Hello dear experts,
I am very new to HCP so I am struggling with a lot of confusion and hope
you can help. I would like to calculate seed-based FC of hippocampus of two
groups (patients/controls) and to perform a group comparison between them.
Now I am not sure about how to proceed. I see two
e based essentially on
>the means and variances of your group).
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa
> Kramarenko <lisa.kramare...@gmail.com>
> Date: Friday, April 7, 2017 at 9:06 AM
> To: "hcp-users@humancon
ubject. You can then do statistics on these maps (e.g. with the FSL PALM
> software tool). You may wish to do the Fisher transform on the correlation
> maps first with wb_command -cifti-math “atanh(x)” -var x
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@human
users-boun...@humanconnectome.org> on behalf of Lisa
> Kramarenko <lisa.kramare...@gmail.com>
> Date: Thursday, July 13, 2017 at 7:25 AM
> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] Calculation of myelin maps
>
&g
Dear Matt,
I completed all three structural pipelines and performed PALM comparison
for myelin maps. However, the result I got was somewhat opposed to
expectations (patients with early MS having significantly stronger
myelination compared to healthy controls).
I wondered that maybe something in
Dear Matt,
I completed all three structural pipelines and performed PALM comparison
for myelin maps. However, the result I got was somewhat opposed to
expectations (patients with early MS having significantly stronger
myelination compared to healthy controls).
I wondered that maybe something in
(just a correction: flip angle 9°, not 90 for MPRAGE)
On 13 July 2017 at 12:19, Lisa Kramarenko <lisa.kramare...@gmail.com> wrote:
> Dear Matt,
>
> I completed all three structural pipelines and performed PALM comparison
> for myelin maps. However, the result I got wa
ris_make_surfaces [options]
>
> DESCRIPTION
> This program positions the tessellation of the cortical surface at
> the
> ...
>
> then I believe you will be able to run mris_make_surfaces and thus the
> pipeline.
>
> Either way, please respond
Hello,
would it cause problems to run Pre-FS, FS, Post-FS, Volume and Surface
Functional and ICA-FIX pipelines with FSL 5.0.9 and the newest FreeSurfer
version? Is there anything I should pay attention to?
Thanks a lot!
Lisa
___
HCP-Users mailing
ou needed to. Note that you must have a field
> map of some kind for the fMRIVolume pipeline to run.
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa
> Kramarenko <lisa.kramare...@gmail.com>
> Date: Thursday, April 27, 2017
On 8 June 2017 at 09:59, Lisa Kramarenko <lisa.kramare...@gmail.com> wrote:
> I wasn't sure about the exact hacking process and just naively commented
> out lines 133-167 in the FreeSurfer script, so that I started with
> recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -n
gt;
> From: "Harms, Michael" <mha...@wustl.edu>
> Date: Wednesday, June 7, 2017 at 12:50 PM
> To: Matt Glasser <glass...@wustl.edu>, Lisa Kramarenko <
> lisa.kramare...@gmail.com>
>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconne
Dear experts,
I am getting the following error when the FreeSurferPipeline comes to the
mris_make surfaces step:
mris_make_surfaces: error while loading shared libraries: libnetcdf.so.6:
cannot open shared object file: No such file or directory
It happens when I run it on Ubuntu 14 and 16,
of the brain as grey or white matter.
>
> Peace,
>
> Matt.
>
> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
> Date: Tuesday, May 30, 2017 at 8:59 AM
>
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@hu
sing fat sat and you
> would need to exclude these subjects or fix the surfaces manually.
>
> Peace,
>
> Matt.
>
> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
> Date: Tuesday, May 30, 2017 at 7:53 AM
> To: Matt Glasser <glass...@wustl.edu&g
fact, I would look at FreeSurfer’s
> documentation.
>
> Peace,
>
> Matt.
>
> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
> Date: Tuesday, May 30, 2017 at 8:49 AM
>
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" &l
recon after my
intervention?
3. I also created some control points to fix missing white matter. Should I
put the control.dat file in the /tmp folder? Will FreeSurfer see
the file automatically or should I add some flag for it?
thanks a lot for your help!
Lisa
On 30 May 2017 at 16:38, Lisa Kramare
l Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173>
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa
sser, Matthew" <glass...@wustl.edu>
> Date: Thursday, June 8, 2017 at 8:30 AM
> To: Lisa Kramarenko <lisa.kramare...@gmail.com>
> Cc: Michael Harms <mha...@wustl.edu>, "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
>
>
ndeed you need to provide a dwell time for fMRI. This is the dwell time
> of the fMRI scan. If that doesn’t fix things up, please post the launcher
> script you are using to call the pipeline.
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on be
ndeed you need to provide a dwell time for fMRI. This is the dwell time
> of the fMRI scan. If that doesn’t fix things up, please post the launcher
> script you are using to call the pipeline.
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on be
s, MO 63110 Email: mha...@wustl.edu
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa
> Kramarenko <lisa.kramare...@gmail.com>
> Date: Monday, May 8, 2017 at 10:11 AM
> To: "Glasser, Matthew" <glass...@wustl.edu>
> Cc: "hcp-users
This tool should help: http://nrg.wustl.edu/software/dicom-browser/
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa
> Kramarenko <lisa.kramare...@gmail.com>
> Date: Thursday, May 4, 2017 at 9:27 PM
> To: "hcp-user
Dear experts,
I have a question about extracting average myelination value from a custom
roi. What I did was the following:
wb_command -cifti-stats merged_myelin_maps_group1.dscalar.nii -reduce -MEAN
-roi
file_with_significant_differences_between_the_groups_thresholded_at_1.3.dscalar.nii
I get
ellation and then
>> parcellating the myelin map and converting the parcellated file to text or
>> whatever you need.
>>
>> Peace,
>>
>> Matt.
>>
>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa
>> Kramarenko <lisa.kramare...@
c.dscalar.nii
>
> Tim
>
>
> On Thu, Oct 19, 2017 at 2:02 AM, Lisa Kramarenko <
> lisa.kramare...@gmail.com> wrote:
>
>> Hey Timothy,
>>
>> thanks for your response. Before continuing with the questions about the
>> exact implementation I am not very
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