External Email - Use Caution
Dear TRACULA experts
I would like to correct my statement in my former email.
The "Error: domainname: Command not found. Too many )’s.“ also occurs if using
TRACULA in FS 7.1.1, but trac-all does not stop (in contrast to FS 7.2.0), and
therefore I wr
Hi John, I would recommend that you use permutation. See
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
In terms of the threshold, "not going higher than .01" means using
between 0 and .01 (eg, don't use .05). For permutation, you can use
whatever thershold you
External Email - Use Caution
Hi Dr Greve,
I would like to correct surface based analyses of PET data for multiple
comparisons. I ran group comparisons in three spaces. left and right
hemispheres and subcortical.
I used the method --cache in mri_glmfit-sim to correct the analyses
you posted soon in all cases.
Many thanks for your help,
Maxime
De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Diamond, Bram Ryder
Envoyé : 16 octobre 2018 14:54
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
Pos
16, 2018 2:48:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
External Email - Use Caution
Hi Bram,
I modified the label of the lateral ventricules because they were mislabeled
too (Freesurfer_S043_test). I didn't change the label of th
urfer-boun...@nmr.mgh.harvard.edu de la part de Diamond, Bram Ryder
Envoyé : 16 octobre 2018 14:36
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
Hi Maxime,
What did you edit in the
aseg? It looks like the CC_* have been mislabeled.
: [Freesurfer] Correction Needed for the Midline
External Email - Use Caution
Sorry. Here are the good links :
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=1maf5ah0hw0
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=abmzg2jvk9t
Maxime
On Oct 16, 2018, at 2:22 PM, Maxime Perron
mailto:maxime.perro
me Perron <maxime.perro...@ulaval.ca>
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
External
Email - Use Caution
Hi Bram,
Thank you very much for the reply, I'm glad yo
e.perro...@ulaval.ca>
Sent: Friday, October 12, 2018 11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
External
Email - Use Caution
Hi Bram,
Thank you very much for the reply, I'm glad you'll ha
11:17:07 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
External Email - Use Caution
Hi Bram,
Thank you very much for the reply, I'm glad you'll have some time to look at
the issue. Please don't hesitate to contact me should
s,
Maxime
De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Diamond, Bram Ryder
Envoyé : 11 octobre 2018 13:18
À : Freesurfer support list
Objet : Re: [Freesurfer] Correction Needed for the Midline
Hi Maxime,
I'll take a look at your data and the issue you're ha
Freesurfer support list
Subject: Re: [Freesurfer] Correction Needed for the Midline
External Email - Use Caution
Hi Freesurfer Experts,
About 2 weeks ago, I sent a question about the midline correction but have not
yet received a feedback. I am wondering if someone had time to check my data
External Email - Use Caution
Hi Freesurfer Experts,
About 2 weeks ago, I sent a question about the midline correction but have not
yet received a feedback. I am wondering if someone had time to check my data or
has an idea on how to correct the bad midline.
I tried to correct
On 6/6/18 7:14 AM, Yann Quidé wrote:
> External Email - Use Caution
>
> Dear all,
>
> Using Freesurfer 5.3, I would like to limit my whole-brain analyses to a mask
> I already defined (ie, small volume correction-like analysis).
> To correct for multiple comparisons, I want to use the m
External Email - Use Caution
Dear all,
Using Freesurfer 5.3, I would like to limit my whole-brain analyses to a mask I
already defined (ie, small volume correction-like analysis).
To correct for multiple comparisons, I want to use the mri_glmfit-sim option.
As I am looking withi
You can try permutation, though it is often more constraining than those
other two options. To do this, you'll need to run mri_glmfit-sim from
the command line using the --sim perm option. Run it with --help to get
examples
On 8/7/15 6:59 AM, pablo najt wrote:
Dear FS experts,
I have a questi
(PNL)
> Brigham and Women's Hospital
>
>
>
> Message: 6
> Date: Tue, 14 Jul 2015 11:33:57 -0400 (EDT)
> From: Bruce Fischl
> Subject: Re: [Freesurfer] Correction with white-matter-points
> To: Freesurfer support list
> Message-ID:
>
> Content-Type: TEX
.
