Hi, I have a question related to this post. Besides an age-group
interaction, wouldn't it also be neccesary to check for an age-gender
interaction?
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Oh, I meant to reply to an older post, but that didn't work
apparently. Below the original post.
This person does a group analysis, with gender and age as
covariates.You adviced to first do a DODS and look for a age-by-group
interaction. If there's no interaction, he/she could continue with
DOSS.
Hi everyone,
I want to analyze with DOSS the relationship between performance on a
cognitive task (called '15wt') and cortical thickness, in one group,
controlling for the effects for age, gender and education. As a
Freesurfer-newbie, it be would really great if someone could check my .sfgd
file a
Thank you Doug!
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Hi everyone,
I run into an error when I try to do the tutorial on ROI group analysis. I
downloaded the tutorial set, but did not put it into
FREESURFER_HOME/subjects, because my computer doesn't allow it. I made my
own folder and copied everything in there. The error arises when I try to
map a lab
It finally worked! Thank you so much Louis. My SUBJECTS_DIR was pointing to
a folder within my TUTORIAL_DATA directory (I thought it was supposed to be
like that when I read the instructions), but now they point to the same
folder and it works. Thanks again!
Anita
_
Dear FreeSurfers,
I have a question regarding conversion from MNI152 coordinates to MNI305
coordinates. I want to take ROIs from a VBM study and use these exact same
ROIs in my vertexwise analysis. So I need to translate the x, y, z
coordinates from MNI152 space into MNI305 space. In previous post
It worked, thanks. I tried to invert it but the coordinates didn't fully
correspond; I must have made an error. Thanks for helping me out!
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Hi all,
I find myself getting quite confused about different coordinates systems.
Is the following correct (when viewing in TkSurfer):
RAS=MNI Talairach=MNI305 (they are all the same?)
Talairach= (non linear) conversion from MNI305
Thanks,
Anita
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Hi all,
I want to measure cortical thickness in 7 volume-defined ROIs (created in
Marsbar). I followed the tutorial
http://freesurfer.net/fswiki/VolumeRoiCorticalThickness. When I want to
visualize my surface-based ROI after mri_vol2surf, for some reason ROI 6
and 7 do not appear in tksurfer (and
Dear Freesurfer experts,
I want to use volume-defined ROIs (obtained in a VBM study) to extract mean
thickness and surface area, in a total group of 138 participants. I
followed the tutorial 'Cortical Thickness of a volume-defined ROI'. I have
a few questions regarding this analysis:
1. The volum
Hi Rujing Zha,
Click this link: http://freesurfer.net/fswiki/VolumeRoiCorticalThickness
Anita
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Hi Bruce,
Thank you for your response. Now at least I know what went wrong; I'll
try your solution.
Thanks!
Anita
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The information
Hi mailinglist,
I want to obtain aparc.stats for pial instead of white matter surface area.
I read that I therefore should adjust mris_anatomical_stats. However, when
I run this command separately, the following error occurs:
cannot allocate memory
Then I tried to put autorecon3 -parcstats in fr
Hi Bruce,
See below. Thank you!
Anita
First I tried:
*aloenhoud@somerenserver:/data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050$
*mris_anatomical_stats -mgz -f stats/lh.aparc.stats -b -a
label/lh.aparc.annot -c label/aparc.annot.ctab 0050 lh pial
INFO: assuming MGZ format for volumes.
co
Hi Bruce,
The wm.mgz was created a while ago with an older version, by another
student.
At the moment I use v5.3.0. Should I recreate wm.mgz with this more recent
version, or is there another option?
Thank you,
Anita
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Dear FreeSurfers,
I’m comparing two groups (patients (N=45) and controls (N=93)) on
cortical thickness using 34 parcelated areas in each hemisphere (i.e.
68 areas in total). When correcting for multiple comparisons using
Bonferroni, only one area remains significant. Bonferroni is quite
conservati
Hi FreeSurfers,
I'm doing an analysis with two groups: patients and controls. When I look
at "Does the average thickness differ between 1 (patients) and 2
(controls)?", I can see blue (negative) and red (positive) correlations. I
know that it means that in some cases, the patients have a higher co
Hi all,
When I do a group analysis and check significant clusters after
performing a Monte Carlo, I see significant areas that were NOT
significant before doing a multiple comparisons correction.
Specifically, after Monte Carlo, the parstriangularis is significant,
while this area was not signific
Hi Doug,
Thanks for your reply. I was using 1.3 for visualization and 2 for
simulation. So that's probably where it went wrong? When I set both
thresholds to 2, significant clusters after Monte Carlo were also
there before the simulation.
Just to double-check: can the values associated with these
Hi Doug,
I mean that before doing any correction, I can press 'Find Clusters
and Goto Max', which will show me clusters based on my visualisation
threshold. As far as I understood, it will go to the most significant
vertex within each cluster and display that value. So before Monte
Carlo, I found
Hi Doug,
It is finally starting to make sense to me. It was indeed the case
that before Monte Carlo, within a cluster there were different values
for each vertex, and after Monte Carlo, each vertex had the same
value. I had difficulty understanding the different functions of the
color scale min/ma
Great! Thank you!
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