Sorry, no.
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110
Hi,
If you are just testing the mean activation, then you need to use the -ise
option to allow sign flipping. Otherwise, by default, PALM does permutations,
but permutations of your model will always generate the exact same mean, which
explains your results.
Cheers,
-MH
--
Michael Harms,
Hi,
There is something in the works:
https://www.biorxiv.org/content/early/2018/01/12/206292
cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box
Hi,
Re (1):
If you want to work with streamlines in MNI space then you have to accept the
"drift" (volume expansion) that is part of MNI space itself.
Re (2):
Maps may be resampled to surfaces in MNI space. But all the FreeSurfer
structural quantities that we provide in the
“functional session A” and “functional session B”. That is related to the
internals of how the data was collected at the scanner.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of
The issue with using FreeSurfer 6.0 in the HCP Pipelines is that some aspects
of the surface generation on HCP-Young Adult data were better using the
FreeSurfer 5.3.0-HCP release. We are in the process of checking the
performance of a beta version of FreeSurfer 6.X on HCP-YA data.
If you use
7T release. Ideally would include
the .txt files.
Thanks v much,
Nina
On Tue, 19 Jun 2018, Harms, Michael wrote:
>
> Hi,
> rfMRI_REST1_7T_PA_Atlas_1.6mm_MSMAll.dtseries.nii is the CIFTI version, using
> MSMAll registration, on a surface mesh with ~ 1.6 mm (average) vertex spacing.
>
&
Hi,
rfMRI_REST1_7T_PA_Atlas_1.6mm_MSMAll.dtseries.nii is the CIFTI version, using
MSMAll registration, on a surface mesh with ~ 1.6 mm (average) vertex spacing.
Note that we've provided CIFTI data on both 1.6 mm and 2.0 mm meshes.
Depending on your research question, the latter may be easier
Hi,
See the “HCP1200 Parcellation+Timeseries+Netmats (PTN)” packages hosted at
https://db.humanconnectome.org/data/projects/HCP_1200
There are “soft parcellations” (ICA-based, and cortical only) computed at
dimensionalities of 15, 25, 50, 100, 200, and 300.
Cheers,
-MH
--
Michael Harms, Ph.D.
Hi guys,
Which of the colormaps currently in Workbench are perceptually uniform and
monotonically increasing in lightness?
In the interest of supporting some of the recent colormaps with considerable
thought behind them, what about including the viridis, plasma, inferno, and
magma colormaps
Hi Tim,
I was wondering about the details of the -cifti-reduce -exclude-outliers
operation. In particular, is it “iterative”? i.e., does it recompute the std
without the outliers from the previous pass(es) and iterate until no further
new outliers are identified?
Thanks,
-MH
--
Michael
Yes, you should be able to use the latest FSL release.
In fact, due to code consolidation in the newest release, FSL 5.0.6 is no
longer allowed for the task-fMRI processing.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of
Hi,
The tasks are triggered by the scanner (so you can assume the start of the
acquisition is at t=0) and you can assume that the spacing between frames is
exactly the TR (0.720 sec for the 3T HCP-Young Adult acquisitions).
Cheers,
-MH
--
Michael Harms, Ph.D.
Hi,
Due to the manner in which the pipeline code developed, the CIFTI files that do
NOT contain “MSMAll” are by default based on “MSMSulc” registration.
Perhaps at some point we will revise the pipeline code to explicitly include
“MSMSulc” as part of the file names, to avoid this confusion.
Hi,
Cortical thickness is purely a surface-based measure, so that particular
dscalar indeed doesn’t contain any volume-based grayordinates.
The task fMRI data would be one example in which volume-based grayordinates are
present in the CIFTI (i.e., cerebellum and subcortical voxels)
Cheers,
Hi,
The entirety of the original FS output is available at
${subject}/T1w/${subject}, which you can obtain via the “Structural Extended”
packages, or as part of “Connectome-in-a-Box” (no longer taking new orders, but
perhaps you already have one) or available on S3.
Cheers,
-MH
--
Michael
Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: "Glasser, Matthew" <glass...@wustl.edu>
Date: Wednesday, April 11, 2018 at 5:35 PM
To: erik lee <erik.lee...@gmail.com>, "Harms, Michael" &
Just to expand on this, since I think I might know why you are asking.
The grand mean is computed on the brain masked volume timeseries, after bias
field correction and jacobian modulation is first applied – see the end of
IntensityNormalization.sh, which is called as the final step in
One thought: Are you sure you are using the “3D” (and not the “2D”) correction
on the scanner?