Psychiatry and Neuroimaging Laboratory (PNL)
Brigham and Women's Hospital
Message: 6
Date: Tue, 14 Jul 2015 11:33:57 -0400 (EDT)
From: Bruce Fischl
Subject: Re: [Freesurfer] Correction with white-matter-points
To: Freesurfer support list
Message-ID:
Content-Type: TEXT/
Hi Pawel
does this happen in both versions? If so, upload a bad subject and we
will take a look
cheers
Bruce
On Tue, 14 Jul 2015, Wrobel, Pawel wrote:
> Dear FreeSurfer Team!
>
> We have a question concerning corrections with white-matter-points.
>
> We are currently working on a T1 data set. A
Dear FreeSurfer Team!
We have a question concerning corrections with white-matter-points.
We are currently working on a T1 data set. After performing
Freesurfer-Segmentations several days ago, we corrected the intensity
normalization in small regions (e.g. Gyrus temporalis superior) with WM-po
] Im Auftrag von clelia pellicano
Gesendet: Freitag, 3. Juli 2015 18:55
An: Freesurfer support list
Betreff: Re: [Freesurfer] correction for field dishomogeneity
I did it. Thank you very much.
C
Il giorno 03/lug/2015 18:51, "Bruce Fischl"
mailto:fis...@nmr.mgh.harvard.edu>> ha s
I did it. Thank you very much.
C
Il giorno 03/lug/2015 18:51, "Bruce Fischl" ha
scritto:
> not sure. Did you use recon-all? If so, then you did use
> "the appropriate pipeline provided by freesurfer"
> On Fri, 3 Jul
> 2015, clelia pellicano wrote:
>
> >
> > Hi Bruce,
> >
> > thank you for your r
not sure. Did you use recon-all? If so, then you did use
"the appropriate pipeline provided by freesurfer"
On Fri, 3 Jul
2015, clelia pellicano wrote:
>
> Hi Bruce,
>
> thank you for your reply. Do you have any idea about what they could mean
> saying "without using the appropriate pipeline pro
Hi Bruce,
thank you for your reply. Do you have any idea about what they could mean
saying "without using the appropriate pipeline provided by freesurfer"?
Thanks
BW
C
Il giorno 03/lug/2015 15:32, "Bruce Fischl" ha
scritto:
> Hi Clelia
>
> yes, we correct for field inhomogeneity. Presumably th
Hi Clelia
yes, we correct for field inhomogeneity. Presumably they mean the B1
receive field, which is what is typically meant in structurals. If they
mean B0, we don't typically correct (nor do most people for structural
imaging - this is more of an issue for diffusion and functional MRI).
ch
Dear experts,
I was wondering how freesurfer corrects for field dishomogeneity.
As long as I know, it's automatically done by the software .
My concern is because a reviewer has made this comment (please find it
below):
"Authors used an old 3 T MRI without using the appropriate pipeline
provided
I don't know what you mean. can you elaborate?
On 04/30/2015 06:41 PM, Ghazal Kiani wrote:
> Hi,
>
> We were wondering when viewing group data on the inflated brain using
> FreeSurfer, if FreeSurfer applies any correction and how we c an
> control the correction value?
>
> Thanks,
> Ghazal
>
>
>
Hi,
We were wondering when viewing group data on the inflated brain using
FreeSurfer, if FreeSurfer applies any correction and how we c an control
the correction value?
Thanks,
Ghazal
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://ma
Here is the proper link.
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/fsaverage.tar.gz
>> Bruce,
>>
>> By "symlink from your /mnt/hgfs/mydata/fsaverage to
>> /usr/local/freesurfer/subjects/fsaverage" you mean "ln -s
>> /mnt/hgfs/mydata/fsaverage /usr/local/
Hi Anna, you can use FDR (ie, Ben-Hoc). You can also use gaussian random
fields (GRF) to do voxel-wise or cluster-wise stats. In our
implementation, we actually use a monte carlo simulation. Run mri_glmfit
and spec the label you want to constrain your results to (--label), then
run mri_glmfit-
You can use FDR correction.
