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
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
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 maxxx...@umn.edu wrote:
Dear HCP experts,
I have a map in volumetric space and I am trying to project it onto the
R440 template. I am
-- Forwarded message --
From: Yizhou Ma maxxx...@umn.edu
Date: Sun, Mar 22, 2015 at 4:56 PM
Subject: Re: [HCP-Users] CIFTIOPEN: NaN values in .dscalar.nii not read
To: Glasser, Matthew glass...@wusm.wustl.edu
Hi Matthew,
I am trying to calculate the correspondence between
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,
Matt.
From: Yizhou Ma maxxx...@umn.edu
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
://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 Ma maxxx
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 maxxx...@umn.edu wrote:
Update: I can not open .dlabel.nii files with ft_read_cifti. Error message
is:
Dot name reference
'LabelTable'.
Best,
Cherry
On Sun, Mar 8, 2015 at 12:27 AM, Yizhou Ma maxxx...@umn.edu 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.dscalar.nii can be opened.
I am confused
might check carefully that all versions of that on your machine are the
latest version.
Peace,
Matt.
From: Yizhou Ma maxxx...@umn.edu
Date: Sunday, March 8, 2015 at 12:27 AM
To: Matt Glasser glass...@wusm.wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject
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 =
-- Forwarded message --
From: Yizhou Ma maxxx...@umn.edu
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 glass...@wusm.wustl.edu
Hi Dr. Glasser,
I moved everything I need
aims to be much more than mine does and will hopefully
end up being the replacement).
Peace,
Matt.
From: Yizhou Ma maxxx...@umn.edu
Date: Sunday, March 8, 2015 at 12:34 AM
To: Matt Glasser glass...@wusm.wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re
formula 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 maxxx...@umn.edu wrote:
Dear HCP experts,
I am trying to reproduce the individual netmats from HCP500-PTN so that I
am sure where the numbers come
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 maxxx...@umn.edu
Date: Monday, March 30, 2015 12:26 PM
To: Stephen Smith st...@fmrib.ox.ac.uk
Cc: hcp-users
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
of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Yizhou Ma maxxx...@umn.edu
Date: Monday, March 30, 2015 6:54 PM
To: Harms, Michael mha...@wustl.edu
Cc: Stephen Smith st...@fmrib.ox.ac.uk, hcp-users@humanconnectome.org
hcp
had some of the changes made to it so I cannot tell you exactly
where to look.
Peace,
Matt.
From: Yizhou Ma maxxx...@umn.edu
Date: Sunday, March 22, 2015 at 5:33 PM
To: Matt Glasser glass...@wusm.wustl.edu
Cc: hcp-users@humanconnectome.org hcp-users@humanconnectome.org
Subject: Re
it.
Tim
On Mon, Mar 2, 2015 at 2:13 PM, Yizhou Ma maxxx...@umn.edu wrote:
Thank you for your suggestion Dr. Harms. It seems that it is the only way
to compare subcortical networks at this moment.
On Mon, Mar 2, 2015 at 12:21 PM, Harms, Michael mha...@wustl.edu wrote:
Not sure
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 maxxx...@umn.edu wrote:
Thank you Michael. My system is failing me at this moment
ICA component; this approach aims to be more robust against
component misalignment (between the group-ICA maps and individual subjects'
data) and artifacts [O’Reilly 2009, Smith OHBM 2014].
Best,
Giles
On 31 Jul 2015, at 15:50, Yizhou Ma maxxx...@umn.edu wrote:
Dear HCP
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 maxxx...@umn.edu
Date: Friday, July 31, 2015 10:16 AM
To: Giles Colclough giles.colclo...@gmail.com
Cc: hcp-users@humanconnectome.org hcp-users
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
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 maxxx...@umn.edu wrote:
I see
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
and ft_write_cifti). This
> issue has been reported to the FieldTrip developers, but as yet there has
> been no fix released.
>
> Best,
>
> Matt
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Yizhou Ma <
> maxxx...@umn.edu>
> Date: Friday, November 13, 2
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
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
> *From:* hcp-users-boun...@humanconnectome.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 propri
and will use the label color 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
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.
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 <maxxx...@umn.edu> wrote:
> Dear HCP experts,
>
> I am following this page to obtain my Amazon S3 credentials. Yet I cannot
>
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
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HCP-Users@humanconnectome.org
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
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
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
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
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: Yi
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
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,
>
>
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"
/science/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.
>
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