not need to be set.
Am I correct? I’d like to make sure I’m doing this right.
Thanks again for this amazing toolset!
Joe
> On Jun 11, 2019, at 15:55, Joseph Dien wrote:
>
> External Email - Use Caution
>
>
> looking further into the archives, I see that the -sd
slices and they are accelerated by a factor of 6, does one specify
-ngroups 6 or -ngroups 10?
Joe
> On Jun 2, 2019, at 19:46, Joseph Dien wrote:
>
> External Email - Use Caution
>
>
> Hi Doug,
>I’m happy to see that FreeSurfer6 provides enhanced suppor
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377.5000
Joseph Dien, PhD
Senior Research Scientist
Department of Human Development and Quantitative Methodology
University of Maryland, College Park
http://joedien.com
Hi,
just a user request for corrected p-values for the mni305 space analyses
(i.e., sig.voxel.nii.gz files).
Thanks!
Joe
Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University
!
Joe
Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
http://joedien.com
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’. I’m guessing some version
update changed the location of this directory. I went into T and performed the
following command:
mkdir 'Cleanup At Startup'
after doing so, everything worked again.
Cheers!
Joe
Joseph
of the rvar term. Can you throw some light on this?
I greatly appreciate your helpful tips and this amazing software that you have
written.
Respectfully,
Joe
> On Mar 17, 2016, at 15:48, Joseph Dien <jdie...@mac.com> wrote:
>
> I did more digging around and came up with a pro
is, would this work? Am I neglecting files other than
ces.nii.gz that would need to be modified? or other fields in the mri data
structure?
When you referred to writing “out a new volume” is this what you meant?
Thanks again for this help!
Joe
> On Mar 15, 2016, at 17:32, Joseph Dien &l
tion for mkcontrast-sess (not mkanalysis-sess)
>
> On 03/13/2016 10:29 PM, Joseph Dien wrote:
>> After a long break, back to this…
>>
>> My goal is still to get the betas for the first and maybe second spm
>> hrf so I can calculate a Calhoun derivative boost measure.
&g
into matlab, make the
> Calhoun computations on each condition, then compute the contrasts, then
> write out the new volume
>
>
> On 07/10/2013 01:40 PM, Joseph Dien wrote:
>> Sounds good!
>>
>> Regarding creating a new volume and computing contrasts fr
<gr...@nmr.mgh.harvard.edu> wrote:
>
> I cannot replicate the error. What version of FS are you using? What
> happens if you run
> mri_glmfit --fsgd RPA-acc.fsgd
> or
> mri_glmfit --fsgd RPA-accGT.fsgd
>
>
>
> On 02/29/2016 09:38 PM, Joseph Dien wrote:
>>
Oops, never mind. User error. I’m too embarrassed to even explain what I did.
:)
Joe
> On Feb 29, 2016, at 21:38, Joseph Dien <jdie...@mac.com> wrote:
>
> Hi,
> I’m having an fsgd error that has totally stumped me. I’m trying to run
> the following command to com
would be greatly appreciated!
Joe
RPA-accGT.fsgd
Description: Binary data
RPA-acc.fsgd
Description: Binary data
Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland
> scanner. Could that be the problem?
>
>
> On 2/10/16 10:40 PM, Joseph Dien wrote:
>> I ran into the same issue:
>>
>> FSLVersion 5.0.4
>> FSLVerMaj 5
>> FSL Version is 5.0.4, must be 3.X or 4.X
>>
>> I downloaded the epidewarp.fsl script from the sug
($status) exit 1;
So apparently this rescaling command is not doing so correctly? The script
comment says it expects the values to be between 0 and 4095 whereas the file
goes to -4096 so perhaps that was a bit more negative than it was expecting?
Joe
> On Feb 11, 2016, at 11:12, Jose
HelpLine
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
---
? But in the case where both samples equal, say, 10,
Leff would end up equalling 100/20=5. Dividing C by 5 seems like too much.
Anyway, very confused. Any guidance would be appreciated.
Respectfully,
Joe
Joseph
Joseph Dien,
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland
E-mail: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com
would have to do to write it out. It won't be something that happens
before I get back from HBM. Can you remind me after HBM?
doug
On 05/31/2013 04:44 PM, Joseph Dien wrote:
It looks like the corrected vertex p-values
(ex: cache.th13.abs.sig.voxel.nii.gz) are only available
...@nmr.mgh.harvard.edu wrote:
The beta's have already been scaled. What do you get if you just
beta/runmean ?
On 07/17/2013 01:45 PM, Joseph Dien wrote:
I implemented the ROI percent signal change formula following the
MarsBaR FAQ (http://marsbar.sourceforge.net/faq.html) but the values
I'm
, 2013, at 3:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
when you ran mkanalysis-sess, what did you set --refeventdur to?
On 07/17/2013 02:50 PM, Joseph Dien wrote:
then I get on the order of .02% difference between the contrasted conditions.
The run mean values are in my expected
analyses.
Thanks!
Joe
On Jul 17, 2013, at 3:58 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
why do you have 20 conditions? And what are the 7 nuisance regressors?
