Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

after recon-all.
by Jamie Hanson 30 Nov '07

30 Nov '07

Hey Folks- So I just finished autorecon-all on a few subjects and wanted to do some prelim analyses. On the tutorial pages, there is some talk of using QDEC or FSGD... I couldn't really find a good page contrasting the two... or is there not a difference? Is FSGD just a dated version? And per the tutorial pages, I need to have pre-smoothed fsaverage surfaces using recon-all -s <subjid> -qcache. I keep getting an output of ERROR: cannot find fsaverage in /study/eemri/freesurfer, which is my subject dir. So I switched to doing mris_preproc for each subject. But I keep getting an ERROR: Cannot find fsaverage (output). So what am I doing wrong? Which target should I specify? Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53706 ***Please note my new email: jamielarshanson(a)gmail.com***

2 1

Error message
by Juergen Haenggi 30 Nov '07

30 Nov '07

Dear Freesurfer experts We had a problem with the preprocessing of one subject. The following error occurred: #-------------------------------------------- #@# Intensity Normalization Fri Nov 30 12:41:05 CET 2007 /Applications/freesurfer/subjects/Handball_Vp02/mri \n mri_normalize -g 1 nu.mgz T1.mgz \n using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.225 0.008 -0.123 0.315; 0.032 1.156 0.002 0.516; 0.073 0.044 1.349 -3.397; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 SPLINE_CUBIC_SET - Fatal error! The number of data points N must be at least 2. The input value is 1. Darwin juergen-haenggis-computer.local 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386 recon-all exited with ERRORS at Fri Nov 30 12:41:09 CET 2007 What does it mean? How to solve that problem? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

2 1

problem viewing in tksurfer
by Sarah Andersen 29 Nov '07

29 Nov '07

Dear FreeSurfers, I am having a problem viewing in tksurfer: I can only see a sliver of the brain. This sliver will rotate and do everything that tksurfer is supposed to do, but I can't view any more of the brain than a tiny piece of the occipital lobe. I have tried this with several different files, and had the same issue for each of them. Tkmedit, on the other hand, works fine. I am using FreeSurfer stable release v4.0.1 on Windows Vista using a virtual machine. FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 I am working through the on-line tutorial and followed the directions to set my environment to /buckner_data/tutorial_subjs I also set SUBJECTS_DIR to $TUTORIAL_DATA . I am working in $SUBJECTS_DIR. The "which" command gives me /usr/local/freesurfer/bin/tksurfer I ran the command "tksurfer good_output lh inflated". The following is the resulting message. surfer: current subjects dir: /usr/local/freesurfer/subjects/freesurfer_tutorial/buckner_data/tutorial_sub js surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects/freesurfer_tutorial/buckner_data/tutorial_sub js surfer: Reading header info from /usr/local/freesurfer/subjects/freesurfer_tutorial/buckner_data/tutorial_sub js/good_output/mri/T1.mgz surfer: vertices=125352, faces=250700 Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... In the email archives I have seen a response that mentioned the NVidia graphics card. I checked and my machine does have an NVidia graphics card. Thanks in advance for the help! Sarah Sarah Andersen Research Specialist Dept. of Neurology Dept. of Speech, Language, and Hearing Sciences (520) 621-9878 sander(a)email.arizona.edu

4 6

Another talairach question . . .
by Dan Dillon 29 Nov '07

29 Nov '07

Dear FreeSurfers, In the course of checking my skull-strips I discovered that one of my subjects does not have a T1.mgz because they did not pass the automatic Talairach failure detection. I checked the transformation with tkregister2 and -fstal, and it actually looks quite good; the brain is tilted, but the Talairach brain follows the tilt nicely. Nonetheless, to move things forward I made a few small edits and saved the registration. I then re-ran autorecon1 using the -notalairach option (at the end of the command line) in order to make use of my edits. However, I got the exact same error back-Talairach transformation ***FAILED***--and consequently there's no T1.mgz. I thought that by specifying -notalairach at the end of the command line while running autorecon1, I would be bypassing the Talairach detector and thus would be able to avoid this problem, but I'm obviously wrong. How do I make use of my edited Talairach and get autorecon1 to continue? Thanks in advance, Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: dillon(a)wjh.harvard.edu

2 2

Gradient Non-Linearity Distortion Correction for Allegra 3T
by Sergei Bogdanov 29 Nov '07

