Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Simple ? about T1.mgz
by Clifford A. Smith, PhD 12 Jan '06

12 Jan '06

I¹ve been going over the tutorials, but my question remains is T1 skull stripped? It seems to check skull stripping brain.mgz is loaded as the main volume with T1.mgz as the aux. Flipping back and forth (control 1/control 2) is used to check the stripped brain.mgz. This implies T1 has the skull still (yet my T1 images are all skull stripped). Thanks. Cliff ------------------ Clifford Smith, PhD Assistant Professor of Behavioral Sciences Rush University Medical Center 312.942.2893

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Calculating area from label
by Jonathan Wisco 12 Jan '06

12 Jan '06

Hi, how can I calculate the area from a label? Thanks, Jon -- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th St. Charlestown, MA 02129 E-mail: jjwisco(a)nmr.mgh.harvard.edu Tel: 617-851-8492 Fax: 617-726-7422

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mri_watershed
by dwakeman＠nmr.mgh.harvard.edu 11 Jan '06

11 Jan '06

Hi, I am having a problem with mri_watershed. The data is @ /space/linus/12/users/dwakeman/subjects/P1B2au1/ I called recon-all -subjid P1B2au1 -autorecon1 The error message is at the bottom. running mri_watershed -atlas T1.mgz brain did not work. There is no brain.mgz file generated, so I cannot look to see what the problem is. I have one other problem on a side note, I am generating a true step by step tutorial, which will serve to both teach people about freesurfer and teach them how to use it. I am using the Recommended ReconTable as a basis for this tutorial. In the table, it says that autorecon1 does 4 iterations of nu_correct; however, when the nu_correct command is run individually it says that it performs 2 iterations. I would like to know if this means that a total of 8 iterations are run in autorecon1 or if the equivalent to autorecon1 is two iterations of the nu_correct command. Thank you for your help on both problems. Dan *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 253666 Find the largest 110-component... heap usage = 243888 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 243349 voxels first estimation of the COG coord: x=128 y=128 z=120 r=87 first estimation of the main basin volume: 2802165 voxels global maximum in x=144, y=108, z=79, Imax=255 CSF=13, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 done Analyze main basin size= 1769198 voxels, voxel volume =1.000 = 1769198 mmm3 = 1769.198 cm3 done PostAnalyze... ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=128,y=134, z=118, r=10259 iterations Problem with the least square interpolation in GM_MIN calculation. before analyzing : CSF_MAX=45, TRANSITION=40, GM_MIN=37, GM=52 after analyzing : CSF_MAX=35, TRANSITION=40, GM_MIN=40, GM=43 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...64 iterations *********************VALIDATION*********************Segmentation fault ERROR: mri_watershed exited with non-zero status Linux megws2 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 Wed Jan 11 17:07:18 EST 2006

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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

1 0

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.

2 1

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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Freesurfer