On 08/14/2013 08:16 AM, Anita van Loenhoud wrote:
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 us
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
Great, thank you for your help!
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 5:39 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error
___
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis
> Sent: Thursday, May 30, 2013 4:50 PM
> To: Douglas N Greve
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Cor
Fotiadis, Panagiotis
Sent: Thursday, May 30, 2013 4:50 PM
To: Douglas N Greve
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error
Great, thanks!
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent
Great, thanks!
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 4:47 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error
yes
On 05/30/2013 04
4:29 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> This is a problem with version 5.0 when you set the clusterwise pvalue
> to something close to 1. I re-rand it with .995 and it work. This is
>
the --2spaces flag does not
apply)?
Best,
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 4:29 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple
gt; Panos
>
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, May 30, 2013 4:10 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> hmm, can't tell from
Definitely, just uploaded it!
Panos
From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 4:10 PM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error
hmm
mail!
>
> Best,
> Panos
>
>
>
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, May 30, 2013 2:55 PM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for
ehalf of Douglas Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, May 27, 2013 10:08 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Correction for multiple comparisons error
>
> what is your cmd line? What version of FS are you using? What is the
>
: Douglas Greve; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Correction for multiple comparisons error
Hi Doug,
1) My cmd line is:
mri_glmfit --y lh.Diseased_gender_age.thickness.10B.mgh --fsgd
Diseased_gender_age.fsgd dods --C CAA_male-vs-female_age_slope.mtx --C
CAA_male-vs
what is your cmd line? What version of FS are you using? What is the
full terminal output?
doug
On 5/25/13 6:55 PM, Fotiadis, Panagiotis wrote:
> Hi!
>
> I have been running the mri_glmfit-sim command to do the correction for
> multiple comparisons for my group analysis and for some voxel-based
Hi!
I have been running the mri_glmfit-sim command to do the correction for
multiple comparisons for my group analysis and for some voxel-based thresholds
(not all) there is an error that comes up when reading the colortable from the
annotation file:
reading colortable from annotation file...
Subject: Re: [Freesurfer] Correction for multiple comparisons question
On 05/13/2013 11:11 AM, Fotiadis, Panagiotis wrote:
> Thanks for the clarifications, Doug!
>
> 1) I am using FS stable version 5.0.0, so I'm assuming that the --2spaces
> flag has probably been implemented for t
r.
>
> Thanks again for all your help.
> Panos
>
>
>
>
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, May 13, 2013 12:22
du
Subject: Re: [Freesurfer] Correction for multiple comparisons question
Hi Panagiotis,
On 5/12/13 9:32 PM, Fotiadis, Panagiotis wrote:
> Hi Freesurfer experts,
>
> I was wondering about three things concerning the use of the mri_glmfit-sim
> command:
>
> 1) I tried running i
Hi Panagiotis,
On 5/12/13 9:32 PM, Fotiadis, Panagiotis wrote:
> Hi Freesurfer experts,
>
> I was wondering about three things concerning the use of the mri_glmfit-sim
> command:
>
> 1) I tried running it with the --2spaces flag in order to Bonferroni correct
> over the two hemispheres but it te
Hi Freesurfer experts,
I was wondering about three things concerning the use of the mri_glmfit-sim
command:
1) I tried running it with the --2spaces flag in order to Bonferroni correct
over the two hemispheres but it tells me that the specific flag is not
recognized. Is there another way to co
Hi Stefano
I believe it's the offset of the center of the color scale. So for
example in the red/positive blue/negative one, the cross-over doesn't
have to be at 0
cheers
Bruce
On Fri, 22 Mar 2013, std...@virgilio.it wrote:
Hi list,
I have a question, probably trivial, on OFFSET in qdec GU
Hi list,
I have a question, probably trivial, on OFFSET in qdec GUI. What's this? And
what I can do using it?
