Hello Freesurfer&#39;s users,<div><br></div><div>I&#39;m starting using FS and I have a problem running recon-all</div><div>I create a folder called <span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; ">hptu_subj001 which contains </span><span class="Apple-style-span" style="border-collapse: collapse; font-family: arial, sans-serif; ">MPRAGE.nii.gz within tutorial_subj</span></div>
<div>First I convert nii.gz to mgz qith the command: </div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><div>recon-all -i MPRAGE.nii.gz -s hptu_subj001</div>
<div><span class="Apple-style-span" style="font-family: arial; border-collapse: separate; ">and then in order to process all, I type:</span></div></span></font></div><div>recon-all –i 001.mgz –subject hptu_subj001 –all</div>
<div><br></div><div>cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj/hptu_subj001_orig&gt; recon-all –i 001.mgz –subject hptu_subj001 –all</div><div><div>ERROR: Flag i unrecognized.</div>
<div>i 001.mgz subject hptu_subj001 all</div><div>Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae #50-Ubuntu SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux</div><div><br></div><div>recon-all -s  exited with ERRORS at Fri Jun 10 12:50:04 COT 2011</div>
</div><div><br></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse; ">then I tried with:</span></font>
</div><div><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse"><br></span></div><div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">cvalencia-Precision-WorkStation-T3400:~/freesurfer/subjects/buckner_data/tutorial_subj&gt; recon-all –i MPRAGE.nii.gz –subject hptu_subj001 –all</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">ERROR: Flag i unrecognized.</span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">i MPRAGE.nii.gz subject hptu_subj001 all</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">Linux cvalencia-Precision-WorkStation-T3400 2.6.35-28-generic-pae #50-Ubuntu SMP Fri Mar 18 20:43:15 UTC 2011 i686 GNU/Linux</span></font></div>
<div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;"><br></span></font></div><div><font class="Apple-style-span" face="arial, sans-serif"><span class="Apple-style-span" style="border-collapse: collapse;">recon-all -s  exited with ERRORS at Fri Jun 10 12:36:24 COT 2011</span></font></div>
<div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; "><br></div></div><div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">How I can fix this error?</div>
<div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; "><br></div><div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">Thanks a lot,</div><div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">
<br></div><div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">Best regards,</div><div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; "><br></div><div style="border-collapse: collapse; font-family: arial, sans-serif; font-size: 13px; ">
Carolina</div>