Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30130 discussions

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by Goldman, Aaron (NIH/NIMH) 02 Nov '05

02 Nov '05

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: aarong(a)mail.nih.gov

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Re: Freesurfer Digest, Vol 21, Issue 3
by Sasha Wolosin 02 Nov '05

02 Nov '05

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 <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] area file To: Marie Schaer <marie.schaer(a)medecine.unige.ch> Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4368FE2E.2020503(a)nmr.mgh.harvard.edu> 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 wolosin(a)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.

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Re: [Freesurfer] help with mris_ca_label
by Sasha Wolosin 02 Nov '05

02 Nov '05

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(a)kennedykrieger.org >>> Bruce Fischl <fischl(a)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(a)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. > > >

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Re: [Freesurfer] help with mris_ca_label
by Sasha Wolosin 02 Nov '05

02 Nov '05

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(a)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.

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subcortical segmentation
by Eliezer Kahn 02 Nov '05

02 Nov '05

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

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Re: [Freesurfer] help with mris_ca_label
by Sasha Wolosin 02 Nov '05

02 Nov '05

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 wolosin(a)kennedykrieger.org >>> "Brian T. Quinn" <btquinn(a)nmr.mgh.harvard.edu> 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 > wolosin(a)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 mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- brian t. quinn

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help with mris_ca_label
by Sasha Wolosin 01 Nov '05

01 Nov '05

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 wolosin(a)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.

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mri_normalize errors
by Eric Feczko 01 Nov '05

01 Nov '05

Hi, Just today I started having problems running mri_normalize within the dev environment using either a centOS or RH computer. Every subject I try to process results in the same error: INFO: Modifying talairach volume c_(r,a,s) based on average_305 Segmentation fault ERROR: mri_normalize exited with non-zero status Linux phrenic 2.6.9-11.ELsmp #1 SMP Wed Jun 8 17:54:20 CDT 2005 i686 i686 i386 GNU/Linux recon-all exited with errors at Tue Nov 1 11:09:57 EST 2005 I even tried re-processing a subject that ran mri_normalize successfully yesterday and recieved the same error. I found nothing wrong with the T1 images in any of the subjects, save for one whose intensity values for white matter greatly exceeded 110; using control points has not fixed that situation. If anyone knows of a solution for this problem, that would be great, thanks! -Eric

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Matlab conflicts with FS-FAST
by Andrew H Bell 31 Oct '05

31 Oct '05

Hello, I'm having strange difficulties with FS-FAST and thought that someone out there might have some suggestions: Specifically - one problem I'm having is viewing the data with SLICEVIEW-SESS The error I get is below (I've pasted the output from the Matlab step on). I don't get this error when using an older version of matlab (which is no longer an option). Is there a way to override this "title" business? Thanks! Andy < M A T L A B > Copyright 1984-2005 The MathWorks, Inc. Version 7.0.4.352 (R14) Service Pack 2 January 29, 2005 Toolbox Path Cache read in 0.00 seconds. Warning: Duplicate directory name: /Users/bellah/matlab. MATLAB Path initialized in 0.06 seconds. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> yvtitle = ruphert100-func_atlas-face_place-sig >> >> >> >> >> yakview: $Id: yakview.m,v 1.4 2003/09/29 00:53:22 greve Exp $ Base /Users/bellah/Documents/HMI_Data/AFNI_Data/Ruphert/face_place1_ru100/ruphert 100/bold/func_atlas//h-offset Overlay /Users/bellah/Documents/HMI_Data/AFNI_Data/Ruphert/face_place1_ru100/ruphert 100/bold/func_atlas//face_place/sig Hemodynamic Data Offset Raw Data RawFunc: Loading Base ... 1.52961 sec Making Base Mosaic ... 0.340587 sec Loading Overlay 1.11081 sec Making Overlay Mosaic ... 0.266878 sec ??? Error: <a href="error:/Applications/freesurfer/fsfast/toolbox/yak.m,427,9">File: yak.m Line: 427 Column: 9</a> "title" previously appeared to be used as a function, conflicting with its use here as the name of a variable. A possible cause of this error is that you forgot to initialize the variable, or you have initialized it implicitly using load or eval. Error in ==> <a href="error:/Applications/freesurfer/fsfast/toolbox/yakview.m,230,1">yakview at 230</a> yak('init',s,'-Nnnc',Nnnc,'-h',hsa,'-dof',dof,... >> > Andrew H. Bell, PhD Laboratory of Brain and Cognition National Institute of Mental Health 49 Convent Drive Building 49, RM 1B80 Bethesda, MD 20892 office: (301) 496-5625 ext.260 mobile: (202) 679-1279 bellah(a)mail.nih.gov

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Re: [Freesurfer] Intensity problems
by Martin Ystad 31 Oct '05

31 Oct '05

Jenni Pacheco wrote: > Hi Martin, > > Control points should fix the problem. Try adding some to this > brighter region, as well as a few to regions currently labeled to > 110. Sometimes this helps. After you've saved your control points (be > sure to save them) then you should run: > > recon-all -normalization -usecontrolpoints -subjid <subjid> > > to make sure that it uses your control points. If you look at your > brain T1 volume now, those bright spots should be taken care of. If > so you'll need to re-run these steps: > recon-all -skullstrip -subcortseg -normalization2 -segmentation > -subjid <subjid> > > If it hasn't worked, let me know, maybe there's another problem. > > good luck, > Jenni > > On Fri, 28 Oct 2005, Martin Ystad wrote: > >> Hi, I'm currently running the latest developmental release for RedHat >> 9, but I seem to have some problems concerning the >> intesity-normalization. Unfortunately, my images have some intensity >> inhomogenities, but the first normalization-step seems to take care >> of most of these. However, some regions inside the white matter has a >> somewhat high value, for example 130 -140. These regions are not >> included in the white matter when I run the recon-all -segmentation >> program. Adding control-points to these areas does not work, >> obviously, since only values lower than 110 are considered when the >> normalization-step is re-runned. (right?) >> Is there any way to include these areas in my final white matter >> whithout manually drawing them onto the wm.mgz -volume? For instance >> raising the threshold for wm-segmentation? >> If so, would this produce any kind new artifacts which I need to be >> aware of? >> >> Thanks, >> >> Martin Ystad >> Medical Student >> University of Bergen >> Institute of Biomedicine >> Jonas Lies vei 91, 5009 >> Bergen, Norway. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > Hi, thanks for your help. I tried what you suggested and it turned out somewhat better. Still, there are large areas that are not included in the wm.mgz. The problem with some of the data sets is that the intensity inhomogenities in the center of the brain also reaches some very low values. I'm worried that if I include these with control-points, some of the gray matter will be misinterpreted as white matter. Is this a legitimate concern, or does the program work in a different way? If so, how low can the control point value be to avoid that this happens? Ps. If I add a control point to one area with a specific high or low value, does this take care of all the other areas with similar values across the brain, or do I have to add a control point to all areas that have discrepancies in intensity? Thanks, Martin

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Freesurfer