No, we were proposing this:
M = cifti map of mean(of Level 2 individual subject copes)
S = cifti map of std(of Level 2 individual subject copes)
Cohen’s d = M/S
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of M
I think this would be done from a level3 file; maybe I'm wrong.
If I understand this correctly, the three steps below would give a Cohen's d
map. Have I understood it right?:
1st) take this file:
HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMAll.dscalar.nii
2nd) transform this file into
Workbench is available for Linux, Windows, and Mac:
http://www.humanconnectome.org/software/get-connectome-workbench.html
It is also open source, so if you want it in some other OS type where QT
compiles, you can try compiling it yourself:
https://github.com/Washington-University/workbench
The
I assumed you were talking about level3 files.
Peace,
Matt.
From: Xavier Guell Paradis mailto:xavie...@mit.edu>>
Date: Monday, January 30, 2017 at 6:25 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, "Harms,
Michael" mailto:mha...@wustl.edu>>, "Elam, Jennifer"
mailto:e...@wustl.edu>>,
"hcp-u
Hi Matthew,
I am sorry, I didn't fully understand your previous message. Do you mean that
the two steps that I mentioned in my last message are correct?
Thank you very much,
Xavier.
From: Glasser, Matthew [glass...@wustl.edu]
Sent: Monday, January 30, 2017 7:22 PM
Hi,
I am a very new user of the workbench. I noticed the availability of the
Workbench Command and went to its home page. The example there shows Operating
System: Linux. Is it not available for WindowsOS? Is it for MacOS?
Thanks,
-Jeff
___
HCP-User
Those are the level 2 copes.
Peace,
Matt.
From: Xavier Guell Paradis mailto:xavie...@mit.edu>>
Date: Monday, January 30, 2017 at 6:20 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, "Harms,
Michael" mailto:mha...@wustl.edu>>, "Elam, Jennifer"
mailto:e...@wustl.edu>>,
"hcp-users@humanconnecto
Dear Matthew,
Thank you very much for the suggestion. To make sure that I understand this
correctly; would this be the correct analysis?:
1st) Obtain a group cope1 file of the S900 group task contrasts (in a previous
message, Michael said he could make this available from the S900 group task
co
No because the non-optimal scaling will divide out in the mean(cope)/std(cope)
ratio.
Peace,
Matt.
From: Xavier Guell Paradis mailto:xavie...@mit.edu>>
Date: Monday, January 30, 2017 at 4:35 PM
To: "Harms, Michael" mailto:mha...@wustl.edu>>, "Elam,
Jennifer" mailto:e...@wustl.edu>>, Matt Glass
The -cifti-find-clusters command assigns a separate integer within each
cluster. You can use -cifti-label-import and then
-cifti-all-labels-to-rois to get each cluster in a separate map. Then,
-cifti-weighted-stats with -spatial-weights and -sum will give you mm^2 for
surface clusters and mm^3 fo
Dear Michael,
Wouldn't using the cope files have the problem that "the released versions are
not optimally scaled (because of a non-optimal intensity bias field
correction)" (as written by Matthew before in this conversation)? Or would this
not matter if Cohen's d were calculated from cope1 file
Hi Moises,
Thanks for the reply!
I also want to know a couple other things - is Sun Grid Engine (SGE) a
particular requirement to ensure bedpostx internally splits the slices among
all available CPU cores? Or will something like Torque and Maui also be fine?
The system administrator in my coll
Dear HCP experts,
After using -cifti-find-clusters, is there a way to know the size of the
clusters that the command has found? We know that the clusters will be larger
than the specified volume-value-threshold, but is there a way to know the mm^3
or number of voxels of the clusters identified?
Dear Michael and Matthew,
Thank you very much for all your replies, your comments were extremely helpful.
Xavier.
From: Harms, Michael [mha...@wustl.edu]
Sent: Monday, January 30, 2017 12:30 PM
To: Elam, Jennifer; Glasser, Matthew; Xavier Guell Paradis;
hcp-users@
Hi,
Just wanted to mention that I’m not promoting the computation of Cohen’s d
effect size maps by dividing the z-stat maps by sqrt(N) as a “formal” solution.
Since the z-stat are computed using ‘flameo’ and multi-level variance
modeling, I think the “proper” way to compute Cohen’s d effect si
Posting this off-list thread about computing effect size task maps for the S900
from the group average zstat maps back to the list in case looking through it
is of interest to other users. If the discussion continues, please include the
list address in the responses so others can follow.
Thank
Dear Sir,
Is it mandatory to have outputs from Resting State Stats pipeline in order
to perform feature based registration using MSM All , is there any
alternative to run the pipeline without the outputs from
RestingStateStats.sh.
Is there any alternate methods which i can use for my analysis t
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