ess?
Thank you very much,
Cherry
On Mon, Apr 22, 2019 at 9:14 PM Yizhou Ma wrote:
> Great that's quick!
>
> On Mon, Apr 22, 2019 at 9:09 PM Glasser, Matthew
> wrote:
>
>> A few weeks maybe if you want a pre-release version.
>>
>> Matt.
>>
>> From
Great that's quick!
On Mon, Apr 22, 2019 at 9:09 PM Glasser, Matthew wrote:
> A few weeks maybe if you want a pre-release version.
>
> Matt.
>
> From: Yizhou Ma
> Date: Monday, April 22, 2019 at 9:06 PM
> To: Matt Glasser
> Cc: "hcp-users@humanconnectome.org&
ience/article/pii/S1053811918303963 for
>examples).
>
> Others in the HCP used different means to identify some of the noise
> components I mentioned above that weren’t being classified correctly by
> regular FIX, and might be able to share their suggestions.
>
> Matt.
>
em all.
>
> Matt.
>
> From: on behalf of Yizhou Ma <
> maxxx...@umn.edu>
> Date: Monday, April 22, 2019 at 3:47 PM
> To: "hcp-users@humanconnectome.org"
> Subject: [HCP-Users] Multi-run ICA-FIX with excessive movement
>
> Dear HCP experts,
>
>
Dear HCP experts,
I am writing for a question with multi-run ICA-FIX for my dataset. I have 4
resting state scans (TR=0.8, length=6.5min each) and 3 task scans (TR=0.8,
length=6min each) that I intend to run multi-run ICA-FIX on. We used
Euclidean norm values to threshold volumes with excessive mo
I see. Thanks. I will stay tuned for that.
On Fri, Mar 15, 2019 at 4:28 PM Glasser, Matthew wrote:
> No that will be a separate pipeline we are working on. We’d like it
> automated, which is an additional research project.
>
> Matt.
>
> From: Yizhou Ma
> Date: Friday, M
th HCP-YA and Lifespan
> datasets to make it a little more generalizable; however, that will be
> released at a later time when it is ready.
>
> Matt.
>
> From: Yizhou Ma
> Date: Tuesday, March 12, 2019 at 7:26 PM
> To: Matt Glasser
> Cc: "hcp-users@humanconn
a couple of last things we want
> to get in there. We will be requiring FSL 6.0.1 going forward for all HCP
> Pipelines, which was released yesterday.
>
> How many total timepoints will you have if you concatenate all of the fMRI
> runs?
>
> Matt.
>
> From: on beha
both sessions?
and
2) If not, will the length of scans in either session be long enough to
allow for adequate ICAFIX performance?
Thank you very much,
Yizhou Ma
PhD Candidate
Clinical Science and Psychopathology Research
Department of Psychology
University of Minnesota
Dear HCP experts,
I am wondering if the item-level data for the Achenbach ASR can be found
somewhere on the ConnectomeDB, or made available at least partially.
Thank you very much,
Cherry
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://
Problem solved. I clicked on "Recreate my Amazon S3 credentials" and got
the secret key there.
On Mon, May 2, 2016 at 4:31 PM, Yizhou Ma wrote:
> Dear HCP experts,
>
> I am following this page to obtain my Amazon S3 credentials. Yet I cannot
> find the AWS icon described i
Dear HCP experts,
I am following this page to obtain my Amazon S3 credentials. Yet I cannot
find the AWS icon described in this page. I clicked on the small button
"Amazon S3 Access Enabled" but that only gave the Access Key ID without the
Secret Key ID.
https://wiki.humanconnectome.org/display/P
lor as the output border
> color. Unfortunately it looks like -border-merge may not currently
> preserve colors (there can be conflicts between files that I'd need to
> figure out what to do with).
