-related dementias a plus) or 
Biomedical Engineering

  *   Experience in structural MRI, resting-state functional MRI, brain 
connectivity

  *   Knowledge of Matlab and/or Python programing

  *   Expertise in statistics (SPSS, R, Nilearn/Nistats, or other)

  *   Team-oriented; excellent organizational, interpersonal and communication 
skills

  *   Experience in multivariate pattern analysis, computational modeling, 
and/or machine learning are all assets



Start duration and salary

The position is available beginning 2021 in the laboratory of Dr. AmanPreet 
Badhwar, located at the Centre de Recherche de l’Institut Universitaire de 
Gériatrie de Montréal (CRIUGM), University of Montreal, Montreal, Canada. 
Funding is available for 1 year, renewable, but selected candidates are 
expected to apply for external fellowships. Candidates must be a Canadian 
citizen/permanent resident or be eligible to work in Canada (after obtaining an 
appropriate visa).



Contact

Applicants should submit a cover letter stating their research interests and 
experience, together with a CV, transcripts, and contact information for two 
reference writers. Please send as a single PDF via email with the subject 
heading “ApplicantName_Postdoctoral_Applicant” to Dr. AmanPreet Badhwar at 
amanpreet.badh...@criugm.qc.ca. 
Applications will be accepted until the position is filled.

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[Freesurfer] remark regarding tcsh with bad locale

[Rovai Antonin]

External Email - Use Caution

Hi,

this is not really a question but rather a comment that, hopefully,
will help those running into the issue I ran into today.

I was using mri_glm-sim with --mczsim 2 option, and got an error saying
that "2,0 must be 1.3, 2.0 ...".
The issue is that printf (used in the mri_glm-sim script) refers to the
LC_NUMERIC locale which, in my unfortunate case, has instructed printf
%2.1f to replace the dot by a comma.

You can check this by typing locale in a terminal.
If, like me, you live in an undercivilized part of the world, then you
may update your locale using e.g.

sudo update-locale LC_NUMERIC=en_US.UTF-8

Log in and out and you'll be back on the right side of the force.

It would be great if a future release of FS could include a locale
check :-)

Hope this help someone, someday.

Best

AR

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

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[Freesurfer] mris_anatomical_stats

[Palin, Tara]

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When using the following command line:


mris_anatomical_stats -th3 -mgz- cortex ../label/?h.cortex.label -f 
../stats/?h.aparc.pial.stats -b -a ../label/?h.aparc.annot -c 
../label/aparc.annot.ctab subject ?h pial


do we generate a pial surface area (for each hemisphere) that excludes the 
medial wall?


Thank you,

Tara

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[Freesurfer] intersubject longitudinal analysis

[KennethSPrice]

External Email - Use Caution

Hello Freesurfers!

I am working through the longitudinal tutorial found here:
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial

To keep it simple, I ran longitudinal processing on 2 timepoints for one 
subject. My qdec file had only two entries. I would like to look at pct 
difference in thickness for one subject. I ran

long_mris_slopes --qdec qdec.dat --meas thickness --hemi lh --do-avg --do-rate 
--do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd 
$SUBJECTS_DIR

When I run the overlay I get an error saying that "the overlay cannot be 
loaded", although the file exists.

freeview -f 
$FREESURFER_HOME/subjects/fsaverage/surf/lh.pial:overlay=$SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-spc.fwhm15.fsaverage.mgh:overlay_threshold=2,5

First of all, is this method sound in order to visualize pct change in 
thickness for one subject? If so, why is the overlay not loading?

Best,
Ken

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