Re: [Freesurfer] help with mris_ca_label
is that *_trans_toSulc.gcs or *.atlas2002_simple.gcs? Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] >>> "Brian T. Quinn" <[EMAIL PROTECTED]> 11/01/05 7:38 PM >>> canonical surface refers to *.sphere.reg (found in $SUBJECTS_DIR/$s/surf) classifier is *.gcs (found in $FREESURFER_HOME/average) On Tue, 1 Nov 2005, Sasha Wolosin wrote: > Dear all, > In calling mris_ca_label, what does 'canonical surface' and > 'classifier' refer to? > Thanks, > Sasha > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 > [EMAIL PROTECTED] > > > > 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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- brian t. quinn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] help with mris_ca_label
*.atlas2002_simple.gcs is Christophe's atlas that we used before the current dev version. On Wed, 2 Nov 2005, Sasha Wolosin wrote: is that *_trans_toSulc.gcs or *.atlas2002_simple.gcs? Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] "Brian T. Quinn" <[EMAIL PROTECTED]> 11/01/05 7:38 PM >>> canonical surface refers to *.sphere.reg (found in $SUBJECTS_DIR/$s/surf) classifier is *.gcs (found in $FREESURFER_HOME/average) On Tue, 1 Nov 2005, Sasha Wolosin wrote: Dear all, In calling mris_ca_label, what does 'canonical surface' and 'classifier' refer to? Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] subcortical segmentation
Hi, As mentioned in a previous message, running the subcortical segmentation takes 10-15 hours, primarily because of the Cannonical Registration (mri_ca_register) step. However, one the freesurfer papers (Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain) states on the very first page that it takes only 30 minutes to label the brain. How essential is the Cannonical Registration part? Can one leave it out and still get a good subcortical segmentation? Thanks, Eli ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] subcortical segmentation
Hi Eli, no, I wouldn't. After that paper we developed a nonlinear registration procedure, which is the long one, that helps things considerably. cheers, Bruce On Wed, 2 Nov 2005, Eliezer Kahn wrote: Hi, As mentioned in a previous message, running the subcortical segmentation takes 10-15 hours, primarily because of the Cannonical Registration (mri_ca_register) step. However, one the freesurfer papers (Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain) states on the very first page that it takes only 30 minutes to label the brain. How essential is the Cannonical Registration part? Can one leave it out and still get a good subcortical segmentation? Thanks, Eli ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] area file
Hello everybody! I have one question about how surface areas are calculated by mris_anatomical stats (release2004). I noticed that the ?h.area file may contain the portion of area corresponding to each different vertex. Actually, the sum of all these areas is around 7'500mm^2 for one hemisphere, which is approximately (but not exactely) the result given by mris_anatomical_stats. However, when I converted the pial surface in matlab, and calculated the sum of the area of each triangle using the following equation http://mathworld.wolfram.com/TriangleArea.html, I obtained a very higher result (~10'000mm^2). Perhaps because the triangles are too big to calculate an accurate area at this stage? So my question was, on which basis is calculated the information contained in lh.area? Does the first row of ?h.area correspond to the piece of area attributable to the first vertice, and so on? Thank you very much for your response! Marie Schaer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] area file
We found a problem with this computation about a year ago (11/12/2004 to be specific). I think I sent an email about it to the list. Any releases prior to that date will have this error in the area computations. Can you try it with a more recent release? Marie Schaer wrote: Hello everybody! I have one question about how surface areas are calculated by mris_anatomical stats (release2004). I noticed that the ?h.area file may contain the portion of area corresponding to each different vertex. Actually, the sum of all these areas is around 7'500mm^2 for one hemisphere, which is approximately (but not exactely) the result given by mris_anatomical_stats. However, when I converted the pial surface in matlab, and calculated the sum of the area of each triangle using the following equation http://mathworld.wolfram.com/TriangleArea.html, I obtained a very higher result (~10'000mm^2). Perhaps because the triangles are too big to calculate an accurate area at this stage? So my question was, on which basis is calculated the information contained in lh.area? Does the first row of ?h.area correspond to the piece of area attributable to the first vertice, and so on? Thank you very much for your response! Marie Schaer ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] area file
