Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

newbie question regarding pooling (analysis over different sessions)
by Sebastian Moeller 20 Sep '05

20 Sep '05

Dear fs-fast wizards, doing monkey fMRI in Bremen (block desing so far) I run into the problem that analysing the data from one session does not lead to well defined activation maps. Therefore I would like to pool over several sessions (always within one subject). Unfortunately I have did not manage to always position the slices at the same position, I recorded a different number of runs each session. Now my assumption is all I need to do is define according df and sf files and be done with. But at what stage (mc-sess, spatialsmooth-sess, mkanalysis-sess.new, selxavg-sess, mkcontrast-sess or stxgrinfer-sess)? Is it advisable to motion correct all session runs together, or combine the data after that step? So excuse me for my uneducated question, but I would be delighted to tap into this list's vast knowledge before debarking into computationally long experiments. One more question, is it necessary/helpful to record low-res anatomicals before functional runs to register separate sessions, or is this step avoidable. Regards Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 97 51 oder 90 95 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

5 6

Atlases and newer releases
by Satrajit Ghosh 20 Sep '05

20 Sep '05

Does one need to recreate custom atlases when changing to a new release? And if so does this process imply reprocessing all the subjects originally used to create the atlas? Thanks, Satra

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

20 Sep '05

Would manually changing the intensities in brain volume using the configure volume brush tool in tkmedit help? Shoudl white matter be re-labelled as 255? What would be a good value for grey matter? -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 9/20/2005 2:19 PM To: Fornito, Alexander Cc: Doug Greve; freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Autorecon re-processing probably susceptibility problems. Try putting some control points in the wm, but there may not be enough g/w contrast to get good surfaces. On Tue, 20 Sep 2005, Fornito, Alexander wrote: > > 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 >> >> >> >> > > >

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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 >> >> >> > > > > > >

2 1

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

2 1

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 > > >

2 1

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.

2 1

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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