Hi all,
I have the same problem, so I split the 4800 volumes in half and used
only 2400 data points so that I have at least two 15-min sessions (2x 1200)
with both phase encoding directions (I'm using the node timeseries
txt-files). I also thought about looking at the other 2400 data points and
mins. Best to do all four though.
Peace,
Matt.
From: David Hofmann davidhofma...@gmail.com
Date: Monday, February 2, 2015 at 3:16 PM
To: Matt Glasser glass...@wusm.wustl.edu
Cc: Chao Liu chao@brunel.ac.uk, hcp-users@humanconnectome.org
hcp-users@humanconnectome.org
Subject: Re
Hi,
I was wondering how much spatial smoothing was applied to the RS data (the
data where the node timeseries are based upon) ?
greetings
David
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HCP-Users@humanconnectome.org
Hi all,
since I want to select an independent subsample from the node-timeseries
data (due to some computational intensive analysis), I was wondering how to
find out which persons are related?
greetings
David
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HCP-Users mailing list
data.
Regards,
Mike
*From:* hcp-users-boun...@humanconnectome.org [mailto:
hcp-users-boun...@humanconnectome.org] *On Behalf Of *Hodge, Mike
*Sent:* Wednesday, June 24, 2015 10:48 AM
*To:* David Hofmann; hcp-users
*Subject:* Re: [HCP-Users] Selecting a subsample of unrelated persons
of Medicine
> 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 David Hofmann <
> davidhofma...@gmail.com>
> Date: Wednesday, J
long rows for better or for worse…
>
> Peace,
>
> Matt.
>
> From: David Hofmann <davidhofma...@gmail.com>
> Date: Thursday, July 14, 2016 at 12:14 PM
>
> To: Matt Glasser <glass...@wustl.edu>
> Cc: Stephen Smith <st...@fmrib.ox.ac.uk>, &q
correct?
>
> Thanks so much for the support :)
>
> David
>
> 2016-07-15 4:50 GMT+02:00 Glasser, Matthew <glass...@wustl.edu>:
>
>> That’s fine, I usually have time along rows for better or for worse…
>>
>> Peace,
>>
>> Matt.
>&
uld recommend using the data with _hp2000_clean in the name. I a
> referring to taking the mean across time at each point in space and
> subtracting that from the data.
>
> Peace,
>
> Matt.
>
> From: David Hofmann <davidhofma...@gmail.com>
> Date: Tuesday
y/
>
> But keep in mind that for neocortex, you can take advantage of the surface
> data the HCP provides (e.g., fsaverage_32k/*surf.gii, *dscalar.nii and
> *dtseries.nii). You can get better inter-subject registration/alignment on
> the surface, if that will be a factor in your st
gt; Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of David Hofmann <
> davidhofma...@gmail.com>
> Date: Saturday, October 29, 2016 at 7:58 AM
> To: hcp-users <hcp-users@humanconnectome.org>
> Subject: [HCP-Users] Question about the multi-moda
near detrend.
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of David Hofmann <
> davidhofma...@gmail.com>
> Date: Thursday, June 29, 2017 at 7:56 AM
> To: hcp-users <hcp-users@humanconnectome.org>
> Subject: [HCP-Users] How t
gt; St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of David Hofmann <
> davidhofma...@gmail.com>
> Date: Friday, June 30, 2017 at 6:04 PM
> To: hcp-users <hcp-users@humanconnectome.org>
> Subject: [HCP-Use
Hi all,
since the final data release is now out, I was wondering what the maximal
number of unrelated subjects is, that have complete 3T resting state and
task data and if there will be an update on the 100 subjects that can be
downloaded so far soon?
greetings
David
Hi all,
I was wondering how to choose the high-pass filter cut-off period (in
seconds) for the task data when the block onset files are used for the 1st
level GLM (with spm12). As far as I understood the period should be around
twice the period until a block repeats.
Based on the .txt onset
Hi all,
I downloaded the preprocessed (bedpostx) DTI data. I used some seeds based
on the anatomy toolbox for the basolateral, centromedial and superficial
amygdala and ran FSL to quantify the structural connections within these
nuclei for the left hemisphere.
It seemed to work, but I have my
Dear all,
as far as I read in previous posts on the list, spatial smoothing of the
volumetric resting state data is not recommended. But this was with regard
to group ICA.
Would you also recommend not to apply any further spatial smoothing for the
(volumetric) resting state data, when running
caused by adding
> volume-based smoothing, because they could be from nearby areas instead.
>
> Tim
>
>
> On Tue, May 29, 2018 at 4:24 PM, David Hofmann
> wrote:
>
>> Dear all,
>>
>> as far as I read in previous posts on the list, spa
hew
> wrote:
>
>> Indeed that is one of the major fallacies in brain imaging. Have a look
>> at this paper in press at PNAS:
>>
>> https://www.biorxiv.org/content/early/2018/04/23/255620
>>
>> Peace,
>>
>> Matt.
