Freesurfer April 2011

freesurfer@nmr.mgh.harvard.edu

121 participants
166 discussions

Fwd: Two Volume Measurement Issues
by Thomas Ballinger 25 Apr '11

25 Apr '11

Hello, I've been asked to obtain freesurfer volume measurements on some cases we've already run with Freesurfer for comparison to VBM measurements. Can anyone direct me to any literature or briefly share knowledge about comparing these two methods? Second question: For said analysis, I'd like to get the total white and grey matter volume from the Freesurfer cases. The cases were run with Freesurfer 4.2, so I don't have access to some of the tools I'm found referenced in discussions of finding total grey matter in the mailing list archives. How does this look for a total grey matter method? somewhat taken from http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg10468.html 1. Get total supratentorial (i.e. sans cerebellum) WM+GM volume. ("BrainSegVolNotVent" in wmparc.stats) 2. Get cerebral WM volume. (wmparc.stats reports the value of total cerebral white matter volume) 3. Subtract 2 from 1 to get total supratentorial GM volume. 4. Get whole brain GM and WM volumes by adding in cerebellar volumes.(wmparc.stats L/R Cerebellum WM/Cortex) 5. Calculate total CSF volumes by summing the individual ventricle and "other" CSF values.(calculate from aseg.stats or wmparc.stats by summing *-Lateral-Ventricle, *-Inf-Lat-Vent, 3rd-Ventricle, 4th-Ventricle, CSF, and 5th-Ventricle) Thanks very much to anyone with time to respond, Thomas Ballinger Research Assistant at PNL at BWH

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surface to native space
by j janssen 25 Apr '11

25 Apr '11

Hi, FS version 4.5 - goal: to transfer the ?h.pial to native ('pre-conformed') space. thus to the space of the image _before_ any FS processing. - what we have done so far: 1) if we convert the T1.mgz (from the FS mri-dir, mri_convert T1.mgz T1.nii) to nifti it coincides perfectly with the native space image. 2) if we then overlay the ?h.pial over the T1.nii it does _not_ match, i.e. it looks like mri_convert includes a translation that shifts the surface with respect to the volume. question: how can we achieve our goal, i.e. get the surface in native space (a perfect overlap with T1.nii)? thanks, -joost

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Tksurfer slow loading.....
by Rongxiang Tang 25 Apr '11

25 Apr '11

Dear all, I met a problem when I tried to load the tksurfer...it doen't give any error, just extremely slow...I also tried the "straces -f....",still very slow... FreeSurfer:~> tksurfer ben lh pial subject is ben hemi is lh surface is pial surfer: current subjects dir: /home/virtualuser/apps/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/virtualuser Reading image info (/home/virtualuser/apps/freesurfer/subjects/ben) Reading /home/virtualuser/apps/freesurfer/subjects/ben/mri/orig.mgz surfer: Reading header info from /home/virtualuser/apps/freesurfer/subjects/ben/mri/orig.mgz surfer: vertices=136724, faces=273444 surfer: single buffered window surfer: tkoInitWindow(ben) surfer: using interface /home/virtualuser/apps/freesurfer/lib/tcl/tksurfer.tcl Reading /home/virtualuser/apps/freesurfer/lib/tcl/tkm_common.tcl Reading /home/virtualuser/apps/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/virtualuser/apps/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/virtualuser/apps/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % the frustration is that I never got to see the surface..since it almost took 10mins..I only see the tksurfer tools and the blank display window. Thanks Catherine

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converting surface label to volume
by Prapti Gautam 25 Apr '11

25 Apr '11

Dear freesurfers, I am trying to convert a surface label into a volume file so that it can subsequently be viewed as a 3-D model. To create the label I've followed the steps from http://www.ci.uchicago.edu/wiki/bin/view/HNL/EditROI and have thus edited my color table LUT file. The command I am using for this is mri_label2volume: mri_label2vol --label test.label --temp brainmask.mgz --reg mni152.register.dat --proj frac 0 1 .001 --subject one --hemi lh --o test.mgz However, the resultant volume file from this command is splotchy and thus does not look ideal when viewed in tkmedit. Decreasing the delta to very small values had no effect in making the volume render better. Is there another way to convert a surface label that has been hand drawn in tksurfer into a volume file that is anatomically correct? Thanks very much for your help Prapti

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Fwd: error with motion correction
by Maryam Vaziri Pashkam 25 Apr '11

