Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Question re' intervention in result of parcelation
by zvalim＠gmail.com 05 Jan '06

05 Jan '06

Hello all, I have a conceptually simple task to accomplish, but can't seem to get it to work via the tkSurfer interface. My goal is to take the result of Freesurfer's default parecelation scheme, remove the Superior Temporal Sulcus label, and partition what was STS into 3 separate regions, with 3 separate labels. Removing the STS label, and generating a new partition of that area into 3 separate labels works OK on the GUI. But I run into problems when trying to save the new partition. First, if I don't assign the new labels to a Structure in the "labels" window, the editing is not saved. However, if I do assign these labels to a structure (e.g., the S_temporal_superior structure) , then after "exporting" the new annotation and reloading it, all three labels will appear as one region called S_temporal_superior. In short, I can't find a way to export the results of my ROI edits into a .annot file. I suspect I might have to create three new structures that correspond to the new labels, but I am not sure in which file I should intervene to create new structures. Any help, much appreciated. Oori

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threshold
by Sasha Wolosin 04 Jan '06

04 Jan '06

Dear all, In group analysis, how are the various thresholds (min, mid, max) related to p-values? 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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tkregister2
by Vasanth Pappu 03 Jan '06

03 Jan '06

Hi, I am using tkregister2 to register two perfusion volumes. I can adjust the brightness of the movable volume, but don't know how to adjust brightness for the target volume. Is this possible? Thanks, Vasanth --

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Re: [Freesurfer] mri_ca_normalize
by Margo McKenna Benoit 03 Jan '06

03 Jan '06

Hi, I'm following up on an earlier email about the mri_ca_normalize step of autorecon2. I am getting an error while running autorecon2 in the developmental freesurfer version on tkmeg at the nmr center. The command I ran was: <recon-all-nmr -subjid avm004 -autorecon2 -nosubcortseg -hemi lh -mail margo> and the output error is below. My directory is /space/lucy/2/users/margo/subjects/ Any advice would be greatly appreciated. Thanks, Margo INFO: SUBJECTS_DIR is /autofs/space/lucy_002/users/margo/subjects Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0/dev2-0-0 -rw-rw-r-- 1 margo smsgp 203951 Dec 22 11:03 /autofs/space/lucy_002/users/margo/subjects/avm004/scripts/recon-all.log Linux tkmeg 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 13:14:25 CDT 2005 i686 athlon i386 GNU/Linux ####################################### GCA RB40_talairach_2005-07-20.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### /autofs/space/lucy_002/users/margo/subjects/avm004 Using mgz format --------------------------------------------- Intensity Normalization2 Tue Jan 3 10:09:16 EST 2006 /autofs/space/lucy_002/users/margo/subjects/avm004/mri mri_normalize -mask brain.mgz norm.mgz T1.mgz reading from norm.mgz... zcat: /autofs/space/lucy_002/users/margo/subjects/avm004/mri/norm.mgz.gz: No such file or directory mghRead(/autofs/space/lucy_002/users/margo/subjects/avm004/mri/norm.mgz, -1): read error mri_normalize: could not open source file norm.mgz using MR volume brain.mgz to mask input volume... ERROR: mri_normalize exited with non-zero status Linux tkmeg 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 13:14:25 CDT 2005 i686 athlon i386 GNU/Linux recon-all exited with errors at Tue Jan 3 10:09:17 EST 2006

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Re: [Freesurfer] tksurfer
by Sasha Wolosin 03 Jan '06

03 Jan '06

I am loading the GDF file from the menu interface. Tksurfer runs correctly before loading the file, including when I load an overlay, but it quits immediately after loading any GDF file. >>> Kevin Teich <kteich(a)nmr.mgh.harvard.edu> >>> Are you loading the GDF file from the menu interface, or from a commandline tool? Does tksurfer run correctly before you load the file? Does it run correctly for other subjects, and with other GDF files? On Tue, Jan 03, 2006 at 09:29:30AM -0500, Sasha Wolosin wrote: > 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. > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Kevin Teich

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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)

3 2

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.

2 1

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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