Freesurfer September 2005

freesurfer@nmr.mgh.harvard.edu

44 participants
91 discussions

RE: [Freesurfer] Autorecon re-processing
by Fornito, Alexander 20 Sep '05

20 Sep '05

Sorry, I missed it - forgive my absent mindedness :( Onto a more valid problem (I hope!), I've had trouble segmenting the olfactory sulcus on some of my images. The wm wolume seems to segment well, but the orig and/or white surface doesn't follow this. Rather than enter the olfacoty sulcus, only partially enters it. I was curious as to why the orig/white surface would not follow the surface of the wm volume, and if there is anyway to fix it? Thanks, Alex -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 9/20/2005 4:03 AM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Autorecon re-processing does your version not tell you these things when you run -help? Fornito, Alexander wrote: >HI, >Just wanted to check a few things re: re-running autorecon. >I'm guessing that re-running autorecon with the -pial flag re-runs make_final_surfaces, which takes about 4-6 hours (correct?). >What is re-run when the -wm and -cp flags are used, and how long do they take? >>From what I understand, -cp would require re-running everything from intensity normalization on, including the subcortical segmentation, while -wm would require re-running the topology fixer and final surfaces. >Does this sound about right? >Thanks, >Alex > >_______________________________________________ >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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RE: [Freesurfer] anatomical stats
by Fornito, Alexander 19 Sep '05

19 Sep '05

Yeah, that's what I meant. That's fine, just wanted to make sure I wasn't doing it wrong! -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Tue 9/20/2005 5:22 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] anatomical stats what do you mean it does not work? Because things aren't aligned? I'm afraid you're on your own if you want the columns to be lined up. I'd suggest a perl script. doug Fornito, Alexander wrote: >-b doesn't seem to work. The command is below, and the format of the output, are below. Is this a bug? > >mris_anatomical_stats -l 1000027_lh_roi.label -b -log roi.log 1000027 lh white > >Output: >% 1000027: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> >592393 124 321 2.582 0.698 0.068 0.022 4.448 0.588 > >-----Original Message----- >From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >Sent: Sat 9/17/2005 10:33 PM >To: Fornito, Alexander >Cc: freesurfer(a)nmr.mgh.harvard.edu >Subject: RE: [Freesurfer] anatomical stats >try -b > >On Sat, 17 Sep 2005, Fornito, Alexander wrote: > > > >>I can create a log file, but in the output, the numbers are out of alignment, so you can't easily figure out what each number refers to. Is there some preferable output format or suffix that I can add to the log file name to adjust this? >> >>Also, I can't seem to use the -f flag to create a table. mris_anatomical_stats runs, but there is no table file output at the end. Is this only for the annotation table (I'm using custom labels)? An example command I've tried is: >> >>mris_anatomical_stats -mgz -l roi.label -f roi_table 1000001 lh white >> >> >>-----Original Message----- >>From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >>Sent: Fri 9/16/2005 9:51 PM >>To: Fornito, Alexander >>Cc: freesurfer(a)nmr.mgh.harvard.edu >>Subject: Re: [Freesurfer] anatomical stats >>p.s. the flags should always come before the mandatory command line args. >> >>On >>Fri, 16 Sep 2005, Fornito, Alexander wrote: >> >> >> >>>Hi, >>>I'm using the 20050905 distribution and it seems like mris_anatomical_stats is trying to look for cor files, when I've run my analyses using mgz. Is there a way to change this, or have I got it wrong?. Here is the output >>> >>>mris_anatomical_stats 1000001 lh white >>>reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/wm... >>>corRead(): can't open file /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/wm/COR-.info >>>mris_anatomical_stats: could not read input volume /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/w >>> >>> >>>Also, I've been having trouble using the -f and -log options (the program runs, but I can't seem to create an output file) with some other surfaces (that I have used cor with). Could you pls give me an example of how to use these flags in the command line? >>>I tried: >>>mris_anatomical_stats 1000027 lh white -l 1000027/label/1000027_roi.label -f roi_stats.log >>>(and I also tried putting the options right after mris_anatomical_stats). >>>Thanks, >>>Alex >>> >>>_______________________________________________ >>>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 > > > > -- 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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RE: [Freesurfer] anatomical stats
by Fornito, Alexander 19 Sep '05