25 Apr '11

Hi, I am running into trouble with motion correction on my Mac and freesurfer 4.5. Originally I ran preproc-sess and got an error from mc-sess in the part (i think) that runs the mcextreg. I ran mc-sess and the same error happened (I have copy pasted the log bellow). It seems like the matlab program that runs mcparams2extreg cannot read the fmc.mcdat file. when I did textread('fmc.mcdat') in matlab, I could open the file and it looked perfectly fine to me with the correct number of TR's. Any idea where the problem might be? Maryam preproc-sess -nosmooth -i f -sf sessid -df sessdir -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.log -------------------------------------------------------------- instem f mc 1 f fmc stc 0 fmc sm 0 mask 1 brain 110419_xu_PDM1_02_PDM MC ----------------------------- Sun Apr 24 20:42:29 EDT 2011 /Users/maryam/mri-space/studies/PDM1/PDM1 mc-sess -fstem f -fmcstem fmc -s 110419_xu_PDM1_02_PDM -d /Users/maryam/mri-space/studies/PDM1/unpackdata -fsd bold -new -update -no-inorm ---------------------------------------- Logfile is /Users/maryam/mri-space/studies/PDM1/PDM1/log/mc-110419_xu_PDM1_02_PDM-bold.log ------------------------------------------- /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM RunList: 005 006 007 008 011 012 013 014 Targ Stem is 005/f Update not needed -rw-r--r-- 1 maryam staff 129203552 Apr 24 20:12 005/fmc.nii -rw-r--r-- 1 maryam staff 64601952 Apr 24 19:12 005/f.nii ------- ************************** ----------- ------- Motion Correcting Run 006 ----------- ------- ************************** ----------- sess = 110419_xu_PDM1_02_PDM Sun Apr 24 20:42:30 EDT 2011 mc-afni2 --i 006/f.nii --t 005/f.nii --frame 0 --o 006/fmc.nii --mcdat 006/fmc.mcdat /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold mri_info --nframes --o /tmp/mriinfo.2758 005/f.nii log file is 006/fmc.nii.mclog mcdat file is 006/fmc.mcdat tmp dir is 006/tmp.mc-afni2.2758 #@# -------------------------------- /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold mri_convert 005/f.nii 006/tmp.mc-afni2.2758/tempvol.nii.gz --nskip 0 --ndrop 205 -odt float mri_convert 005/f.nii 006/tmp.mc-afni2.2758/tempvol.nii.gz --nskip 0 --ndrop 205 -odt float nskip = 0 ndrop = 205 $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 005/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0.000171665, -3.15037e-05) j_ras = (0.000174532, -0.983572, -0.180519) k_ras = (-2.07852e-18, -0.180519, 0.983572) changing data type from 4 to 3 (noscale = 0)... Dropping last 205 frames writing to 006/tmp.mc-afni2.2758/tempvol.nii.gz... #@# -------------------------------- /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold mri_convert 006/f.nii 006/tmp.mc-afni2.2758/invol.nii.gz -odt float mri_convert 006/f.nii 006/tmp.mc-afni2.2758/invol.nii.gz -odt float $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 006/f.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0.000171665, -3.15037e-05) j_ras = (0.000174532, -0.983572, -0.180519) k_ras = (-2.07852e-18, -0.180519, 0.983572) changing data type from 4 to 3 (noscale = 0)... writing to 006/tmp.mc-afni2.2758/invol.nii.gz... #@# -------------------------------- /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold 3dvolreg -verbose -dfile 006/fmc.mcdat -base 006/tmp.mc-afni2.2758/tempvol.nii.gz -prefix 006/tmp.mc-afni2.2758/outvol.nii.gz 006/tmp.mc-afni2.2758/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_02_01_1144 (Jul 3 2008) [32-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 006/tmp.mc-afni2.2758/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:006/tmp.mc-afni2.2758/tempvol.nii.gz is 10.399981 degrees from plumb. ++ Reading in base dataset 006/tmp.mc-afni2.2758/tempvol.nii.gz ++ Oblique dataset:006/tmp.mc-afni2.2758/invol.nii.gz is 10.399981 degrees from plumb. ++ Reading input dataset 006/tmp.mc-afni2.2758/invol.nii.gz ++ Edging: x=4 y=4 z=2 ++ Creating mask for -maxdisp + Automask has 57667 voxels + 10333 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 206 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205.. ++ CPU time for realignment=16.6 s [=0.0808 s/sub-brick] ++ Min : roll=-0.008 pitch=-0.103 yaw=-0.096 