Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

tksurfer
by Sasha Wolosin 03 Jan '06

03 Jan '06

Dear all, I am running into some problems with tksurfer in the x86_64 dev release (oct 03). Whenever I attempt to load a group descriptor file the program quits. Below is the command line output. Any idea what might be happening? Thanks, Sasha surfer: current subjects dir: /data/final_surfs_30_60_20 surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/final_surfs_30_60_20 surfer: Reading header info from /data/final_surfs_30_60_20/average_306020_all//mri/T1.mgz surfer: vertices=163842, faces=327680 surfer: single buffered window surfer: using interface /freesurfer_dev/lib/tcl/tksurfer.tcl Reading /freesurfer_dev/lib/tcl/tkm_common.tcl Reading /freesurfer_dev/lib/tcl/tkm_wrappers.tcl Reading /freesurfer_dev/lib/tcl/fsgdfPlot.tcl Reading /freesurfer_dev/lib/tcl/tkUtils.tcl Read /freesurfer_dev/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % surfer: Interpreting overlay volume /data/final_surfs_30_60_20/stats_all_30/sigt_Group_doss-thickness-100rh.mgz as encoded value file. min value=-3.646420 max value=4.032682 gdfReadHeader: reading /data/final_surfs_30_60_20/stats_all_30/y_doss-thickness-100rh_000.fsgd INFO: ignoring tag Creator INFO: ignoring tag SmoothSteps INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed 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] tkregister-sess failing, can't tell why
by Kathryn Devaney 02 Jan '06