>
> Tim
>
>
> On Mon, Nov 30, 2015 at 4:30 PM, Yizhou Ma wrote:
>
Dear HCP experts,
I am trying to create borders based on HCP's .dlabel files. I am working on
the FTB labels in the ICA PTN results. The reference surface I use is the
R440 template, inflated surface. Here's the command I used:
wb_command -label-to-border Q1-Q6_R440.L.inflated.32k_fs_LR.surf.gii
manconnectome.org <
> hcp-users-boun...@humanconnectome.org> on behalf of Yizhou Ma <
> maxxx...@umn.edu>
> *Sent:* Monday, November 23, 2015 2:08 PM
> *To:* arch...@mir.wustl.edu; hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] Is proprietary aspera browser plug
Hi Kevin,
It's been more than two years and I am wondering if there has been any
updates for downloading the HCP data via command line?
Thanks,
Cherry
___
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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/lis
has been reported to the FieldTrip developers, but as yet there has
> been no fix released.
>
> Best,
>
> Matt
>
> From: on behalf of Yizhou Ma <
> maxxx...@umn.edu>
> Date: Friday, November 13, 2015 at 10:03 PM
> To: "hcp-users@humanconnectome.org"
>
Dear all,
I am writing to report what I think of as a problem when using "wb_command
-cifti-convert -to-nifti" on cifti files created with "ft_write_cifti" in
matlab.
This scenario arises when someone creates a new cifti file in matlab (with
ft_write_cifti), and convert it to nifti for use (For e
I demeaned the timeseries of each run before concatenating them and now my
DR results are identical to HCP's (though the scaling is different, which I
don't think matters). Thank you all for your help!
Best,
Cherry
On Fri, Jul 31, 2015 at 12:07 PM, Yizhou Ma wrote:
> I see. Tha
I see. That makes sense. I'll give it a try. Thanks!
On Fri, Jul 31, 2015 at 12:06 PM, Glasser, Matthew
wrote:
> The steps are because the mean image is not the same across the four runs,
> so you need to demean the data before combining across runs.
>
> Peace,
>
> Ma
ing?
>
> Peace,
>
> Matt.
>
> From: on behalf of Yizhou Ma <
> maxxx...@umn.edu>
> Date: Friday, July 31, 2015 at 11:57 AM
> To: "Harms, Michael"
>
> Cc: "hcp-users@humanconnectome.org"
> Subject: Re: [HCP-Users] failure to replicate dua
alone.
I have no idea if this is something with how dual_regression work with
cifti transferred data or if I am doing something wrong.
Thanks,
Cherry
On Fri, Jul 31, 2015 at 11:04 AM, Yizhou Ma wrote:
> I have just plotted the timeseries and it seems that my results doesn't
> really
I have just plotted the timeseries and it seems that my results doesn't
really make sense - they look like square oscillations. HCP's results look
like real timeseries.
On Fri, Jul 31, 2015 at 10:48 AM, Yizhou Ma wrote:
> Thank you Michael. My system is failing me at this moment a
-
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From:
ries for each ICA map [Filippini 2009].
>2.
>
>A newer approach based on estimating the principal eigen-timeseries
>within each ICA component; this approach aims to be more robust against
>component misalignment (between the group-ICA maps and individual subjects'
>d
Dear HCP experts,
I am trying to run my own dual regression on HCP's rsfMRI data. What I did
is use wb_command -cifti-convert -to-nifti to convert group ICA maps and
individual rsfMRI scans to NifTI and use FSL's dual_regression command.
*dual_regression melodic_IC.nii.gz 1 -1 0 ./test 100307_rsf
---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: Yizhou Ma
>
>
> --
> 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: 314-747-
FSLNets doc and the PTN release
> doc.
> Cheers.
>
>
> On 30 Mar 2015, at 18:17, Glasser, Matthew
> wrote:
>
> Hi Steve,
>
> What about the correction for temporal autocorrelation?
>
> Matt.
>
> From: Stephen Smith
> Date: Monday, March 3
ormula is .5*ln((1+r)/(1-r)), which after some log
> identities becomes .5*(ln(1+r)-ln(1-r)).