dS=+0.255 dL=-0.019 dP=-0.151 ++ Mean: roll=+0.031 pitch=-0.011 yaw=-0.045 dS=+0.619 dL=+0.037 dP=-0.055 ++ Max : roll=+0.060 pitch=+0.112 yaw=-0.010 dS=+0.693 dL=+0.075 dP=+0.015 ++ Max displacements (mm) for each sub-brick: 0.49 0.65 0.63 0.74 0.69 0.75 0.71 0.77 0.70 0.76 0.67 0.77 0.72 0.73 0.66 0.67 0.67 0.67 0.69 0.70 0.72 0.66 0.71 0.68 0.72 0.67 0.73 0.68 0.73 0.66 0.73 0.66 0.70 0.64 0.72 0.69 0.71 0.71 0.72 0.66 0.66 0.67 0.72 0.70 0.71 0.72 0.71 0.69 0.72 0.72 0.71 0.72 0.72 0.69 0.71 0.74 0.73 0.69 0.72 0.72 0.76 0.76 0.79 0.73 0.75 0.74 0.75 0.75 0.71 0.74 0.67 0.72 0.65 0.72 0.65 0.69 0.69 0.65 0.68 0.64 0.72 0.67 0.67 0.68 0.69 0.65 0.73 0.67 0.71 0.69 0.73 0.72 0.76 0.74 0.72 0.66 0.68 0.69 0.69 0.68 0.68 0.70 0.73 0.70 0.73 0.78 0.74 0.73 0.75 0.74 0.72 0.74 0.63 0.66 0.68 0.74 0.72 0.74 0.79 0.74 0.74 0.76 0.79 0.79 0.74 0.76 0.70 0.75 0.72 0.78 0.74 0.78 0.76 0.80 0.76 0.79 0.77 0.76 0.76 0.75 0.73 0.80 0.78 0.81 0.78 0.84 0.76 0.79 0.77 0.79 0.76 0.83 0.77 0.79 0.77 0.84 0.76 0.80 0.77 0.81 0.72 0.79 0.74 0.80 0.77 0.83 0.81 0.82 0.76 0.81 0.75 0.78 0.74 0.75 0.71 0.75 0.73 0.77 0.77 0.80 0.77 0.80 0.75 0.73 0.77 0.72 0.76 0.72 0.76 0.72 0.72 0.69 0.66 0.68 0.65 0.68 0.64 0.70 0.62 0.70 0.62 0.69 0.67 0.74 0.75 0.74 ++ Max displacement in automask = 0.84 (mm) at sub-brick 145 ++ Wrote dataset to disk in 006/tmp.mc-afni2.2758/outvol.nii.gz #@# -------------------------------- /Users/maryam/mri-space/studies/PDM1/unpackdata/110419_xu_PDM1_02_PDM/bold mri_convert 006/tmp.mc-afni2.2758/outvol.nii.gz 006/fmc.nii --in_like 005/f.nii mri_convert 006/tmp.mc-afni2.2758/outvol.nii.gz 006/fmc.nii --in_like 005/f.nii reading info from 005/f.nii... $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from 006/tmp.mc-afni2.2758/outvol.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0.000171665, -3.15037e-05) j_ras = (0.000174532, -0.983572, -0.180519) k_ras = (-2.07852e-18, -0.180519, 0.983572) writing to 006/fmc.nii... ... cleaning up .... Sun Apr 24 20:43:59 EDT 2011 mc-afni2 done INFO: Making external regressor from mc params mcparams2extreg -mcfile 006/fmc.mcdat -northog 6 -extreg 006/mcextreg Logfile is 006/mcparams2extreg.log ----------- Matlab file -------------- mcfile = '006/fmc.mcdat'; extreg = '006/mcextreg'; nkeep = []; northog = [6]; pctorthog = []; monly = 0; mc = textread(mcfile); mc = mc(:,2:7); ntrs = size(mc,1); if(ntrs < 6) fprintf('ERROR: ntrs = %d < 6\n',ntrs); if(~monly) fprintf('Quiting matlab\n'); quit; fprintf('should not be here\n'); end end if(~isempty(nkeep)) x = mc(:,1:nkeep); elseif(~isempty(northog)) [u s v] = svd(mc); ds = diag(s); pct = 100*cumsum(ds)/sum(ds); x = u(:,1:northog); nkeep = northog; fprintf('INFO: northog = %d, pct = %g\n',northog,pct(nkeep)); else [u s v] = svd(mc); ds = diag(s); pct = 100*cumsum(ds)/sum(ds); nkeep = min(find(pct > pctorthog)); x = u(:,1:nkeep); fprintf('INFO: pctorthog = %g, nkeep = %d\n',pctorthog,nkeep); end x2 = zeros(1,1,nkeep,ntrs); x2(1,1,:,:) = x'; %' %fmri_svbvolume(x2,extreg); mri.vol = permute(x2,[1 3 2 4]); mri.tr = 0; mri.flip_angle = 0; mri.te = 0; mri.ti = 0; mri.vox2ras0 = eye(4); mri.xsize = 1; mri.ysize = 1; mri.zsize = 1; mri.volres = [1 1 1]; mri.volsize = [size(mri.vol,1) size(mri.vol,2) size(mri.vol,3)]; fname = sprintf('%s.bhdr',extreg); MRIwrite(mri,fname); quit; ----------------------------------- ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.9.0.529 (R2009b) 64-bit (maci64) August 12, 2009 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> >> ??? Error using ==> textread at 167 File not found. >> ??? Undefined variable mc. >> ??? Undefined function or variable 'mc'. >> ??? Undefined function or variable 'ntrs'. >> >> ??? Undefined function or variable 'mc'. >> >> ??? Undefined function or variable 'ntrs'. >> ??? Undefined function or variable 'x'. >> >> >> ??? Undefined function or variable 'x2'. >> >> >> >> >> >> >> >> >> >> ??? Reference to non-existent field 'vol'. >> >> ??? Reference to non-existent field 'vol'. Error in ==> MRIwrite at 70 bmri.voldim = [size(mri.vol,1) size(mri.vol,2) size(mri.vol,3)]; >> >> ------------------------------------------ ERROR: output not created ERROR: mc-sess failed

