try running recon-all -make all On Thu, 12 Sep 2013, Rudolph Pienaar wrote:
> Hmmm... I'm sorry, but I can't really help/comment on why your specific > run of recon-all resulted in those two files having different sizes. > > > > On 9/12/13 16:00 , std...@virgilio.it wrote: >> OK. But, I have run a simple command (recon-all) for cortical >> parcellation. >> I have already used this command for other structural images. >> This is the image features: >> data_type FLOAT32 >> dim1 212 >> dim2 320 >> dim3 320 >> dim4 1 >> datatype 16 >> pixdim1 0.8000000119 >> pixdim2 0.8000000119 >> pixdim3 0.8000000119 >> pixdim4 0.0109999999 >> cal_max 0.0000 >> cal_min 0.0000 >> file_type NIFTI-1+ >> >> Thanks, >> >> >> Stefano >> >> >> ----Messaggio originale---- >> Da: rudo...@nmr.mgh.harvard.edu >> Data: 12-set-2013 17.50 >> A: <std...@virgilio.it> >> Cc: <freesurfer@nmr.mgh.harvard.edu> >> Ogg: Re: R: Re: [Freesurfer] mris_calc erroe in recon-all >> >> The file 'lh.area' contains 126850 elements. The file 'lh.area.pial' >> contains 126355 elements. >> >> You cannot add them together since they have different sizes. >> >> On 9/12/13 11:14 , std...@virgilio.it wrote: >>> Thanks. >>> >>> These are the output >>> [iMac-di-Stefano:Con28/SUBJECTS_DIR/surf] Stefano% mris_calc lh.area >> stats >>> Size [ 126850 ] >>> Min@(index) [ -0.322716 >>> (56402) ] >>> Max@(index) [ 12.367171 >>> (123284) ] >>> Mean [ 0.587518 ] >>> Std [ 0.402374 ] >>> Sum [ 74526.703125 ] >>> Prod [ 0.000000 ] >>> [iMac-di-Stefano:Con28/SUBJECTS_DIR/surf] Stefano% mris_calc >>> lh.area.pial stats >>> Size [ 126355 ] >>> Min@(index) [ 0.000000 (97676) ] >>> Max@(index) [ 22.833410 >>> (119901) ] >>> Mean [ 0.785660 ] >>> Std [ 0.738523 ] >>> Sum [ 99272.054688 ] >>> Prod [ 0.000000 ] >>> >>> but I do not understand what's happen. >>> >>> Stefano >>> >>> ----Messaggio originale---- >>> Da: rudo...@nmr.mgh.harvard.edu >>> Data: 12-set-2013 14.49 >>> A: <std...@virgilio.it> >>> Cc: <freesurfer@nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] mris_calc erroe in recon-all >>> >>> The error would indicate that the number of elements in 'lh.area' and >>> 'lh.area.pial' are not the same. You can check this also with mris_calc: >>> >>> mris_calc lh.area stats >>> >>> mris_calc lh.area.pial stats >>> >>> which will provide some basic statistical output, including the size >>> (i.e. number of elements) of each. The sizes have to match in order to >>> add. >>> >>> HTH >>> -=R >>> >>> On 9/12/13 02:56 , std...@virgilio.it wrote: >>>> Hi list, >>>> >>>> I have a problem during recon-all >>>> >>>> #@# Surf Volume lh Thu Sep 12 08:25:31 CEST 2013 >>>> >> /Applications/freesurfer/subjects/subject_prova/Con28/SUBJECTS_DIR/surf >>>> \n mris_calc -o lh.area.mid lh.area add lh.area.pial \n >>>> >>>> mris_calc: >>>> Sorry, but I seem to have encountered an error. >>>> While checking on input filetype sizes, >>>> I found a size mismatch, i.e. len(input1)!=len(input2) >>>> >>>> Darwin iMac-di-Stefano.local 12.4.0 Darwin Kernel Version 12.4.0: Wed >>>> May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 >>>> >>>> recon-all -s SUBJECTS_DIR exited with ERRORS at Thu Sep 12 08:25:31 >>>> CEST 2013 >>>> >>>> For more details, see the log file >>>> >>> >> /Applications/freesurfer/subjects/subject_prova/Con28/SUBJECTS_DIR/scripts/recon-all.log >>>> To report a problem, see >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> >>>> >>>> Thanks, >>>> >>>> >>>> >>>> Stefano >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> -- >>> Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu >>> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >>> 149 (2301) 13th Street, Charlestown, MA 02129 USA >>> >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is >>> addressed. If you believe this e-mail was sent to you in error and the >>> e-mail >>> contains patient information, please contact the Partners Compliance >>> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to you >>> in error >>> but does not contain patient information, please contact the sender >>> and properly >>> dispose of the e-mail. >>> >>> >>> >> >> >> -- >> Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu >> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >> 149 (2301) 13th Street, Charlestown, MA 02129 USA >> >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
