, Donald N.
*Sent:* Thursday, February 11, 2021 1:16 PM
*To:* Freesurfer support list
*Subject:* Re: [Freesurfer] cortical thickness values for each point
in a ctx label file
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Thanks for getting back so quickly, Doug.
Creating pial label files will enable me
between the white and pial vertex with the same label as a
cortical thickness?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Krieger, Donald N.
Sent: Thursday, February 11, 2021 1:16 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] cortical thickness values for each point in a
tical thickness.
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Douglas N. Greve
Sent: Thursday, February 11, 2021 1:04 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] cortical thickness values for each point in a ctx
label file
Not sure what you mean as the pial file
Not sure what you mean as the pial files are surfaces not labels or
annotations. If you want to extract labels from the annotations you can
use mri_annotation2label
On 2/11/2021 12:55 PM, Krieger, Donald N. wrote:
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Dear freesurfer group,
I wish to measure
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Dear freesurfer group,
I wish to measure a cortical thickness value for each entry in a label file,
e.g. SubNo/wmparc/ctx-lh-lateraloccipital_1011.label .
Is there a function in the freesurfer distribution which includes this
capability?
Also, is the
Best wishes,
> AIcha
>
> *Van:* freesurfer-boun...@nmr.mgh.harvard.edu
> namens Greve, Douglas
> N.,Ph.D.
> *Verzonden:* donderdag 31 oktober 2019 19:16
> *Aan:* freesurfer@nmr.mgh.harvard.edu
> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a verte
31 oktober 2019 19:16
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Cortical thickness values on a vertex base level
You can run mri_surfcluster with your fdr threshold as the --thmin
value. This will output cluster number (ocn) map. This will assign the
cluster number to a
>
> ?
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> 0.001
>
> Right parahippocampal gyrus
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>
>
> ?
>
>
>
> ?
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>
>
> ?
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> 0.002
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>
> Does this clarify my question?
>
> Best wishes,
> Aicha
>
>
, Douglas N.,Ph.D.
Verzonden: donderdag 31 oktober 2019 16:25
Aan: freesurfer@nmr.mgh.harvard.edu
Onderwerp: Re: [Freesurfer] Cortical thickness values on a vertex base level
I'm not sure what you mean. Do you want the mean thickness of a cluster
and/or its surface area?
On 10/30/19 6:
I'm not sure what you mean. Do you want the mean thickness of a cluster
and/or its surface area?
On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote:
>
> External Email - Use Caution
>
> Dear developers,
>
> For a case-control study we are comparing the cortical thickness and
> cortical surface
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Dear developers,
For a case-control study we are comparing the cortical thickness and cortical
surface area on a vertex-base level, for which we found significant differences
throughout the brain.
Is it possible that, in addition to the significance
sure, you need to rerun mris_thickness with -max where N is the
threshold you want to use (making it big enough and nothing will get
thresholded)
On Fri, 5 Apr
2019, Gonzalo Rojas Costa wrote:
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Hi:
How can I get cortical thickness surface image
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Hi:
How can I get cortical thickness surface image with values more than 5 mm?
Sincerely
Gonzalo Rojas Costa
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probably easiest to use matlab. see
FREESURFER_HOME/matlab/read_annotation.m, which has an example
On 4/5/2019 11:29 AM, Gonzalo Rojas Costa wrote:
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>
> Hi:
>
>How can I get the different values of cortical thickness in the
> insula? Not the mean and SD.
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Hi:
How can I get the different values of cortical thickness in the
insula? Not the mean and SD...
Sincerely
Gonzalo Rojas Costa
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THank you so much for your help!
Le lun. 18 mars 2019 à 16:32, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :
> The vertices chosen for the cluster depend only on the cluster forming
> threshold (CFT). Once that is chosen, the vertices in
The vertices chosen for the cluster depend only on the cluster forming
threshold (CFT). Once that is chosen, the vertices in the cluster are fixed.
The permutation judges how likely the cluster as a whole would be seen by
chance. There are other ways to do permutation, but this is the way we do
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Ok, well then I do not understand the purpose of the permutation testing if
the number of permutation would not change the size of the clusters. What
is it doing if not refining what vertices are significant? Perhaps I am
just missing a key idea.
