Sounds like it can't find the freesurfer executables. This page might help:
https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration On Feb 17, 2015, at 11:14 AM, Dr Sampada Sinha <drsampadasi...@gmail.com> wrote: > Dear HCP team members, > > Sorry for bothering you all again. But this time the analysis got stuck in > its initial FreeSurfer processing with the following error: > > /xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPipeline.sh: > line 78: recon-all: command not found. > > Ful details of the error is given below: > > xxx@ndy10 > [/xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/Examples/Scripts] % > ./FreeSurferPipelineBatch.shThis script must be SOURCED to correctly setup > the environment prior to running any of the other HCP scripts contained here > > LS2001 > About to use fsl_sub to queue or run > /xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPipeline.sh > /xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/FreeSurfer/FreeSurferPipeline.sh: > line 78: recon-all: command not found > set -- --subject=LS2001 > --subjectDIR=/xxx/xxx/xxx/xxx/HCP_data/LS2001/T1w > --t1=/xxx/xxx/xxx/xxx/HCP_data/LS2001/T1w/T1w_acpc_dc_restore.nii.gz > --t1brain=/xxx/xxx/xxx/xxx/HCP_data/LS2001/T1w/T1w_acpc_dc_restore_brain.nii.gz > --t2=/xxx/xxx/xxx/xxx/HCP_data/LS2001//T1w/T2w_acpc_dc_restore.nii.gz > --printcom= > . > /xxx/xxx/xxx/xxx/HCP_data/scripts/Pipelines-3.4.0/Examples/Scripts/SetUpHCPPipeline.sh > > Also, will you please let me know if there are separate scripts for the > analysis of lifespan data without the gradient distortion correction. > > Thank you so much for your patience and your time… > > With kind regards, > > Sampada > > -- > Sampada Sinha > Post-Doctoral Associate > University of Minnesota (East Bank) > Molecular and neuroimaging laboratory > Department of Psychiatry > Minneapolis-55415 > > > > > > > > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
