hi, I have tried to make prefrotnal cortex label by doing first
mri_annotation2label --subject "$subject" --hemi rh --outdir "$subject"/label
mri_mergelabels -i lh.caudalanteriorcingulate.label -i lh.caudalmiddlefrontal.label -i lh.lateralorbitofrontal.label -i lh.medialorbitofrontal.label -i lh.parsopercularis.label -i lh.parsorbitalis.label -i lh.parstriangularis.label -i lh.rostralanteriorcingulate.label -i lh.rostralmiddlefrontal.label -i lh.superiorfrontal.label -i lh.lateralorbitofrontal.label -o lh.prefrontalcortex.label -d /directory/subject/label
which does create a label called x.prefrontalcortex.label in each persons directory. then however when i try to do
mris_anatomical_stats -l $SUBJECTS_DIR/"$subject"/label/lh.prefrontalcortex.label "$subject" lh pial | grep "thickness" >> left_prefrontal
i get error and say it cant find label. any pointers on what im doing wrong?
thank you
What is the full terminal output and error msg?
On 11/21/2014 04:14 AM, Anna Jonsson wrote:
hi, I have tried to make prefrotnal cortex label by doing first
mri_annotation2label --subject "$subject" --hemi rh --outdir "$subject"/label
mri_mergelabels -i lh.caudalanteriorcingulate.label -i lh.caudalmiddlefrontal.label -i lh.lateralorbitofrontal.label -i lh.medialorbitofrontal.label -i lh.parsopercularis.label -i lh.parsorbitalis.label -i lh.parstriangularis.label -i lh.rostralanteriorcingulate.label -i lh.rostralmiddlefrontal.label -i lh.superiorfrontal.label -i lh.lateralorbitofrontal.label -o lh.prefrontalcortex.label -d /directory/subject/label
which does create a label called x.prefrontalcortex.label in each persons directory. then however when i try to do
mris_anatomical_stats -l $SUBJECTS_DIR/"$subject"/label/lh.prefrontalcortex.label "$subject" lh pial | grep "thickness" >> left_prefrontal
i get error and say it cant find label. any pointers on what im doing wrong?
thank you
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hi the full error message is reading input surface /XXXXXXXXXX/surf/lh.pial... reading input pial surface /XXXXXXXXXX/surf/lh.pial... reading input white surface //XXXXXXXXX/surf/lh.white... mris_anatomical_stats: could not parse 1697283th line '60529 -5.365 -17' in label file subj: could not read label file (null)
On Mon, Nov 24, 2014 at 4:56 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
What is the full terminal output and error msg?
On 11/21/2014 04:14 AM, Anna Jonsson wrote:
hi, I have tried to make prefrotnal cortex label by doing first
mri_annotation2label --subject "$subject" --hemi rh --outdir "$subject"/label
mri_mergelabels -i lh.caudalanteriorcingulate.label -i lh.caudalmiddlefrontal.label -i lh.lateralorbitofrontal.label -i lh.medialorbitofrontal.label -i lh.parsopercularis.label -i lh.parsorbitalis.label -i lh.parstriangularis.label -i lh.rostralanteriorcingulate.label -i lh.rostralmiddlefrontal.label -i lh.superiorfrontal.label -i lh.lateralorbitofrontal.label -o lh.prefrontalcortex.label -d /directory/subject/label
which does create a label called x.prefrontalcortex.label in each persons directory. then however when i try to do
mris_anatomical_stats -l $SUBJECTS_DIR/"$subject"/label/lh.prefrontalcortex.label "$subject" lh pial | grep "thickness" >> left_prefrontal
i get error and say it cant find label. any pointers on what im doing wrong?
thank you
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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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.
It looks like there is something wrong with that label file (there should not be 1.7 million lines). Check to see whether the first couple of lines look similar to the other labels. it might be that mergelabels is not quite doing the right thing.
doug
On 11/26/14 11:38 AM, Anna Jonsson wrote:
hi the full error message is reading input surface /XXXXXXXXXX/surf/lh.pial... reading input pial surface /XXXXXXXXXX/surf/lh.pial... reading input white surface //XXXXXXXXX/surf/lh.white... mris_anatomical_stats: could not parse 1697283th line '60529 -5.365 -17' in label file subj: could not read label file (null)
On Mon, Nov 24, 2014 at 4:56 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What is the full terminal output and error msg? On 11/21/2014 04:14 AM, Anna Jonsson wrote: > hi, I have tried to make prefrotnal cortex label by doing first > > > > mri_annotation2label --subject "$subject" --hemi rh --outdir > "$subject"/label > > > > mri_mergelabels -i lh.caudalanteriorcingulate.label -i > lh.caudalmiddlefrontal.label -i lh.lateralorbitofrontal.label -i > lh.medialorbitofrontal.label -i lh.parsopercularis.label -i > lh.parsorbitalis.label -i lh.parstriangularis.label -i > lh.rostralanteriorcingulate.label -i lh.rostralmiddlefrontal.label -i > lh.superiorfrontal.label -i lh.lateralorbitofrontal.label -o > lh.prefrontalcortex.label -d /directory/subject/label > > > which does create a label called x.prefrontalcortex.label in each > persons directory. then however when i try to do > > mris_anatomical_stats -l > $SUBJECTS_DIR/"$subject"/label/lh.prefrontalcortex.label "$subject" lh > pial | grep "thickness" >> left_prefrontal > > i get error and say it cant find label. any pointers on what im doing > wrong? > > thank you > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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