Freesurfer January 2007

freesurfer@nmr.mgh.harvard.edu

51 participants
74 discussions

lesions
by Joan Fisher 14 Jan '07

14 Jan '07

Lots of questions about lesions: 1) What is the best way to measure the size of a lesion in Freesurfer? Or should it be drawn in afni and transported to Freesurfer somehow? 2) What is the best way to measure how much of each ROI is affected by the lesion? 3) Line 25 lists "Left-lesion" and Line 57 lists "Right-lesion" in aseg.stats, but these are currently all zeros in brains that have clear lesions -- why? And why are those lines there if Freesurfer isn't recognizing a hole in the head as a lesion? Is there some option that must be selected to make this work? 4) Is it true that cortical lesions can throw off Freesurfer's ability to see landmarks, so that not only the lesion area might be mislabeled, but surrounding tissue and even distant tissue too? If so, is there a way around this problem built into Freesurfer? I have one brain with a large cortical lesion that looks like it parcellated okay, and another with a huge lesion that doesn't look right at all. Periventricular lesions look fine -- is this what others have found? 5) What is the best way to dump the parcellation data and the subcortical segmentation data back into afni (which files specifically) so that it can be viewed in 3D on the original structural brain as a mask? Help would be much appreciated. Many thanks, Joan Fisher University of Chicago

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Recon-all -i ... command does not create all 10 folders
by Juergen Haenggi 12 Jan '07

12 Jan '07

Dear Freesurfer users we are running Freesurfer 3.0.4 on a supercomputer. the problem is that the first recon-all command (recon-all -i ...) do not create all 10 folders per subjects, so that Freesurfer crashed when trying to write lh.aparc.annot, because there is no folder called label. We then created the "label" folder in advance, but after running the analysis, this folder is no longer available. The first recon-all command generated only the following five folders: mri, scripts, stats, surf, touch. When running locally on my workstation, everthing works fine. Any idea what is wrong. The owners of the supercomputer asked me whether there is a possibility to test the Freesurfer software in a shorter time, i.e. not to run the whole pipe with a brain because it takes about 30 hours to complet. Therefore my question: Is it possible to do a shorter test of the whole pipe or to run a evaluation tool? Thanks a lot in advance Best regards Juergen ---------------------------------------------- Juergen Haenggi, Ph.D. student Neuropsychology and Imaging Division of Psychiatry Research Psychiatric University Hospital University of Zurich, Switzerland P.O. Box 1931 Lenggstrasse 31, 8032 Zurich 0041 44 384 26 10 (office phone) 0041 76 445 86 84 (mobile phone) 0041 44 384 26 86 (fax) H 115 (office room number) juergen.haenggi(a)bli.unizh.ch (division email) http://www.dpr.unizh.ch/ (division website) http://www.juergenhaenggi.ch (private website) ----------------------------------------------

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mni305 template large than normalized MRI data ?
by tulu 10 Jan '07

10 Jan '07

Dear Freesurfer experts, I use fs 3.0.4 stable version on FC4. In recon-all stage 1, I check tkregister2 for my subject's MRI. I found the MNI305 template is large than normalized T1. Is it right ? Thanks replay KL Chen

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How to get masks on cerebral white matter and cortex?
by Kai Li 09 Jan '07

09 Jan '07

Hi, I wonder how to get masks on the cerebral white matter and the cerebral cortex. In particular, I'd like to have the masks in the space of the original input image. I noticed that in the asegm.mgz cerebral white matter and cerebral cotex are explicitly labeled, but I'm not sure if this is the final result instead of an intermediate result of less accuracy. If I should use aseg.mgz, do I need to do some transformation to go back to the original space, and how to? Thanks, Kai

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Freesurfer Installation Problem
by Jaakko Karras 09 Jan '07

