If you're studying thickness, I'm a fan of using mean cortical thickness as
the covariate (since thickness is what you're studying). I've posted on
this in the past.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Hi,
Sorry, but I don't understand what you're asking.
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South
Hi Doug,
There are approaches/methods available for permutation testing with
non-orthogonal design matrices -- see for example the documentation for
FSL's randomise and the references cited therein.
cheers,
-MH
--
Michael Harms,
e the difference
between groups using appropriate contrasts.
2) If you want to control for all 3 covariates simultaneously, then all of
them should be included (as separate, de-meaned columns) in the design
matrix.
cheers,
-MH
--
Michael Harms,
Goghari VM et al, Cereb Cortex 2007; 17:415-24
Kuperberg GR et al, Arch Gen Psych 2003; 60:878-88
Harms MP et al, Brit J Psychiatry 2010; 196:150-157 and related
correspondence (196:414-415)
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte
ot; in the first
Normalization stage, if for example using an expert options file for
mri_normalize?
thanks,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Dep
compare the two surfaces directly -- e.g., the
rms distance between matched vertices.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatr
ystem using
freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 distribution.
I can't change the FDR "Rate" either.
thanks,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington
L 5.9 system
using the qdec in FS 5.1 as well.
So, must be something about the libraries qdec uses not quite playing nice
in RHEL 5.9 ?
thanks,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washi
Thanks Nick -- that fixed it.
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747
I'm curious: For comparison to the results in that paper, has anyone
quantified the variability that results when one runs the same FS
version repeatedly on the same subject, but with a different random seed
each time? That is, how much of the difference is related to math
libraries vs. intrinsic
Hi Peter,
This sounds very familiar (including the effect on the opposing
hemisphere) to something I've observed previously under FS v5.1 -- see
the posts titled "control point guidance" from late Jan 2012. This may
be related to a change in how CP's were used in FS v5.1, which I believe
they are
Hi Mark,
Did you see my post from 1/10/2012 ("anterior temporal lobe problems")?
We had good success (albeit not perfect) in improving our anterior
temporal surfaces using the options mentioned there.
cheers,
-MH
On Mon, 2012-08-20 at 14:43 -0500, Mark Fletcher wrote:
> Dear FreeSurfers,
>
> I
And in your second set of images, you probably need to edit the wm.mgz.
I suspect that there is a topology problem that is messing up the wm.orig
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental
mical
orientation, not according to which axis was readout and which was phase
encode.
Hope that helps,
-MH
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Departme
well, one would need to use the backwards compatability flag
that Nick introduced in relation to the CP issue.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medi
Hi Bruce,
How are you matching the BW for T2-SPACE vs. MPRAGE -- the former
typically has a BW around 700+ Hz/Px, while the latter is typically around
200 Hz/Px.
thanks,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience
Just wanted to mention that, to my knowledge no commercial stat package
will mean center by group (Donald's case (C)) if you request an
interaction model. Mean centering by group is a very unusual operation.
cheers,
-MH
--
Michael Harms,
Re 1) See the Wiki on the longitudinal stream
Re 2) That syntax will result in registration and averaging of the input
images to yield a single volume that is then run through recon-all
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte
ickness as a
covariate for studies involving thickness as the dependent variable.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psych
Hi Laura,
If you're looking for another reference that has used this approach, you
could see our 2010 paper:
http://www.ncbi.nlm.nih.gov/pubmed/20118463
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of M
Hi Corey,
You may be interested in the recent thread on the SPM list discussing
similar issues about why one shouldn't put too much stock in Brodman
area labels unless they are derived from actual histology (e.g., the
work of Julich/Amunts/Zilles et al).
https://www.jiscmail.ac.uk/cgi-bin/webadmi
Regarding #2: Yes, if you a have global difference in thickness between
groups, then it is appropriate to control for that in the same manner that
one frequently controls for total brain volume in volumetric analyses.
cheers,
-MH
> Dear list,
>
> I have two question:
>
> 1. Is it possible to do
Hi Sheeva,
The pial surface is not designed to include the hippocampus and
amygdala.
