Freesurfer April 2006

freesurfer@nmr.mgh.harvard.edu

50 participants
83 discussions

Cortical surface measurement.
by Goradia, Dhruman D 19 Apr '06

19 Apr '06

Hello All, Is it possible to find ROI based cortical surface measures using freesurfer? I am interested in manually tracing ROI and then obtaining thickness, surface area and curvature measures for the ROI. Is there a way to do this in freesurfer? Thank you -Dhruman

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using Analyze
by Chacko Cherian 18 Apr '06

18 Apr '06

Hello all, Can freesurfer use data in Analyze format or does everything have to be converted to .mgz?? Thanks in advance. Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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masking regions on volume data
by trinity＠nmr.mgh.harvard.edu 18 Apr '06

18 Apr '06

Hi - I'm trying to make a picture for a manuscript submission. We'd like to show group amygdala activation on a volume but we'd only like to show the amygdala activation and mask all the other activation out of the picture. How do we do this? Thank you. Trinity

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aparc2aseg -hemi
by Sasha Wolosin 18 Apr '06

18 Apr '06

Dear FreeSurfers, I am using freesurfer stable 3.0.1 for 64-bit linux, and I would like to run aparc2aseg on just the right hemisphere. I ran "recon-all -hemi rh -subjid 2600test -autorecon-all" and when it got to aparc2aseg it exited with the following error: MRISread(/data/subjects/2600test/surf/lh.white): could not open file No such file or directory I then tried to run mri_aparc2aseg separately using the flag "-hemi rh" and it said option "-hemi" is unknown. Does aparc2aseg require both hemispheres be run through all the previous steps? 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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segmentation fault for: mris_convert
by Dahlia Sharon 14 Apr '06

14 Apr '06

Hi, I'm trying to use mris_convert and am getting a segmentation fault error. The precise steps are pasted below. Can anyone figure out why this is happening now? Thanks! Dahlia. mirabai:dahlia[81] setenv SUBJECTS_DIR ~/structurals/ mirabai:dahlia[82] nmrenv -------- freesurfer-Linux-centos4-stable-v3.0.1c-20060329 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/stable FSFAST_HOME /usr/local/freesurfer/stable/fsfast SUBJECTS_DIR /homes/6/dahlia/structurals/ FUNCTIONALS_DIR /usr/local/freesurfer/stable/sessions MINC_BIN_DIR /usr/local/freesurfer/stable/mni/bin MINC_LIB_DIR /usr/local/freesurfer/stable/mni/lib PERL5LIB /usr/local/freesurfer/stable/mni/lib/perl5/5.8.0 GSL_DIR /usr/local/freesurfer/stable/lib/gsl QTDIR /usr/local/freesurfer/stable/lib/qt TCLLIBPATH /usr/local/freesurfer/stable/lib/tcltktixblt/lib FSL_DIR /usr/local/freesurfer/stable/fsl [mirabai:~] (nmr-std-env) cd structurals/subj06_bay2/surf/ [mirabai:surf] (nmr-std-env) mris_convert rh.occip.patch.flat rh.occip.patch.flat.asc Segmentation fault [mirabai:surf] (nmr-std-env)

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{Disarmed} stats
by Sasha Wolosin 14 Apr '06

14 Apr '06

Dear FreeSurfers, We are running FreeSurfer on CentOS 4.2 and are currently in the process of updating from CentOS 4.2 to 4.3. To check stability, we ran the same data on multiple machines with the different versions of CentOS using recon-all. We also ran the same data twice on the same machine (on the following day, with no changes made). We actually found slight differences in the ROI stats for the data run twice on the same machine, (in addition to slight differences between machines.) While these differences do not seem to be significant, we are concerned about them because we do not know of any reason to expect random effects in our analysis. here is an example of the differences found: [root@bwy-1-113mm subjects]$ grep -s caudalmid 2606/stats/lh.aparc.stats caudalmiddlefrontal 3873 2648 6807 2.155 0.735 0.119 0.023 41.641 3.388 [root@bwy-1-113mm subjects]$ grep -s caudalmid apr11run2606/stats/lh.aparc.stats caudalmiddlefrontal 3877 2644 6994 2.212 0.736 0.118 0.023 41.228 3.411 Does anyone know what may cause these differences? Is there any standard method you would use to test for stability other than looking at data such as these? 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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RE: [Freesurfer] aseg.auto.mgz
by Jenni Pacheco 14 Apr '06

