Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

Re: [Freesurfer] white matter volume per lobe...
by Gonzalo Rojas Costa 28 May '13

28 May '13

Hi Doug: I use the instructions that you told me... But, why I get the gray colored region (red arrow) ?... Sincerely, Gonzalo Rojas Costa > Message: 15 > Date: Mon, 27 May 2013 22:41:41 -0400 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] white matter volume per lobe... > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <51A41965.6050808(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > you will need to run mri_annotation2label and specify the output to be > an annotation file instead of a segmentation. Then you will have to run > mri_aparc2aseg, specifying your lobes annotation as well as --labelwm > (look in the recon-all.log file for an example of how wmparc.mgz is > created). Then run mri_segstats (you can also get an example from the > recon-all.log file). > doug -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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resampling surfaces to native space, mri_surf2surf not scaling properly?
by Gunter, Geoffrey 28 May '13

28 May '13

Hello, I'm trying to resample Freesurfer output volumes and surfaces back into their native anatomical space using mri_vol2vol and mri_surf2surf. The volumes appear to be resampled correctly, their resolution and orientation match the original images'. However, the resampled surfaces do not appear to have been transformed correctly by mri_surf2surf. When I visually compare them to the Freesurfer-space surfaces overlaid on the brain images in FreeView, TKMEdit, Paraview-CAWorks, etc., they seem to be identical to the un-transformed, Freesurfer-space surfaces. In addition, when I check the list of vertices for transformed and untransformed surfaces, the coordinates of each vertex are unchanged. These are the commands that I'm using: mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o resamp_brain.mgz mri_surf2surf --sval-xyz pial --reg resamp_brain.mgz.reg --tval resamp_lh_pial --tval-xyz --hemi lh --s 1158119_3_6 The registration file, "resamp_brain.mgz.reg" looks like this: subject-unknown 0.937500 0.937500 1.000000 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 0 0 0 1 round My Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Could it be that mri_surf2surf is not applying scaling transformations correctly? Thanks for your help, Geoff

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area measurements FS5.1
by Benjamín Garzón 28 May '13

28 May '13

Hi, I have processed a sample with FS 5.1 and would like to do a group analysis of surface-based area. According to the release notes ( ** ) there is an issue with the conversion into standard space. I found a former post pointing to a version of preproc-sess that to my understanding should fix that, but the file is not there any more. Is there any quick fix for this problem without having to move to 5.3 / could I get that file? Thanks, Benjamin ** There is a bug in the way that FS converts surface-based area (eg, lh.area) and volume (eg, lh.volume) into standard space. The files themselves are fine, it is the way they are transfered to standard space that is the problem. You will not need to re-analyze any of your individual subject data. The volumes of the subcortical structures are unaffected by this problem. Global measures of cortical volume are also unaffected. -- Benjamín Garzón, Ph.D. Karolinska Institutet Department of Neuroscience Retzius Väg 8 17177 Stockholm (SWEDEN)

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Re: [Freesurfer] BBR Register failing
by Salil Soman 28 May '13