>
> Tim
>
>
> On Mon, Mar 30, 2015 at 11:02 AM, Yizhou Ma wrote:
>
>> Dear HCP experts,
>>
>> I am trying to reproduce the individual netmats from HCP500-PTN so that
Dear HCP experts,
I am trying to reproduce the individual netmats from HCP500-PTN so that I
am sure where the numbers come from. I used individual node timeseries in
/ts2/subjID and did correlation in matlab. I then used fisher's z
transformation: .5*ln(1+r)-ln(1-r). The resulting netmat is differ
has already had some of the changes made to it so I cannot tell you exactly
> where to look.
>
> Peace,
>
> Matt.
>
> From: Yizhou Ma
> Date: Sunday, March 22, 2015 at 5:33 PM
> To: Matt Glasser
> Cc: "hcp-users@humanconnectome.org"
>
> Subject:
iles you might wish to use in your analysis (even
> if it was, the data inside it wouldn’t be valid as it wouldn’t be cerebral
> cortex). Let me know if you don’t follow the instructions below for
> converting your dlabel files into 91282 grayordinates space.
>
> Peace,
>
>
${StudyFolder}/${Subject}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz and as the
> label volume the same volume where you’ve set all voxels to zero.
>
> Peace,
>
> Matt.
>
> From: Yizhou Ma
> Date: Sunday, March 22, 2015 at 4:56 PM
> To: Matt Glasser
> Subject: Re: [HCP
actually
have different ideas as to what is the medial wall. They label brain
structures on what HCP considered the medial wall (this doesn't seem to
make sense but it is true in the data).
Best,
Cherry
On Sun, Mar 22, 2015 at 4:58 PM, Yizhou Ma wrote:
>
> -- Forwar
-- Forwarded message --
From: Yizhou Ma
Date: Sun, Mar 22, 2015 at 4:56 PM
Subject: Re: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read
To: "Glasser, Matthew"
Hi Matthew,
I am trying to calculate the correspondence between the HCP ICA
parcellations
Dear HCP experts,
I'd like to report what seems to me a problem with ciftiopen. When I opened
a .dscalar.nii file with ft_read_cifti, I got 96854 grayordinates. Yet when
I used ciftiopen, I got 91282 grayordiantes. It seems to me that ciftiopen
automatically left out where there is a "NaN" in the
nd also upload the dense
> label file that is giving you problems. If file size is a problem, please
> send the file (preferably off-list) to me.
>
> Best wishes,
> Jan-Mathijs
>
>
> On Mar 8, 2015, at 7:37 PM, Yizhou Ma wrote:
>
> Update: I can not open .dlabel.nii file
Update: I can not open .dlabel.nii files with ft_read_cifti. Error message
is:
Dot name reference on non-scalar structure.
Error in ft_read_cifti (line 930)
key = NamedMap.LabelTable.Key;
On Sun, Mar 8, 2015 at 12:49 PM, Yizhou Ma wrote:
> Hi Dr. Schoffelen,
>
> T
://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB
Also just to mention that both yours and Timothy's email never got into my
mailbox. I wouldn't have seen them if I did not read the HCP digest.
Thanks,
Cherry
On Sun, Mar 8, 2015 at 12:38 AM, Yizhou
much more than mine does and will hopefully
> end up being the replacement).
>
> Peace,
>
> Matt.
>
> From: Yizhou Ma
> Date: Sunday, March 8, 2015 at 12:34 AM
> To: Matt Glasser
> Cc: "hcp-users@humanconnectome.org"
> Subject: Re: [HCP-Use
k carefully that all versions of that on your machine are the
> latest version.
>
> Peace,
>
> Matt.
>
> From: Yizhou Ma
> Date: Sunday, March 8, 2015 at 12:27 AM
> To: Matt Glasser
> Cc: "hcp-users@humanconnectome.org"
> Subject: Re: [HCP-U
tent field 'LabelTable'.
Best,
Cherry
On Sun, Mar 8, 2015 at 12:27 AM, Yizhou Ma wrote:
> Hi,
>
> Since "melodic_IC.dscalar.nii" for d=25 seemed to be the only file that I
> could not open, I just unzipped all my group ICA maps and now the new
> "melodic_IC.ds
ad by ciftiopen.