29 Nov '07

Dear Freesurfers, I have downloaded grad_unwarp_bash.tar.gz from the NBIRN site and am trying to follow the instructions on http://www.nbirn.net/tools/gradient_non_linearity/index.shtm and https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping?action=highligh… to create the displacement table for Allegra .. I do have the spherical harmonics expansion file for Allegra .. allegra.coef .. I have done: $ perl gradient_unwarp_converter.pl allegra.coef which created grad_unwarp_tables/allegra.coef Now I am trying to run: $ ./scripts/create_displacement_table siemens allegra and I get: Table names: avanto, sonata, trio, brm, crm If you would like to use a different table name, please contact czanner(at)nmr.mgh.harvard.edu for further information Which table name I should use for Allegra 3T or are there any other options? .. I did contact Silvester but sounds like he's been off the project for a year and might not be able to help ... Thank you, Sergei Bogdanov Research Assistant Lewis Center for Neuroimaging University of Oregon sbogdano(a)uoregon.edu

1 0

FS & group feat
by oxro03＠yahoo.com 29 Nov '07

29 Nov '07

Hi, I have a 3 level feat analysis with 2 runs in each subject on the first level. At the second level these two get combined with a fixed effect analysis to produce a mean for each subject. At the third level, the second level results are combined with FLAME to produce group maps. I was able to paint the first and second level results onto the individual subjects' surface by following the excellent instructions on the FS wiki. But how do I paint the 3rdlevel FLAME results onto the fsaverage brain? (Without using group analysis in surface space). Thanks a lot, Sandy --------------------------------- Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See how.

2 1

flat map issue
by romain valabregue 29 Nov '07

29 Nov '07

Hello, I define a patch of the occipital lob flat_patch and run the comand mris_flatten lh.occip.patch.3d lh.occip.flat.patch.3d why do I end up with a 'closed' flattened surface flatten result points around the cutting line stay close and not far away like in classical view like this one : flat clasic What's wrong ? Thank for your help Romain

2 4

Cluster thresholding
by Alex Fornito 28 Nov '07

28 Nov '07

Hi, I have run qdec for a simple contrast comparing thickness across the cortical surface between a patient and control group. Not much survives vertex-wise FDR correction, and I would like to try cluster- based thresholding. I would like to make sure I understand the inputs to the command. Am I correct on the following? --in = the signifcance values (i.e., contrast_name.sig.mgh file) --thmin = the vertexwise threshold for determining clusters, where 2 corresponds to p=.01 --minarea = the cluster extent threshold - Am I correct in assuming this should not be smaller than the smoothing kernel? When I run the command below, I get the following output. Only one (whole hemi) cluster is identified. I'm not sure if its a problem in my command line, or with my data. Also, I seem to have the --cwsig flag wrong, but can't figure out the error (appending .w or .label to the end of the output filename does not change the error). I greatly appreciate your help. mri_surfcluster --in qdec/MF_group_lh/contrasts.sig.mgh --subject fsaverage --hemi lh --surf white --annot aparc --sign abs --thmin 2 -- minarea 25 --sum stats/qdec_run/cluster/summary.txt --o stats/ qdec_run/cluster/cluster_output --cwsig stats/qdec_run/cluster/cwsig --olab stats/qdec_run/cluster/MF_group_lh_thk thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ hemi = lh srcid = qdec/MF_group_lh/contrasts.sig.mgh paint srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = abs thmin = 2 thmax = -1 fdr = -1 minarea = 25 xfmfile = talairach.xfm nth = -1 outid = stats/qdec_run/cluster/cluster_output paint sumfile = stats/run2/cluster/summary.txt subjectsdir = /data/kang/work/struct/alex/freesurfer/subjects_cann FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/mri/ transforms/talairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/surf/lh.white.avg.area.mgh Done reading source surface Reading annotation /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsaverage/label/lh.aparc.annot reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/ buckner_cortical_atlas/scripts/colortable_final.txt) Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 43.1907 at vertex 101931 overall min = 7.66111 at vertex 28089 surface nvertices 163842 surface area 65416.985991 surface area 65416.985976 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, minarea=25.000000 Found 1 clusters Max cluster size 103339.460938 INFO: fixing MNI talairach coordinates Saving thresholded output to stats/qdec_run/cluster/cluster_output avg = 35.029, stdev = 4.669, min = 7.661, max = 43.191 Saving cluster pval stats/qdec_run/cluster/cwsig unknown file type for file (stats/qdec_run/cluster/cwsig) LabelWrite: saving to stats/qdec_run/cluster/MF_group_lh_thk-0001.label Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne Postal address: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 fornitoa(a)unimelb.edu.au