Quoting from http://www.freesurfer.net/fswiki/FsTutorial/OutputData :
There are regions where the surfaces are not intended to be accurate
that you should be aware of:
* Areas around the hippocampus and
more concrete to take to the admins of each system.
thanks,
-MH
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
Renard Hospita
Hi Josh,
With sophisticated mixed modeling procedures that use MLE estimation
(e.g., SAS's PROC MIXED) it would be possible to use all your data while
still modeling the necessary covariances. If you extracted ROI-based
measures that would be a possible approach you could take. However, I
don't
mris_volume returns the volume interior to the entire surface (whichever
surface is provided as input), which in the case of Xh.white as input
will include subcortical gray matter, ventricles, etc.
mris_wm_volume subtracts out the volume of non-wm voxels based on the
aseg.
Here is the usage stat
They are separate labels, so they would need to be added together.
cheers,
-MH
On Mon, 2011-09-26 at 19:21 +, victor del brutto wrote:
> Hello all,
>
> Quick question, does the Lateral Ventricle volume include the volume
> of the Inferior Lateral Ventricle (i.e. temporal horn) or do they n
Typically one uses either a measure of "brain volume" or an estimate of
intracranial volume -- the choice depends on whether or not you want to
control for whole brain atrophy when making your interpretations, in
which case you would use "brain volume" rather than ICV. There have
been numerous po
is any literature about area
> (surface) analysis in particular. Am I at the right track at all?
>
> Best wishes,
> Tanja.
>
> On Wed, Nov 2, 2011 at 2:15 PM, Michael Harms wrote:
> >
> > Typically one uses either a measure of "brain volume" or an estimate o
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
Renard Hospital, Room 6604 Tel: 314-747-6173
660 South Euclid Ave
Hello,
What is the difference between the mris_ms_surface_CNR and mri_cnr
functions? (I couldn't find any descriptive info for either). And are
either of them useful for identifying datasets with "poor"
gray/white/csf contrast?
thanks,
-MH
--
Mich
Hi Irene,
To add to what Martin wrote, the issue is that the conform stage of
mri_convert automatically interpolates "oblique acquisitions" and the
user has no control to turn off this behavior. You may be interested in
the following thread in which I inquired about this interpolation:
http://ww
/scripts
directory so that the directory already existed. However, in
conjunction with the -i flag this then triggers the error of "existing
subject" and the -force option no longer exists to force the process to
proceed.
cheers,
-MH
--
Michael H
at 14:52 -0600, Michael Harms wrote:
> Hi guys,
> There is an issue with recon-all abending if you use the -expert option
> on the very first call to recon-all, because recon-all attempts to copy
> to $subjid/scripts/expert-options before the scripts directory has been
> created.
>
Hi Jordan,
I just had a similar discussion (off-list) with Nick recently.
The distinction only matters if you end up trimming cerebellum voxels
out of the aseg, and want your aseg for cerebellum to be correct.
Quoting Nick:
"it [brain.finalsurfs.manedit.mgz] is used only in the instance (which
ha
stripping.
Should 4 GB be sufficient?
thanks,
-MH
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
Renard Hospital, Room 6604
If you only made edits to the aseg, then you can run:
recon-all -s subject_name -autorecon2-aseg -autorecon3
which omits some stages that don't need to be redone (but which would
otherwise be included if you use the -autorecon2 flag).
If you in addition added control points, then you would run
re
Thanks Doug. And good question that I've wondered about myself Jeff.
The part about the high-resolution volume that is created "under the
hood" explains why mris_wm_volume takes substantially longer to complete
than would be expected relative to just running `mris_volume Xh.white`
and then subtr
You need to specify 'pial' as the surface name argument in
mris_anatomical_stats
cheers,
-MH
On Thu, 2011-12-15 at 10:52 -0500, Robustelli, Briana (NIH/NIMH) [F]
wrote:
> Dear FreeSurfer team,
> I have been looking at area.pial differences in two groups using qdec.
