OK. But, I have run a simple command (recon-all) for cortical parcellation.<br>
I have already used this command for other structural images.<div>This is the image features:</div><div><div>data_type &nbsp; &nbsp; &nbsp;FLOAT32</div><div>dim1 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 212</div><div>dim2 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 320</div><div>dim3 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 320</div><div>dim4 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; 1</div><div>datatype &nbsp; &nbsp; &nbsp; 16</div><div>pixdim1 &nbsp; &nbsp; &nbsp; &nbsp;0.8000000119</div><div>pixdim2 &nbsp; &nbsp; &nbsp; &nbsp;0.8000000119</div><div>pixdim3 &nbsp; &nbsp; &nbsp; &nbsp;0.8000000119</div><div>pixdim4 &nbsp; &nbsp; &nbsp; &nbsp;0.0109999999</div><div>cal_max &nbsp; &nbsp; &nbsp; &nbsp;0.0000</div><div>cal_min &nbsp; &nbsp; &nbsp; &nbsp;0.0000</div><div>file_type &nbsp; &nbsp; &nbsp;NIFTI-1+</div></div><div><br></div><div>Thanks,</div><div><br></div><div><br></div><div>Stefano</div><div><br><br>
----Messaggio originale----<br>Da: rudolph@nmr.mgh.harvard.edu<br>Data: 12-set-2013 17.50<br>A: &lt;stdp82@virgilio.it&gt;<br>Cc: &lt;freesurfer@nmr.mgh.harvard.edu&gt;<br>Ogg: Re: R: Re: [Freesurfer] mris_calc erroe in recon-all<br><br>The file 'lh.area' contains 126850 elements. The file 'lh.area.pial' <br>contains 126355 elements.<br><br>You cannot add them together since they have different sizes.<br><br>On 9/12/13 11:14 , stdp82@virgilio.it wrote:<br>&gt; Thanks.<br>&gt;<br>&gt; These are the output<br>&gt; [iMac-di-Stefano:Con28/SUBJECTS_DIR/surf] Stefano% mris_calc lh.area stats<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Size&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [ 126850 ]<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Min@(index)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [ -0.322716 <br>&gt; (56402) ]<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Max@(index)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [ 12.367171 <br>&gt; (123284) ]<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Mean&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [ 0.587518 ]<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Std&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [ 0.402374 ]<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Sum&nbsp;&nbsp;&nbsp;&nbsp; [ 74526.703125 ]<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Prod&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [ 0.000000 ]<br>&gt; [iMac-di-Stefano:Con28/SUBJECTS_DIR/surf] Stefano% mris_calc <br>&gt; lh.area.pial stats<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Size&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [ 126355 ]<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Min@(index) [ 0.000000 (97676) ]<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Max@(index)&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [ 22.833410 <br>&gt; (119901) ]<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Mean&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [ 0.785660 ]<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Std&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [ 0.738523 ]<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Sum&nbsp;&nbsp;&nbsp;&nbsp; [ 99272.054688 ]<br>&gt;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Prod&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; [ 0.000000 ]<br>&gt;<br>&gt; but I do not understand what's happen.<br>&gt;<br>&gt; Stefano<br>&gt;<br>&gt; ----Messaggio originale----<br>&gt; Da: rudolph@nmr.mgh.harvard.edu<br>&gt; Data: 12-set-2013 14.49<br>&gt; A: &lt;stdp82@virgilio.it&gt;<br>&gt; Cc: &lt;freesurfer@nmr.mgh.harvard.edu&gt;<br>&gt; Ogg: Re: [Freesurfer] mris_calc erroe in recon-all<br>&gt;<br>&gt; The error would indicate that the number of elements in 'lh.area' and<br>&gt; 'lh.area.pial' are not the same. You can check this also with mris_calc:<br>&gt;<br>&gt; mris_calc lh.area stats<br>&gt;<br>&gt; mris_calc lh.area.pial stats<br>&gt;<br>&gt; which will provide some basic statistical output, including the size<br>&gt; (i.e. number of elements) of each. The sizes have to match in order to <br>&gt; add.<br>&gt;<br>&gt; HTH<br>&gt; -=R<br>&gt;<br>&gt; On 9/12/13 02:56 , stdp82@virgilio.it wrote:<br>&gt; &gt; Hi list,<br>&gt; &gt;<br>&gt; &gt; I have a problem during recon-all<br>&gt; &gt;<br>&gt; &gt; #@# Surf Volume lh Thu Sep 12 08:25:31 CEST 2013<br>&gt; &gt; /Applications/freesurfer/subjects/subject_prova/Con28/SUBJECTS_DIR/surf<br>&gt; &gt; \n mris_calc -o lh.area.mid lh.area add lh.area.pial \n<br>&gt; &gt;<br>&gt; &gt; mris_calc:<br>&gt; &gt; Sorry, but I seem to have encountered an error.<br>&gt; &gt; While checking on input filetype sizes,<br>&gt; &gt; I found a size mismatch, i.e. len(input1)!=len(input2)<br>&gt; &gt;<br>&gt; &gt; Darwin iMac-di-Stefano.local 12.4.0 Darwin Kernel Version 12.4.0: Wed<br>&gt; &gt; May&nbsp; 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64<br>&gt; &gt;<br>&gt; &gt; recon-all -s SUBJECTS_DIR exited with ERRORS at Thu Sep 12 08:25:31<br>&gt; &gt; CEST 2013<br>&gt; &gt;<br>&gt; &gt; For more details, see the log file<br>&gt; &gt; <br>&gt; /Applications/freesurfer/subjects/subject_prova/Con28/SUBJECTS_DIR/scripts/recon-all.log<br>&gt; &gt; To report a problem, see<br>&gt; &gt; http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting<br>&gt; &gt;<br>&gt; &gt;<br>&gt; &gt; Thanks,<br>&gt; &gt;<br>&gt; &gt;<br>&gt; &gt;<br>&gt; &gt; Stefano<br>&gt; &gt;<br>&gt; &gt;<br>&gt; &gt; _______________________________________________<br>&gt; &gt; Freesurfer mailing list<br>&gt; &gt; Freesurfer@nmr.mgh.harvard.edu<br>&gt; &gt; https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<br>&gt;<br>&gt;<br>&gt; -- <br>&gt; Rudolph Pienaar, M.Eng, D.Eng / email: rudolph@nmr.mgh.harvard.edu<br>&gt; MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging<br>&gt; 149 (2301) 13th Street, Charlestown, MA 02129 USA<br>&gt;<br>&gt;<br>&gt;<br>&gt; The information in this e-mail is intended only for the person to whom <br>&gt; it is<br>&gt; addressed. If you believe this e-mail was sent to you in error and the <br>&gt; e-mail<br>&gt; contains patient information, please contact the Partners Compliance <br>&gt; HelpLine at<br>&gt; http://www.partners.org/complianceline . If the e-mail was sent to you <br>&gt; in error<br>&gt; but does not contain patient information, please contact the sender <br>&gt; and properly<br>&gt; dispose of the e-mail.<br>&gt;<br>&gt;<br>&gt;<br><br><br>-- <br>Rudolph Pienaar, M.Eng, D.Eng / email: rudolph@nmr.mgh.harvard.edu<br>MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging<br>149 (2301) 13th Street, Charlestown, MA 02129 USA<br><br><br><br>
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