1 0

Re: [Freesurfer] recon-all Flirt Error
by skenny＠uchicago.edu 28 Nov '07

28 Nov '07

i have installed version freesurfer-Linux-rh9-stable-pub-v4.0.1 and i do not see a dir for fsl, only fsafd and fsfast. i tend to get the flirt error but this does not seem to affect the completion of recon-all so i've ignored it 'til now. but just wondering why i don't see an fsl directory if there is meant to be one in the distribution package... thanks sarah ---- Original message ---- >Date: Mon, 26 Nov 2007 19:38:45 -0500 >From: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> >Subject: Re: [Freesurfer] recon-all Flirt Error >To: Anil Roy <aroy85(a)gmail.com> >Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > >Anil, > >flirt is an FSL utility that is included in the freesurfer distribution >in the $FREESURFER_HOME/fsl directory (in bin). Normally, freesurfer >will setup a path to it. Make sure it is in your path. > >Nick > >On Mon, 2007-11-26 at 16:26 -0600, Anil Roy wrote: >> Hello All, >> >> I wanted to test the Freesurfer installation by running recon-all but >> I received an error saying flirt no found. Can someone point me to the >> cause of this problem, is it a missing library or some other issue? >> >> I have posted the output from running recon-all on bert below. >> >> Thanks, >> >> Anil. >> >> [root@wonglinux1 freesurfer]# recon-all -s bert -autorecon1 >> INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects >> Actual FREESURFER_HOME /usr/local/freesurfer >> -rw-rw-rw- 1 root root 657949 Aug 18 >> 23:25 /usr/local/freesurfer/subjects/bert/scripts/recon-all.log >> Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 >> i386 GNU/Linux >> flirt: Command not found. >> INFO: current FREESURFER_HOME does not match that of previous >> processing. >> Current: /usr/local/freesurfer >> Previous: /space/freesurfer/build/pub-releases/freesurfer >> #-------------------------------------------- >> #@# MotionCor Mon Nov 26 16:17:47 CST 2007 >> Found 3 runs >> /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz >> /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz >> /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz >> #----------------------------------------------- >> /usr/local/freesurfer/subjects/bert >> >> mri_motion_correct.fsl - >> o /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz - >> wild /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz >> >> tmpdir is /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009 >> -------------------------------------------------------------- >> mri_motion_correct.fsl logfile >> is /usr/local/freesurfer/subjects/bert/mri/rawavg.mgz.mri_motion_correct.fsl.log >> -------------------------------------------------------------- >> ----------------------------------------- >> Converting /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz >> Mon Nov 26 16:18:28 CST 2007 >> /usr/local/freesurfer/subjects/bert >> mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- 1.img -odt float >> $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ >> reading from /usr/local/freesurfer/subjects/bert/mri/orig/001.mgz... >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-1, -0, -0) >> j_ras = (0, 0, -1) >> k_ras = (-0, 1, -0) >> changing data type from 0 to 3 (noscale = 0)... >> writing to /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor-1.img... >> Analyze Output Matrix >> - 1.000 0.000 -0.000 134.400; >> -0.000 0.000 1.000 -111.000; >> -0.000 -1.000 -0.000 129.000; >> 0.000 0.000 0.000 1.000; >> -------------------- >> INFO: set hdr.hist.orient to -1 >> ----------------------------------------- >> Converting /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz >> Mon Nov 26 16:18:33 CST 2007 >> /usr/local/freesurfer/subjects/bert >> mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- 2.img -odt float >> $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ >> reading from /usr/local/freesurfer/subjects/bert/mri/orig/002.mgz... >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-1, -0, -0) >> j_ras = (0, 0, -1) >> k_ras = (-0, 1, -0) >> changing data type from 0 to 3 (noscale = 0)... >> writing to /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor-2.img... >> Analyze Output Matrix >> - 1.000 0.000 -0.000 134.400; >> -0.000 0.000 1.000 -111.000; >> -0.000 -1.000 -0.000 129.000; >> 0.000 0.000 0.000 1.000; >> -------------------- >> INFO: set hdr.hist.orient to -1 >> ----------------------------------------- >> Converting /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz >> Mon Nov 26 16:18:40 CST 2007 >> /usr/local/freesurfer/subjects/bert >> mri_convert /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/cor- 3.img -odt float >> $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ >> reading from /usr/local/freesurfer/subjects/bert/mri/orig/003.mgz... >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-1, -0, -0) >> j_ras = (0, 0, -1) >> k_ras = (-0, 1, -0) >> changing data type from 0 to 3 (noscale = 0)... >> writing to /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor-3.img... >> Analyze Output Matrix >> - 1.000 0.000 -0.000 134.400; >> -0.000 0.000 1.000 -111.000; >> -0.000 -1.000 -0.000 129.000; >> 0.000 0.000 0.000 1.000; >> -------------------- >> INFO: set hdr.hist.orient to -1 >> ----------------------------------------- >> Motion Correcting /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor-2.img >> Mon Nov 26 16:18:45 CST 2007 >> /usr/local/freesurfer/subjects/bert >> fsl_rigid_register -maxangle 90 - >> r /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor- 1.img - >> i /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor-2.img - >> o /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/resampled.img - >> tmpdir /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009 -cleanup >> >> >> >> $Id: fsl_rigid_register,v 1.26 2007/06/12 15:11:07 greve Exp $ >> Mon Nov 26 16:18:46 CST 2007 >> /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/resampled.img >> -------------------------------------- >> /usr/local/freesurfer/subjects/bert >> mri_convert /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor-1.img /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/refvol.fsl_rigid_register.nii >> mri_convert /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor-1.img /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/refvol.fsl_rigid_register.nii >> $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ >> reading from /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor-1.img... >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-1, 0, 0) >> j_ras = (0, 0, -1) >> k_ras = (0, 1, 0) >> writing to /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/refvol.fsl_rigid_register.nii... >> -------------------------------------- >> /usr/local/freesurfer/subjects/bert >> mri_convert /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor-2.img /usr/local/freesurfer/subjects/bert/mri/tmp-mri_motion_correct.fsl-9009/invol.fsl_rigid_register.nii >> mri_convert /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor- >> 2.img /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/invol.fsl_rigid_register.nii >> $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ >> reading from /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor- 2.img... >> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >> i_ras = (-1, 0, 0) >> j_ras = (0, 0, -1) >> k_ras = (0, 1, 0) >> writing to /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/invol.fsl_rigid_register.nii... >> -------------------------------------- >> /usr/local/freesurfer/subjects/bert >> tkregister2_cmdl --targ /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor-1.img -- >> mov /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor- 2.img -- >> reg /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/tkregister.dat -- >> fslregout /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/initxfm.fslmat --regheader --noedit --s >> doesnotmatter >> target volume /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor-1.img >> movable volume /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor-2.img >> reg file /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/tkregister.dat >> LoadVol 0 >> ZeroCRAS 0 >> $Id: tkregister2.c,v MailScanner has detected a possible fraud attempt >> from "1.86.2.1" claiming to beMailScanner warning: numerical links are >> often malicious: 1.86.2.1 2007/08/15 15:39:42 nicks Exp $ >> Diagnostic Level -1 >> INFO: loading target /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor- 1.img >> Ttarg: -------------------- >> -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; >> INFO: loading movable /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/cor- 2.img >> 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 = 1, float2int = 0 >> Computing reg from header (and possibly input matrix) >> ---- Input registration matrix (computed) -------- >> 1.000 0.000 0.000 0.000; >> 0.000 1.000 0.000 0.000; >> 0.000 0.000 1.000 0.000; >> 0.000 0.000 0.000 1.000; >> --------------------------------------- >> ---- Input registration matrix -------- >> 1.000 0.000 0.000 0.000; >> 0.000 1.000 0.000 0.000; >> 0.000 0.000 1.000 0.000; >> 0.000 0.000 0.000 1.000; >> subject = doesnotmatter >> RegMat --------------------------- >> 1.000 0.000 0.000 0.000; >> 0.000 1.000 0.000 0.000; >> 0.000 0.000 1.000 0.000; >> 0.000 0.000 0.000 1.000; >> register: file /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/tkregister.dat written >> FSLOUTPUTTYPE NIFTI >> tkreg2FSL: mov det = -1, ref det = -1 >> Init FSL Mat based on geometry ------------------- >> 1.00000000 -0.00000000 -0.00000000 -0.00000000 >> -0.00000000 1.00000000 -0.00000000 -0.00000000 >> -0.00000000 -0.00000000 1.00000000 -0.00000000 >> 0.00000000 0.00000000 0.00000000 1.00000000 >> ------------------------------------------------- >> -------------------------------------- >> /usr/local/freesurfer/subjects/bert >> calling eval flirt -in /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/invol.fsl_rigid_register.hdr - >> out /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/outvol.fsl_rigid_register.hdr -bins 256 - >> cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 - >> interp trilinear -dof 6 - >> ref /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/refvol.fsl_rigid_register.hdr - >> init /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/initxfm.fslmat - >> omat /usr/local/freesurfer/subjects/bert/mri/tmp- >> mri_motion_correct.fsl-9009/outvol.fsl_rigid_register.fslmat >> flirt: Command not found. >> ERROR: running flirt >> Linux wonglinux1 2.4.20-8 #1 Thu Mar 13 17:54:28 EST 2003 i686 i686 >> i386 GNU/Linux >> >> recon-all exited with ERRORS at Mon Nov 26 16:18:55 CST 2007 >> >> _______________________________________________ >> 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

2 1

BrainMaskVol vs BrainSegVol
by Akram Bakkour 28 Nov '07

28 Nov '07

Hi all, I want to pull the measure of whole brain volume. In the aseg.stats there is a BrainMaskVol and a BrainSegVol. Which one do I want? As I understand it, BrainMaskVol is the volume of the brainmask (including the ventricles) whereas BrainSegVol is the volume of brain matter and not including the ventricles, so I think this is the one I want, but I want to make sure and I couldn't find a straight answer on the wiki. Thanks! Akram. -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org

3 3

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