Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30060 discussions

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)

4 22

{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.

2 2

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 >

3 2

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

3 4

yakview ttrouble
by Sebastian Moeller 13 Apr '06

13 Apr '06

Dear freesurfers, ran into troubles with yakview (centos4_x86_64-3.0.1-pub-full under Suse 9.3 x86_64) the -nosplash option in line 398 of fsfast/bin/yakview causes a "Warning: Type-ahead buffer overflow." from the installed matlab 7.1 and, not completely unexpected, some corruption. The corruption I observed was a wrong TR and a way off scaling of the colorbar, BTW. Anyway, putting a hash before the -nosplash helps (with the caveat that the splash window opens, albeit transiently). I still see other issues with my install of yakview.m, like the help window (and any other msgbox) gets a copy of the statusline written over line 7. It seems like set_text() gets periodically called with 'gca' as argument, a bit b0rked, if set_text(gca, ud) is called while the help window is active, as gca now points to this window. A Q&D cure is to secure the two call to se_text(gca,ud), with the following construct: if (gcf == ud.hThisYakFig), set_text(gca,ud); end Oh yeah zooming does not really work, but I did not investigate further One more thing though, what to use -v1 or -v2? Ahoi & thanks Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 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

1 0

RE: [Freesurfer] FW: FW: Recon-all longitudinal script
by Nguyen, Thang Q 12 Apr '06

12 Apr '06

Hi Jenni, Yes I have tried it. I guess I should have been clearer when I wrote "I have added the mgz extension", my mistake. Thanks, -Thang -----Original Message----- From: Jenni Pacheco [mailto:jpacheco@nmr.mgh.harvard.edu] Sent: Wednesday, April 12, 2006 3:13 PM To: Nguyen, Thang Q Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: Recon-all longitudinal script Hi Thang, I'm not sure if you've tried this, but try adding -mgz to the command line when running recon-all-nmr-long. Jenni On Wed, 12 Apr 2006, Nguyen, Thang Q wrote: > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Tuesday, April 11, 2006 5:42 PM > To: Nguyen, Thang Q > Subject: Re: FW: Recon-all longitudinal script > > Hi Thang, > > please post this to the list > > Bruce > On Tue, 11 Apr 2006, Nguyen, Thang Q wrote: > >> Hello Bruce Fischl, >> I was wondering if you could help me with this Freesurfer issue. I am >> trying to run the longituduinal script (recon-all-nmr-long) that Xiao >> sent me. We have installed the latest 2006 version of Freesurfer > which >> works in mgz format. I have tried running recon-all on one subject > and >> running the longitudinal script on the second subject. Unfortunately, >> it errors out saying that the script can't find the mgz format. I > have >> added the mgz extension and it also gives me the same problem. >> I have tried recon-all on the second subject as well and then running >> the longitudinal script but it gives me this error: >> >> ***************************************************** >> Sphere rh Mon Apr 10 18:04:19 PDT 2006 >> > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S >> zetoR2/scripts >> cp >> > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S >> zetoR/surf/rh.sphere >> > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S >> zetoR2/surf/rh.sphere >> --------------------------------------------- >> Surf Reg rh Mon Apr 10 18:04:19 PDT 2006 >> > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S >> zetoR2/scripts >> Too many )'s. >> >> ***************************************************** >> Since Xiao left, I no longer have a contact for this problem. I have >> contacted Karl Helmer and he hasn't responded. I was wondering if you >> could help me. Thank you, >> Thang Nguyen >> >> >> ________________________________ >> >> From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] >> Sent: Friday, April 07, 2006 3:36 PM >> To: Nguyen, Thang Q >> Subject: Re: Recon-all longitudinal script >> >> >> I think you run recon-all on the first time point, then -long on the >> subsequent ones. But I've never actually run it myself :). >> >> doug >> >> >> >> >> Nguyen, Thang Q wrote: >> Hello Doug Greve, >> I am trying to run a longitudinal analysis using the > recon-all-nmr-long >> binary from Xiao. I was wondering if you could answer some questions > I >> have. Do I need to process each longitudinal scan using recon-all > first >> and then apply the longitudinal analysis to the first scan or can I >> simply run the recon-all-nmr-long for the subsequent subjects without >> running recon-all on those datasets? >> Thank you for your time, >> -Thang >> >> >> >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

1 0

FW: FW: Recon-all longitudinal script
by Nguyen, Thang Q 12 Apr '06

12 Apr '06

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, April 11, 2006 5:42 PM To: Nguyen, Thang Q Subject: Re: FW: Recon-all longitudinal script Hi Thang, please post this to the list Bruce On Tue, 11 Apr 2006, Nguyen, Thang Q wrote: > Hello Bruce Fischl, > I was wondering if you could help me with this Freesurfer issue. I am > trying to run the longituduinal script (recon-all-nmr-long) that Xiao > sent me. We have installed the latest 2006 version of Freesurfer which > works in mgz format. I have tried running recon-all on one subject and > running the longitudinal script on the second subject. Unfortunately, > it errors out saying that the script can't find the mgz format. I have > added the mgz extension and it also gives me the same problem. > I have tried recon-all on the second subject as well and then running > the longitudinal script but it gives me this error: > > ***************************************************** > Sphere rh Mon Apr 10 18:04:19 PDT 2006 > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S > zetoR2/scripts > cp > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S > zetoR/surf/rh.sphere > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S > zetoR2/surf/rh.sphere > --------------------------------------------- > Surf Reg rh Mon Apr 10 18:04:19 PDT 2006 > /raid2/research/analysis/GE-SiemensCalibration/Freesurfer_longitudinal/S > zetoR2/scripts > Too many )'s. > > ***************************************************** > Since Xiao left, I no longer have a contact for this problem. I have > contacted Karl Helmer and he hasn't responded. I was wondering if you > could help me. Thank you, > Thang Nguyen > > > ________________________________ > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Friday, April 07, 2006 3:36 PM > To: Nguyen, Thang Q > Subject: Re: Recon-all longitudinal script > > > I think you run recon-all on the first time point, then -long on the > subsequent ones. But I've never actually run it myself :). > > doug > > > > > Nguyen, Thang Q wrote: > Hello Doug Greve, > I am trying to run a longitudinal analysis using the recon-all-nmr-long > binary from Xiao. I was wondering if you could answer some questions I > have. Do I need to process each longitudinal scan using recon-all first > and then apply the longitudinal analysis to the first scan or can I > simply run the recon-all-nmr-long for the subsequent subjects without > running recon-all on those datasets? > Thank you for your time, > -Thang > > > > > >

2 1

unpacking anonymized data
by Doug Greve 12 Apr '06

12 Apr '06

I just wanted to give people some warning about unpacking/converting anonymized Siemens dicom files. Siemens inserts some ascii information into their dicom files (what I call the "ascii header"). This is inserted into a "private" field in the dicom header. Some anonymizers will strip this information out of the dicom file. If the dicom file contains a mosiac (eg, as with functionals), then it will not be possible to unpack it using the tools in freesurfer if the ascii header is gone. If the dicom file contains individual slice images (non-mosaics), then it is possible to unpack it correctly even if their is no ascii header. There is currently a bug in mri_convert/unpacksdcmdir that might cause a slice reversal if the ascii header is not there. If you acquired data sagitally, this would mean a left-right flip. This bug has been fixed (live in dev and stable tomorrow). Even so, be very careful when anonymizing your data. You should do some sort of check against unanonymized data to assure that nothing funny has happened. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer