chmod (as many other linux/unix commands) do not return anything except eventual errors.

Try './optseq2 --help' when you are in the optseq dierctory. Else write the full path before optseq2.

Pål

Pål G. Larsson M.D., Dr. philos. Head of Clinical Neurophysiology Department of Neurosurgery Division of Surgery and Clinical Neuroscience

Oslo University Hospital Po.box 4950 Nydalen 0424 Oslo Norway Tel: (+47) 23074407 Mobile: (+47) 93429791 E-mail: pall@ous-hf.nomailto:pal.gunnar.larsson@ous-hf.no non-sensitive

Fra: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] På vegne av Lukito, Steve Sendt: 12. august 2013 12:31 Til: freesurfer@nmr.mgh.harvard.edu Emne: [Freesurfer] Optseq2 with Cygwin

Dear optseq2 developers,

I would like to use optseq2 to develop optimal sequence for my MRI experiment. I have a windows machine (Windows 7, SP1, 64-bit OS) so I installed Cygwin-64 to run the optseq2. What I've done so far:

- Downloaded optseq2.exe (Cygwin version) and put this into the Cygwin-64 folder

- I run Cygwin and change my directory to Cygwin-64 where the optseq2 is

- I followed instructions from previous email trails so I typed in chmod a+x optseq2 (to make optseq2 executable within the shell?)

- Then I typed in ./optseq2 (since typing in optseq2 on its own results in -bash: optseq2: command not found)

On both occasions (chmod... and ./optseq2), the command prompt returns without output. As I understand it, at least, for the second command I should get the help text for optseq? Have I done something wrong?

Would really appreciate you help! Steve

PS I am not familiar with UNIX so please be patient if my question is trivial :).

Steve Lukito, MSc. PhD Candidate | Institute of Psychiatry | King's College London Department of Child and Adolescent Psychiatry - PO85 16 De Crespigny Park London SE5 8AF

Phone: 0207 848 0469