02 Jan '06

Ok, I changed the subject name in the register.dat file too and now I'm getting this, other error: Can't connect to xDisplay! register: ### tkoInitWindow(name) failed ERROR: tkregister2 failed Full text is below: [whatever:MYSTUDY] (nmr-std-env) tkregister-sess -sf sessid -df sesspar -------------------------------------------------------------- tkregister-sess logfile is /autofs/space/ship_006/users/kdevaney/Migraine_Aura/MYSTUDY/log/tkregister-sess.log -------------------------------------------------------------- Session: /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630 ---------------- Mon Jan 2 20:15:48 EST 2006 INFO: anatdir set to /space/orsay/2/knutsen/falco/old/mri/T1 ________________________________________________ /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630/bold/006 tkregister2 --targ /autofs/space/orsay_002/knutsen/falco/old/mri/T1 --mov ./f bshort --reg ../register.dat --plane cor --title old--Falco050630--006 --volview targ --surf white ________________________________________________ INFO: Volume /tmp/mritotal_9679/T1_8_dxyz.mnc cannot be found. INFO: Volume /homes/nmrnew/home/inverse/local/lib/model/average_305_8_dxyz.mnc cannot be found. INFO: found the orig volume (mri/orig) to get c_(ras) information for src INFO: added info to the surface. INFO: Volume /tmp/mritotal_9679/T1_8_dxyz.mnc cannot be found. INFO: Volume /homes/nmrnew/home/inverse/local/lib/model/average_305_8_dxyz.mnc cannot be found. INFO: found the orig volume (mri/orig) to get c_(ras) information for src INFO: added info to the surface. surfname set to white target volume /autofs/space/orsay_002/knutsen/falco/old/mri/T1 movable volume ./f reg file ../register.dat LoadVol 1 $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.348 0.013 0.005 -1.504; 0.014 0.325 0.078 20.196; 0.003 -0.073 0.337 10.458; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /autofs/space/orsay_002/knutsen/falco/old/mri/T1 INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ./f INFO: bvolumeRead: min = 0, max = 12970 INFO: changing move type to float Tmov: -------------------- -1.250 0.000 0.000 40.000; 0.000 0.000 1.250 -28.125; 0.000 -1.250 0.000 40.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.348 0.013 0.005 -1.504; 0.014 0.325 0.078 20.196; 0.003 -0.073 0.337 10.458; 0.000 0.000 0.000 1.000; subject = old Reading lh surface white INFO: The transform was made with average_305.mnc. Done reading surface Reading rh surface white INFO: The transform was made with average_305.mnc. Done reading surface Zoom Factor = 2 FOV = 256 Opening window old Can't connect to xDisplay! register: ### tkoInitWindow(name) failed ERROR: tkregister2 failed > the register.dat: > > cat > /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630/bold/register.dat > falco > 1.250000 > 1.250000 > 0.010000 > -3.479126e-01 1.338825e-02 5.119526e-03 -1.504414e+00 > 1.396347e-02 3.252346e-01 7.814508e-02 2.019644e+01 > 2.820157e-03 -7.263381e-02 3.366362e-01 1.045828e+01 > 0.000000e+00 0.000000e+00 0.000000e+00 1.000000e+00 > round > > > On > Mon, 2 Jan 2006, Kathryn Devaney wrote: > >> Hi Bruce, >> The subjectname is in >> /space/ship/6/users/kdevaney/Migrane_Aura/analysis/Falco050630 >> and there it is "old" - is it stored somewhere else as well? (I think I >> might have a migraine aura before this analysis is over) >> K >> >>> the register.dat lists the subject name as "falco", not "old". >>> On Mon, 2 Jan >>> 2006, Kathryn Devaney wrote: >>> >>>> Hi - >>>> I've actually set the subject_dir to /space/orsay/2/knutsen/falco/ and >>>> used "old" for the subject name, which seemed to me like it would work >>>> - >>>> is there a reason that it shouldn't? >>>> Kathryn >>>> >>>>> Hi Kathryn, >>>>> >>>>> it looks to me like the register.dat has the wrong subject name. >>>>> There >>>>> is >>>>> no "falco" subject, rather a subject named "old" in the falco >>>>> SUBJECTS_DIR: >>>>> >>>>> ls /space/orsay/2/knutsen/falco/old/surf/ >>>>> lh.area* lh.qsphere* rh.curv* rh.sphere* >>>>> lh.curv* lh.rh.sphere.reg* rh.inflated* >>>>> rh.sphere.reg* >>>>> lh-dt_lop.label* lh.smoothwm* rh.orig* rh.sulc* >>>>> lh.inflated* lh.sphere* rh.patch* >>>>> rh.temporal.label* >>>>> lh.MT* lh.sphere.reg* rh.patch.3d* >>>>> rh.thickness* >>>>> lh.orig* lh.sulc* rh.patch.flat* rh.white* >>>>> lh.patch* lh-temporal.label* rh.pial* surfer.log* >>>>> lh.patch.3d* lh.thickness* rh.qsphere* >>>>> lh.patch.flat* lh.white* rh.rh.sphere.reg* >>>>> lh.pial* rh.area* rh.smoothwm* >>>>> >>>>> cheers, >>>>> Bruce >>>>> >>>>> On Mon, 2 Jan 2006, Kathryn Devaney wrote: >>>>> >>>>>> Below is the text of the process - it fails with no explanation. If >>>>>> anyone has any insight into this, it would be greatly appreciated! >>>>>> >>>>>> [whatever:MYSTUDY] (nmr-std-env) tkregister-sess -sf sessid -df >>>>>> sesspar >>>>>> -------------------------------------------------------------- >>>>>> tkregister-sess logfile is >>>>>> /autofs/space/ship_006/users/kdevaney/Migraine_Aura/MYSTUDY/log/tkregister-sess.log >>>>>> -------------------------------------------------------------- >>>>>> >>>>>> Session: >>>>>> /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630 >>>>>> ---------------- >>>>>> Mon Jan 2 19:41:16 EST 2006 >>>>>> INFO: anatdir set to /space/orsay/2/knutsen/falco/old/mri/T1 >>>>>> ________________________________________________ >>>>>> /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630/bold/006 >>>>>> tkregister2 --targ /autofs/space/orsay_002/knutsen/falco/old/mri/T1 >>>>>> --mov >>>>>> ./f bshort --reg ../register.dat --plane cor --title >>>>>> old--Falco050630--006 >>>>>> --volview targ --surf white >>>>>> ________________________________________________ >>>>>> MRISread(/space/orsay/2/knutsen/falco/falco/surf/lh.white): could >>>>>> not >>>>>> open >>>>>> file >>>>>> No such file or directory >>>>>> tkregister2: could not read surface white >>>>>> No such file or directory >>>>>> surfname set to white >>>>>> target volume /autofs/space/orsay_002/knutsen/falco/old/mri/T1 >>>>>> movable volume ./f >>>>>> reg file ../register.dat >>>>>> LoadVol 1 >>>>>> $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ >>>>>> Diagnostic Level -1 >>>>>> ---- Input registration matrix -------- >>>>>> -0.348 0.013 0.005 -1.504; >>>>>> 0.014 0.325 0.078 20.196; >>>>>> 0.003 -0.073 0.337 10.458; >>>>>> 0.000 0.000 0.000 1.000; >>>>>> float2int = 0 >>>>>> --------------------------------------- >>>>>> INFO: loading target >>>>>> /autofs/space/orsay_002/knutsen/falco/old/mri/T1 >>>>>> INFO: changing target type to float >>>>>> Ttarg: -------------------- >>>>>> -1.000 0.000 0.000 128.000; >>>>>> 0.000 0.000 1.000 -128.000; >>>>>> 0.000 -1.000 0.000 128.000; >>>>>> 0.000 0.000 0.000 1.000; >>>>>> INFO: loading movable ./f >>>>>> INFO: bvolumeRead: min = 0, max = 12970 >>>>>> INFO: changing move type to float >>>>>> Tmov: -------------------- >>>>>> -1.250 0.000 0.000 40.000; >>>>>> 0.000 0.000 1.250 -28.125; >>>>>> 0.000 -1.250 0.000 40.000; >>>>>> 0.000 0.000 0.000 1.000; >>>>>> mkheaderreg = 0, float2int = 0 >>>>>> ---- Input registration matrix -------- >>>>>> -0.348 0.013 0.005 -1.504; >>>>>> 0.014 0.325 0.078 20.196; >>>>>> 0.003 -0.073 0.337 10.458; >>>>>> 0.000 0.000 0.000 1.000; >>>>>> subject = falco >>>>>> Reading lh surface white >>>>>> ERROR: tkregister2 failed >>>>>> [whatever:MYSTUDY] (nmr-std-env) >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>> >>> >>> >> >> >> > > >

