Dear HCP experts,
we got some images from a different center, and their T1 MPRAGE has voxel
dimensions of 1mm in all directions, but their T2 image is 0.5mm*0.5mm*1mm.
Would this be fine for structural HCP pipelines, or would it be a problem
that the resolution is different?
Thanks in advance!
>
> Matt.
>
> From: on behalf of Darko Komnenić
>
> Date: Monday, October 8, 2018 at 8:33 AM
> To: "hcp-users@humanconnectome.org"
> Subject: [HCP-Users] archiving the results from HCP pipellines
>
> Dear HCP experts,
> in my lab, we are trying to free
Dear HCP experts,
in my lab, we are trying to free up disk space, and are looking into
archiving some of the previous analyses we did with HCP pipelines. Since
the complete data is quite large, we were considering just saving the
initial T1 and T2 nifti images and the myelin maps that get produced
Dear HCP experts,
after obtaining myelin maps for the participants in my sample, I was
wondering if there's an easy way to turn the visual information that we see
when we overlay the maps on a surface, into numerical information? For
instance, having the average myelin value per region for each
Great, thanks!
On Tue, Aug 21, 2018 at 4:13 PM, Glasser, Matthew
wrote:
> Right 1mm in all directions and preferably 0.8mm or less in all directions.
>
> Matt.
>
> From: Darko Komnenić
> Date: Tuesday, August 21, 2018 at 9:12 AM
> To: Matt Glasser
> Cc: "
won’t work well.
>
> Matt.
>
> From: on behalf of Darko Komnenić
>
> Date: Tuesday, August 21, 2018 at 4:42 AM
> To: "hcp-users@humanconnectome.org"
> Subject: [HCP-Users] A 2D T2-scan for HCP Pipelines?
>
> Dear HCP experts,
> I got asked today if the
Dear HCP experts,
I got asked today if the HCP pipelines can also be used with a 3D T1 scan
and a 2D T2 scan. Based on what I saw in the FAQ, I said no, but I would
like to double check with you, so as not to give out any misinformation.
So, if the dimensions of the T2 scan are only 2D, can that
g the L/R
> differences. Assuming you had a larger sample size and the pattern stayed
> the same, the differences would be bilateral.
>
> Matt.
>
> From: Darko Komnenić
> Date: Friday, August 10, 2018 at 1:18 PM
> To: "Harms, Michael"
> Cc: Matt Glasser , &qu
> All the best,
>
>
>
> Anderson
>
>
>
>
>
> *From: *"Glasser, Matthew"
> *Date: *Wednesday, August 8, 2018 at 17:05
> *To: *"Harms, Michael" , Darko Komnenić <
> komnen...@gmail.com>
>
> *Cc: *"Winkler, Anderson (NIH/NIMH)
g>.
> Tel: 314-747-6173
>
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> *From: * on behalf of Darko
> Komnenić
> *Date: *Tuesday, August 7, 2018 at 6:50 AM
> *To: *"Glasser, Matthew"
>
> *Cc: *"hcp-users@humanconnectome.org
, Aug 6, 2018 at 9:03 PM, Glasser, Matthew wrote:
> Can you just make a simple effect size map with + and – and no
> thresholding?
>
> Matt.
>
> From: Darko Komnenić
> Date: Monday, August 6, 2018 at 12:09 PM
>
> To: Matt Glasser
> Cc: "hcp-users@humanconnect
contrast changing with
> post-mortem MRI imaging.
>
> Peace,
>
> Matt.