19 Sep '05

-b doesn't seem to work. The command is below, and the format of the output, are below. Is this a bug? mris_anatomical_stats -l 1000027_lh_roi.label -b -log roi.log 1000027 lh white Output: % 1000027: <wm vol> <surf area> <gray vol> <thick mean> <thick var> <integ rect. mean curv> <integ rect. Gauss curv> <fold index> <intr curv ind> 592393 124 321 2.582 0.698 0.068 0.022 4.448 0.588 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Sat 9/17/2005 10:33 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] anatomical stats try -b On Sat, 17 Sep 2005, Fornito, Alexander wrote: > I can create a log file, but in the output, the numbers are out of alignment, so you can't easily figure out what each number refers to. Is there some preferable output format or suffix that I can add to the log file name to adjust this? > > Also, I can't seem to use the -f flag to create a table. mris_anatomical_stats runs, but there is no table file output at the end. Is this only for the annotation table (I'm using custom labels)? An example command I've tried is: > > mris_anatomical_stats -mgz -l roi.label -f roi_table 1000001 lh white > > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Fri 9/16/2005 9:51 PM > To: Fornito, Alexander > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] anatomical stats > p.s. the flags should always come before the mandatory command line args. > > On > Fri, 16 Sep 2005, Fornito, Alexander wrote: > >> Hi, >> I'm using the 20050905 distribution and it seems like mris_anatomical_stats is trying to look for cor files, when I've run my analyses using mgz. Is there a way to change this, or have I got it wrong?. Here is the output >> >> mris_anatomical_stats 1000001 lh white >> reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/wm... >> corRead(): can't open file /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/wm/COR-.info >> mris_anatomical_stats: could not read input volume /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/w >> >> >> Also, I've been having trouble using the -f and -log options (the program runs, but I can't seem to create an output file) with some other surfaces (that I have used cor with). Could you pls give me an example of how to use these flags in the command line? >> I tried: >> mris_anatomical_stats 1000027 lh white -l 1000027/label/1000027_roi.label -f roi_stats.log >> (and I also tried putting the options right after mris_anatomical_stats). >> Thanks, >> Alex >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > > > >

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Autorecon re-processing
by Fornito, Alexander 19 Sep '05

19 Sep '05

HI, Just wanted to check a few things re: re-running autorecon. I'm guessing that re-running autorecon with the -pial flag re-runs make_final_surfaces, which takes about 4-6 hours (correct?). What is re-run when the -wm and -cp flags are used, and how long do they take? >From what I understand, -cp would require re-running everything from intensity normalization on, including the subcortical segmentation, while -wm would require re-running the topology fixer and final surfaces. Does this sound about right? Thanks, Alex

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RE: [Freesurfer] anatomical stats
by Fornito, Alexander 17 Sep '05

17 Sep '05

I can create a log file, but in the output, the numbers are out of alignment, so you can't easily figure out what each number refers to. Is there some preferable output format or suffix that I can add to the log file name to adjust this? Also, I can't seem to use the -f flag to create a table. mris_anatomical_stats runs, but there is no table file output at the end. Is this only for the annotation table (I'm using custom labels)? An example command I've tried is: mris_anatomical_stats -mgz -l roi.label -f roi_table 1000001 lh white -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Fri 9/16/2005 9:51 PM To: Fornito, Alexander Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] anatomical stats p.s. the flags should always come before the mandatory command line args. On Fri, 16 Sep 2005, Fornito, Alexander wrote: > Hi, > I'm using the 20050905 distribution and it seems like mris_anatomical_stats is trying to look for cor files, when I've run my analyses using mgz. Is there a way to change this, or have I got it wrong?. Here is the output > > mris_anatomical_stats 1000001 lh white > reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/wm... > corRead(): can't open file /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/wm/COR-.info > mris_anatomical_stats: could not read input volume /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/w > > > Also, I've been having trouble using the -f and -log options (the program runs, but I can't seem to create an output file) with some other surfaces (that I have used cor with). Could you pls give me an example of how to use these flags in the command line? > I tried: > mris_anatomical_stats 1000027 lh white -l 1000027/label/1000027_roi.label -f roi_stats.log > (and I also tried putting the options right after mris_anatomical_stats). > Thanks, > Alex > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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new stable release
by Sasha Wolosin 16 Sep '05

16 Sep '05

Dear all, I am having trouble installing/setting up the stable release v2.1 for CentOS 4 x86_64. I seem to be missing all the mni and fsl tools, they are not included in my freesurfer home folder. Should I just copy these from the dev version? When I try to run setup I get this error: [root@bwy-1-113mm /freesurfer]$ source SetUpFreeSurfer.csh Setting up enviroment for FreeSurfer/FS-FAST $Id: FreeSurferEnv.csh,v 1.3.6.6 2005/07/29 17:40:57 kteich Exp $ FREESURFER_HOME /freesurfer FSFAST_HOME /freesurfer/fsfast FSL_DIR /freesurfer/fsl SUBJECTS_DIR /freesurfer/subjects WARNING: /freesurfer/fsl/bin does not exist. Any help is greatly appreciated. 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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anatomical stats
by Fornito, Alexander 16 Sep '05

16 Sep '05

Hi, I'm using the 20050905 distribution and it seems like mris_anatomical_stats is trying to look for cor files, when I've run my analyses using mgz. Is there a way to change this, or have I got it wrong?. Here is the output mris_anatomical_stats 1000001 lh white reading volume /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/wm... corRead(): can't open file /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/wm/COR-.info mris_anatomical_stats: could not read input volume /data/flanders/work/alex/freesurfer/subjects_fe/1000001/mri/w Also, I've been having trouble using the -f and -log options (the program runs, but I can't seem to create an output file) with some other surfaces (that I have used cor with). Could you pls give me an example of how to use these flags in the command line? I tried: mris_anatomical_stats 1000027 lh white -l 1000027/label/1000027_roi.label -f roi_stats.log (and I also tried putting the options right after mris_anatomical_stats). Thanks, Alex

