Re: [Freesurfer] May you help me with 'recon-all' errors

2015-12-09 Thread Peng Zan
Thank you! Hopefully, I can either figure it out myself or be helped by someone. Thanks! Best, Peng On Wednesday, December 9, 2015, Bruce Fischl wrote: > Hi Peng > > nifti should be fine as input, but definitely don't use analyze. It > doesn't preserve the direction cosines so once you convert

Re: [Freesurfer] May you help me with 'recon-all' errors

2015-12-09 Thread Bruce Fischl
Hi Peng nifti should be fine as input, but definitely don't use analyze. It doesn't preserve the direction cosines so once you convert to it you will never be sure which side of the image is the left hemim and which is the right. I can't help with the 'can't locate MNI/Startup.pm ' error. H

Re: [Freesurfer] May you help me with 'recon-all' errors

2015-12-09 Thread Bruce Fischl
Hi Peng it looks like we can't read your input dicom. For example, the log says: reading from /Users/Peng/Documents/MNE/MNE_analysis/MRI/R2261_S0283/m000-gm_A0136_N12518_S0283_20120817_P5716_averageCBF_normalized.dcm... Starting DICOMRead2() dcmfile = /Users/Peng/Documents/MNE/MNE_analysis/MRI/R

[Freesurfer] May you help me with 'recon-all' errors

2015-12-09 Thread Peng Zan
Dear freesurfer expert, I am a student from University of Maryland, learning freesurfer for MNE analysis recently. I have a perhaps silly problem and could not solve by myself. The problem occurred as 'recon-all -s R2261_S0283 exited with errors...' when I was running 'recon-all -autorecon-all -su