14 Apr '06

Hi Tom, What kind of scans are you working with? How were they collected? Have you averaged more than one acquisition? Jenni _____ From: Tom Bayer [mailto:tabayer@gmail.com] Sent: Thursday, April 13, 2006 7:41 PM To: Jenni Pacheco Subject: Re: [Freesurfer] aseg.auto.mgz autorecon2 ran all the way through. I first noticed a problem because the wm.mgz file is only a narrow band of voxels and its distorted. The brain.mgz file is missing some areas of white matter. aseg.auto.mgz is missing a hemisphere, and aseg.mgz is very similar in shape to wm.mgz, which is an irregularly shaped blob that occupies about 1/4 of the coronal section, and is roughly centered in the image. I am fairly certain that the failure occured in the step generating aseg.auto.mgz or one of the steps just prior, because nu_noneck.mgz looks good. I created brainmask.mgz and brainmask.auto.mgz using manual thresholding and they are exactly to my specifications. Strangely, the output file brain.mgz still has problems. It looks exactly as it did before manual thresholding. on a previous post to the list, it was suggested that default thresholding took over because brainmask.mgz and brainmask.auto.mgz do not match. I assure you that they do match. I cop[ied the mask that I manually created so that both files match exactly. -tom On 4/13/06, Jenni Pacheco <jpacheco(a)nmr.mgh.harvard.edu> wrote: Hi Tom, We're going to need a little more info. Did autorecon2 finish? Did it fail part way through? When you say everything has problems, what kind of problems? go here to see the types of information we need in order to best help you: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting thanks, -- Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 jpacheco(a)nmr.mgh.harvard.edu On Thu, 13 Apr 2006, Tom Bayer wrote: > I'm having problems with the output of recon-all -autorecon2. proceeding > down the recon-all dev table, I checked the outputs of each step. > everything looks good until aseg.auto.mgz everything after has problems. > What kind of manual intervention do I need to do for this? > > -Tom >

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tksurfer overlay display
by anthony gallo 13 Apr '06

13 Apr '06

Hello, How can the color scale bar of the overlay display be changed so that it only shows positive values? I know if you use the truncate function in "Configure Overlay Display" that takes the color for the negative values off the display but the scale itself still shows negative values. If further clarity is needed please let me know. Thanks! -Anthony

2 1

aseg.auto.mgz
by Tom Bayer 13 Apr '06

13 Apr '06

I'm having problems with the output of recon-all -autorecon2. proceeding down the recon-all dev table, I checked the outputs of each step. everything looks good until aseg.auto.mgz everything after has problems. What kind of manual intervention do I need to do for this? -Tom

2 1

Manual intervention for skull stripping
by Lee HL 13 Apr '06

13 Apr '06

Hi, I'm a freesurfer newbie. I was following the instructions from the beginners guide to fix bad output from skull stripping. However, it didn't work as it should be as described below (see italics) when I clicked on my middle button. Is there any option that I could do to re-assign my buttons to perform the operation? Thank you very much for your help! "Use Ctrl-1 and Ctrl-2 to cycle between the two volumes. Find a place in the image where the cerebellum is missing in the output volume, then use the middle button on the mouse to paint in cerebellum from the auxiliary volume. Cycle back and forth between the volumes frequently so you know where you are." -- extracted from the internet source. -- Best wishes, HweeLing Research Scientist Cognitive Neuroscience Laboratory Singapore Health Services

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Freesurfer April 2006