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.
---
Conte Center
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 Euclid Ave
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, Ph.D
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, Ph.D
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
Department
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 Psychiatry
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 University School
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
Washington
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.
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 have
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
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
Department
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 Medicine
Department
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, Ph.D
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
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 Psychiatry, Box
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 Mental
of the mri/orig.mgz, which brings with
it blurring (i.e., the same sort of concerns that prompt one to use a
single MPRAGE, rather than the average of two MPRAGEs)
Just curious...
thanks,
-MH
--
Michael Harms, Ph.D.
Conte
Just as an FYI, we also recently encountered the same problem, also
using mri_convert as our DICOM to NIFTI converter. Our work-around was
to just switch to dcm2nii.
Jolinda: I don't know why mri_convert is populating a slice_code entry
for a Siemens MPRAGE acquisition, since an MPRAGE is a
so
that we could always depend on voxel coordinates having some anatomical
meaning, regardless of what crazy slice orientation was prescribed. Not
sure if Doug has some easier work around for you to prevent the rotation.
cheers
Bruce
On Thu, 16 Jun 2011, Michael Harms wrote:
Hi
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).
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 the
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
,
-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
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
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
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 need
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 posts
I at the right track at all?
Best wishes,
Tanja.
On Wed, Nov 2, 2011 at 2:15 PM, Michael Harms mha...@conte.wustl.edu wrote:
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
--
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
--
Michael Harms, Ph.D
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:
/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 Harms, Ph.D
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.
As an attempted
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
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
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
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
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,
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
Parc 2 . what do you think is the problem ? i
attached the log
thanks
--- En date de : Jeu 29.12.11, Michael Harms mha...@conte.wustl.edu
a écrit :
De: Michael Harms mha...@conte.wustl.edu
Objet: Re: [Freesurfer] aparc.a2009s+aseg problem
À: LAOUCHEDI
Harms mha...@conte.wustl.edu
a écrit :
De: Michael Harms mha...@conte.wustl.edu
Objet: Re: [Freesurfer] aparc.a2009s+aseg problem
À: LAOUCHEDI MAKHLOUF laouma...@yahoo.fr
Cc: freesurfer@nmr.mgh.harvard.edu
Date: Vendredi 30 décembre 2011, 16h57
On Wed, Nov 2, 2011 at 4:02 PM, Michael Harms mha...@conte.wustl.edu
wrote:
Hi guys,
We have a sample of 150+ pediatric brains that we pumped through FS 5.1,
and in an easy majority of them the white/pial surface accuracy in the
anterior temporal lobe is poor
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
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
Renard Hospital, Room 6604
it helps.
-SK
On Fri, Jan 27, 2012 at 12:06 PM, Michael Harms mha...@conte.wustl.edu
wrote:
Hi guys,
We are currently trying to fix some errors in the white/pial surfaces
where there are thin white matter strands by using control points, and
are noticing
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
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
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
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
qdec
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 ASEG
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, Michael Harms
mha...@conte.wustl.edu wrote
--
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
;
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;
}
}
}
return(vol);
}
Michael Harms wrote:
Hi Doug or Nick,
I was wondering
-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.
Conte Center
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 in which
--
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
#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 in wm.mgz
represent? For example, I know that if you manually add a voxel, it
gets set to 255
a solution
to this, so I just wanted to give you a heads up. One possible
work-around is to make an edit that causes the surface to change.
It is
probably the case that even a small change causes the hole to fill and
everything works out.
doug
Michael Harms wrote:
Hello,
Anyone
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
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 Harms
mha...@conte.wustl.eduwrote:
Hi Jeff,
I
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
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
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?
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] subjectname hemi
[surfacename]
On Fri, 2012-05-18 at 15:18 +0100, Inês Violante wrote:
Hi,
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 mha...@conte.wustl.edu wrote:
The last argument of mris_anatomical_stats allows you to specify the
surface to use (pial in your case)
cheers
Here is an approach that will be easier, and involves less back and
forth between the surface and volume-based streams (and thus should be
more accurate): Just use 'mris_volume' to get the volume of everything
enclosed by the pial surface, which if I recall correctly will include
the lateral
rh.pial): part of two important brain structures, amygdala
and
hippocampus, is not enclosed in the pial surface. Is there a way to
resolve
this issue?
Thanks,
Xiangchuan
-Original Message-
From: Michael Harms [mailto:mha...@conte.wustl.edu]
Sent: Friday, January 08, 2010 15:55
To: Bruce Fischl
Cc: Michael Harms; Xiangchuan Chen; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] ICV/brain volume
Or you can fix the talairach transform and get the icv the standart way.
When dividing by total brain vol, you undo atrophy. That's why icv is
used.
Martin
On Jan 9
Hello,
What do geometry differences represent in the output of mri_diff?
i.e., What do the numbers in the following output from mri_diff
represent?
Volumes differ in geometry 1 4 0.15
Volumes differ in geometry 2 1 0.00
thanks,
-Mike H.
--
Michael Harms, Ph.D
axes...
MRIreorder: incorrect dst width
error reordering axes
I've checked the archives, and read through the mri_convert help, but
just can't seem to figure out if reordering from one orientation to
another (without resampling) is possible using mri_convert.
thanks,
-MH
--
Michael Harms
) in combination with --out_orientation. --out_orientation
should not resample.
doug
Michael Harms wrote:
Hello Doug,
Is it possible using mri_convert to just reorder the way in which the
data is stored, without any resampling of the actual voxel values?
i.e., I have Siemen's MPRAGE
,
-MH
On Fri, 2010-02-05 at 14:30 -0500, Douglas N Greve wrote:
Michael Harms wrote:
Hi Doug,
Is --reorder4 a new feature in one of the more recent releases?