I tried with mris_anatomical_stats from freesurfer-Linux-rh9-v2.1 and I obtained exactly the same result for total surface area as in matlab with the sum of all the triangles, thanks for the advice! In the mean time I was just wondering how folding index returned by mris_anatomical_stats is calculated? Thank you! Marie Schaer Quoting Doug Greve <[EMAIL PROTECTED]>: > > We found a problem with this computation about a year ago (11/12/2004 to > be specific). I think I sent an email about it to the list. Any releases > prior to that date will have this error in the area computations. Can > you try it with a more recent release? > > > > Marie Schaer wrote: > > >Hello everybody! > > > >I have one question about how surface areas are calculated by > mris_anatomical > >stats (release2004). > >I noticed that the ?h.area file may contain the portion of area > corresponding to > >each different vertex. Actually, the sum of all these areas is around > 7'500mm^2 > >for one hemisphere, which is approximately (but not exactely) the result > given > >by mris_anatomical_stats. However, when I converted the pial surface in > matlab, > >and calculated the sum of the area of each triangle using the following > equation > >http://mathworld.wolfram.com/TriangleArea.html, I obtained a very higher > result > >(~10'000mm^2). Perhaps because the triangles are too big to calculate an > >accurate area at this stage? > > > >So my question was, on which basis is calculated the information contained > in > >lh.area? Does the first row of ?h.area correspond to the piece of area > >attributable to the first vertice, and so on? > > > >Thank you very much for your response! > > > >Marie Schaer > > > > > > > >___ > >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 > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] help with mris_ca_label
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 [EMAIL PROTECTED] surf]$ pwd /home/wolosin/subjects/dec1877J_prac/surf [EMAIL PROTECTED] 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 [EMAIL PROTECTED] surf]$ Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] help with mris_ca_label
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 [EMAIL PROTECTED] surf]$ pwd /home/wolosin/subjects/dec1877J_prac/surf [EMAIL PROTECTED] 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 [EMAIL PROTECTED] surf]$ Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] area file
Hi Marie, the folding indices are taken from one of the original Van Essen and Drury papers. Sorry I don't have the ref handy. Bruce On Wed, 2 Nov 2005, Marie Schaer wrote: I tried with mris_anatomical_stats from freesurfer-Linux-rh9-v2.1 and I obtained exactly the same result for total surface area as in matlab with the sum of all the triangles, thanks for the advice! In the mean time I was just wondering how folding index returned by mris_anatomical_stats is calculated? Thank you! Marie Schaer Quoting Doug Greve <[EMAIL PROTECTED]>: We found a problem with this computation about a year ago (11/12/2004 to be specific). I think I sent an email about it to the list. Any releases prior to that date will have this error in the area computations. Can you try it with a more recent release? Marie Schaer wrote: Hello everybody! I have one question about how surface areas are calculated by mris_anatomical stats (release2004). I noticed that the ?h.area file may contain the portion of area corresponding to each different vertex. Actually, the sum of all these areas is around 7'500mm^2 for one hemisphere, which is approximately (but not exactely) the result given by mris_anatomical_stats. However, when I converted the pial surface in matlab, and calculated the sum of the area of each triangle using the following equation http://mathworld.wolfram.com/TriangleArea.html, I obtained a very higher result (~10'000mm^2). Perhaps because the triangles are too big to calculate an accurate area at this stage? So my question was, on which basis is calculated the information contained in lh.area? Does the first row of ?h.area correspond to the piece of area attributable to the first vertice, and so on? Thank you very much for your response! Marie Schaer ___ 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 [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] area file
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9278543&query_hl=1 I got it, thank you very much! Marie Quoting Bruce Fischl <[EMAIL PROTECTED]>: > Hi Marie, > > the folding indices are taken from one of the original Van Essen and Drury > papers. Sorry I don't have the ref handy. > > Bruce > > On Wed, 2 Nov 2005, Marie Schaer wrote: > > > > > > > I tried with mris_anatomical_stats from freesurfer-Linux-rh9-v2.1 and I > obtained > > exactly the same result for total surface area as in matlab with the sum of > all > > the triangles, thanks for the advice! > > > > In the mean time I was just wondering how folding index returned by > > mris_anatomical_stats is calculated? > > > > Thank you! > > > > Marie Schaer > > > > > > Quoting Doug Greve <[EMAIL PROTECTED]>: > > > >> > >> We found a problem with this computation about a year ago (11/12/2004 to > >> be specific). I think I sent an email about it to the list. Any releases > >> prior to that date will have this error in the area computations. Can > >> you try it with a more recent release? > >> > >> > >> > >> Marie Schaer wrote: > >> > >>> Hello everybody! > >>> > >>> I have one question about how surface areas are calculated by > >> mris_anatomical > >>> stats (release2004). > >>> I noticed that the ?h.area file may contain the portion of area > >> corresponding to > >>> each different vertex. Actually, the sum of all these areas is around > >> 7'500mm^2 > >>> for one hemisphere, which is approximately (but not exactely) the result > >> given > >>> by mris_anatomical_stats. However, when I converted the pial surface in > >> matlab, > >>> and calculated the sum of the area of each triangle using the following > >> equation > >>> http://mathworld.wolfram.com/TriangleArea.html, I obtained a very higher > >> result > >>> (~10'000mm^2). Perhaps because the triangles are too big to calculate an > >>> accurate area at this stage? > >>> > >>> So my question was, on which basis is calculated the information > contained > >> in > >>> lh.area? Does the first row of ?h.area correspond to the piece of area > >>> attributable to the first vertice, and so on? > >>> > >>> Thank you very much for your response! > >>> > >>> Marie Schaer > >>> > >>> > >>> > >>> ___ > >>> 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 > >> [EMAIL PROTECTED] > >> Phone Number: 617-724-2358 > >> Fax: 617-726-7422 > >> > >> > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] help with mris_ca_label
