[HCP-Users] GradientDistortionUnwarp error help.

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

Re: [HCP-Users] GradientDistortionUnwarp error help.

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: > >

[HCP-Users] The coordinates of surface time-series of Resting State fMRI FIX-Denoised (Compact)

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

Re: [HCP-Users] GradientDistortionUnwarp error help.

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

Re: [HCP-Users] GradientDistortionUnwarp error help.

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} -

Re: [HCP-Users] The coordinates of surface time-series of Resting State fMRI FIX-Denoised (Compact)

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

Re: [HCP-Users] GradientDistortionUnwarp error help.

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.

Re: [HCP-Users] Recon-all Errors in Freesurfer HCP pipeline

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-

Re: [HCP-Users] access to hcp-openaccess-temp

>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

[HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

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

Re: [HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

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

[HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

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

[HCP-Users] Generating Field Maps for PreFreeSurferPipelineBatch.sh input

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.