> I would now like to e
As you noted, the surfaces bisect the hippocampus and amygdala, so the
small amount of tissue outside the pial surface is not included in the
surface based measures of total GM volume. Compared to the overall
variation in brain size, this should be inconsequential.
cheers,
-MH
On Mon, 2011-12-1
Hi Andreia,
The XhCortexVol measures in the aseg.stats of FS v5.1 are identical to:
`mris_volume Xh.pial` - `mris_volume Xh.white`
To my knowledge, that measure is therefore simply the difference of the
volume encapsulated by the two surfaces. My point was that the surface
"inaccuracies" in the
The problem is apparently that the Xh.aparc.a2009s.annot wasn't created.
Look in scripts/recon-all.log and make sure that the section "Cortical
Parc 2" is present, and if it is, look for clues as to why the .annot
wasn't created.
cheers,
-MH
On Thu, 2011-12-29 at 16:03 +, LAOUCHEDI MAKHLOUF
Michael
> i looked in the job.log file (i am using a condor
> cluster) that i attached, and there is no such section!
>
> thanks
>
> --- En date de : Jeu 29.12.11, Michael Harms
> a écrit :
>
> De: Michael Harms
> Objet: Re:
ical Parc 2" . what do you think is the problem ? i
> attached the log
>
> thanks
>
>
>
> --- En date de : Jeu 29.12.11, Michael Harms
> a écrit :
>
> De: Michael Harms
> Objet: Re: [Freesurfer] aparc.a2009s+aseg problem
&g
; file.
>
> thanks for all
>
> --- En date de : Ven 30.12.11, Michael Harms
> a écrit :
>
> De: Michael Harms
> Objet: Re: [Freesurfer] aparc.a2009s+aseg problem
> À: "LAOUCHEDI MAKHLOUF"
> Cc: freesurfer@nmr.mgh.h
he frontal lobes. Much like you I looked at possible
> >> explanations and a medical physicist and a radiologist I worked with
> >> blamed inaccuracies entirely on chemical shift. Adding control points
> >> at least in temporal lobes generally provided only moderate
&
Hi Clare,
I just posted something you may want to try, detailing some flags/expert
options that we tried that yielded dramatically better temporal lobe
surfaces for us.
cheers,
-MH
On Tue, 2012-01-10 at 15:38 +, Gibbard, Clare wrote:
> Hi Bruce,
>
> Thank you for your quick reply. I instal
#x27;s (which would be my expectation).
This is version 5.1.
thanks,
-MH
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
R
Does FS have a generic binary for natively getting simple stats from mgz
files -- e.g., min, max, range, percentiles, etc? i.e., something
analogous to 'fslstats', but which works directly on mgz files?
thanks,
-MH
--
Michael H
ough the link below.
> >
> > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-August/011695.html
> >
> >
> > Hope it helps.
> >
> > -SK
> >
> > On Fri, Jan 27, 2012 at 12:06 PM, Michael Harms
> > wrote:
> >
&
's.
cheers,
-MH
On Mon, 2012-01-30 at 11:55 -0500, Bruce Fischl wrote:
> I don't think so, but if you write out a list we can put them into
> mri_info (at least the easy ones for now).
>
> On Mon, 30 Jan 2012, Michael
> Harms wrote:
>
> >
> > Does FS
Hi Nick,
I found a small bug in recon-all that prevents the -showedits flag from
working in conjunction with expert-options:
Line 785 in recon-all of v5.1 currently has an extraneous closing
parenthesis:
if (-e $XOptsFile)) then
but should be:
if (-e $XOptsFile) then
Also, I'm puzzled
t; 5 brainmask-OFF 0 64 2550
> 6 brainmask-ON255 26 00
> 7 brain.finalsurf-OFF 0 128 2550
> 8 brain.finalsurfs-ON 255 128 00
> 9 aseg-CHANGED 255 255 1280
>
> N.