>
> From: on behalf of Darko Komnenić
>
> Date: Tuesday, July 3, 2018 at 4:51 PM
> To: "hcp-users@humanconnectome.org"
> Subject: [HCP-Users] Comment on the paper by Righart et a
Dear HCP experts,
I've just read the paper by Righart et al. where they correlated the T1/T2
ratio to histopathological data acquired from post mortem brains. They
report that the only parameter that correlated with T1/T2 ratio was
dendrite density, whereas myelin content/density as measured
I would delete ${StudyFolder}/${Subject}/T1w/${Subject}
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Darko Komnenić
> <komnen...@gmail.com>
> Date: Monday, May 7, 2018 at 10:36 AM
> To: "hcp-users@humanconnectome.org
Dear HCP experts,
I am comparing cortical myelin content between patients and controls. I
manually corrected some brainmasks and tried to rerun the FS pipeline,
which failed at the HiResPial step, because I forgot that some lines of the
script have been commented out.
Can I just rerun everything
att.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Darko Komnenić
> <komnen...@gmail.com>
> Date: Wednesday, February 28, 2018 at 8:16 AM
> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subjec
Dear HCP experts,
if the PreFreeSurferPipelineBatch script finished successfully, and then
the FreeSurfer one finished with errors, but made some new output files
before stopping, is it OK to just simply rerun FreeSurferPipeline script on
the same participants? Or should I first delete all the new
hout
error, or at least return a different error than before.
I am not sure why this problem arose, since, as I mentioned, this pipeline
completed successfully several months ago.
Cheers,
Darko
On Sat, Feb 24, 2018 at 12:32 AM, Darko Komnenić <komnen...@gmail.com>
wrote:
> Thanks, Tim, I'll t
script has the unmatched quote.
>
> Tim
>
>
> On Fri, Feb 23, 2018 at 1:03 PM, Darko Komnenić <komnen...@gmail.com>
> wrote:
>
>> Alright, thank you!
>> Darko
>>
>> On Fri, Feb 23, 2018 at 6:20 PM, Glasser, Matthew <glass...@wustl.edu>
>>
nother computer/or in a VM where you install stuff from
> scratch and see if the issue persists.
>
> Peace,
>
> Matt.
>
> From: Darko Komnenić <komnen...@gmail.com>
> Date: Friday, February 23, 2018 at 6:25 AM
>
> To: Matt Glasser <glass...@wustl
> Peace,
>
> Matt.
>
> From: Darko Komnenić <komnen...@gmail.com>
> Date: Thursday, February 22, 2018 at 4:49 AM
> To: Matt Glasser <glass...@wustl.edu>
>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Use
Hi Matt,
yes, I am using bash.
On Wed, Feb 21, 2018 at 9:56 PM, Glasser, Matthew <glass...@wustl.edu>
wrote:
> That is the shell command to source a script. Are you using bash as your
> shell?
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome
n Mon, Jan 29, 2018 at 10:39 PM, Glasser, Matthew <glass...@wustl.edu>
wrote:
> gedit with bash shell highlighting (sh).
>
> Matt
>
> On 1/29/18, 11:50 AM, "Darko Komnenić" <komnen...@gmail.com> wrote:
>
> >Hi Matt,
> >could you please tell me whi
es, so you must have done something
> to your version of the script.
>
> Peace,
>
> Matt.
>
> From: Darko Komnenić <komnen...@gmail.com<mailto:komnen...@gmail.com>>
> Date: Friday, January 26, 2018 at 11:58 AM
> To: Matt Glasser <glass...@wustl.edu<m
Hi Michael and Matt,
if I'm interpreting the output correctly, the “$var” resolve as following:
"$SubjectID" --->
--subject=VIMS_HC_034
"$SubjectDIR" --->
--subjectDIR=/home/lisak/Desktop/NMDA_HCP/controls/VIMS_HC_034/T1w
"$T1wImage" ---> there are actually two things here
t; Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of Darko Komnenić
> <komnen...@gmail.com>
> Date: Monday, January 22, 2018 at 10:59 AM
> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: [HCP
Dear HCP experts,
I am trying to compare the cortical myelin content between patients and
healthy controls. I ran the pre-FreeSurfer and FreeSurfer pipelines, and
they finished without reporting an error. When I tried to run the
Post-FreeSurfer pipeline, I received the following error note after
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