Best,
The size of the cluster is not going to be affected by the number of
iterations (only by the threshold). Why would you think that the cluster
size is affected by the number of iterations?
On 3/14/19 5:45 AM, Giuliana Klencklen wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> A
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Hi Douglas,
According to your suggestion, I used the permutation simulation approach. I
chose a cluster forming threshold set at 0.05 and explored how the number
of iterations effects the data. For example, I used this command for 1,000
iterations:
mr
You can make the bonferroni correction from of mri_glmfit-sim the same as qdec
by not including --2spaces (the bonferroni correction in qdec is actually 1,
not 0). Also, if you want to use such a low cluster forming threshold
(1.3=p<.05), then you should use permutation and not MC (MC is not val
This can happen if the label is small and/or you've used a lot of smoothing. It
is better to do this kind of thing in fsaverage space rather than moving the
labels back to the individual space. If you've run mri_glmfit-sim, then it
should have created a table file (something.y.ocn.dat). This fi
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Hi FS experts,
I did group-level, surface-based, vertex-wise analysis for baseline and
longitudinal data. I used Qdec and do the same work with the fsgd version
(mri_glmfit-sim command) to double-check the data.
I created label files with tksurfer for
Look in the QDEC output folder. In each contrast folder, you should see
a summary file. I think the info you want is in that file.
doug
On 02/11/2014 03:08 PM, Natasha Haris wrote:
> Dear Freesurfers,
>
> Is there anyway to get a compiled list of all the significant clusters
> with information
Dear Freesurfers,
Is there anyway to get a compiled list of all the significant clusters with
information about their maximum thickness value, x/y/z vertices, t
statistic etc on QDEC? Does this have anything to do with a SaveClusterFile
command? All of this information must be stored somewhere for
your interpretation is correct. Here's the matlab code
cd glmdir/yourcontrast
X = load('../Xg.dat');
C = load('C.dat');
y = load('cache.th20.abs.y.ocn.dat');
[beta rvar] = fast_glmfit(y,X);
[F pvalues] = fast_fratio(beta,X,rvar,C);
pvalues will be an array with the pvalue for each cluster
make s
Hi Doug,
thank you for your reply. It is unusual as I also get a significant result
in SPSS for a non-significant cluster in mri-glmfit. Just to make sure I am
doing things correctly - I am interpreting each column in the xxx.y.ocn.dat
file as a cluster in the xxx.sig.cluster.summary file (in nume
That is the right file to use, and one would expect to see significant
results. Are you sure you are using exactly the same model? If you have
matlab, I can give you some code to do the analysis using the exact
model that mri_glmfit uses.
doug
On 12/9/13 10:43 PM, Sinead Kelly wrote:
D
Dear Freesurfer users,
I have just ran mri-glmfit on cortical thickness data and corrected for
multiple comparisons using Monte Carlo Simulation. I have significant
clusters (cwp < .05), however, when I analyse the average thickness
measures from the xxx.y.ocn.dat file in SPSS, there are no signif
Hi Gonzalo, we don't have anything that will do this easily. If you have
matlab you can load in the annot with read_annotation.m, read in the
thickness with read_curv.m, then extract the values you need from that.
doug
Gonzalo Rojas Costa wrote:
> Hi:
>
>In rh.aparc.a2009s.stats file, appear
Hi Gonzalo
I would do it in matlab, with read_curv.m and read_annotation.m
cheers
Bruce
On Wed, 23
Nov 2011, Gonzalo Rojas Costa wrote:
> Hi:
>
> In rh.aparc.a2009s.stats file, appears the average cortical thickness
> (ThickAvg) value for frontal middle gyrus (G_front_middle): how can I
> get
Hi:
In rh.aparc.a2009s.stats file, appears the average cortical thickness
(ThickAvg) value for frontal middle gyrus (G_front_middle): how can I
get the values of the cortical thickness in that gyrus (for example),
not the average value ?...
Sincerely,
Gonzalo Rojas Costa
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