Freesurfer

freesurfer@nmr.mgh.harvard.edu

7 participants
30057 discussions

update patch for freesurfer
by tulu 11 Jan '06

11 Jan '06

Dear freesurfer experts, I wonder if there any update patch I need to download after I install the latest release of dev version of freesurfer ? Thanks replay Kl chen

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problem with stxgrinder-sess
by Michael Ho 10 Jan '06

10 Jan '06

Hi, I'm having a problem with stxgrinder-sess. Here is some relevant info: tkmeg:mikeho[82] source /usr/local/freesurfer/nmr-dev-env SUBJECTS_DIR /space/canada/5/users/mikeho/subjects FUNCTIONALS_DIR /space/canada/5/users/mikeho/brainmapper [tkmeg:~] (nmr-dev-env) which stxgrinder-sess /usr/local/freesurfer/dev/fsfast/bin/stxgrinder-sess [tkmeg:~] (nmr-dev-env) cd /space/canada/5/users/mikeho/vtw_study When I type: [tkmeg:vtw_study] (nmr-dev-env) stxgrinder-sess -contrast words_vs_nonwords -analysis vtw_eng_syn_vis_all -sf sessid -df sesspar stxgrinder-sess logfile is /autofs/space/canada_005/users/mikeho/vtw_study/log/stxgrinder-sess.060110114213.log nthsess = 1 vtw006_eng_syn_vis time=0.012953 -------- /autofs/space/canada_005/users/mikeho/brainmapper/vtw006_eng_syn_vis contrast words_vs_nonwords (time=0.135684) slice 0 ??? Error using ==> fmri_svbfile Too many output arguments. Error in ==> /usr/local/freesurfer/dev/fsfast/toolbox/fast_svbslice.m On line 35 ==> err = fmri_svbfile(y,fname); Error in ==> /usr/local/freesurfer/dev/fsfast/toolbox/fast_stxgrinder2_sess.m On line 167 ==> fast_svbslice(tmp,cesstem,slice,'',mristruct); omnibus contrasts f and fsig can be generated, however, nothing is generated in the vtw_eng_syn_vis_all contrast directory. I get the same error with the bert tutorial data, and in both std and dev environments. Oddly (or maybe not) stxgrinder0-sess works. Thanks. Mike Ho

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Re: [Freesurfer] multiple comparisons
by Sasha Wolosin 09 Jan '06

09 Jan '06

When I set FDR = .05, or anything under .85, and select "set threshold using FDR" the min threshold is always set to 4.03, which is about p= .0001, correct? Would you normally require such low p-values for this type of analysis? Why would such varied FDRs result in the same min threshold? We do not see any results when the min>2.0 (p=.01), so this is very problematic for us. Also, at just over FDR = .85 (I realize this is absurdly high) the min threshold jumps down to 1.23, do you have any idea why this jump might occur? Thanks, Sasha >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> .05 is fairly standard I think. On Mon, 9 Jan 2006, Sasha Wolosin wrote: > Is this something you apply frequently at MGH? What FDR value would you > typically require? > >>>> Doug Greve <greve(a)nmr.mgh.harvard.edu> >>> > > Currently, mris_glm does not attempt to correct for multiple > comparisons, though this feature will be in the next release. In the > mean time, you can correct for multiple comparisons using FDR in > tksurfer. > > > > Sasha Wolosin wrote: > >> Dear all, >> I would like to learn more about group analysis using mris_glm. How >> does the program correct for the problem of multiple comparisons? Is >> there any way to determine the rate of false positives? >> 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 >> >> >> >> > >

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Re: [Freesurfer] multiple comparisons
by Sasha Wolosin 09 Jan '06

09 Jan '06

Is this something you apply frequently at MGH? What FDR value would you typically require? >>> Doug Greve <greve(a)nmr.mgh.harvard.edu> >>> Currently, mris_glm does not attempt to correct for multiple comparisons, though this feature will be in the next release. In the mean time, you can correct for multiple comparisons using FDR in tksurfer. Sasha Wolosin wrote: >Dear all, > I would like to learn more about group analysis using mris_glm. How >does the program correct for the problem of multiple comparisons? Is >there any way to determine the rate of false positives? >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 > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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multiple comparisons
by Sasha Wolosin 09 Jan '06

09 Jan '06

Dear all, I would like to learn more about group analysis using mris_glm. How does the program correct for the problem of multiple comparisons? Is there any way to determine the rate of false positives? 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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inorm-sess trouble
by Kathryn Devaney 06 Jan '06

06 Jan '06

Hi all, I posted a message earlier today from the end of my rope and I think it was a bit terse. Apologies. I'm hoping that someone might have some insight into a (different) problem that's come up with inorm. I'm analyzing three identical subjects. The first two went through fine, but the third is running into an error when I try to run inorm. I'm not sure what is causing this and I'm hoping someone has seen it before or can understand what is going wrong. Any help would be much appreciated. Thanks, Kathryn [whatever:mystudy] (nmr-std-env) inorm-sess -sf sessid -df sesspar -fsd bold -funcstem fmc -motioncor ------------------------------------------------ ------------------------------------------------ ------------------------------------------------ /autofs/space/annecy_014/users/kdevaney/color_flail/cf3 Fri Jan 6 22:19:26 EST 2006 Filesystem 1K-blocks Used Available Use% Mounted on annecy:/local_mount/space/annecy/14 127983336 3073920 124909416 3% /autofs/space/annecy_014 RunList 007 008 009 010 011 012 013 014 set: No match. [whatever:mystudy] (nmr-std-env)

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Scientific Linux vs. Fedora Core
by Renat Yakupov 06 Jan '06

06 Jan '06

Hello everybody, Does anybody have any experience with Scientific Linux? How does it compare with Fedora Core in terms of computational performance? Will I still be able to use Red Hat FreeSurfer release on a PC running Scientific Linux? Thank you. Regards, Renat.