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
Hi,
We didn’t create the HCP Pipeline BIDS app, and have no experience using it.
Users should be aware that the current BIDS App “hides” various choices that
one would normally have to make when running the HCP Pipelines, and I’m not
sure what particular choices it has implemented. In that
That feature isn’t yet in the released wb_command.
Try using the latest “released” version of the Pipelines from GitHub, rather
than the master branch.
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University
That page appears to be down for the moment. We’ll get it fixed.
The Echo Spacing for the dMRI from the Lifespan1a pilot was 0.69 ms.
(Although, FWIW, if you already processed your data using 0.78 ms, it doesn’t
matter in this particular case. You’ll still get a completely correct
, 2018 at 12:08 PM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: hcp-users <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Convert activation cifti data to volume nifti
Thank you for the clarification.
Here is a tree structure of one subject folder
"tfMRI_EMOTION
: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Yassine Benhajali <yanama...@gmail.com>
Date: Tuesday, March 27, 2018 at 11:05 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: NEUROSCIENCE tim <tsc...@mst.edu>, hcp-users <hcp-use
Hi,
“AP” (short for anterior-to-posterior) and “PA” (short for
posterior-to-anterior) refer to the phase encoding direction.
In general, as Jenn said, we recommend using both the AP and PA data, so that
your results aren’t “biased” toward a particular phase-encoding direction.
Is there a
Hi,
Not in wb_command at the current time. You could of course load the data into
Matlab and run a regression there, if all you care about is the effect size of
the relationship. What PALM nicely gives you is the ability to control for
multiple comparisons in a statistically rigorous manner
I think the issue, as I read it, is that Will’s data is only NIFTI currently,
so he doesn’t have any subject CIFTI that he could use for the stage 1 of dual
reg.
Our suggestion of course to remedy that would be that you process your data
into CIFTI, using the HCP Pipelines. ☺
Cheers,
-MH
--
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Timothy Coalson <tsc...@mst.edu>
Date: Wednesday, March 7, 2018 at 5:19 PM
To: "Harms, Michael" <mha...@wust
mann <davidhofma...@gmail.com>
Cc: "Harms, Michael" <mha...@wustl.edu>, hcp-users
<hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Concatenating resting state runs
The basic idea for variance normalization is to equalize the variance of the
noise. It is very hel
...@wustl.edu>
Date: Wednesday, March 7, 2018 at 11:24 AM
To: "Harms, Michael" <mha...@wustl.edu>, David Hofmann <davidhofma...@gmail.com>
Cc: hcp-users <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Concatenating resting state runs
Hi Mike,
Not
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: <hcp-users-boun...@humanconnectome.org> on behalf of "Harms, Michael"
<mha...@wustl.edu>
Date: Wednesda
Matt,
Don’t we compute an estimate of the unstructured noise variance as part of
RestingStateState, and then place that into one of the packages?
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School
;
Date: Wednesday, February 28, 2018 at 11:03 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: "Glasser, Matthew" <glass...@wustl.edu>, hcp-users
<hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Concatenate sessions from Emotion task
Hey again,
how can I
Hofmann <davidhofma...@gmail.com>
Date: Wednesday, February 28, 2018 at 8:45 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: "Glasser, Matthew" <glass...@wustl.edu>, hcp-users
<hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Concatenate sessions fro
-747-6173
St. Louis, MO 63110 Email:
mha...@wustl.edu
From: David Hofmann <davidhofma...@gmail.com>
Date: Wednesday, February 28, 2018 at 7:50 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: "Glasser, Matthew" <glass..
Well, you know the TR, and the number of frames in the first run, so just add
the product of those two to the times in the 2nd run (unless you are manually
deleting additional frames at the start of either run).
Cheers,
-MH
--
Michael Harms, Ph.D.
What tools are you planning on using for the GLM fitting? Concatenating the
runs will lead to some inaccuracies in the auto-correlation modeling at the
point of concatenation, although I don’t know if anyone has ever investigated
whether it matters much empirically.
Cheers,
-MH
--
Michael
.Tel: 314-747-6173
St. Louis, MO 63110 Email:
mha...@wustl.edu
From: redhatw <redh...@gmail.com>
Date: Friday, February 23, 2018 at 9:37 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: "Glasser, Matthew"
Email:
mha...@wustl.edu
From: redhatw <redh...@gmail.com>
Date: Friday, February 23, 2018 at 8:03 AM
To: "Glasser, Matthew" <glass...@wustl.edu>
Cc: "Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org"
<hcp-users
The files without any “registration suffix” came first temporally and were
generated using “MSMSulc” registration. When the “MSMAll” registration was
added later, we then added “MSMAll” as part of the file name.
