a 1 somewhere in columns 1-8 to indicate the class
>(ie, site/dx) that the subject is in.
On 05/26/2016 12:57 PM, Timothy Hendrickson wrote:
> Hi Doug,
>
> Thank you for such a prompt response. Just to be clear you are
> recommending that I manually create the matrix file right?
>
like this for LGI?
If I take the mean of all of the ROIs would that be equivalent to a
hemispheric LGI measure?
Thanks!
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
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>Columns 1-16 model the intercepts for all your classes
>Columns 17-20 model the ages for your gender-x-diagnosis subclasses
>Columns 21-24 model the ICV for your gender-x-diagnosis subclasses
On 07/06/2016 02:04 PM, Timothy Hendrickson wrote:
> Freesurfer Support,
>
> Thank yo
the best thing to do is to set a mask representing the
clusters from the first GLM and then run the second GLM on the mask.
Is this a reasonable thing to do? What steps/commands would I perform in
order to do something like this?
Respectfully,
-Tim Hendrickson
Timothy Hendrickson
Department of
t;
of thresholds and I have not found much literature that decimates this
either.
Are there any general best practices I should follow when determining these
thresholds?
Respectfully,
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-
that it must be done via command line with mri_glmfit and
the --pvr flag. I am confused as to what sort of file I should input into
the --pvr flag (do I run a separate analysis?, etc).
Any advice would be extremely helpful.
Respectfully,
-Tim
Timothy Hendrickson
Department of Psychiatry
t"
command and using that co-variate data to input into the FSGD file?
Respectfully,
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
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illCondMatrix_twoStage_years_10_31_16.txt.
Additionally I've included my fsgd file for stage two and my qdec file for
stage one.
Any assistance would be extremely helpful,
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
Normalized m
-archive.com/hcp-users@humanconnectome.org/msg03477.html.
<http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html>
Are there any workflows or development versions that I can download in
order to perform something like this.
Respectfully,
-Tim
Timothy Hendrickson
Department of Psyc
e into fs_average space, however I
am running to problems visualizing it in freeview or tksurfer. Please see
the error message in the forwarded message below?
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
-- Forwarded m
Aww thank you for clarifying Michael. I definitely misread Matthew's post.
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
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It seems that this message has been ignored. I really do need an answer on
this.
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
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Freesurfer
lay/PublicData/HCP+Users+FAQ>
I believe I have resampled the GIFTI file into fs_average space, however I
am running to problems visualizing it in freeview or tksurfer. Please see
the error message in the forwarded message below?
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
cript, all timepoint qdec file,
temporal average qdec file, fsgd file, and design matrix.
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
Design matrix --
0.000 0.000 1.000 0.000 0.000
lh.testretest.fsaverage.cortex.label --surf fsaverage lh
The error message is attached within file
AllSite_twoStageLongitudinal_DsgnMtxErr.txt
Additionally I've included my analysis script, all timepoint qdec file,
temporal average qdec file, fsgd file, and design matrix.
-Tim
Timothy Hendrickson
Department of Psych
neficial.
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
Design matrix --
0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000
0.000 0.000 0.000 0.000 0.000 0.000
emporal average qdec file, fsgd file, and design matrix.
Any help would be extremely beneficial.
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
Design matrix --
0.000 0.000 0.000 1.000
Doug,
That did it! Thank you so much for your help!
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
On Wed, Dec 21, 2016 at 12:47 PM, Douglas N Greve wrote:
> your 10th column is all 0s
>
>
> On 12/2
determine the outline of said cluster.
2) In QDEC one is able to visualize a scatter plot for a particular
cluster. Is there any way to do this via the command line option?
Thank you,
-Tim Hendrickson
--
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434
I'm just following up on this e-mail. I have not heard anything yet.
-Tim
On Mon, May 9, 2016 at 3:16 PM, Timothy Hendrickson
wrote:
> Free Surfer Support,
>
> I have been using the command line version for group analysis since my
> data set has too many factors for QDEC.
&g
Tim
--
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
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The information in t
d
age) contrast like
[0 0 0 0 0 0 0 0 1 -1]
On 05/24/2016 02:30 PM, Timothy Hendrickson wrote:
>
> Freesurfer Support,
>
> I'd like to create a design matrix for a group analysis outside of the
> DODS and DOSS models. I understand that in order to do this the -X
> flag must b
follows:
0 0 1 1 0 0
0 0 0 0 1 1
Is this correct?
-Tim
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
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Hi Doug,
Yes thank you this was my contrast matrix, not my design matrix. I've taken
your advice by multiplying the co-variates together.
Thanks for the help!
-Tim
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freesurfer 6 and
5.3.0 - HCP
2) Is there any way that I can download/install the newer version of
mri_convert used for freesurfer 6 within 5.3.0 - HCP?
-Tim
Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S
External Email - Use Caution
Hello,
I notice that within TRACULA 6.0 that eddy_correct is used for the eddy
current correction. This is an older tool as compared to eddy, is there a
reason that eddy_correct is still used? Have you done cross comparisons
between eddy_correct and ed
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