09 Jan '07

I recently installed FreeSurfer 3.0.4 for CentOS 4 x86_64 on a server running Fedora Core 3 (w/ x86_64), but ran into the following error upon testing the installation with the command "tkmedit bert orig.mgz": $ tkmedit bert orig.mgz Talairach transform /autofs/space/freesurfer/subjects/bert/mri/transforms/talairach.xfm does not exist ... Loading tal xfm file /home/fmri/fmrihome/dti/software/freesurfer/subjects/bert/mri/transforms/talairach.xfm The setup script ran flawlessly, producing the following output: $ source SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4-stable-pub-v3.0.4 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/fmri/fmrihome/dti/software/freesurfer FSFAST_HOME /home/fmri/fmrihome/dti/software/freesurfer/fsfast SUBJECTS_DIR /home/fmri/fmrihome/dti/software/freesurfer/subjects MNI_DIR /home/fmri/fmrihome/dti/software/freesurfer/mni GSL_DIR /home/fmri/fmrihome/dti/software/freesurfer/lib/gsl FSL_DIR /home/fmri/fmrihome/fsl I was able to locate the "missing" talairach.xfm file in the appropriate directory. On another note, I run into the following tcl/tk error when running tksurfer: Tk_Init failed: Can't find a usable tk.tcl in the following directories: /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 /home/ fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 ./lib/tk8.4 ./li b/tk8.4 ./library ./library ./tk8.4.6/library ./tk8.4.6/library /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk.tcl: ca n't access "::tk::Priv.::ffff:171.65.48.253:0": parent namespace doesn't exist can't access "::tk::Priv.::ffff:171.65.48.253:0": parent namespace doesn't exist while executing "upvar #0 ::tk::Priv.::ffff:171.65.48.253:0 ::tk::Priv" ("uplevel" body line 1) invoked from within "uplevel #0 upvar #0 ::tk::Priv.$disp ::tk::Priv" (procedure "tk::ScreenChanged" line 9) invoked from within "tk::ScreenChanged [winfo screen .]" (file "/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 /tk.tcl" line 277) invoked from within "source /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk .tcl" ("uplevel" body line 1) invoked from within "uplevel #0 [list source $file]" /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk.tcl: ca n't import command "mc": already exists can't import command "mc": already exists while executing "namespace import ::msgcat::mc" (in namespace eval "::tk::msgcat" script line 21) invoked from within "namespace eval msgcat { namespace export mc mcmax if {[interp issafe] || [catch {package require msgcat}]} { # The msgcat..." (in namespace eval "::tk" script line 3) invoked from within "namespace eval ::tk { # Set up the msgcat commands namespace eval msgcat { namespace export mc mcmax if {[interp issafe] || [..." (file "/home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4 /tk.tcl" line 20) invoked from within "source /home/fmri/fmrihome/dti/software/freesurfer/lib/tcltktixblt/lib/tk8.4/tk .tcl" ("uplevel" body line 1) invoked from within "uplevel #0 [list source $file]" This probably means that tk wasn't installed properly. I run into the same error when opening the FSL 3.3 GUI, so I assume the error from FreeSurfer is related. I understood that the latest FreeSurfer is packaged with the required tcl/tk libraries, so this shouldn't be an issue. Any thoughts? Note: I also installed the standard CentOS 4 (non 64 bit) distribution, but encountered the same problems. Thanks, Jaakko __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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RE: [Freesurfer] problem with mris_anatomical_stats
by Nick Schmansky 09 Jan '07