>>
>> From: David
Hi all,
I'm having trouble finding the data with the partial correlations of e.g.
the 300 ROI ICA for each subject. Can someone point me in the right
direction here?
Very much appreciated :).
greetings
David
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t;
> I doubt that matters for this application of making an unstructured noise
> timeseries for the purpose of variance normalization.
>
> Matt.
>
> From: "Harms, Michael" <mha...@wustl.edu>
> Date: Wednesday, March 7, 2018 at 12:09 PM
>
> To: Matt Gla
tps://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>.
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
>
>
> *From: *Timothy Coalson <tsc...@mst.edu>
> *Date: *Wednesday, March 7, 2018 at 5
8134
>
> 660 South Euclid Ave
> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>.
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO 63110 Email:
> mha...@wustl.edu
>
>
>
> *From: *David Hofmann
ral standard deviation of the unstructured noise
> timeseries and divide the data by it to get the variance normalized data.
>
> Peace,
>
> Matt.
>
> From: David Hofmann <davidhofma...@gmail.com>
> Date: Wednesday, March 7, 2018 at 10:47 AM
>
> To: Matt Glasser &
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of David Hofmann <
> davidhofma...@gmail.com>
> Date: Wednesday, March 7, 2018 at 2:32 AM
> To: hcp-users <hcp-users@humanconnectome.org>
> Subject: [HCP-Users] Concatenating resting state runs
&g
Hi all,
for a later analysis where I extract ROIs with SPM, I need to concatenate
the resting state runs and want to make sure I'm doing it correctly. SPM
extracts the first eigenvariate of a ROI, i.e. the component that explains
the most variance.
I'm using the* Resting State fMRI 1
know if the order
> matters. If you are interested in effects that might be related to order
> (e.g. drowsiness being higher in later scans, then order might matter).
>
> Peace,
>
> Matt.
>
> From: David Hofmann <davidhofma...@gmail.com>
> Date: Wednesday, March 7, 2018
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of David Hofmann <
> davidhofma...@gmail.com>
> Date: Tuesday, February 27, 2018 at 4:52 AM
> To: hcp-users <hcp-users@humanconnectome.org>
> Subject: [HCP-Users] Concatenate sess
Hi all,
I would like to concatenate the RL and LR files from the Emotion task
(modelling the sessions separately is not an option for the analysis I want
to do later on) and thus have to change the onsets in fear.txt and neu.txt
for the second session accordingly. I'm not quite sure how to do
icine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>.
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO 63110 Email:
> mha...@wust
hiatry, Box 8134
>
> 660 South Euclid Ave
> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>.
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO 63110 Email:
> mha...@wustl.edu
>
>
>
> *From: *<h
of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>.
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO 63110 Email:
> mha...@wust
Hi all,
I was taking a look at the ICA (100) node time series and noticed that some
ROIs have relatively large magnitude while others have a smaller magnitude
(see attached pictures). Can someone explain to me how these differences
arise? In other words, is this the "natural" BOLD activity within
sorry, I meant the differences in scaling across nodes within a subject.
Thanks!
Am Do., 25. Okt. 2018 um 10:27 Uhr schrieb Steve Smith :
> Hi - do you mean differences in scaling across nodes, or within-node
> differences across subjects?
> Cheers.
>
>
> On 25 Oct 2018, at 09
ave different amplitudes, but the scaling (for any
> given node) is consistent across subjects.
>
> btw it looks like the actual stddev of those two timeseries are not
> massively different.
>
> Cheers.
>
>
>
> > On 24 Oct 2018, at 23:46, David Hofmann wrote:
> >
>
Hi all,
I want to calculate some seed-based functional connectivity using the RS
fix-extended dataset for 3T and 7T. Would you recommend filtering in the
frequency range 0.01-0.1 Hz as it is normally in the preprocessing of RS
data before FC calculation?
Thanks in advance,
David
I see. Thanks very much :)
2018-09-22 13:44 GMT+02:00 Steve Smith :
> Hi - In this case the FIX-cleaned data supplied by HCP.
> Cheers.
>
>
> On 22 Sep 2018, at 12:27, David Hofmann wrote:
>
> Hi Steve,
>
> thanks for the quick reply. Just one follow-up question:
I personally am not a believer in lowpass
> filtering clean data.
> Cheers, Steve.
>
> On 22 Sep 2018, at 11:29, David Hofmann wrote:
>
> Hi all,
>
> I want to calculate some seed-based functional connectivity using the RS
> fix-extended dataset for 3T and 7T. Would you recommend fil
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