Cheers,
-MH
--
Michael Harms, Ph.D.
Hi,
While the documentation is overall very good, I don’t know if I’d rely on that
pdf for a detailed list of all the files that we recommend “keeping”. For
that, you could download and unpack the packages for a subject with complete
data (e.g., 100307), and see what you all get.
As a
An importable protocol for Siemens is available here:
http://protocols.humanconnectome.org/CCF/
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of
nned in each
scanner. Thank you so much for your help.
Best
Luo
-- Original ----------
From: Harms, Michael <mha...@wustl.edu>
Date: 周四,1月 18,2018 0:14 下午
To: 罗 <963619...@qq.com>, hcp-users <hcp-users@humanconnectome.org>
Subject: Re: [HCP
Hi,
It’s an indication of the “quarter” (Q) of the project that the data was
acquired.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of
We suggest using the latest version of the HCP Pipelines with the latest
version of Workbench.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
What subject are you looking at that has a “T1w_MPR1_reorient_sformMod.nii.gz”
file? I’m not seeing that file in our “unprocessed” packages for any of a
handful of HCP-Young Adult subjects that I just checked…
The other files are as Matt explained, and are also explained in the release
:
mha...@wustl.edu
From: <hcp-users-boun...@humanconnectome.org> on behalf of "Harms, Michael"
<mha...@wustl.edu>
Date: Tuesday, November 28, 2017 at 8:49 AM
To: Live Eikenes <live.eike...@ntnu.no>, "hcp-users@humanconnectome.org"
<hcp-users@humanconnectome.o
Hi,
We have a VE11C protocol, but built on a Prisma, that various sites have used a
starting point available here:
http://protocols.humanconnectome.org/CCF/
You can try importing it, and see what sort of adaptations it makes, due to the
lower strength gradients of the Skyra. (The main
Hi,
In FS, “Intracranial volume”, renamed to “EstimatedTotalIntraCranialVol” (aka
“eTIV”) in more recent FS versions, is solely based on the determinant of a
talairach transform that is internal to FS. That particular transform does not
necessarily need to be accurate for FS to generate
Hi,
It’s a standard Cohen’s d calculation -- mean of the individual subject (lev2)
copes, divided by the std of the individual subject copes
In terms of FSL code, if $mergedcope is the 4D file containing all the
individual subject cope estimates, the code is just:
fslmaths $mergedcope
Sure, you can download individual files using REST calls – see previous posts
in the list for example syntax. Or, you could access the files via Amazon S3
and identify the subjects that way.
The Movement_RelativeRMS_mean.txt file that accompanies each fMRI run is the
mean of the relative
Hi,
No. I believe the switch to using FSL’s ‘mcflirt’ as the “default” motion
correction was around release 3.15. I’d suggest you switch to using the latest
release in the 3.x line, which is 3.22.
For additional context, since the original post referenced the ABCD study, I
assume that the
Hi,
I don’t think the following is necessarily your problem, but know that the
simple tensor model is not appropriate at high b-values. You should either
1) use the “—kurt” or “—kurtdir" flags which will add a “mean kurtosis” or
“parallel/perpendicular kurtosis” parameters that can account
Yes, there was a ‘melodic’ failure for the rfMRI_REST1_RL run that we were
never able to resolve.
Thanks,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
f of 罗 <963619...@qq.com>
Date: Tuesday, October 24, 2017 at 9:23 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: hcp-users <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] about the hcp data
I'm sorry.
I question is that whether all the 1113 subjects with MRI are av
Hi,
Can you rephrase your question? Are you asking if the S1200 data release is
available for purchase as part of the “Connectome in a Box” program?
If so, the answer is yes:
https://store.humanconnectome.org/data/
cheers,
-MH
--
Michael Harms, Ph.D.
Germane to this discussion is that using the same methodology, but a different
sample of subjects, the same Yale group has recently reported that the
correlation of predicted gF (from netmats) and observed gF was r=0.22.
https://www.ncbi.nlm.nih.gov/pubmed/28968754
cheers,
-MH
--
Michael
Also, if you fitting a simple tensor model via ‘dtifit’, you may want to
consider limiting yourself to just the b=1000 shell (+ b=0’s), because the
simple tensor model breaks down for high b-values. There should be a post in
the archive about this.
Cheers,
-MH
--
Michael Harms, Ph.D.