09 Jan '07

Abdel, Indeed mris_fix_topology had the same bug as mris_anatomical_stats (when running on Slackware Linux). I've posted a fixed version of mris_fix_topology here: http://surfer.nmr.mgh.harvard.edu/pub/dist/ named: mris_fix_topology.gz mv this to your $FREESURFER_HOME/bin, then type: gunzip mris_fix_topology.gz chmod a+x mris_fix_topology Let me know if you encounter similar bugs. This fixed binary will appear in the next release. Nick On Fri, 2007-01-05 at 14:43 +0000, Abdel Douiri wrote: > Hi Nick > We have done a new update to our Linux system and i have found the same error that i report a while ago (see bellow) But this time is for mris_fix_topology program. > Can you please check it again for mris_fix_topology.c file, the error that you found was problem with sprintf! (sprintf(fname,"%s.mgz",fname) to strcat(fname,".mgz") > ). > Thanks > Abdel > > > > > Abdel, > > Thanks for testing this. The bug fix will appear in an upcoming > release, but you can continue using the mris_anatomical_stats that you > have now. > > For those interested in the perils of testing a multi-platform app, the > buggy line of code was: > > sprintf(fname,"%s.mgz",fname) > > Here the source and destination are the same, which, according to glibc > docs for sprintf, is undefined behavior. The odd thing is that these > Linux variants: RedHat 7.3, RedHat 9, Centos4, Debian and SuSE; and Mac > OS X, all have a shared libc lib that handles the line of code properly. > The libc included with Slackware, however, did not (and understandably > so). libc.so is included not with Freesurfer, but with the OS, so this > means that testing even on a half-dozen different platforms doesn't > guarantee trouble-free performance on a seemingly identical platform. > > The proper code in this case is: > > strcat(fname,".mgz"); > > N. > > > On Fri, 2006-08-18 at 18:40 +0100, A. Douiri wrote: > > that s works! > > Cheers! > > > > > > At 01:51 18/08/2006, Nick Schmansky wrote: > > >Abdel, > > > > > >I don't think there is a matlab alternative to mris_anatomical_stats. > > > > > >However, there is a suspicious line of code in mris_anatomical_stats that > > >I have fixed, and I'm wondering if you can give a new binary a try. It is > > >found here: > > > > > > http://surfer.nmr.mgh.harvard.edu/pub/dist/ > > > > > >and named: > > > > > > mris_anatomical_stats.gz > > > > > >To install, after downloading: > > > > > > gunzip mris_anatomical_stats.gz > > > chmod o+x mris_anatomical_stats > > > mv mris_anatomical_stats $FREESURFER_HOME/bin > > > > > >While I cannot recreate the error you see, I do not have a Slackware > > >installation, and I am wondering if its core libs are revealing a bug in > > >our code. > > > > > >Let me know if it works. > > > > > >Thanks, > > > > > >Nick > > > > > > > > > > Hi Nick, > > > > Thanks in advance for your help and i would like to ask is there an > > > > alternative in matlab for example to do mris_anatomical_stats? > > > > The detail of the outjkputs is: > > > > > > > > the output of: > > > > $ mris_anatomical_stats --all-info > > > > ProgramName: mris_anatomical_stats ProgramArguments: --all-info > > > > ProgramVersion: $Name: stable3 $ TimeStamp: 06/08/17-10:28:55-GMT CVS: > > > > $Id: > > > > mris_anatomical_stats.c,v 1.35.2.1 2006/04/21 19:45:19 nicks Exp $ User: > > > > douiri Machine: img-179 Platform: Linux PlatformVersion: 2.6.16.22 > > > > CompilerName: GCC CompilerVersion: 30400 > > > > > > > > I tried with other subjects and also bert and i get the same problem: > > > > > > > > $ mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a > > > > ../label/lh.aparc.annot -c ../stats/aparc.annot.ctab bert lh > > > > INFO: assuming MGZ format for volumes. > > > > computing statistics for each annotation in ../label/lh.aparc.annot. > > > > reading volume .mgz... > > > > zcat: /home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz.gz: > > > > No > > > > such file or directory > > > > mghRead(/home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz, > > > > -1): > > > > read error > > > > mris_anatomical_stats: could not read input volume .mgz > > > > > > > > > > > > the freesurfer version > > > > $ cat $FREESURFER_HOME/build-stamp.txt > > > > freesurfer-Linux-centos4-stable-pub-v3.0.3 > > > > > > > > > > > > and the linux version is: > > > > $ cat /etc/slackware-version > > > > Slackware 10.2.0 > > > > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > From: [EMAIL PROTECTED] > > > > [mailto:[EMAIL PROTECTED] On Behalf Of Nick > > > > Schmansky > > > > Sent: 17 August 2006 00:06 > > > > To: Abdel Douiri > > > > Cc: Freesurfer Mailing List > > > > Subject: RE: [Freesurfer] problem with mris_anatomical_stats > > > > > > > > Abdel, > > > > > > > > This problem is truly strange. The filename seems to just disappear. > > > > > > > > Can you send me the output of: > > > > > > > > mris_anatomical_stats --all-info > > > > > > > > Also, does this error repeat? That is, if you try: > > > > > > > > cd $SUBJECTS_DIR/01_00/scripts > > > > mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats \ > > > > -b -a ../label/lh.aparc.annot \ > > > > -c ../stats/aparc.annot.ctab 01_00 lh > > > > > > > > does it fail again? And does this happen for other subjects? > > > > > > > > Also, which freesurfer version is being used? To find out, type: > > > > > > > > cat $FREESURFER_HOME/build-stamp.txt > > > > > > > > And which Linux OS is it installed upon? > > > > > > > > Nick > > > > > > > > > > > > On Wed, 2006-08-16 at 17:16 +0100, Abdel Douiri wrote: > > > >> Thanks Bruce > > > >> I have put the subject and that is "01_00" and the first and second > > > >> autorecon was OK only the autorecon3 where it was the problem. Attached > > > > the > > > >> log file. > > > >> Thanks a lot for your help > > > >> Abdel > > > >> -----Original Message----- > > > >> From: [EMAIL PROTECTED] > > > >> [mailto:[EMAIL PROTECTED] On Behalf Of Bruce > > > >> Fischl > > > >> Sent: 16 August 2006 14:01 > > > >> To: Abdel Douiri > > > >> Cc: freesurfer(a)nmr.mgh.harvard.edu > > > >> Subject: Re: [Freesurfer] problem with mris_anatomical_stats > > > >> > > > >> Hi Abdel, > > > >> > > > >> is that the full command line? If so, you need to specify a subject with > > > >> -subjid. If not, could you send us the full command line and > > > > recon-all.log? > > > >> > > > >> cheers, > > > >> Bruce > > > >> > > > >> > > > >> On Wed, 16 Aug 2006, Abdel Douiri wrote: > > > >> > > > >> > Hi all, > > > >> > > > > >> > > > > >> > > > > >> > I will be grateful if someone can tell me what going wrong in the > > > >> following > > > >> > problem: > > > >> > > > > >> > When running "recon-all -autorecon3" the program stop with error > > > >> exactly > > > >> in > > > >> > the "mris_anatomical_stats" cmd stage and I have the following error: > > > >> > > > > >> > > > > >> > > > > >> > mris_anatomical_stats -mgz -f ../stats/lh.aparc.stats -b -a > > > >> > ../label/lh.aparc.annot -c ../stats/aparc.annot.ctab 01_00 lh > > > >> > > > > >> > > > > >> > > > > >> > computing statistics for each annotation in ../label/lh.aparc.annot. > > > >> > > > > >> > reading volume .mgz... > > > >> > > > > >> > zcat: > > > >> /home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz.gz: > > > >> No > > > >> > such file or directory > > > >> > > > > >> > mghRead(/home/samba/user/douiri/freesurfer/subjects/01_00/scripts/.mgz, > > > >> -1): > > > >> > read error > > > >> > > > > >> > mris_anatomical_stats: could not read input volume .mgz > > > >> > > > > >> > INFO: assuming MGZ format for volumes. > > > >> > > > > >> > Linux img-179 2.6.16.22 #2 SMP Mon Jun 26 15:49:31 BST 2006 i686 > > > >> unknown > > > >> > unknown GNU/Linux > > > >> > > > > >> > > > > >> > > > > >> > recon-all exited with ERRORS at Tue Aug 15 20:52:49 BST 2006 > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > > > > >> > Thanks > > > >> > > > > >> > A > > > >> > > > > >> > > > > >> _______________________________________________ > > > >> 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 > > > > > > > > _______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > >

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mri_convert and nifti
by Doug Greve 08 Jan '07

08 Jan '07

I have just discovered a small bug in the NIFTI reader in FreeSurfer. The bug caused the sform/qfrom matrix to be slightly off for oblique volumes that are non-isotropic (the more oblique and the more non-isotropic, the worse). Part of the error involves the matrix being slightly non-orthogonal. There is NO effect of this bug if any of the following apply: 1. You use mri_convert to convert from DICOM (or any other non-NIFTI format) to NIFTI 2. Your volumes are not oblique 3. Your volumes are isotropic This bug can manifest itself only when using NIFTI as input to a freesurfer tool. I have fixed this bug in both our DEV and STABLE versions. 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

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talairach registration
by Cameron Ellis 08 Jan '07

08 Jan '07

Hi, Hopefully this is something simple. When I try to check the talairach transform for my subjects I type: tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig and then I get this error: subject = SM1C2_autoreconall Reading lh surface orig MRISread(/space/troy/3/users/retrievalnewest/SM1C2_autoreconall/surf/lh.orig): could not open file No such file or directory /usr/local/freesurfer/stable/bin/tkregister2.bin: could not read surface orig No such file or directory orig.mgz is in the mri folder. why is it looking for lh.orig? Without the surf tag, tkregister loads the transform fine but I do not get the green surface outlines to assist with the registration. A more detailed transcription of the error is pasted below if needed. Thanks, Cameron [troy:SM1C2_autoreconall] (nmr-std-env) cd .. [troy:retrievalnewest] (nmr-std-env) pwd /autofs/space/troy_003/users/retrievalnewest [troy:retrievalnewest] (nmr-std-env) tkregister2 --mgz --s SM1C2_autoreconall --fstal --surf orig surfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 %Mon Jan 8 14:55:02 2007>>> /usr/local/freesurfer/dev/mni/bin/minctracc -clobber -debug /tmp/mritotal_2618/src_8_dxyz.mnc /usr/local/freesurfer/dev/mni/bin/../share/mni_autoreg/average_305_8_dxyz.mnc transforms/talairach.auto.xfm -transformation /tmp/mritotal_2618/src_8tmp2c.xfm -lsq9 -xcorr -model_mask /usr/local/freesurfer/dev/mni/bin/../share/mni_autoreg/average_305_8_mask.mnc -center -2.114464 54.148323 -58.055290 -step 4 4 4 -tol 0.004 -simplex 2 talairach.xfm --------------------- 0.790 -0.163 0.022 8.207; 0.189 0.845 -0.535 -58.555; 0.093 0.573 0.939 13.334; 0.000 0.000 0.000 1.000; INFO: loading target /space/troy/3/users/retrievalnewest/SM1C2_autoreconall/mri/orig.mgz INFO: changing target type to float Ttarg: -------------------- -1.000 -0.000 0.000 125.117; 0.000 -0.000 1.000 -84.596; -0.000 -1.000 0.000 84.914; 0.000 0.000 0.000 1.000; INFO: loading movable /usr/local/freesurfer/stable/average/mni305.cor.mgz INFO: changing move type to float Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 0.790 -0.163 0.022 8.207; 0.189 0.845 -0.535 -58.555; 0.093 0.573 0.939 13.334; 0.000 0.000 0.000 1.000; subject = SM1C2_autoreconall Reading lh surface orig MRISread(/space/troy/3/users/retrievalnewest/SM1C2_autoreconall/surf/lh.orig): could not open file No such file or directory /usr/local/freesurfer/stable/bin/tkregister2.bin: could not read surface orig No such file or directory

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ca normalize
by Don Hagler 08 Jan '07

08 Jan '07

I have a subject that has gotten stuck on the CA Normalize step. I have tried running it several times and it always gets stuck in the same place, running away for days if I let it, using 99.9% of the CPU. We are running RH4-x86_64-R302. Is this something that has been observed / dealt with before? This is the screen output for the CA Normalize step up to the point of getting stuck: #-------------------------------------- #@# CA Normalize Fri Jan 5 11:02:19 PST 2007 /space/emc1/4/data/MMILDB/ADNI/Containers/FREESURFERRECON_005_S_0448_20060504.085355_1/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R302/average/RB_all_2006-02-15.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R302/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type reading transform from 'transforms/talairach.lta'... INFO: compute sample coordinates transform 1.405 -0.358 0.038 35.157; 0.193 0.687 -0.595 80.138; 0.176 0.895 1.062 -269.933; 0.000 0.000 0.000 1.000; INFO: transform used _________________________________________________________________ Fixing up the home? Live Search can help http://imagine-windowslive.com/search/kits/default.aspx?kit=improve&locale=…

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Flag: -subjectid unrecognized
by Chunchun Ni 08 Jan '07

08 Jan '07

hi, I converted one analyze file to MGZ format, then try use the recon-all -autorecon-all -subjid bert (replace subjectid by myid ), but the command run nothing but Flag: -subjectid unrecognized. Anybody has some idea how to fix it? Thanks for any help! Chunchun

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Freesurfer January 2007