&
Hi Nick,
Why does mri_compile_edits (-showedits flag) report edits to
brainmask.mgz (both in the edits.mgz volume and its text output) if no
manual edits were actually performed -- i.e, if brainmask.mgz and
brainmask.auto.mgz are identical?
thanks,
-MH
--
Michael Harms, Ph.D
HI Ed,
I believe that you are referring to the RA measure of anisotropy.
FA is theoretically limited to the range 0-1.
FA's greater than 1 can arise when you have negative estimates of the
eigenvalues, which can arise when using linear least squares estimation
of the tensor.
cheers,
-MH
On Fri,
Hi Jeff,
make_average_subject is just if you want to visualize results on a
surface presenting the average of your own subjects, rather than using
the provided 'fsaverage'. It is not necessary (and not related) to
performing group statistical comparisons per se.
You can use the 'qdec' utility to
Sorry, but no.
On Wed, 2012-02-15 at 13:50 -1000, Jeff Sadino wrote:
> Hello,
>
>
> I have 200 subjects and I am analyzing their cortex in qdec. I have
> several subjects that have poor cortical surfaces on a local basis.
> Is there a way for exclude just one area for just one subject during
Hi Alan,
What version of FS are you using? And did you run from scratch each
time on the original inputs? (Or did you run it on top of the previously
processed version?)
cheers,
-MH
On Tue, 2012-02-21 at 11:04 -0500, Alan Francis wrote:
> Dear Bruce:
>
> I ran 3 brains twice and checked the AS
Francis wrote:
> Hi Michael:
>
>
> We are running 4.3 for this particular study (for continuity) although
> we have 5.1 for other studies. We ran each of them from scratch each
> time.
>
>
> thanks,
>
>
> Alan
>
> On Tue, Feb 21, 2012 at 11:09 AM, Micha
!
-MH
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
Renard Hospital, Room 6604 Tel: 314-747-6173
660 South Eucli
gt; if(SegId == Right_Hippocampus) vol += VoxSize;
> if(SegId == Left_Amygdala) vol += VoxSize;
> if(SegId == Right_Amygdala) vol += VoxSize;
> if(SegId == Left_Accumbens_area) vol += VoxSize;
> if(SegId == Right_Accumbens_area) vol += VoxSize;
> }
> }
>
popped up, but got the message "unknown option -v".
Any idea what is going wrong here? So you can see for yourself, I went
ahead and uploaded the subject's processed data to your FTP server
(110107_L206.tgz)
thanks,
-MH
--
Michael Harms, Ph.D.
--
Hello,
Anyone have a chance to look at this? Should we just forget about
trying to get an accurate lhCorticalWhiteMatterVol value for this
subject?
thanks,
-MH
On Tue, 2012-02-21 at 15:35 -0600, Michael Harms wrote:
> Hi guys,
>
> We have a subject processed with FS v5.1
nd 250?
thanks,
-MH
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
Renard Hospital, Room 6604 Tel: 314-747-6173
250
> #define PRETESS_FILL 215
> #define WM_EDITED_ON_VAL 255
> #define WM_EDITED_OFF_VAL 1
>
> On Tue, 13 Mar 2012,
> Michael Harms wrote:
>
> >
> > Hello,
> > Is there a "key" for what all the various altered voxel values
tial
> >>>> volume that are really WM. So far so good. I think the problem is that
> >>>> the shell for this subject has a hole in it, so the flood leaks into
> >>>> most the interior. When inverted, there are very few voxels left
> >>>>
Hi Jeff,
I personally like the idea of using average thickness as a covariate to
control for a reduction in "whole brain" thickness, and have used that
approach in a paper. If the Abstract that you mentioned indicated that
this is flawed, I'd be curious to know what the reason was...
cheers,
-MH
tical
thickness differences between groups" -- see references [1,4] in our
Reply.