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tkregister-sess failing, can't tell why
by Kathryn Devaney 02 Jan '06

02 Jan '06

Below is the text of the process - it fails with no explanation. If anyone has any insight into this, it would be greatly appreciated! [whatever:MYSTUDY] (nmr-std-env) tkregister-sess -sf sessid -df sesspar -------------------------------------------------------------- tkregister-sess logfile is /autofs/space/ship_006/users/kdevaney/Migraine_Aura/MYSTUDY/log/tkregister-sess.log -------------------------------------------------------------- Session: /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630 ---------------- Mon Jan 2 19:41:16 EST 2006 INFO: anatdir set to /space/orsay/2/knutsen/falco/old/mri/T1 ________________________________________________ /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630/bold/006 tkregister2 --targ /autofs/space/orsay_002/knutsen/falco/old/mri/T1 --mov ./f bshort --reg ../register.dat --plane cor --title old--Falco050630--006 --volview targ --surf white ________________________________________________ MRISread(/space/orsay/2/knutsen/falco/falco/surf/lh.white): could not open file No such file or directory tkregister2: could not read surface white No such file or directory surfname set to white target volume /autofs/space/orsay_002/knutsen/falco/old/mri/T1 movable volume ./f reg file ../register.dat LoadVol 1 $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.348 0.013 0.005 -1.504; 0.014 0.325 0.078 20.196; 0.003 -0.073 0.337 10.458; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /autofs/space/orsay_002/knutsen/falco/old/mri/T1 INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ./f INFO: bvolumeRead: min = 0, max = 12970 INFO: changing move type to float Tmov: -------------------- -1.250 0.000 0.000 40.000; 0.000 0.000 1.250 -28.125; 0.000 -1.250 0.000 40.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.348 0.013 0.005 -1.504; 0.014 0.325 0.078 20.196; 0.003 -0.073 0.337 10.458; 0.000 0.000 0.000 1.000; subject = falco Reading lh surface white ERROR: tkregister2 failed [whatever:MYSTUDY] (nmr-std-env)

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cma colors
by Sasha Wolosin 28 Dec '05

28 Dec '05

Dear all, I am interested in using the CMA parcellation. Is the atlas lh.curvature.buckner40.filled.desikan_killany.gcs equivalent to the CMA parcellation? Thanks, Sasha 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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CMA parcellation
by Sasha Wolosin 27 Dec '05

27 Dec '05

Dear all, I am interested in using the CMA parcellation to create ROI's. Is it possible to create ?h.aparc.annot files using the CMA parcellation scheme instead of the surface-based parcellation scheme? Thanks, Sasha 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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overlay thickness maps
by Kirk, Gregory 24 Dec '05

24 Dec '05

I would like to overlay lh.thickness, rh.thickness on inflated for single subject, not the glm results, how to do that is well documented from the tutorial/tutorial group study tried tksurfer subject lh inflated - got the gray surface next file->load overlay -> $SUBJECTS_DIR/subject/surf choose lh.thickness * calculate identity map it redraws the surface but there is no colormap of the thickness can I do what I am trying ? Happy Holidays Greg.