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RE: [Freesurfer] intensity normalization failure
by Fornito, Alexander 15 Sep '05

15 Sep '05

Hi, Just had a couple of questions re: the -pvvol flag in mri_segstats: How does it take account of partial voluming? Is there anyway to visualize what the partial volume-corrected volume would look like? Would you recmmoned using this falg routinely to obtain subcortical volumes? Finally, on a completely unrelated question, is there any reason to think that surfaces created using the same freesurfer distribution on a Mac would be incompatible with those created using a Linux machine (ie., would you be able to pool them for one study without any problems, and could you start creating surfaces on one, and then re-run afdter manual edits on the other?) Thanks, Alex -----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Thu 9/15/2005 10:11 AM To: Bruce Fischl Cc: Fornito, Alexander; freesurfer(a)nmr.mgh.harvard.edu; Tracy Wang Subject: RE: [Freesurfer] intensity normalization failure You should be able to use mri_segstats somehow. You'll need a segmentation, though. You could tell it to report on the aseg wm values. You could also use the fill volume (127 and 255?). Check out the --help doug On Wed, 14 Sep 2005, Bruce Fischl wrote: > should be easy enough to do in matlab. Just load the wm volume, then find all > the T1 voxels that are nonzero in it. > > Bruce > On Thu, 15 Sep 2005, Fornito, Alexander wrote: > >> Is it possible to obtain and intensity histogram of the wm voxels, or >> descriptive stats (eg., Mean, SD) as a quick check? >> >> -----Original Message----- >> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Sent: Thursday, September 15, 2005 3:33 AM >> To: Tracy Wang >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] intensity normalization failure >> >> if it succeeds then the intensity in the wm should be exactly 110 over >> much of the brain, and 90<wm<120 pretty much everywhere >> >> Bruce >> >> On Wed, 14 Sep >> 2005, Tracy Wang wrote: >> >>> Hi >>> >>> What is a typical example of when the intensity normalization process >> fails? >>> Does the over-all image seem brighter? What is a good indicator of >> success >>> or failure? >>> >>> Thanks, >>> Tracy >>> >>> >>> Tracy Wang >>> Research Assistant >>> Cognitive Neuroscience Laboratory >>> >>> Washington University >>> Department of Psychology, Campus Box 1125 >>> One Brookings Drive >>> St. Louis MO 63130-4899 >>> 314-935-5019 >>> twang(a)artsci.wustl.edu >>> >> _______________________________________________ >> 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 > > > -- 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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average curvatures
by Sheeva Azma 15 Sep '05

15 Sep '05

Hello, I am trying to superimpose an average curvature on the inflated brain surface of another subject. I know that you can use mris_average_curvature to create an average curvature of some specified brains, but I would like to use an average curvature that is not an average of the subjects' curvatures; instead, I'd like it to be an average of curvatures from a general atlas. How do I create, based on this average, the lh.avg_curv and rh.avg_curv files in a subject's surf/ directory? Thanks, Sheeva Azma

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tkregister2
by Sasha Wolosin 15 Sep '05

15 Sep '05

Dear all, I am having trouble running tkregister2. I get an error when I run tkregister2 on a subject after running autorecon1 (see below.) However, I also get an error when I run it on bert. It seems tkregister2 is searching for COR files, but I am using mgz format. Am I not using the correct flags? My subjects directory contains the talairach subject included in the dev release. Do I need to download talairach separately? Here is the output for subject 2335 and bert: [root@bwy-1-113mm talairach]$ tkregister2 --mgz --s 2335 --fstal INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.002 0.050 -0.017 -3.539; -0.053 1.034 -0.076 -12.275; 0.014 0.081 1.091 -14.424; 0.000 0.000 0.000 1.000; corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 [root@bwy-1-113mm subjects]$ tkregister2 --mgz --s bert --fstal INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.37 2005/08/29 21:38:09 greve Exp $ Diagnostic Level -1 talairach.xfm --------------------- 1.154 -0.024 0.046 -5.813; 0.014 0.941 0.131 -21.893; -0.048 -0.155 1.123 -0.730; 0.000 0.000 0.000 1.000; WARNING: can't find the talairach xform '/autofs/space/minerva_001/users/nicks/subjects/bert/mri/transforms/talairach.xfm' WARNING: transform is not loaded into mri corRead(): can't open file /freesurfer/subjects/talairach/mri/orig/COR-.info ERROR: could not read /freesurfer/subjects/talairach/mri/orig as 0 [root@bwy-1-113mm subjects]$ Any help is greatly appreciated. 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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Freesurfer September 2005