cheers,
-MH
> Hi Michael and others,
>
> maybe it's this one:
>
> http://bjp.rcpsych.org/content/196/5/414.1.long
>
> best,
> -joost
>
>
> On Fri, Mar 23, 2012 at 2:15 AM, Michael
Note that a bug in the calculation of the supratentorial volume was
recently identified (see archives), so if you want to use that measure
you should get the fixed version of mri_segstats and regenerate the
aseg.stats files.
cheers,
-MH
On Fri, 2012-03-30 at 09:12 -0400, Bruce Fischl wrote:
> Hi
For going from MNI to Talairach (or vice-versa) there are also the
transforms that Lancaster derived -- these are citable because they are
published.
See
http://brainmap.org/icbm2tal/
which contains links to the relevant matlab scripts.
cheers,
-MH
On Thu, 2012-05-03 at 12:54 -0400, Douglas N
Hi Gabor,
dcm2nii's default setting for VB17 DICOMs should be to rotate the bvecs
that it returns into the voxel/image axes if you have a modern version of
it.
See item 8 under Sample Datasets of
http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html
for some notes on this issue and a sug
Hi Jorg,
I think the Siemens tfl (MPRAGE) sequence automatically sets the TE to
the lowest possible value consistent with the choosen bandwidth,
gradient mode, and performance of your gradient set.
In all likelihood, I'm guessing that the value was still less than 4 ms
on your system, right?
ch
The last argument of mris_anatomical_stats allows you to specify the
surface to use (pial in your case)
cheers,
-MH
NAME
mris_anatomical_stats
SYNOPSIS
mris_anatomical_stats [options]
[]
On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
> Hi,
>
> I need to know the s
utput of the aparcstats2table for the surface area
> using the pial surface.
>
> Perhaps I am not using the correct command
>
> Thanks for the help.
>
> ines
>
>
> On Fri, May 18, 2012 at 3:41 PM, Michael Harms wrote:
> >
> > The last argument o
ation is stored in ribbon.mgz (and it overrides the aseg
> definition). At some point, we will use the surfaces to directly
> refine the aseg boundaries.
>
> doug
>
>
>
>
> Michael Harms wrote:
> > Hi Chris,
> > Doug, please correct me if I'm wr
Yes, tkmedit shows the image volume in native space. What you are
seeing regarding the corresponding talairach coordinates is consistent
with that.
cheers,
Mike H.
On Tue, 2008-10-07 at 16:54 +0200, Juergen Haenggi wrote:
> Dear FS experts
>
> I posted another email about my confusion with the
Hi John,
To my knowledge, there is no mechanism of manual editing that can force
the pial surface out further (provided that it wasn't a problem of missing
pial tissue due to an overly aggressive skull-stripping).
cheers,
Mike H.
> By the way, here is a matching picture of T1.mgz. Just to show
At some point in early 2008, Doug had created a version of tkregister2
that he graciously provided us, which had --gca-skull and --gca flags,
which greatly simplified the process of confirming the accuracy of
either the talairach_with_skull.lta and talairach.lta transforms
(respectively). However
Hello,
A clarification about this (based on my understanding/reading of the
recon-all code) to help avoid any potential confusion about how the -
clean-bm flag operates more generally:
If you rerun the skull stripping without the -clean-bm flag, recon-all
will preserve any edits previously made
s was observed using QDEC from v4.1.0, although I believe that I've
experienced behavior consistent with this in previous versions as well.
cheers,
Mike H.
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Me
this behavior, so that one can simply rotate the surface without the
scatterplot opening and obscuring the screen?
In the QDEC with previous FS versions (e.g., v4.0.2), one had to do
Control+left mouse to get the scatterplot (which was fine by me)...
cheers,
Mike H.
--
Michael Harms, Ph.D
ing just one of the two continuous
covariates instead, no problem...
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
Renard
Hello,
What is the role of the spatial AR1 that is automatically computed as
part of a QDEC analysis?
thanks,
Mike H.
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School
h to satisfy the necessary inequality
for the specified FDR Rate?