On 07/17/2013 03:54 PM, Joseph Dien wrote:
It's a boxcar design so 20.265.
mkanalysis-sess -fsd bold -analysis CPA.sm05.lh
file is something different.
Thanks!
Joe
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com
-CS_HC.HC.th2.neg.cluster1/junk.label
1311
mri_label2label: Done
Ended at Fri Jul 12 18:23:48 EDT 2013
funcroi-sess completed
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
, at 7:34 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
Hi Joe,
On 07/12/2013 06:51 PM, Joseph Dien wrote:
I'm using Freesurfer 5.3.0
(well, actually I ran the original analyses with 5.2.0 and then am
running this ROI follow-up with 5.2.0, could that be a problem? From
a consistent format.
Not a big deal, but consistency would be helpful for scripts.
Cheers!
Joe
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 202-297-8117
http
and regenerate the
contrasts. But what are you planning to do the the beta file? It sounds
like a potentially bad idea
doug
On 07/09/2013 10:26 PM, Joseph Dien wrote:
It looks as though selxavg3-sess generates the contrast analyses at
the same time as the beta weights. Would it be possible
be a numerical issue (it is
not computed analytically). Why do you need the 2nd derivative?
doug
On 07/10/2013 12:47 PM, Joseph Dien wrote:
I'm thinking of generating a modified beta.nii.gz file where the
primary betas have been replaced with the Calhoun et al (2004)
derivative boost
Sounds good!
Regarding creating a new volume and computing contrasts from it, what do you
mean? I didn't follow that.
Thanks!
Joe
On Jul 10, 2013, at 1:33 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
On 07/10/2013 01:29 PM, Joseph Dien wrote:
Sorry, not following what you
you can give me!
Joe
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com
PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
On 07/09/2013 04:11 PM, Joseph Dien wrote:
Hi,
I have a question about how mkcontrast-sess works. I ran an
analysis using the mkanalysis-sess option spmhrf 2 so there are three
regressors for each predictor, the primary, the latency
this mean I should avoid the spmhrf 2 option entirely to avoid loss of
statistical power?
Thanks for the help!
Joe
On Jul 9, 2013, at 4:34 PM, Joseph Dien jdie...@mac.com wrote:
Thanks for the quick response! So if I wanted to use the Calhoun 2004
approach, I should be able to use
(as the default threshold
was also the reason the suparmarginal gyrus cluster was not being displayed).
Cheers!
Joe
On Jun 15, 2013, at 12:07 AM, Joseph Dien jdie...@mac.com wrote:
I'm getting some puzzling discrepancies when comparing the ocn and the
cluster outputs. The summary file indicates
On May 31, 2013, at 12:09 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
On 05/30/2013 04:37 PM, Joseph Dien wrote:
Just to make sure I'm doing this right, I'm going to summarize what
I've taken away from your answers and to ask some new questions. In
order to present the results
On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
On 05/31/2013 01:49 AM, Joseph Dien wrote:
I was able to make more progress so I'm mostly good at this point but
I have a remaining question:
I assume the contents of sig.nii.gz (which I assume are the vertex
Dien jdie...@mac.com wrote:
On May 31, 2013, at 12:11 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
On 05/31/2013 01:49 AM, Joseph Dien wrote:
I was able to make more progress so I'm mostly good at this point but
I have a remaining question:
I assume the contents of sig.nii.gz
:
On 5/29/13 10:42 PM, Joseph Dien wrote:
On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Hi Joe,
On 05/29/2013 01:00 AM, Joseph Dien wrote:
I need to extract the beta weights from a cluster identified with
FS-Fast in order to compute percentage signal
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
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https
space if that would make it easier (but you
can't surface smooth).
doug
On 05/30/2013 05:08 PM, Joseph Dien wrote:
I tried using MRIread to look at the contents of the analysis files (using
Fressurfer 5.2.0 under OS X 10.8.3 and Matlab 2013a):
mri = MRIread('ces.nii.gz',0);
but I'm
available?
Thanks again for your patience!
Joe
On May 30, 2013, at 4:37 PM, Joseph Dien jdie...@mac.com wrote:
Just to make sure I'm doing this right, I'm going to summarize what I've
taken away from your answers and to ask some new questions. In order to
present the results, I need two things
On May 29, 2013, at 11:40 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
Hi Joe,
On 05/29/2013 01:00 AM, Joseph Dien wrote:
I need to extract the beta weights from a cluster identified with
FS-Fast in order to compute percentage signal change.
1) I see a file called beta.nii.gz
I was wondering if someone could give me a summary as to how SUMA and FSFAST
differ? In other words, user interface aside, what would be reasons to use one
or the other?
Joe
Joseph Dien,
Senior Research
a
dummy analysis run with a single event of the desired duration and then look in
the X variable in the resulting X.mat file?
Sorry for all the questions!
Joe
Joseph Dien,
Senior Research Scientist
University
Compliance HelpLine
at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
Joseph
Compliance HelpLine
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properly
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Joseph
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