Stefano --- Begin Message ---
Hi list,
I have a question, probably trivial, on onset in qdec GUI. What's this? And
what I can do using it?
Stefano
___
We'd like to obtain total cerebellar volumes. There are errors within the
cerebellar segmentation as revealed in the aseg.mgz file. Is there a
method Is there a method to manually edit the cerebellar segmentation?
Thank You,
Rachel Steinhorn
___
Freesu
No, that looks correct.
doug
On 06/27/2012 12:05 PM, Jörg Pfannmöller wrote:
> P.S.:I executed the following sequence to achieve the first level analysis
> with a correct registration.
>
> preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage
> lhrh -mni305 -fwhm 0 -per-run
P.S.:I executed the following sequence to achieve the first level analysis with
a correct registration.
preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage
lhrh -mni305 -fwhm 0 -per-run
register-sess -s session_id -fsd bold -per-run -init-header
preproc-sess -s session
You should run preproc-sess again to make sure that all the files that
need to be updated after the registration are properly updated. This
should not change the registration -- it should just look at the time
stamps of the files and update any that need updating. However, if the
files earlie
Dear Doug,
I have tested the various options of register-sess. The result was a succesful
registration of the functional
to the anatomical image. This registration with register-sess is performed
after preproc-sess failed to achieve
a proper registration. The register.dof6.dat file is updated
That is just the name. It must be different for each call so that the
files are not overwritten. It does not have to match the sign, but it
will be less confusing if it does.
doug
On 06/18/2012 12:38 PM, mdkrue...@uwalumni.com wrote:
> Freesurfers-
>
> When choosing the simulation type does the
Freesurfers-
When choosing the simulation type does the ending have to match the sim
sign? for instance i see examples with
--sim mc-z 1 3 mc-z.pos.3 --sim sign pos
or
--sim mc-z 1 3 mc-z.neg.3 --sim sign neg
I guess what i am asking is what does the first sign (in the mc-z.(SIGN).3
me
Here are a couple
Hayasaka 2003 Neuroimage
Hagler 2006 Neuroimage
The Hagler reg is specifically for surfaces
doug
On 06/14/2012 03:13 AM, Marie Schneider wrote:
> Thanks very much for your help and your advice.
>
> Are there any publications which describe the principles of the Monte
> Carlo si
Thanks very much for your help and your advice.
Are there any publications which describe the principles of the Monte Carlo
simulation when used for correction of multiple comparisons?
-Marie
2012/6/12 Douglas N Greve
> yes, though I would probably do it outside of qdec as it can take a whi
doug-
thanks for all the help on this. another quick question:
when choosing the simulation type does the ending have to match the sim
sign? for instance i see examples with
--sim mc-z 1 3 mc-z.pos.3 --sim sign pos
or
--sim mc-z 1 3 mc-z.neg.3 --sim sign neg
I guess what i am asking i
If you run it with --help, you will see this. let me know if this is not
clear.
6. Select the threshold sign (--sim-sign). This is the sign of the
threshold used to create the clusters for cluster-wise correction
of multiple comparisons. Options are abs (unsigned), pos
(positive), and
Freesurfers-
When correcting for multiple comparisons using:
mri_glmfit-sim \
--glmdir lh.gender_age.glmdir \
--sim mc-z 5 4 mc-z.negative \
--sim-sign neg --cwpvalthresh 0.4\
--overwrite
What does the sign mean (ie - the neg, pos, abs). Also for the mc-z
simulation type do we no longer
It includes them in the model as regressors, so, for example, the Group
1 mean (beta) is computed simultaneously with the slope. Think of a
bunch of dots that form a line. You fit it to y = x*m + y0. y0 is the
intercept (ie, expected y at x=0). In your case you have two y0's (one
for each group
Hey all-
This may be a simple question to answer, but in an analysis looking at say
cortical thickness between Group 1 and Group 2 with say 3 continues
variables (age, anxiety, IQ) there would be a contrast matrix of 1 -1 0 0 0
. How does free surfer correctly remove the effects of the continues
v
yes, though I would probably do it outside of qdec as it can take a
while (hours or days)
On 06/12/2012 08:03 AM, Marie Schneider wrote:
> Thank you very much for your answer.
