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
__
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
---
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 of
!
Joe
Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
http://joedien.com
___
Freesurfer mailing list
000gn’. 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
-----
he inclusion 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 wrote:
>
> I did more digging around and came up with a procedure.
, 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 wr
sis-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.
>>
>> As a first
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 from it, what
>> do you mean? I d
ote:
>
> 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:
>> Hi,
>>I’m having an
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 wrote:
>
> Hi,
> I’m having an fsgd error that has totally stumped me. I’m trying to run
> the following command to compute the second l
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
($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 1
;
>
> 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 suggested ftp site and
>> repl
ttp://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 Di
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
/Applications/freesurfer/bin/tksurfer
Joseph Dien,
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland
E-mail: jdie...@mac.com
Phone: 202-297-8117
http://joedien.com
not sure what to expect from FSFAST analyses.
Thanks!
Joe
On Jul 17, 2013, at 3:58 PM, Douglas N Greve 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.
>>
ul 17, 2013, at 3:50 PM, Douglas N Greve 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 b
:
>
> 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.htm
> 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.ni
but it yielded too many
numbers so I'm thinking a curvature file is something different.
Thanks!
Joe
--------
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail
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
, at 7:34 PM, Douglas N Greve 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 t
5.lh/tmp.funcroi-sess.roi.AR-v-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 Mary
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 wrote:
>
> On 07/10/2013 01:29 PM, Joseph Dien wrote:
>> Sorry, not following what you are sug
must 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
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
weights?
Joe
On Jul 9, 2013, at 5:08 PM, Joseph Dien wrote:
> I tried correlations and the 2nd derivative is definitely not orthogonal.
>
> >> corrcoef([X(1:207,4) X(1:207,5) X(1:207,6)])
>
> ans =
>
> 1. -0. -0.5427
>-0.1.
o does 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 wrote:
> Thanks for the quick response! So if I wanted to use the Calhoun 2004
> approach, I should be able to use the St
PM, Douglas N Greve 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
ks for any help you can give me!
Joe
----
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 202-297-8117
http://j
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 wrote:
> I'm getting some puzzling discrepancies when comparing the ocn and the
> cluster outputs. The summary file indicates t
oseph Dien wrote:
>
> On May 31, 2013, at 12:11 PM, Douglas N Greve
> 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:
>>>
On May 31, 2013, at 12:11 PM, Douglas N Greve 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
On May 31, 2013, at 12:09 PM, Douglas N Greve 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
tions available?
Thanks again for your patience!
Joe
On May 30, 2013, at 4:37 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,
hat 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):
>>
&
are expecting a
four-dimensional matrix.
Thanks!
Joe
--------
Joseph Dien,
Senior Research Scientist
University of Maryland
E-mail: jdie...@mac.com
Phone: 301-226-8848
Fax: 301-226-8811
http://joedien.com//
___
Free
e wrote:
>
> On 5/29/13 10:42 PM, Joseph Dien wrote:
>>
>> On May 29, 2013, at 11:40 AM, Douglas N Greve
>> wrote:
>>
>>> Hi Joe,
>>>
>>> On 05/29/2013 01:00 AM, Joseph Dien wrote:
>>>> I need to extract the beta weights fr
On May 29, 2013, at 11:40 AM, Douglas N Greve 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 c
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
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
t; >> gr...@nmr.mgh.harvard.edu
> >> <mailto:gr...@nmr.mgh.harvard.**edu
> >> >
> >> Phone Number: 617-724-2358
> >> Fax: 617-726-7422
> >>
> >> Bugs:
> >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<
you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners 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
48 matches
Mail list logo
