I wouldn¹t use hp=pd2 unless you know what you are doing, as that option
has not been fully tested. I run with hp=0.
Matt.
On 4/13/19, 10:41 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Marta Moreno" <hcp-users-boun...@humanconnectome.org on behalf of
mmorenoort...@icloud.com> wrote:
>Dear Experts,
>
>I am running the following script MSMAllPipelineBatch.sh from
>${StudyFolder}/${Subject}/scripts after running MR ICA+FIX with success,
>and I am getting the following error:
>
>ERROR: failed to open file
>'/Volumes/data/data3/NTTMS/NTTMS_s002/NTTMS_s002_170812/MNINonLinear/Resul
>ts/RS_fMRI_MR/RS_fMRI_MR_Atlas_hppd2_clean_vn_tempcompute.dscalar.nii',
>file does not exist, or folder permissions prevent seeing it
>
>I set up the script as follow:
>
>fMRINames="RS_fMRI_MR"
>OutfMRIName="RS_fMRI_MR_REST"
>HighPass="pd2"
>fMRIProcSTRING="_Atlas_hppd2_clean"
>MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
>RegName="MSMAll_InitalReg"
>HighResMesh="164"
>LowResMesh="32"
>InRegName="MSMSulc"
>MatlabMode="1" #Mode=0 compiled Matlab, Mode=1 interpreted Matlab
>
>I checked and the file called: *tempcompute.dscalar.nii¹, is not there.
>
>What am I doing wrong? Something went wrong in the previous step while
>running MR ICA+FIX that I am not aware of?
>
>Thanks a lot!
>
>Leah.
>
>
>
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