Best,
Cherry
On Sun, Mar 8, 2015 at 12:18 AM, Glasser, Matthew
wrote:
> I’m puzzled by that as well, unless you don’t have write permission to
> the location which can mess things up.
>
> Peace,
>
> Matt.
>
> From: Yizhou Ma
> Date: Sunday,
-- Forwarded message --
From: Yizhou Ma
Date: Sun, Mar 8, 2015 at 12:07 AM
Subject: Re: [HCP-Users] Difficulties reading cifti into matlab with
ft_read_cifti or ciftiopen
To: "Glasser, Matthew"
Hi Dr. Glasser,
I moved everything I need to open under the /bin just to
Dear HCP experts,
I am experiencing difficulties reading cifti into matlab.
For the ICA maps (melodic_IC.dscalar.nii). I used:
cifti=ft_read_cifti('melodic_IC.dscalar.nii')
The error I got was:
Error using read_nifti2_hdr (line 56)
cannot open melodic_IC.dscalar.nii as nifti file, hdr size = 16
subjects) for the PTN release but it never got done yet -
> maybe we should make sure that gets done for the next PTN release."
>
> Peace,
>
> Matt.
>
> From: Yizhou Ma
> Date: Friday, March 6, 2015 at 11:11 AM
> To: Matt Glasser
> Cc: Timothy Coalson , "
t; (because we don’t apply any volume-based smoothing), however as soon as you
> try to average these maps across subjects (to create melodic_IC_sum.nii.gz)
> you aren’t aligning like with like any more and hence get an inaccurate
> result.
>
> Peace,
>
> Matt.
>
> F
file from an existing cifti file, rather than
> downloading it.
>
> Tim
>
>
> On Mon, Mar 2, 2015 at 2:13 PM, Yizhou Ma wrote:
>
>> Thank you for your suggestion Dr. Harms. It seems that it is the only way
>> to compare subcortical networks at this moment.
>
ool of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: Yizhou Ma
> Date: Sunday, March 1, 2015 10:23 PM
> To: Matt Glasser
>
> Cc: "hcp-users@humanconnectome.org"
&
ve two gyri where others have
> only one). Thus, it’s really better to do your cortical analysis on the
> surface to begin with, as we do in the HCP with CIFTI.
>
> Peace,
>
> Matt.
>
> From: Yizhou Ma
> Date: Sunday, March 1, 2015 at 9:27 PM
> To: Timothy Coa
Hi,
I am still looking forward to getting help on this issue. Is an "Atlas_ROIs.
2.nii.gz" or similar files provided for volume to surface mapping onto R440
group template? If not, will there be any in the future?
Thanks,
Cherry
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HCP-Users mailing l
ce, instead the cerebellum is included as voxels), as it is
> currently not feasible to segment subject cerebellums into surfaces.
>
> Tim
>
>
> On Mon, Feb 2, 2015 at 8:22 AM, Yizhou Ma wrote:
>
>> Dear HCP experts,
>>
>> I have a map in volumetric space and
Dear HCP experts,
I have a map in volumetric space and I am trying to project it onto the
R440 template. I am trying to use wb_command -volume-to-surface-mapping
&-cifti-create-dense-scalar. It works fine for the two hemispheres. Yet for
subcortical volume, I can not find a label volume file for t
Dear HCP experts,
I am looking at the group ICA maps released by HCP, which as I understand
should be mapped on to the R440 group-average template (?).
I am wondering if the label files for structural parcellation, including
aparc, aparc.a2009s, and BA can be generated on this template so that I
e using the Aspera
> download tool when the download was interrupted, if you open the Aspera
> tool again, it will already have the remaining cases already queued up.
>
> -Dan
>
> From: Yizhou Ma
> Date: Saturday, December 27, 2014 4:10 PM
> To: "hcp-users@humanconnect
Dear HCP users,
I am wondering if I can download a portion of the S500 data by specifying
the subject IDs. My download of the S500 data got interrupted and I am left
with 100+ subjects not downloaded. I have figured out their subject IDs.
Just wondering if it is possible to use some kind of filter
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