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Paracingulate Gyri Parcellating
by Faden, Eric (NIH/NIMH) [F] 23 Dec '05

23 Dec '05

After reading the paper I am still a little confused about how the Subcortical Parcellation labels the parasingulate gyri when some people have one and others have two? Can anyone shed a little light on this issue? -Eric

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wmfill problem
by Sven Panis 22 Dec '05

22 Dec '05

Hi surfers, I experience a problem during the first step of the create surface routine : fill white matter. Specifically, the ponscall.dat file in mri/tmp is empty and at the start of step two (tessellate RH white matter) I'm asked to confirm that "the images in .../mri/filled/COR-0 cannot be found .... wmfill first." I have already tried to enter the coordinates of the corpus callosum and the pons manually (paying attention to the fact that xTal = coronal, yTal = horizontal, zTal = saggital + to make sure the cc is disconnected), without result... (I use the values in the Volume Index, no Talairachs). Do I have to pay attention to other things when entering coordinates manually? Or does anyone of you have an idea about what's going wrong? Any help appreciated! Thanks and enjoy the holidays, Sven Panis University of Leuven Department of Psychology Tiensestraat 102 3000 Leuven BELGIUM tel: +32-16-32.60.94 Mailto: sven.panis(a)psy.kuleuven.be Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

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RE: [Freesurfer] Sulcal depth
by Bagnato, Francesca (NIH/NINDS) [F] 22 Dec '05

22 Dec '05

Yes, this is what I mean. Thanks, -francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 22, 2005 5:37 PM To: Bagnato, Francesca (NIH/NINDS) [F] Cc: Fornito, Alexander; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth you mean in a parcellation unit? It's whatever the parcellation unit is defined to be. On Thu, 22 Dec 2005, Bagnato, Francesca (NIH/NINDS) [F] wrote: > As far as the cortical thickness of sulci is concerned, the program > refers to the cortex in between two giry, right? > Thanks, > -francesca > > Francesca Bagnato, MD > NIB-NINDS-NIH > 10 Center Drive > Building 10, Room 5B16 > Bethesda, MD, 20892 > USA > ph #: 001-301-402.6391 > fax #: 001-301-402.0373 > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Thursday, December 22, 2005 5:30 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Sulcal depth > > not all that easily, although I guess we could write out something from > mris_inflate that has the units of mm. > > On Fri, 23 Dec 2005, Fornito, Alexander wrote: > >> Hi all, >>> From my understanding, ?h.sulc can be used to measure sulcal depth. >> I'm wandering if it is possible to use this to get the depth of a > sulcus within an ROI, and if so, how you would extract the relevant > measures, i.e.., would it be obtainable through mris_anatomical_stats? >> Thanks, >> Alex >> >> Alex Fornito >> M.Psych/PhD (clin. neuro.) candidate >> Melbourne Neuropsychiatry Centre and Department of Psychology >> The University of Melbourne >> alexander.fornito(a)wh.org.au >> >> ________________________________ >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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RE: [Freesurfer] Sulcal depth
by Bagnato, Francesca (NIH/NINDS) [F] 22 Dec '05

22 Dec '05

As far as the cortical thickness of sulci is concerned, the program refers to the cortex in between two giry, right? Thanks, -francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 22, 2005 5:30 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth not all that easily, although I guess we could write out something from mris_inflate that has the units of mm. On Fri, 23 Dec 2005, Fornito, Alexander wrote: > Hi all, >> From my understanding, ?h.sulc can be used to measure sulcal depth. > I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? > Thanks, > Alex > > Alex Fornito > M.Psych/PhD (clin. neuro.) candidate > Melbourne Neuropsychiatry Centre and Department of Psychology > The University of Melbourne > alexander.fornito(a)wh.org.au > > ________________________________ > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer