[Freesurfer] volume, surface area, and thickness

[Woo-Suk Tae]

Dear FreeSurfer experts and developers

I am confronted with some technical question of a reviewer.
I am not sure about "volume = thickness-by-surface area" and the review's
opinion (attached below) about volume, surface area, and thickness was
correct.
Any comments from FreeSurfer's experts would help me.

Sincerely yours

Woo-Suk Tae
Seoul, Korea

I added the reviewer's comments.
-
1. Volume/thickness: The authors cite many papers that show volume and
thickness differences in MDD. The unresolved part here, however, is the
RELATION between cortical thickness and cortical volume: There is no doubt,
that both measures are found affected in MDD. This is, because cortical
thickess multiplied by the surface area of a gyrus results in its volume,
so volumse = thickness-by-surface area. Surface area values themselves are
technically more noisy and usually thus less sensitive (due to the problem
of false attributions to an area).

So, volume is influenced by thickness and surface and is the less specific
measure. If a volume effect is detected in a study, it is unclear, if it is
driven by thickness, or surface area, or both. In this respect, the study
of Schmaal et al. is telling, as it analyzed BOTH measures, finding only
thickness effects of MDD, and (practically) no surface area changes except
for adolescent MDD. In the adolescent MDD samples gross surface area
differences were detected.

This means, that the question of "superiority" is rather a question of
"specificity": (Cortical) volume findings in adult MDD are mostly driven by
thickness differences and are in on way independent from thickness
differences. In this respect, the authors should follow the basic geometric
principles of morphometry and point out the relatedness of the two. They
can simply check this in their FreeSurfer variables (e. g. for total grey
matter volume). Not reporting surface area is leaving an interpretational
gap as surface area differences could in addition drive volume differences.
The authors may want to decide not to present surface area results, but
then they should discuss this as limitation to disentangle the origin of
volumetric (cortical) effects. This seems important as methylation effects
and FKBP5 interact with early life time stress, so effects on surface area
as seen in adolescent MDD highlight that surface area effects could play
in.








Woo-Suk, Tae  Ph.D.  Research Professor
Brain Convergence Research Center, Medical Research Center
Anam Hospital, Korea University Medical Center, Seoul, Korea
mobile: 82-10-9120-4629
office: 82-2-920-6831
email: woosuk@gmail.com, woos...@gmail.com 

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Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

[Anastasia Yendiki]

No need to rerun anything. It's an issue with the format of those mean 
path files. Just view them in the standard 5.3 version of freeview for 
now.


On Fri, 26 Aug 2016, Elijah Mak wrote:


Hi Anastasia,

Yes indeed. I am using a dev version of freeview. I could give it another go 
with the freeview that came
with v5.3. But does this mean that I shoudl also I re-run the tracula -stat on 
a v5.3? 

Thanks!

Best Wishes,
Elijah



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Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

[Elijah Mak]

Hi Anastasia,

Yes indeed. I am using a dev version of freeview. I could give it another
go with the freeview that came with v5.3. But does this mean that I shoudl
also I re-run the tracula -stat on a v5.3?

Thanks!

Best Wishes,
Elijah
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Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

[Anastasia Yendiki]

Hi Elijah - Glad to hear that things worked out! Are you by any chance 
using the dev version of freeview?


a.y

On Fri, 26 Aug 2016, Elijah Mak wrote:


Hi Anastasia and others,
I am trying to visualise the *.path.mean.txt on MNI template after running 
trac-all -stat. I used this
command:

freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w 
stats/*.path.mean.txt
However, it looks like something has gone wrong with the labelling and position 
of the tracts (note the
CST highlighted in green).

https://www.dropbox.com/s/ndpkfgbrfgvt5q1/Screen%20Shot%202016-08-22%20at%2014.41.37.png?dl=0

Everything was fine and correctly labelled when I checked the merged tracks.

Thanks again for your help!


Best Wishes,
Elijah

P.S. On another note, the reinit=1 trick works very well and I was able to 
reconstruct the tracts in
almost all cases. Thanks!




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Re: [Freesurfer] PET surface sampling

[Jonathan DuBois]

Hi Doug, 

Thank you. I ran sampled the data and ran mri_glmfit as you suggested, although 
the resulting bp file seems to only have binary clusters (in the attached image 
the red cluster all have a value of 1 and everywhere else is 0). Is this the 
normal output? I expected a more varying map. 

Thanks 
Jonathan

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[Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

[Elijah Mak]

Hi Anastasia and others,

I am trying to visualise the *.path.mean.txt on MNI template after running
trac-all -stat. I used this command:

freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w
stats/*.path.mean.txt

However, it looks like something has gone wrong with the labelling and
position of the tracts (note the CST highlighted in green).

https://www.dropbox.com/s/ndpkfgbrfgvt5q1/Screen%20Shot%202016-08-22%20at%2014.41.37.png?dl=0

Everything was fine and correctly labelled when I checked the merged tracks.

Thanks again for your help!


Best Wishes,
Elijah

P.S. On another note, the reinit=1 trick works very well and I was able to
reconstruct the tracts in almost all cases. Thanks!
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Re: [Freesurfer] sig.sum files shows more clusters than sig.mgh image

[Oana Georgiana Rus]

Dear Doug,

I tried using --o instead of --ocp.

*Neither the sig.sum nor the sig.mgh file change.*

*So i dont see the postcentral cluster neither after running it with --o 
in sig.mgh.*


But the cluster is present in the sig.sum file. i am not sure why it 
could be like that.


Best Georgiana


Am 25.08.2016 um 16:32 schrieb Douglas N Greve:

Try using --o instead of --ocp


On 08/25/2016 05:50 AM, Oana Georgiana Rus wrote:

Dear Doug,

thanks a lot for responding. Here my command lines and attached the image.

*So command line to perform the GLM analysis and get the sig.mgh file
was:*

mri_glmfit --y
/data_august/Geo/freesurfer_OCD/freesurf_steps/2_mris_preproc/education_out/rh.all_gender_age.volume.10.mgh
\
   --fsgd diagnosis_gender_scanner_age.fsgd dods\
   --surf average_subjects rh \
   --C
/data_august/Geo/freesurfer_OCD/subjects_converted/difference_OCD_nonOCD_regressing_gender_scanner_age.mat
\
   --C
/data_august/Geo/freesurfer_OCD/subjects_converted/difference_Muc_Jen_regressing_group_gender_age.mat
\
   --glmdir
/data_august/Geo/freesurfer_OCD/freesurf_steps/3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir


*Then to see the sig.mgh FDR corrected(0.05) and with corresponding
clusters in a text file sig.sum the command line was:*

mri_surfcluster --src
3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/sig.mgh
\
   --subject average_subjects \
   --annot aparc \
   --fdr .05 \
   --hemi rh \
   --sum
3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/FDR_corrected/sig.cluster.sum
\
   --ocp
3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/FDR_corrected/sig.cluster.mgh


*The result output file sig.cluster.sum file looks like: *

# Cluster Growing Summary (mri_surfcluster)
# $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
# $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $
# CreationTime 2016/08/10-12:44:41-GMT
# cmdline mri_surfcluster --src
3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/sig.mgh
--subject average_subjects --annot aparc --fdr .05 --hemi rh --sum
3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/FDR_corrected/sig.cluster.sum
--ocp
3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/FDR_corrected/sig.cluster.mgh

# cwd /data_august/Geo/freesurfer_OCD/freesurf_steps
# sysname  Linux
# hostname dnepr.mri.tu-muenchen.de
# machine  x86_64
# FixVertexAreaFlag 1
# FixSurfClusterArea 1
#
# Input
3_glmfit/education_out/account_for_scanner/rh.gender_age_scanner_Vol.glmdir/difference_OCD_nonOCD_regressing_gender_scanner_age/sig.mgh
# Frame Number  0
# srcsubj average_subjects
# hemi rh
# surface white
# annot aparc
# SUBJECTS_DIR /data_august/Geo/freesurfer_OCD/subjects_converted
# FDR 0.05
# SearchSpace_mm2 68665.3
# SearchSpace_vtx 163842
# Bonferroni 0
# Minimum Threshold 2.90905
# Maximum Threshold infinity
# Threshold Signabs
# AdjustThreshWhenOneTail 1
# Area Threshold0 mm^2
# Overall max 2.17264 at vertex 97170
# Overall min -5.57963 at vertex 38757
# NClusters  23
# Total Cortical Surface Area 68665.3 (mm^2)
# FixMNI = 1
#
# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZ NVtxs   Annot
1   -5.580   38757312.19 20.1  -49.79.0   738 precuneus
2   -5.264  112198798.03 28.5  -80.4   18.9  1067
lateraloccipital
*3   -4.536 37472126.77 45.4   -7.8   14.7   286  postcentral*
4   -4.2932509149.21 53.8  -44.96.3   296 bankssts
5   -4.238  130081120.67  9.5  -81.0   37.6   171
superiorparietal
6   -4.176   70319 89.19 43.6  -45.1   -9.9   127 fusiform
7   -4.142   99571 56.31 55.7  -13.9   18.5   135
postcentral
8   -3.903  114823128.09 49.5  -28.9  -19.9   189
inferiortemporal
9   -3.6012614 30.73 10.5   18.1   57.156
superiorfrontal
   10   -3.540   17914118.52 32.3   13.2   50.3   193
caudalmiddlefrontal
   11   -3.477   73193101.62 44.7   38.5   -5.6   124
parstriangularis
   12   -3.422  162554 56.81 62.7  -36.1   -1.7   100
middletemporal
   13   -3.420   49413 32.19 44.1   -0.3  -17.680
superiortemporal
   14   -3.416   19541 59.40 12.9  -50.9   60.8   129
superiorparietal
   15   -3.351   99261 28.03 38.3   40.64.636
rostralmiddlefrontal
   16   -3.291   44544 46.46  4.3  -57.2   22.485 precuneus
   17   -3.275   28430 29.87 39.4  -14.7  -22.447 fusiform
   18   

[Freesurfer] modifying wm.mgz after editing aseg

[Julian Jäckle]

Dear all

my question would be whether editing wm.mgz and running autorecon2-wm will
affect a previous edit of aseg?

Further can aseg and wm.mgz be processed simultaneously as it is possible
for wm.mgz and pial surface using autorecon2-wm?

Greetings

Julian
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