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RE: [Freesurfer] average thickness
by Goldman, Aaron (NIH/NIMH) [F] 06 Jan '06

06 Jan '06

The command line is: mris_glm --design $df --surfmeas thickness --hemi $h --trgsubj $ts --nsmooth 300 --beta beta.mgh --var var.mgh And each column of the design file is: subject_name 1 And then, when I try to run mris_convert -c beta.mgh beta.asc, it just gives me the usage instruction line. When I take out the -c, it does a segmentation fault. Thanks, -Aaron- ________________________________ From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Friday, January 06, 2006 12:00 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness what was your command-line? For mris_glm, specify --beta beta.mgh. btw, the rvar output will be the variance of the thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I downloaded the new version of mris_convert, but I'm having trouble getting it to run successfully. When I start with bfloats it says freadFloat: fread failed a bunch of times, and starting with a COR file it says it can't allocate memory. How do I specify the mgh format you recommended when I run mris_glm? Thanks, -Aaron- ________________________________ From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, January 05, 2006 4:30 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness I'd recommend using mgh instead of bfloat, but in either case you'd do something like: mris_convert -c beta.mgh $SUBJECTS_DIR/yoursubject/surf/lh.white beta.asc (or use beta.bhdr for bfloat). The ability of mris_convert to read any "volume" format was added fairly recently, so if yours does not do it, you can get a new one from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert doug Goldman, Aaron (NIH/NIMH) [F] wrote: Great, thanks. One more question. Doing it the mris_glm way, is there somehow I can turn the beta files (bfloat) into ascii surface format? Thanks, -Aaron- ________________________________ From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, January 05, 2006 3:08 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness The easiest way is probably to build an average subject (make_average_subject). This will create ?h.thickness in the surf dir which will be the average across the input subjects. You could also use mris_glm with a design matrix of all 1s. The beta output will then be the average thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I feel like I used to know this, but how do I make a map of average thickness for a group of subjects? Also, is there a way I can make a similar map showing the variance of thickness values? 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 ________________________________ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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stxgrinder - Error using betainc
by Kathryn Devaney 06 Jan '06

06 Jan '06

I'm not sure how to explain this one, so I'll just include the output: [whatever:mystudy] (nmr-std-env) stxgrinder-sess -analysis color01 -contrast color_bw_01 -sf sessid -df sesspar -------------------------------------------------------------- stxgrinder-sess logfile is /autofs/space/ship_006/users/kdevaney/Color_Flail/Color_Flail_1/mystudy/log/stxgrinder-sess.060106032655.log -------------------------------------------------------------- Contrast List: color_bw_01 MLF is /tmp/stxgrinder-sess-18701.m ----------------------------------------------------- < M A T L A B > Copyright 1984-2003 The MathWorks, Inc. Version 6.5.1.199709 Release 13 (Service Pack 1) Aug 4 2003 Using Toolbox Path Cache. Type "help toolbox_path_cache" for more info. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspblks. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspmasks. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspmex. Warning: Name is nonexistent or not a directory: /autofs/space/lyon_006/pubsw/common/matlab/6.5.1/toolbox/dspblks/dspdemos. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> nthsess = 1 Color_Flail_1 time=0.037307 -------- /autofs/space/ship_006/users/kdevaney/Color_Flail/Color_Flail_1 contrast color_bw_01 (time=0.160157) slice 0 ??? Error using ==> betainc X must be in the interval [0,1]. Error in ==> /usr/local/freesurfer/beta/fsfast/toolbox/tTest.m On line 37 ==> p = betainc(z,dof/2,0.5); Error in ==> /usr/local/freesurfer/beta/fsfast/toolbox/fast_stxgrinder2_sess.m On line 156 ==> prow = sign(trow).*tTest(DOF,abs(trow),tTestDOFMax); >> >> Started at Fri Jan 6 03:26:57 EST 2006 Ended at Fri Jan 6 03:27:05 EST 2006 stxgrinder-sess completed

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RE: [Freesurfer] average thickness
by Goldman, Aaron (NIH/NIMH) [F] 06 Jan '06

06 Jan '06

Hi, I downloaded the new version of mris_convert, but I'm having trouble getting it to run successfully. When I start with bfloats it says freadFloat: fread failed a bunch of times, and starting with a COR file it says it can't allocate memory. How do I specify the mgh format you recommended when I run mris_glm? Thanks, -Aaron- ________________________________ From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, January 05, 2006 4:30 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness I'd recommend using mgh instead of bfloat, but in either case you'd do something like: mris_convert -c beta.mgh $SUBJECTS_DIR/yoursubject/surf/lh.white beta.asc (or use beta.bhdr for bfloat). The ability of mris_convert to read any "volume" format was added fairly recently, so if yours does not do it, you can get a new one from: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_convert doug Goldman, Aaron (NIH/NIMH) [F] wrote: Great, thanks. One more question. Doing it the mris_glm way, is there somehow I can turn the beta files (bfloat) into ascii surface format? Thanks, -Aaron- ________________________________ From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thursday, January 05, 2006 3:08 PM To: Goldman, Aaron (NIH/NIMH) [F] Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] average thickness The easiest way is probably to build an average subject (make_average_subject). This will create ?h.thickness in the surf dir which will be the average across the input subjects. You could also use mris_glm with a design matrix of all 1s. The beta output will then be the average thickness. Goldman, Aaron (NIH/NIMH) [F] wrote: Hi, I feel like I used to know this, but how do I make a map of average thickness for a group of subjects? Also, is there a way I can make a similar map showing the variance of thickness values? 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 ________________________________ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

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Freesurfer