(Currently, I'm using mri_convert from v4.1.0, and I don't see a --
reorder4 flag).
Yes, it is. It is actually only
And for the comparison to be appropriate, you further have to make sure
that you are using the exact same main and interaction terms in SPSS as
are being used in QDEC. The mere presence of interaction terms in a model
can have big effects on the significance (or lack thereof) of the main
Hi Joost,
If you want to control for possible global differences in thickness,
then an appropriate covariate of some sort is need. To me, a logical
covariate for a thickness analysis is the mean cortical thickness, as
this is more directly related to the measure of interest than something
like
Hi Massieh,
There were some posts related to this a while back.
If I recall correctly, the vertex-wise area measure (and likewise the
vertex-wise volume measure) is highly dependent on the local mesh
triangulation, and thus is not really a meaningful variable from a
biological perspective. So,
The data in aparc.stats contain surface area, gray matter volume, and
average thickness for whole regions, and are not intended for surface
display. If you want to analyze those regional values use
'aparcstats2table' and then import the data into your preferred
statistical package for further
Hi Kelly,
See also these threads where I advocate using mean cortical thickness as
an appropriate covariate for a thickness analysis:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11987.html
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13459.html
Mean cortical
Sorry, my initial reply went to just to Laura, and not the list.
-MH
Forwarded Message
From: Laura Verga ildestinodiunombre...@gmail.com
To: Michael Harms mha...@conte.wustl.edu
Subject: Re: [Freesurfer] Different slices number for control group
Date: Tue, 8 Jun 2010 17:13:14
I'll help Bruce out here :)
See
Panizzon et al, Cerebral Cortex, 2009, 19:2728-35
http://www.ncbi.nlm.nih.gov/pubmed/19299253
and
Winkler et al, Neuroimage, 2009 (in press)
http://www.ncbi.nlm.nih.gov/pubmed/20006715
cheers,
-MH
On Wed, 2010-06-23 at 17:06 -0400, Matthew Ku wrote:
Dear
DODS: Different offset, different slope; This models (potentially)
differing slopes against the covar and allows you to check for a group-
by-covar interaction
DOSS: Different offset, same slope; This assumes that both groups have
the exact same slope against the covar (but differing
'dcm2nii' would be another DICOM to nifti converter to try.
good luck,
-MH
On Thu, 2010-09-02 at 17:54 -0400, Douglas N Greve wrote:
Sorry, I don't have an easy solution. I think philips does something
that breaks our 3rd party dicom reader, so there's not an easy way for
me to fix it.
The 'fsledithd' utility (of FSL) can be used to edit the number of
frames (as well as a host of other fields) in a Nifti file.
cheers,
-MH
On Wed, 2010-09-22 at 09:02 -0400, Douglas Greve wrote:
Hi Tommi, that's going to be a problem because all the tools look at
the number of frames to
Jeff,
Posting this back to the list so that others can see your reply.
cheers,
-MH
Forwarded Message
From: Jeff Sadino jsadino.que...@gmail.com
To: Michael Harms mha...@conte.wustl.edu
Subject: Re: [Freesurfer] Surface Area and Cortical Volume
Date: Wed, 29 Sep 2010 17:29:45
usage: mris_anatomical_stats [options] subject name hemi [surface
name]
So, just end your command with the word 'pial'.
cheers,
-MH
On Thu, 2010-09-30 at 17:09 +, Zhang, Yuning wrote:
Hi,experts,
I am trying to get the total surface area of pial surface using the
following
at 18:23 +, Zhang, Yuning wrote:
Does the surface area calculated here include the non-cortical area along the
medial wall ?
Thank you very much.
From: Michael Harms [mha...@conte.wustl.edu]
Sent: Thursday, September 30, 2010 5:24 PM
Hello,
Deniz mentioned T2-SPACE rather than the multi-echo MPRAGE (memprage).
Can you do something similar using the 3D T2-SPACE?
cheers,
-MH
Hi Deniz,
yes, it should be in the mris_make_surfaces of that version. You need to
run it with -dura memprage_echo%d.mgz 4
where 4 is the # of
Hi Jay,
Permutation testing will give the most accurate results.
cheers,
-MH
Hi Experts,
Which option is best to use: mc-z or perm?
I have read that perm gives more accurate results than mc-z, as it uses
the actual data rather than fake data to estimate the null distribution.
When I use
on the use of permutation,
unless there is some tutorial I haven't found.
How many permutations should one run?
Any other helpful hints?
Cheers...J
On Mon Oct 11 9:05 , Michael Harms sent:
Hi Jay,
Permutation testing will give the most accurate results
If you're referring to VERTEX-WISE analyses of area and volume, there
are issues with the interpretability of those measures.
Don Hagler has posted on this several times.
For example, most recently see:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15205.html
cheers,
-MH
On
Hi Mira,
If the map you provided is of uncorrected p-values at say p=0.05, then
you appear to have just a couple small regions of group differences, so
it isn't surprising that after FDR nothing would survive.
The result is what it is, and unless you had specific a priori
hypotheses regarding
Hi Ed,
Is there a distinction in FreeSurfer between cortical and
subcortical white matter? I thought that white matter was simply
white matter...
You wrote that the white matter values in aseg.stats are identical to
the output of mris_wm_volume, which is exactly what I would expect.
You do NOT
thickness by its proportion of the total surface area.
cheers,
-MH
On Thu, 2010-12-16 at 11:57 -0600, Michael Harms wrote:
Yes, I think that using average cortical thickness is a reasonable
covariate to use in thickness analyses. And total cortical surface area
likewise if you are analyzing
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