In the context of the long resting state runs that we have available, I would
argue that throwing in additional possible confounds is the appropriate thing
to do. Are you suggesting that sex, age, age^2, sex*age, sex*age^2, brain
size, head size, and average motion shouldn’t all be included?
Email:
mha...@wustl.edu
From: hercp <he...@uw.edu>
Date: Thursday, October 5, 2017 at 3:39 PM
To: "Harms, Michael" <mha...@wustl.edu>
Subject: Re: [HCP-Users] Mean and variance normalization
Hi Michael,
Thanks for the input. Are you aware of any utility t
Re (2) (expanding on Matt’s response): Demeaning and variance normalizing a
parcellated timeseries (or equivalently the time series for a single ROI), and
then concatenating those, is not the same as demeaning and variance normalizing
the dense time series, concatenating those, and then
And it is all handled automatically for the dMRI data in the HCP Pipeline.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box
Hi Tim,
We plan on creating at least a structural pipeline that will support the use of
FreeSurfer’s longitudinal processing. Unfortunately, there is no beta version,
and I don’t want to speculate at this time on a timeline.
Cheers,
-MH
--
Michael Harms, Ph.D.
@Matt: The minimally preprocessed subcortical data in the CIFTI was smoothed
with a 2 mm FWHM “parcel-constrained” kernel, right? (i.e, the smoothing does
not cross boundaries of subcortical structures). In that case, if they were to
then further smooth the subcortical data, but smooth
IntraCranial volume is based entirely on the determinant of the talairch
transform. We don’t check the accuracy of that transform because it doesn’t
even need to be accurate for FreeSurfer to generate correct surfaces and
segmentations.
So, frankly, I wouldn’t use the IntraCranial volume
Hi,
We don’t have a single average head motion for each subject stored as a
variable in ConnectomeDB. You can find the average frame-to-frame motion for
each fMRI run (rfMRI or tfMR) in the Movement_RelativeRMS_mean.txt file for
that run.
Cheers,
-MH
--
Michael Harms, Ph.D.
See the --combine-data-flag in DiffPreprocPipeline.sh
The default value of 1 is intended for acquisitions in which you have acquired
the full vector table with both polarities, which isn’t how you acquired your
data.
In your case, you’ll need to use a value of ‘2’ for that flag.
Cheers,
-MH
There is no “modeling” of the rfMRI data, and thus no residuals (unlike the
task data).
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of
FYI: We are switching over to using ‘dcm2niix’, which is Chris Rorden’s newer,
actively maintained conversion tool.
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Creating an “average-surface” is fine, and we in fact to that and provide it as
part of our “group-average” data (available for download from ConnectomDB).
But, those average surfaces are just a “back-drop” for overlaying/visualizing
the metric/cifti data, and aren’t intended to be used as a
Yes, unless you want to deal with the NaNs.
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel:
Sure, we have data, but I'm not sure how useful it would be to you without
getting into various details. e.g., What type of preprocessing are you
intending? Does it include any denoising? How are you going to define your
spatial mask? Etc...
How exactly were you thinking of quantifying
Hi,
A couple extensions to Tim’s recipe.
PALM has a “transposedata” option, so you can always transpose at the PALM
stage if you prefer to not explicitly create a transposed CIFTI file.
PALM can indeed accept CIFTI files “as is”, *if* you want to do permutation on
the max statistic across
Hi,
There are actually 4 different maps in that file. If you load it into
Workbench, the name associated with each map tells you what each map is.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental
Hi,
Is there a particular reason that you can’t provide all the dMRI scans at once,
and let the pipeline handle the merging for you?
If you process each dMRI run separately, then the individual runs will not be
in optimal alignment. (You would be relying on the registration of each run to
the
one 300 GB system hard disk,
3. one 300 GB hard disk for database,
4. one 300 GB hard disk for image data and
5. one CD-R/DVD-R drive for image storage,
Any relevant information and idea would help a lot. Thank you very much!
Looking forward to your reply.
--
Meizhen Han
PhD Candida
What banding artifact are you referring to? Could you post a picture to a
sharing site?
thx
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of
Essa Yacoub from CMRR sent me the following for distribution to the HCP-User
list on this issue:
"A lot of investigators have done comparisons between the sequences. Most of
this data is not public, although there are some sites that have published
things - e.g.
Which version of FSL are you using? I believe that the
eddy_unwarped_images.eddy_rotated_bvecs file will be created by the version of
‘eddy’ that comes with the newest FSL (5.0.10), but if you are using FSL 5.0.9,
you needed to install the “eddy patch” to get that functionality.
cheers,
-MH
multiple nifti
files contains only cerebellar data, which is not surface information.
