thanks, I created a label directory and that solved the problem. It looks like all our subjects are missing a label directory. Do you know why that might happen?
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Bruce Fischl fischl@nmr.mgh.harvard.edu 11/02/05 1:46 PM >>>
Hi Sasha,
it gets written into the label dir by default. Are you sure that directory exists (should be at the same level as surf)
Bruce On Wed, 2 Nov 2005, Sasha Wolosin wrote:
I'm having trouble specifying the output file when running mris_ca_label- should it be in the surf folder or somewhere else? (output below) Thanks, Sasha
[root@localhost surf]$ pwd /home/wolosin/subjects/dec1877J_prac/surf [root@localhost surf]$ mris_ca_label dec1877J_prac rh rh.sphere.reg /freesurfer/ average/rh.atlas2002_simple.gcs rh.aparc.annot reading atlas from /freesurfer/average/rh.atlas2002_simple.gcs... reading color table from GCSA file.... input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 9230 changed, 125897 examined... 001: 2224 changed, 34779 examined... 002: 681 changed, 11344 examined... 003: 275 changed, 3817 examined... 004: 160 changed, 1602 examined... 005: 76 changed, 937 examined... 006: 31 changed, 434 examined... 007: 18 changed, 193 examined... 008: 15 changed, 103 examined... 009: 7 changed, 86 examined... 010: 2 changed, 46 examined... 011: 3 changed, 16 examined... 012: 0 changed, 10 examined... 000: 286 total segments, 189 labels (2604 vertices) changed 001: 107 total segments, 12 labels (195 vertices) changed 002: 95 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 121 changed) writing output to rh.aparc.annot... could not write annot file /home/wolosin/subjects/dec1877J_prac/surf/../label/rh .aparc.annot No such file or directory mris_ca_label: could not write annot file rh.aparc.annot for dec1877J_prac No such file or directory [root@localhost surf]$
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
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no. The mksubjdirs script should create a label dir.
On Wed, 2 Nov 2005, Sasha Wolosin wrote:
thanks, I created a label directory and that solved the problem. It looks like all our subjects are missing a label directory. Do you know why that might happen?
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Bruce Fischl fischl@nmr.mgh.harvard.edu 11/02/05 1:46 PM >>>
Hi Sasha,
it gets written into the label dir by default. Are you sure that directory exists (should be at the same level as surf)
Bruce On Wed, 2 Nov 2005, Sasha Wolosin wrote:
I'm having trouble specifying the output file when running mris_ca_label- should it be in the surf folder or somewhere else? (output below) Thanks, Sasha
[root@localhost surf]$ pwd /home/wolosin/subjects/dec1877J_prac/surf [root@localhost surf]$ mris_ca_label dec1877J_prac rh rh.sphere.reg /freesurfer/ average/rh.atlas2002_simple.gcs rh.aparc.annot reading atlas from /freesurfer/average/rh.atlas2002_simple.gcs... reading color table from GCSA file.... input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... relabeling using gibbs priors... 000: 9230 changed, 125897 examined... 001: 2224 changed, 34779 examined... 002: 681 changed, 11344 examined... 003: 275 changed, 3817 examined... 004: 160 changed, 1602 examined... 005: 76 changed, 937 examined... 006: 31 changed, 434 examined... 007: 18 changed, 193 examined... 008: 15 changed, 103 examined... 009: 7 changed, 86 examined... 010: 2 changed, 46 examined... 011: 3 changed, 16 examined... 012: 0 changed, 10 examined... 000: 286 total segments, 189 labels (2604 vertices) changed 001: 107 total segments, 12 labels (195 vertices) changed 002: 95 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 121 changed) writing output to rh.aparc.annot... could not write annot file /home/wolosin/subjects/dec1877J_prac/surf/../label/rh .aparc.annot No such file or directory mris_ca_label: could not write annot file rh.aparc.annot for dec1877J_prac No such file or directory [root@localhost surf]$
Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin@kennedykrieger.org
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Sasha Wolosin