Dear Experts:
I have a question for MSMAll alignment for MultiRunICAFIX cleaned data.
Once I run the MultiRunICAFIX pipeline, I get the output like
"${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii".
But I want to align the data (e.g.,
${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii)
Dear Experts:
We’re acquiring HCP-style data, and running HCP pipelines. We are following the
order of pipelines as Matt suggested.
But I have concerns about final output of MSMAll pipeline for rfMRI data set.
Once we run the MSMAllPipeline and DeDriftAndResamplePipeline, we get final
output
stion about the MSMAll pipeline inputs, I would need to see what you have.
>
> Matt.
>
> From: <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Sang-Young Kim
> mailto:sykim...@gmail.com>>
> Date: Friday, September 28, 2018 at 6:55 PM
> T
t; the native mesh surfaces to achieve the most fidelity to the original
> segmentation, and then resample afterward, but the 32k surfaces are probably
> good enough.
>
> Tim
>
>
> On Fri, Sep 28, 2018 at 6:04 PM, Sang-Young Kim <mailto:sykim...@gmail.com>> wrote:
> De
Dear Experts:
I have a certain kinds of volume maps in MNI space. I would like to mapping
this map to surface.
I know how to use wb_command -volume-to-surface-mapping.
My question is that if I use following command, is this also multi-modal
surface matched map?
t}/MNINonLinear/xfms/standard2acpc_dc.nii.gz to
> warp the data to structural space (and can use a 2mm reference volume in
> that space if you wish to keep it at the same resolution).
>
> Peace,
>
> Matt.
>
> On 7/24/18, 12:27 PM, "hcp-users-boun...@humanconnecto
ace, which is normally located in ${Subject}/MNINonLinear/xfms after
fMRIVolume pipeline.
Could you please let me know where to find it?
Thanks.
Sang-Young Kim, Ph.D.
Postdoctoral Fellow
Department of Radiology
University of Pittsburgh
___
HCP-Users ma
Dear experts:
I’m trying to do tfMRI volume-based analysis and have tried to run the script
"TaskfMRIAnalysisBatch.sh".
When I set the variable VolumeBasedProcessing="NO" in the script, I was able to
run the tfMRI data on grayordinate space without any error. But if I changed
the variable to
for that purpose? Or could someone kindly provide
an example script for converting EPrime text file to EV file (e.g.,
${Subject}/unprocessed/${tfMRIName}/LINKED_DATA/EPRIME/EVs)?
If not available, please give me some advise how to do that.
Thanks in advance.
Sang-Young Kim, Ph.D
Postdoctoral Fellow
> to run the job on a machine with more RAM.
>
> Peace,
>
> Matt.
>
> From: Sang-Young Kim <sykim...@gmail.com <mailto:sykim...@gmail.com>>
> Date: Monday, October 9, 2017 at 9:58 AM
> To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu&
r/Results/${fMRIName}/${fMRIName}.nii.gz@${StudyFolder}/${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}.nii.gz
> 2000
> ${StudyFolder}/${Subject}/MNINonLinear/Results/${ConcatName}/${ConcatName}.nii.gz
>
> Peace,
>
> Matt.
>
> From: Sang-Young Kim <sykim...@
is is all that the multi-run
> ICA+FIX pipeline does differently from regular ICA+FIX.
>
> I’ll let Steve answer that other question.
>
> Matt.
>
> From: Sang-Young Kim <sykim...@gmail.com <mailto:sykim...@gmail.com>>
> Date: Friday, October 6, 2017 at 11:06 AM
&
<mailto:st...@fmrib.ox.ac.uk>>
> Date: Friday, October 6, 2017 at 1:49 AM
> To: Sang-Young Kim <sykim...@gmail.com <mailto:sykim...@gmail.com>>
> Cc: "hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>"
> <hcp-users@humanconnect
we do group ICA using each data processed with ICA+FIX?
What is the optimal way to do combining analysis across each run?
Any insights would be greatly appreciated.
Thanks.
Sang-Young Kim
***
Postdoctoral Research Fellow
Department
the -volume-all
> data_sub.nii portion of the command.
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org
> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Sang-Young Kim
> <sykim...@gmail.com <mailto:sykim...@gmail.com>&
vertices
Could anyone please explain what’s wrong with data processing?
Since I didn't see any error messages when I ran the HCP pipeline, I have no
idea why CIFTI file does not contain volume data.
Thanks in advance.
Sang-Young Kim
Postdoctoral Research Fellow
Department of Radiology, University
son <kjami...@umn.edu> wrote:
>
> In your FSL FIX installation, you can try making the same change in line #307
> of call_matlab.sh
>
> -Keith
>
> On Mon, Sep 11, 2017 at 6:34 PM, Sang-Young Kim <sykim...@gmail.com
> <mailto:sykim...@gmail.com>> wrot
ipeline.sh from:
>
> ML_PATHS="addpath('${FSL_MATLAB_PATH}'); addpath('${FSL_FIX_CIFTIRW}');"
>
> to
>
> ML_PATHS="restoredefaultpath; addpath('${FSL_MATLAB_PATH}');
> addpath('${FSL_FIX_CIFTIRW}');"
>
> -Keith
>
> On Mon, Sep 11,
t; Matt.
>
> On 9/11/17, 4:19 PM, "hcp-users-boun...@humanconnectome.org
> <mailto:hcp-users-boun...@humanconnectome.org> on behalf of
> Sang-Young Kim" <hcp-users-boun...@humanconnectome.org
> <mailto:hcp-users-boun...@humanconnectome.org> on behalf of
&
t;ciftiopen" function directly on the matlab. It
worked in matlab.
But I have no idea why above error came up while running FIX.
Any insights would be greatly appreciated.
Thanks.
Sang-Young Kim, Ph.D.
Postdoctoral Fellow
Department of Radiology, Universi
6173
> St. Louis, MO 63110Email: mha...@wustl.edu
>
> On 8/25/17, 11:23 AM, "hcp-users-boun...@humanconnectome.org on behalf of
> Sang-Young Kim" <hcp-users-boun...@humanconnectome.org on behalf of
> sykim...@gmail.com> wrote:
>
> Dear HCP users:
>
&
opposite direction (e.g., PA) for topup. So I
have 1x113 bval and 3x113 bvec for DWI AP data, and 1x1 bval (e.g., 0 value)
and 3x1 bvec (also 0 values) for DWI PA data.
Something is wrong in bval and/or bvec file?
It will be greatly appreciated if you can help me.
Thanks in advance.
Sang
Dear HCP experts:I’m trying to install FSL FIX on my Mac in order for applying ICA+FIX on rfMRI data. I have installed R packages and MATLAB Runtime Componentas indicated in README text file of FSL FIX folder. And I have edited the "settings.sh" script to reflect my system setup as
ion to recommend it.
>
> I'm sorry for your frustration in dealing with this issue. Thank you for
> asking this on the list. Hopefully, this reply will prevent some others from
> experiencing the same frustration.
>
> Tim
>
> On 05/17/2017 09:31 AM, Sang-Young Kim wrot
Dear HCP users:
In FreeSureferPipeline script (e.g., FreeSurferHiresWhite), it looks like that
cp --preserve=timestamps option does not work in Mac OSX.
I have spent lots of times to fix this problem and cause a lot of frustration.
My question is that whether I can use the option rsync -t to
Dear all:
I’m running HCP pipeline script on our Siemens Prisma data. I would like to see
whether gradient nonlinearity on Siemens Prisma scanner would cause visible
error on segmentation result. I got the gradient coefficient file from the
scanner.
If I set the variable of
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