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 [EMAIL PROTECTED] >>> Bruce Fischl <[EMAIL PROTECTED]> 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 > > [EMAIL PROTECTED] surf]$ pwd > /home/wolosin/subjects/dec1877J_prac/surf > [EMAIL PROTECTED] 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 > [EMAIL PROTECTED] surf]$ > > Sasha Wolosin > Research Assistant > Developmental Cognitive Neurology > Kennedy Krieger Institute > 707 N. Broadway > Baltimore, MD 21205 > ph: (443) 923-9270 > [EMAIL PROTECTED] > > > > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] help with mris_ca_label
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 [EMAIL PROTECTED] Bruce Fischl <[EMAIL PROTECTED]> 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 [EMAIL PROTECTED] surf]$ pwd /home/wolosin/subjects/dec1877J_prac/surf [EMAIL PROTECTED] 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 [EMAIL PROTECTED] surf]$ Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
Hi, I have a script that basically opens up tksurfer and tkmedit for manual editing, and then runs recon-all stage2 once you’re done editing. We recently tried to run the script on a different computer with the same freesurfer distribution, and got an error I’m not used to seeing. It says: WARNING: Couldn't not load orig volume from ///surf/../mri/orig.mgz Talairach coords will be incorrect. (the ‘’ was edited in by me) I was just wondering if this error will create problems, either with correct manual editing or with running stage2. Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Freesurfer Digest, Vol 21, Issue 3
Regarding this issue with the old version of mris_anatomical_stats, will problems with rh.area effect any of the other results? Or are there any bugs effecting other anatomical stats besides rh.area? Message: 2 Date: Wed, 02 Nov 2005 12:58:06 -0500 From: Doug Greve <[EMAIL PROTECTED]> Subject: Re: [Freesurfer] area file To: Marie Schaer <[EMAIL PROTECTED]> Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset=us-ascii; format=flowed We found a problem with this computation about a year ago (11/12/2004 to be specific). I think I sent an email about it to the list. Any releases prior to that date will have this error in the area computations. Can you try it with a more recent release? Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 [EMAIL PROTECTED] 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] (no subject)
Hi Aaron, First, is it something simple and annoying like that your script doesn't look for an orig.mgz volume (vs. the 'orig' which was standard until fairly recently)? I have needed to edit my scripts to accommodate for this. okay! On Wed, 2 Nov 2005, Goldman, Aaron (NIH/NIMH) wrote: Hi, I have a script that basically opens up tksurfer and tkmedit for manual editing, and then runs recon-all stage2 once you're done editing. We recently tried to run the script on a different computer with the same freesurfer distribution, and got an error I'm not used to seeing. It says: WARNING: Couldn't not load orig volume from ///surf/../mri/orig.mgz Talairach coords will be incorrect. (the '' was edited in by me) I was just wondering if this error will create problems, either with correct manual editing or with running stage2. Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: [EMAIL PROTECTED] -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] freesurfer + fsl
Hi All,
I have installed Freesurfer for Mac OS X (2 Oct 2005) on my system
(running 10.4.2) - thanks for the OS X release!
Unfortunately, fsl doesn't work after the installation of Freesurfer.
This is the error message I get when I try to open the fsl GUI:
Error in startup script: no suitable image found. Did find:
/Applications/freesurfer/lib/tcltktixblt/lib/
libtix8.1.8.4.a: unknown fi
le type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A
while executing
"load /Applications/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix"
("package ifneeded" script)
invoked from within
"package require Tix"
invoked from within
"if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] !
= 0 } {
package require Tix
tix configure -scheme TixGray
option add ..."
(file "/usr/local/fsl/tcl/fslstart.tcl" line 3)
invoked from within
"source [ file dirname [ info script ] ]/fslstart.tcl"
(file "/usr/local/fsl/tcl/fsl.tcl" line 71)
invoked from within
"source ${FSLDIR}/tcl/${origname}.tcl"
(file "/usr/local/fsl/bin/fsl" line 19)
FSL was installed in the recommended directory /usr/local/fsl/ and
worked well before.
Any help to get FSL working again is highly appreciated!!
Peter
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[Freesurfer] automated parcellation
Dear Freesurfers, We have used the automated parcellation (Fischl et al, 2004) in several subjects and noticed in some cases labeling of the lateral part of a gyrus (i mean the part that's visible on the folded surface), as belonging to a sulcus. The example I have in mind is the labeling of a gyrus that could be the middle temporal or the angular gyrus as the posterior part of the superior temporal sulcus (STS). I figured the program could not find the correspondence between that particular gyrus and any labels and, since it happened to be close and, sometimes, between two branches of STS, it was labeled as such. Or we made a mistake somewhere ... ? Could anyone please comment on this ? thanks ! Goulven Josse (U of Chicago) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
