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 FLOAT32dim1 212dim2 320dim3 320dim4 1datatype 16pixdim1 0.8000000119pixdim2 0.8000000119pixdim3 0.8000000119pixdim4 0.0109999999cal_max 0.0000cal_min 0.0000file_type NIFTI-1+ Thanks,
Stefano
----Messaggio originale---- Da: rudolph@nmr.mgh.harvard.edu Data: 12-set-2013 17.50 A: stdp82@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 , stdp82@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: rudolph@nmr.mgh.harvard.edu Data: 12-set-2013 14.49 A: stdp82@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 , stdp82@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: rudolph@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.
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 , stdp82@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: rudolph@nmr.mgh.harvard.edu Data: 12-set-2013 17.50 A: stdp82@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 , stdp82@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: rudolph@nmr.mgh.harvard.edu Data: 12-set-2013 14.49 A: stdp82@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 , stdp82@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: rudolph@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: rudolph@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA
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 , stdp82@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: rudolph@nmr.mgh.harvard.edu Data: 12-set-2013 17.50 A: stdp82@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 , stdp82@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: rudolph@nmr.mgh.harvard.edu Data: 12-set-2013 14.49 A: stdp82@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 , stdp82@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: rudolph@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: rudolph@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA
Try
recon-all -make all
On Sep 12, 2013, at 4:00 PM, stdp82@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: rudolph@nmr.mgh.harvard.edu Data: 12-set-2013 17.50 A: stdp82@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 , stdp82@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: rudolph@nmr.mgh.harvard.edu Data: 12-set-2013 14.49 A: stdp82@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 , stdp82@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: rudolph@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: rudolph@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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Rudolph Pienaar -
stdp82＠virgilio.it