>
> Are 10 000 iterations also used when I am running a Monte Carlo
> simulation in qdec?
>
> Thanks, Marie
>
> 2012/6/9
Thank you very much for your answer.
Are 10 000 iterations also used when I am running a Monte Carlo simulation
in qdec?
Thanks, Marie
2012/6/9 Douglas N Greve
> they are two different correction schemes. If they gave the same answer,
> then it would not make sense to have both. the monte carl
they are two different correction schemes. If they gave the same answer,
then it would not make sense to have both. the monte carlo tries to
compute the probability of a cluster of the given size under the null
hypothesis. FDR controls for the number of false positives relative to
the total num
Dear FreeSurfer experts,
I have some questions about corrections for multiple comparisons in
FreeSurfer. I have two samples, one consisting of two groups and one
consisting of three groups.
I do the comparison with the sample of two groups in qdec. Correcting for
multiple comparisons, I get a sig
You can't do directly from preproc-sess, but you can do it from
register-sess if you have an additional whole brain acquisition in the
same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc)
as long as it is whole brain. If your anatomical was acquired in the
same session, then
Dear Doug,
I am having a partial field of view and a full brain scan. How can I integrate
the results in the preproc-sess sequence in order to complete the preprocessing
correctly?
Cheers pfannmoe
On Mon, 04 Jun 2012 11:42:32 -0400
Douglas N Greve wrote:
> You can try running register-sess
You can try running register-sess outside of preproc-sess, something like
register-sess -s session -fsd bold -per-run -init-spm
before you do that, you need to have spm5 and matlab, and change your
matlab/startup.m to add the spm5 path
path(path,'/usr/pubsw/common/spm/spm5');
doug
ps. Is this w
Dear Doug,
indeed the initialization fails. I was able to initiate bbregister manually,
giving a good registration result. Can you give me a hint how to
modify the registration and keeping the preproc-sess stream intact?
Cheers
pfannmoe
___
Fr
They rely on the registration. What is failing? It is usually the
initialization that fails. If you're using FSL, you can try using the
SPM registration (though it's a little trickier to set up).
doug
On 06/04/2012 05:20 AM, Jörg Pfannmöller wrote:
> Dear freesurfers,
>
> I have a simple questio
Dear freesurfers,
I have a simple question concerning the freesurfer 5.1 FSFAST preprocessing. In
the preprocessing the functional images are registered to the anatomical ones
using bbregister. This is the 3rd in a series of 8 preprocessing steps. If the
preproc-sess registration fails it is po
Hi Viola,
there's some detailed info if you run
mri_glmfit-sim --help
mri_glmfit --help
mri_glmfit-sim runs mri_glmfit.
When you use mri_glmfit-sim with the --cache option, it uses simulations
that are based on 10,000 iterations.
Here are some slides that give more detail
http://surfer.nmr.mgh
Dear Freesurfers,
could you please give me detailed information about the Bonferroni or
clusterwise correction we can do in Freesurfer? How much iterations? Is that
cluster- oder voxelwise? Is there anywhere a detailed description about the
correction options?
Best regards,
Viola
_
right?
Please advise.
Thank you.