In that case, is the resulting "min" just set to the -log10(p) of the
most significant p-value?
If easy to implement, it would be handy if the output to the terminal
reported the number of vertices with P < than the FDR
ertices
in the two surfaces.
Is there some relationship between these two different definitions of
distortion?
thanks,
Mike H.
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington Universit
matter"? Or both?
thanks for clarifying,
-Mike H.
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
Renard Hospital, Roo
ness-age-
Cor)
cheers,
Mike H.
--
Michael Harms, Ph.D.
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
Renard Hospital, Room 6615 Tel:
y displayed
surface?
Does the 'mri_path2label' binary use the same algorithm?
And, is there any mechanism for taking curvature or sulcal depth into
account? (e.g., connect points along a line of minimum or maximum
curvature change, rather than using geodesic distance)
t
Hi Anthony,
For cortical gray matter volume, compute statistics using the
{lh,rh}.cortex.label file.
i.e.,
mris_anatomical_stats -l lh.cortex.label -f $subj/stats/lh.cortex.stats
$subj lh
That will be roughly similar to computing the volume difference between
the pial and white surfaces, except
Hello Rysia,
I'll add a comment by calling your attention to one statistical
"subtlety". When using a DODS ("separate slopes") model in the presence
of a continuous covariate, and then examining the significance of the
group effect, the interpretation (and results) depend critically on the
meani
> I have a final question: the DOSS with age covaried (and DODS with
> > mean-centred age) comparison between patients and controls is almost
> > identical to a straight (no covariates considered) analysis between
> > patients and controls. Can I necessarily conclud
Nick,
This is great -- you probably also noticed that the version of the
transform used (without or with skull) can make a big difference in the
computed scale factor.
Was variability assessed by comparing eTIV values computed from multiple
MR sessions from the same subject? Or by comparison to
Is there now actually a "mid" surface available in between the white and
pial surfaces? (i.e., akin to Caret)? Or by "area of the mid-point" are
you just referring to the average at each vertex of the ?h.area and ?
h.area.pial "curv" files?
thanks,
-Mike H.
On Tue, 2009-02-17 at 13:17 -0500, Ni
It seems like the issue of whether or not to correct the volume when
mapping to fsaverage is akin to the choice of "modulated" vs. "non-
modulated" VBM, as it's called...
-MH
On Tue, 2009-02-17 at 13:17 -0500, Nick Schmansky wrote:
> Devdutta,
>
> The 'area' of a vertex on a surface in freesurf
Here is a question related to this whole discussion (prompted by what
Darren wrote):
As a practical matter, have you found the localized (i.e., vertex-based)
measures of area and volume to be biologically useful and meaningful?
Have they been used in any published studies? (I don't recall seeing
Hello Nathan,
If you want stats related to the ?h.cortex.label (e.g., average cortical
thickness) you can do the following:
mris_anatomical_stats -l {$hemi}h.cortex.label -f
$id/stats/{$hemi}h.cortex.stats $id {$hemi}h
The resulting ?h.cortex.stats file will contain all the same
measures (e.
The recent paper by Wonderlick et al. (Neuroimage 44:1324-1333, 2009) is
relevant to your situation. They show that differing voxel geometry can
definitely lead to bias in the results (as Bruce noted).
cheers,
Mike H.
On Tue, 2009-03-17 at 21:26 -0600, Jeff Sadino wrote:
> Hi Bruce,
>
> Yes, w
And just to bring this discussion full circle, how does the training set
for the subcortical segmentation relate?? Is the training set (and
associated manual labeling) that is used for the subcortical
segmentation composed of the same 39 subjects used for both the current
spherical template and
As an aside, in a Alzheimer/ elderly cohort of ~250, we had 12 subjects
that we had to exclude for what sounds like a very similar reason -- we
just couldn't get the pial surface in the anterior temporal lobe to
properly encapsulate the gray matter.
-Mike H.
On Fri, 2009-05-15 at 12:24 +1000, Ol
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