Would there be any way of converting that to multiple nifti files?
Thank you very much,
Xavier.
____
From: Harms, Michael [mha...@wustl.edu<mailto:mha...@wustl.edu>]
Sent:
Hi,
No plans to provide such a subject group in the interface, but it is easy
enough to compute such a group using the variables that we have provided in the
database.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the
We have a more recent (and importable) protocol available here that I would
suggest you use as a starting point:
http://protocols.humanconnectome.org/CCF/
Your Prisma should already come with GPUs. Are you using the 64 channel coil?
That will be a slower recon than the 32 ch coil, but I
We’ve run InfoMap on them, but I haven’t had a chance to review them.
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South
ural Protocol
Thanks Michael.
Do you think my study would be eligible for registration with the HCP? If so,
how would I go about setting this up?
Best wishes,
Rachel
On 22 June 2017 at 18:46, Harms, Michael
<mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote:
Hi,
Check out the vario
hed sighted controls is actually more difficult than
recruiting patients.
Best wishes,
Rachel
On 21 June 2017 at 14:33, Harms, Michael
<mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote:
Hi,
You can find an importable protocol here:
http://protocols.humanconnectome.org/CCF/
The pr
Hi,
You can find an importable protocol here:
http://protocols.humanconnectome.org/CCF/
The protocols that we are using for the HCP-Aging/Development projects are
highly similar, but include a few additions (e.g., switch to
navigator-corrected anatomicals; addition of PCASL scan). Those will
Hi,
We will not be releasing any additional data that hasn’t already been released.
(Such subjects have been reported to our IRB as excluded from the Young Adult
HCP, and are not eligible for release). Information on existing released
subjects with identified quality control issues can be
This is via Essa:
It is the same as what is done in the Siemens product - these are Siemens
code/algorithms. But yes - they do B0 corrections, including in post-processing.
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of
In theory, the resolutions and matrix size don’t need to match. But I thought
that, as a practical matter, the Pipelines don’t work if they don’t match. At
least that was the case at some point in the past...
--
Michael Harms, Ph.D.
---
tional if it doesn’t already
exist.
Peace,
Matt.
From: Lisa Kramarenko
<lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>
Date: Thursday, June 8, 2017 at 4:21 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "Harms,
ce tuning happens in between –white and –smooth2 whereas the
pial surface tuning happens between -pial and -surfvolume on this table:
http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3
Peace,
Matt.
From: Lisa Kramarenko
<lisa.kramare...@gmail.com<mailto:lisa.kramare...
Unfortunately, the HCP Pipelines do not currently support rerunning FreeSurfer
after editing. It is on our list of “things to do” to add that functionality.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of
Jesper’s plan is to release an updated version of ‘eddy’ that includes the
slice-to-volume registration after OHBM.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School
Hi Ariana,
If you were referring to asymmetry in the ventricles, I passed an image on to
our radiologist, and he confirmed that the ventricular asymmetry is within
normal variability.
If there was something else that you were referring to, please let us know off
the list.
thanks,
-MH
--
They were acquired with opposite phase encoding (PE) directions, and thus will
have differing areas of susceptibility dropout. We recommend using them
together, as a *pair* of scans, so as to avoid potential biases from using just
one of the two PE directions.
cheers,
-MH
--
Michael Harms,
{fMRIName}_{LR,RL}__{L,R}.native.func.gii?
Thanks,
Jiang Jian
At 2017-05-23 22:31:34, "Harms, Michael"
<mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote:
Hi,
Do you want the “Level 1” results processed through the task model (GLM)?
Or, do you just want the “minimally p
Hi,
Do you want the “Level 1” results processed through the task model (GLM)?
Or, do you just want the “minimally preprocessed” data that entered into the
task analysis scripts? These are available in:
Yes, in DiffPreprocPipeline_PostEddy.sh you’ll need to use
“--combine-data-flag=2”
Also, I want to caution you about collecting only half of the total dMRI data
that we collected in the UMN Lifespan piloting. There is a reason that we
collected a full 20 min of dMRI when using 1.5 mm
Yes, you can use the subject IDs in a public document, PROVIDED that NOTHING
that comes from the RESTRICTED data is associated with that subject ID in your
public document.
cheers,
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the
Hi,
Are you using the latest gifti library available via the link mentioned here?
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?
cheers,
-MH
--
Michael Harms, Ph.D.
---
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