Antonella
From: Douglas N Greve
To: Antonella Kis
Cc: "freesurfer@nmr.mgh.harvard.edu"
Sent: Tuesday, August 23, 2011 4:33 PM
Subject: Re: [Freesurfer] correction for multiple comparisons
Yes, that is correct, you sh
Yes, that is correct, you should use .025 if you are correcting for both
hemispheres.
doug
Antonella Kis wrote:
>
> Hi Doug,
>
> I would like to run the correction for multiple comparisons. I know
> glmfit-sim corrects for multiple comparisons. My question is:
>
> the corrections for multiple co
Hi Doug,
I would like to run the correction for multiple comparisons. I know glmfit-sim
corrects for multiple comparisons. My question is:
the corrections for multiple comparisons will be done while running
mri_glmfit-sim \
--glmdir rh.age.glmdir \
--cache 2 neg \
--overwrite
or I need t
Hi Antonella,
it's hard to say just looking at a single slice. Why do you think you
need to correct it?
Bruce
On Wed, 3 Aug 2011, Antonella Kis wrote:
Hi Bruce,
I will be very grateful if you or someone else can give me an advise if I
should do some corrections for the optic nerve in the f
Hi,
I have two questions regarding ICV correction for total hippocampal volume
(from aseg.stats) and for hippocampal subfield volumes.
1) Total hippocampal volume: I am using the mri_label_volume script that
uses the atlas normalization factor as an estimate for total ICV two
T1-weighted scans (T
Yes, we use simulation-based. Look at the group analysis tutorial. You
will have to run mri_glmfit-sim (or run the script that QDEC creates).
doug
Olivier Colliot wrote:
> Hi Freesurfers,
>
> I was wondering if there exists a procedure in Freesurfer to have
> corrections for multiple comparison
Hi Freesurfers,
I was wondering if there exists a procedure in Freesurfer to have
corrections for multiple comparisons at the cluster level (as in SPM for
example).
Many thanks
Olivier
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https:
Gonzalo,
It's difficult to tell on just this one slice and I'm more used to viewing
scans in the coronal plane. If you turn the aseg.mgz on, is that part of
the subcortical gm? If not and you believe it to be cortical gm, let me
know and we'll take a look.
Allison
--
On Wed, 24 Feb 2010, Gon
It looks like there might be some wm that is not labeled as wm. If you fix
this first (by adding wm to the wm.mgz or adding control points if it is
an intensity problem), that should fix the pial surface.
--
On Wed, 24 Feb 2010, Gonzalo Rojas wrote:
> Hi:
>
> How can I correct the pial surf
ind this out?
> rosa
> Original-Nachricht
>
>> Datum: Tue, 4 Aug 2009 08:13:01 -0400 (EDT)
>> Von: Bruce Fischl
>> An: Rosa Steimke
>> CC: freesurfer@nmr.mgh.harvard.edu
>> Betreff: Re: [Freesurfer] correction for behavioral varialbles i
Bruce Fischl
> An: Rosa Steimke
> CC: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] correction for behavioral varialbles in qdec
> Hi Rosa,
>
> you have to select them.
>
> cheers,
> Bruce
>
> On Tue, 4 Aug 2009, Rosa Steimke wrote:
>
> >
Hi Rosa,
you have to select them.
cheers,
Bruce
On Tue, 4 Aug 2009, Rosa Steimke wrote:
>
> HI,
> i have a question regarding qdec. If i load a designfile with 4 variables,
> but than i only select 1 for analysis, does qdec then correct for the other
> variables that i did not select? or do i
HI,
i have a question regarding qdec. If i load a designfile with 4 variables, but
than i only select 1 for analysis, does qdec then correct for the other
variables that i did not select? or do i have to select them?
thanks in advance!!
rosa
--
Jetzt kostenlos herunterladen: Internet Explorer 8
Hi, this is Jared again at the Brigham. Quick correction. The error
says "pbsubmit: Command not found." not "psubmit: Command not found."
Thanks
-Jared
Jared Price
Center for Neurological Imaging
Brigham and Women's Hospital
Harvard Medical School
1249 Boylston Street
Boston, MA 02115
617-5
Dear Freesurfer users
In my former email, I meant that I can not change from bash to tcsh shell on
Mac OS X. Sorry!
Thanks
Regards
Juergen
---
Juergen Haenggi, Ph.D. student
Department of Neuropsychology
Institute of Psycho
93 matches
Mail list logo