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Re: [Freesurfer] Change the default SUBJECTS_DIR...
by Rongxiang Tang 23 Apr '11

23 Apr '11

Hi Bruce, Thanks for your prompt reply. I'm running the freesurfer in a virtual box in windows 7. When I plug the usb in, the computer just called it (E:)...and i just directly copy that directory"E:\data\Ventricle-freesurfer\ben\1.3.12.2.1107.5.2.7.20418.30000009010518365025000028507" to the command line... Is this correct? Thanks Catherine

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Change the default SUBJECTS_DIR...
by Rongxiang Tang 22 Apr '11

22 Apr '11

Dear All, All my data is on a USB hard drive and I do not want to put them in the "/home/virtualuser/apps/freesurfer/subjects" directory, which is the default... Also, I would like to save all my results on that USB hard drive... I was wondering if I would be able to do that... I tried this: FreeSurfer:~> setenv SUBJECTS_DIR E:\data\Ventricle-freesurfer\ben\1.3.12.2.1107.5.2.7.20418.30000009010518365025000028507 And when I want to start the process...it gave me this FreeSurfer:~> recon-all \ -i /data/Ventricle-freesurfer/ben/1.3.12.2.1107.5.2.7.20418.30000009010518365025000028507 ERROR: cannot find /data/Ventricle-freesurfer/ben/1.3.12.2.1107.5.2.7.20418.30000009010518365025000028507 Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s exited with ERRORS at Fri Apr 22 21:00:35 EDT 2011 Is there any way to fix this? Or do I have to save all my data and results in the default directory? Thanks Catherine

2 1

Could I run several freesurfers at the same time?
by Rongxiang Tang 22 Apr '11

22 Apr '11

Dear All, I was wondering if I can run several freesurfers in my virtualbox simultaneously by setting up several virtual machines...my computer has 16G RAM and it's Windows 7 64-bit. Would working multiple freesurfers at the same time slow down the calculations? Moreover, I was wondering if my computer could afford these loads... Thanks Catherine

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Trilinear interpolation of mri_convert and ribbon/surface coordinates
by Evan Luther 21 Apr '11

21 Apr '11

Hello FreeSurfer community, When using mri_convert to convert a .img file with a voxel size of .7 mm^3 and 252x300x300 dimensions to a nifti file for further FreeSurfer processing, mri_convert uses trilinear imterpolation to force the image to have 301x301x301 dimensions. Can anyone explain why this occurs and/or if the brain is actually being stretched in one dimension or if the image is simply being padded? Also why does it become an isotropic volume of 301 voxels rather than 300? Furthermore, once the ribbon files have been created they appear to be oriented about an origin that is at the center of the field of view. Are the surface files produced in the same coordinate system? Thank you! -- *Evan Luther* Ress High-Resolution Neuroimaging Laboratory Undergraduate Research Assistant B.S. Biomedical Engineering, 2012 University of Texas at Austin eluther13(a)gmail.com <bethvansant(a)yahoo.com> 210-602-4372

2 1

Setup configuration error
by Jade 21 Apr '11

21 Apr '11

Hi, After I installed FreeSurfer ( freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0.dmg) in my Macbook (Snow Leopard, Version 10.6.7), I got the message saying " The software was successfully installed" but while I tried to configure my shell, after I typed setenv FREESURFER_HOME <freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh I got this message "freesurfer_installation_directory: No such file or directory". I tired it in both X11 and terminal. Please help me to use Freesurfer. Thank you. Jade

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Freesurfer April 2011