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Hello Freesurfer developers,
I wanted to extract mean thickness values of all participants from the
uncorrected significance maps obtained from mri glmfit for structural data
instead of extracting it from the corrected maps from glmfit sim. Is there
a
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Across all activations since the pcc map was generated by an osgm.
On Friday, November 1, 2019, Greve, Douglas N.,Ph.D.
wrote:
> you mean the average across all activations or clusters of activation?
>
> On 10/31/2019 9:18 PM, Amrita B
n cluster?
>
> On 10/31/2019 3:15 PM, Amrita Bedi wrote:
>
> External Email - Use Caution
> Thank you Dr Greve, that issue is resolved.
>
> I do have another question. I’m now trying to extract mean correlation
> values to the seed from each individual subje
.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz file correctly
> Try
> mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i
> */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz
>
> Where you have "bilat*", that should only be one folder
>
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-- Forwarded message --
From: *abedi...@citymail.cuny.edu * <
abedi...@citymail.cuny.edu>
Date: Thursday, October 31, 2019
Subject: Fw: glm error
To: Amrita Bedi
Amrita Bedi
*Biomedical Engineering - Class of 2018*
*Th
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Hi Freesurfer developers,
I’m using the glmfit tutorial to see clusters for my data. I’m trying to
view the uncorrected clusters on tksuefer using the command line tksurfer
fsaverage lh inflated -overlay /path to data/cache.th13.abs.sig.ocn.annot
but
5-10mm of smoothing. If you really want that much
> smoothing, you should use permutation. See https://surfer.nmr.mgh.
> harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>
> On 5/21/2019 10:09 AM, Amrita Bedi wrote:
>
> External Email - Use Caution
>
>
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-- Forwarded message --
From: *abedi...@citymail.cuny.edu * <
abedi...@citymail.cuny.edu>
Date: Tuesday, May 21, 2019
Subject:
To: "amibedi...@gmail.com"
Hi Freesurfer developers,
While running the mri glmfit sim command for a
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Hi Freesurfer developers,
My question is related to creation of an fsgd file for glm analysis. I have
approximately 500 subjects and 10 variables. I was wondering whats the most
time efficient way of creating an fsgd file given my data currently
. You need to reduce it down to one column. In the
Xg.dat that you sent, the two columns are the last two columns; in this
case, you can just remove the last column. Your contrast matrix will
then need one less column.
On 4/11/19 2:08 PM, Amrita Bedi wrote:
>
> External Email - Use Caution
case, you can just remove the last column. Your contrast matrix will
then need one less column.
On 4/11/19 2:08 PM, Amrita Bedi wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve,
>
> I can’t do the Fsgd in the DOSS format since it won’t be ok for my
> other
ales. This is not a problem for the NSI_1 variable because
> there is no slope for females. If you think this is ok for CAPS_C, then
> just do it. If not, then things get harder, but I can probably step you
> through it.
>
> On 4/11/19 8:40 AM, Amrita Bedi wrote:
&g
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-- Forwarded message --
From: *abedi...@citymail.cuny.edu * <
abedi...@citymail.cuny.edu>
Date: Thursday, April 11, 2019
Subject: Fw: mriglmfit error
To: Amrita Bedi
Amrita Bedi
*Biomedical Engineering - Class of 2018*
*Th
gt; system('mris_fwhm')
>
>
>
> On 1/29/19 9:39 AM, Amrita Bedi wrote:
> >
> > External Email - Use Caution
> >
> > Hi Drs Greve and Fischl,
> >
> > I tried the mris_fwhm command and got the following. Not sure if this
> > is helpful or not
message --
From: *Amrita Bedi*
Date: Friday, January 25, 2019
Subject: Functional connectivty walkthrough step 8 error
To: Freesurfer support list
Ok hopefully, the text is visible now.
bash-4.2$ mris_fwhm
USAGE: mris_fwhm
Smooths surface data and/or estimates FWHM
--i input
check options and exit
--help print out information on how to use this program
--version print out version and exit
$Id: mris_fwhm.c,v 1.40.2.4 2016/12/08 22:02:40 zkaufman Exp $
On Friday, January 25, 2019, Amrita Bedi wrote:
> Sorry for the confusion. The Va doesn’t let us acc
d send us that. Just copy and
> paste the text directly into the email. This is *much* more useful for us.
>
> cheers
> Bruce
>
>
> On Fri, 25 Jan 2019, Amrita Bedi wrote:
>
>
>> External Email - Use Caution
>>
>>
>> [0a440090-c896-4f22-8b
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Pasted the text in the email but not sure if you can view it
On Friday, January 25, 2019, Amrita Bedi wrote:
>
>
> On Friday, January 25, 2019, Amrita Bedi wrote:
>
>>
>>
>> Here you go.
>> On Friday, Janu
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On Friday, January 25, 2019, Amrita Bedi wrote:
>
>
> Here you go.
> On Friday, January 25, 2019, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> Hi Amrita, can you just paste the text into the email?
&
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Here you go.
On Friday, January 25, 2019, Greve, Douglas N.,Ph.D.
wrote:
> Hi Amrita, can you just paste the text into the email?
> thanks
> doug
>
> On 1/25/19 10:51 AM, Amrita Bedi wrote:
>
> External Email - Use
; /share/VA_Imaging/Projects/salat/2389_TRT/abedi
> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm:
> /home/apps/matlab/MATLAB/R2011b/sys/os/glnxa64/libstdc++.so.6: version
> `GLIBCXX_3.4.11' not found (required by
> /home/apps/freesurfer-6.0/freesurfer/bin/mris_fwhm)
>
>
>
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Hi Dr Greve,
Attached is the log file.
On Tuesday, January 22, 2019, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:
> Can you send the full terminal output and/or the log file?
>
> On 1/22/19 2:53 PM, Am
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Hello Freesurfer developers,
I was following the functional connectivity walkthrough for resting stage
BOLD data and I got the attached error when I ran step 8 (selxavg3-sess).
Does anyone have any thoughts on how to trouble shoot this?
Not sure if
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