Hello All,
I am having a bug with my Gradient Distortion Unwarp process in prefreesurfer
and wanted to reach out for ideas.
This is what is shows:
START: GradientDistortionUnwarp
gradunwarp-INFO: Parsing
/mnt/md126p2/Ubuntu/home/functionalspinelab/NecessaryDownloads/HCPpipelines-master/coeff_A
HI - looks like maybe the fieldmap inputs are not setup correctly?
Cheers.
> On 17 Jul 2018, at 12:19, Hawasli, Ammar wrote:
>
> Hello All,
>
> I am having a bug with my Gradient Distortion Unwarp process in prefreesurfer
> and wanted to reach out for ideas.
>
> This is what is shows:
>
>
Dear all,
We already downloaded the data of Resting State fMRI FIX-Denoised (Compact)
of 100 unrelated subjects. We wanted to do some analysis on these data
(rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii), so we need the coordinates of
these surface time-series. Could you please explain where I c
Hi Ammar,
Please post your .bat call to the pipeline script. Most likely you need to set
somethings to NONE
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Steve Smith mailto:st...@fmrib.ox.ac.uk>>
Date: Tuesday, July 17, 2018 at 11:23 AM
To: "Hawasli, Ammar" mailto:h
Here is the batch script
get_batch_options() {
local arguments=("$@")
unset command_line_specified_study_folder
unset command_line_specified_subj
unset command_line_specified_run_local
local index=0
local numArgs=${#arguments[@]}
local argument
while [ ${index} -
For any given subject, the coordinates of the surfaces are given in the surface
file, e.g.
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.midthickness_MSMAll.32k_fs_LR.surf.gii.
Note that you should be using the MSMAll FIX cleaned data.
Peace,
Matt.
From:
m
Hi Ammar,
Check these paths:
SpinEchoPhaseEncodeNegative="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_AP.nii.gz"
SpinEchoPhaseEncodePositive="${StudyFolder}/${Subject}/unprocessed/3T/T1w_MPR1/${Subject}_3T_SpinEchoFieldMap_PA.nii.gz”
Matt.
Thanks Tim, That was so detailed and helpful, so appreciated !
However, other libraries are still missing: libhdf5_hl.so.6 and libhdf5.so.6.
I have tried to link these libraries to existing ones (after copying) as
suggested in here:
https://sr6033.github.io/linux/2017/05/26/Installing-libhdf5-in-
>From what I recall, the s3fs mounting doesn't give feedback when it fails,
and the nitrc-ce web interface assumes it succeeds. Double check for typos
in both your access ID and secret access key (BOTH will have changed, I
believe). After this, use the command line to issue the mount command, and
Dear All,
I am new to the HCP MR pipelines and was wondering if anyone can provide
guidance on how to generate magnitude and phase field maps for input to
PreFreeSurferPipelineBatch.sh
The files that I currently have from the Siemens 3T scanner are:
SpinEchoFieldMap_PA
SpinEchoFieldMap_AP
Tha
Hi,
If you are using SEFMs, you don't need to generate magnitude and phase field
maps. It is handled internally. See the Batch script in the Examples
directory.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Thank you, Michael!
Do you know for this section:
# "Effective" Echo Spacing of *Spin Echo Field Maps*. Specified in
seconds.
# Set to "NONE" if not used.
# SEEchoSpacing = 1/(BWPPPE * ReconMatrixPE)
# where BWPPPE is the "BandwidthPerPixelPhaseEncode" = DIC
Hi Michael,
Another quick question…
What would be appropriate values for:
DwellTime
SEUnwarpDir
TopupConfig
Thanks!
Marc
On 18 Jul 2018, at 0:20, Harms, Michael wrote:
> Hi,
> If you are using SEFMs, you don't need to generate magnitude and phase
> field maps. It is handled internally.
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