Hello,
Upon starting to analyse our data, which was acquired with an HCP-like
protocol, with the HCP pipelines, we were wondering if there is an
available script or tool that converts DICOM to NIFTI in the HCP dir
structure.
Hope to hear from you.
Shachar Gal,
Tel Aviv University
ask that on the FreeSurfer list as that is not an HCP
> Pipeline issue. Please tell them what version of FreeSurfer you are using.
>
> Matt.
>
> From: Shachar Gal
> Date: Monday, August 20, 2018 at 10:53 AM
> To: Matt Glasser
> Cc: Niv Tik
> Subject: Re: [HCP-Users
FreeSurferLabels
ReferenceMyelinMaps
CorrectionSigma
RegName
InflateExtraScale
Thanks,
Shachar Gal, Tel Aviv University
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ctions
as to the correct workflow for using the FIX pipelines.
thank you
On Mon, 10 Dec 2018 at 23:13, Glasser, Matthew wrote:
> Did you use the hcp_fix script or some other method of running FIX on HCP
> data.
>
> Matt.
>
> From: Shachar Gal
> Date: Monday, December 10, 2018 at 7:
, Matthew wrote:
> You can still do training after running hcp_fix. As for not using hcp_fix
> initially and just running the main fix script, I haven’t tried that. You
> might need to ask on the main FSL list.
>
> Matt.
>
> From: Shachar Gal
> Date: Tuesday, December 11, 20
2018 at 21:58, Glasser, Matthew wrote:
> See lines 177-193 from the hcp_fix script.
>
> Matt.
>
> From: Shachar Gal
> Date: Tuesday, December 11, 2018 at 6:33 AM
> To: Matt Glasser
> Cc: "Harms, Michael" , "hcp-users@humanconnectome.org" <
> h
clid Ave. Tel: 314-747-6173
>
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
>
>
> *From: * on behalf of Shachar Gal <
> gal.shac...@gmail.com>
> *Date: *Friday, November 23, 2018 at 2:37 AM
> *To: *"Glasser, Matt
nd we will have new versions announced soon. PostFix generates the
> Workbench scenes for hand classification of components.
>
> Matt.
>
> From: on behalf of Shachar Gal <
> gal.shac...@gmail.com>
> Date: Monday, November 19, 2018 at 3:30 AM
> To: "hcp-users@humanco
y
>
> 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: * on behalf of
our data.
but in the hcp_fix script, i saw it calls melodic by itself, so im a
bit confused about the parallel step-by-step procedure, that includes the
hcp_fix script and the PostFix script.
hope this clears things up.
thanks,
Shachar
On Thu, 22 Nov 2018 at 17:43, Shachar Gal wrote:
>
, is there any similar documentation regarding postfix?
I'm not sure what's its purpose in the cleaning and applying procedure.
thanks.
Shachar Gal
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but regarding this repository, you mean MSM_HOCR/src/MSM ?
because the files there are .cc, which is not what the pipeline codes look
for..
On Mon, 25 Mar 2019 at 13:35, Glasser, Matthew wrote:
> It should point to where the compiled MSM binary is.
>
> Matt.
>
> From: Shac
hey
following this issue, should the $MSMBINDIR point to this whole directory,
or only to the src folder inside of it?
thanks,
Shachar
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hey,
what is the current recommendation regarding group analysis for task fmri
data?
converting to fake-nifty and analysing using fsl tools?
or is there any available tool for doing this on with CIFTI files?
cheers,
Shachar Gal
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Dear experts,
while running the fMRISurface pipeline (using the latest pipeline release)
I encountered an issue where the subcortical-processing script takes a
really long while (now running for more than 6 hours).
this is the command on which it is stuck
${CARET7DIR}/wb_command
some further information that might be useful - the output file
rfMRI_REST_AP_temp_atlas.dtseries.nii, has already been created. its in the
target folder. but the command won't stop "running"
On Sun, 31 Mar 2019 at 16:13, Shachar Gal wrote:
> Dear experts,
>
> while runn
i think the problem is somehow related to the fact that im connecting by
ssh to our server (from home..)
because when i started another session, the path to the lost file was ok
i hope thats all of it, ill update if its more than that
On Sat, 23 Mar 2019 at 21:10, Shachar Gal wrote:
> la
hey,
using the FreeSurferPipline in the new version of the Pipelines i get the
error bellow.
furthermore, the fsaverage folder is empty, so nothing was created in
there, so not only this file is missing...
Reporting on 70 segmentations
Using PrintSegStat
mri_segstats done
label mri mri.2mm scripts surf xhemi
On Sat, 23 Mar 2019 at 21:03, Glasser, Matthew wrote:
> What is present in here:
>
> /usr/local/freesurfer/subjects/fsaverage
>
> Matt.
>
> From: on behalf of Shachar Gal <
> gal.shac...@gmail.com>
> Date: Saturday, Mar
and i have a feeling you might ask, so this is my FS version
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
On Sat, 23 Mar 2019 at 20:54, Shachar Gal wrote:
> hey,
> using the FreeSurferPipline in the new version of the Pipelines i get the
> error bellow.
>
mber)
is this a bug, or am i missing something?
thanks,
Shachar Gal
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> Associate Professor of Psychiatry
>
> 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
>
>
>
>
gt;
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Associate Professor of Psychiatry
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave.
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