28 May '13

Done. Thank you for your consideration. The best I can figure so far is 1) the script's attempt to make the tmp.bbregister.7392 directory fails and 2) (after I manually make this directory), there seems to be something going wrong at the level of fslregister I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run freesurfer and tracula (using only the flirt method, the bbr method was giving me trouble as well). The code is all running on a sun grid engine, with individual ubuntu 12.04.1 LTS machines. Your help on this matter would be greatly appreciated. Sal On Sat, May 25, 2013 at 8:23 PM, Douglas Greve <greve(a)nmr.mgh.harvard.edu>wrote: > Hi Sal, can you post this to the list instead of me directly? > thanks! > doug > > > > On 5/25/13 11:00 PM, Salil Soman wrote: > > Dear Doug, > > I attempted to run the process we discussed earlier today for registering > a different tissue contrast to the T1 after freesurfer 5.3 was run. > > I had run an FSSPGR for my subject using the following command: > > recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm > -openmp 50 -hippo-subfields -all > > It finished without any problems. > > Then I tried running the bbrregister command: > > bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg > register.dat --bold > > (this version was with bold contrast, but I get the same error if I try > t1 or t2). > > The process fails and I get the following error log (below). Any > suggestions on what I am doing wrong? > > Thanks, > > Sal > > ---------- Forwarded message ---------- > From: Salil Soman <salsoman(a)stanford.edu> > Date: Sat, May 25, 2013 at 7:54 PM > Subject: bbregister fail log > To: salsoman(a)stanford.edu > > > Logfile for bbregister > Sat May 25 19:51:15 PDT 2013 > > setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS > cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS > /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov > QSM_906.nii.gz --init-fsl --reg register.dat --bold > > $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $ > Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 > 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer > mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii > mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from QSM_906.nii.gz... > TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0.313177, 0.949695) > k_ras = (0, -0.949695, 0.313177) > writing to ./tmp.bbregister.26724/template.nii... > fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii > --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 > --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol > brainmask > > Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log > > Sat May 25 19:51:17 PDT 2013 > --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg > ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov > --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask > $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ > corn18.stanford.edu > Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8 > 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux > nIters 1 > -------------------------------------- > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS > mri_convert ERROR: could not determine file for > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: > ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii > mri_convert ERROR: could not determine file for > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR: > ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii > > mri_convert: extra arguments ("not" and following) > > type mri_convert -u for usage > > -------------------------------------- > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS > mri_convert ./tmp.bbregister.26724/template.nii > ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 > mri_convert ./tmp.bbregister.26724/template.nii > ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0 > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > reading from ./tmp.bbregister.26724/template.nii... > TR=98.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (-1, 0, 0) > j_ras = (0, 0.313177, 0.949695) > k_ras = (0, -0.949695, 0.313177) > keeping frame 0 > writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii... > Mov determinant is -0.984886 > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS > tkregister2_cmdl --mov > ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg > ./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout > ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit > tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl > INFO: no target volume specified, assuming FreeSurfer orig volume. > target volume orig > movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii > reg file ./tmp.bbregister.26724/fslregister/reg0.26760.dat > LoadVol 0 > ZeroCRAS 0 > $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ > Diagnostic Level -1 > INFO: loading target > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/orig.mgz > 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 > ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii > Tmov: -------------------- > -1.000 0.000 0.000 112.000; > 0.000 0.000 0.985 -83.715; > 0.000 -1.000 0.000 112.000; > 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 1.591; > -0.000 -0.950 0.313 0.719; > 0.000 -0.313 -0.950 -5.896; > 0.000 0.000 0.000 1.000; > --------------------------------------- > ---- Input registration matrix -------- > 1.000 -0.000 -0.000 1.591; > -0.000 -0.950 0.313 0.719; > 0.000 -0.313 -0.950 -5.896; > 0.000 0.000 0.000 1.000; > Determinant 1 > subject = WMR3T_0015z_FS > RegMat --------------------------- > 1.000 -0.000 -0.000 1.591; > -0.000 -0.950 0.313 0.719; > 0.000 -0.313 -0.950 -5.896; > 0.000 0.000 0.000 1.000; > FSLOUTPUTTYPE NIFTI > tkreg2FSL: mov det = -0.984886, ref det = -1 > Sat May 25 19:51:22 PDT 2013 > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS > flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii > -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 > -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 > -verbose 0 -omat ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat > -schedule /mnt/glusterfs/salsoman/fsl/etc/flirtsch/xyztrans.sch -init > ./tmp.bbregister.26724/reg.init.dat.fsl.mat0 > ** ERROR (nifti_image_read): failed to find header file for > './tmp.bbregister.26724/fslregister/refvol.fslregister' > ** ERROR: > nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): > bad header info > ERROR: failed to open file > ./tmp.bbregister.26724/fslregister/refvol.fslregister > ERROR: Could not open image > ./tmp.bbregister.26724/fslregister/refvol.fslregister > Image Exception : #22 :: Failed to read volume > ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > Abort > Sat May 25 19:51:22 PDT 2013 > /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS > flirt.fsl -ref ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii > -in ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii -bins 256 > -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 > -verbose 0 -omat ./tmp.bbregister.26724/reg.init.dat.fsl.mat -init > ./tmp.bbregister.26724/fslregister/fslmat0.trans.mat -schedule > /mnt/glusterfs/salsoman/freesurfer/bin/flirt.newdefault.20080811.sch > ** ERROR (nifti_image_read): failed to find header file for > './tmp.bbregister.26724/fslregister/refvol.fslregister' > ** ERROR: > nifti_image_open(./tmp.bbregister.26724/fslregister/refvol.fslregister): > bad header info > ERROR: failed to open file > ./tmp.bbregister.26724/fslregister/refvol.fslregister > ERROR: Could not open image > ./tmp.bbregister.26724/fslregister/refvol.fslregister > Image Exception : #22 :: Failed to read volume > ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii > terminate called after throwing an instance of 'RBD_COMMON::BaseException' > Abort > tkregister2_cmdl --s WMR3T_0015z_FS --mov > ./tmp.bbregister.26724/template.nii --reg > ./tmp.bbregister.26724/reg.init.dat --fslreg > ./tmp.bbregister.26724/reg.init.dat.fsl.mat --noedit > tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl > ERROR: cannot open ./tmp.bbregister.26724/reg.init.dat.fsl.mat > cat: ./tmp.bbregister.26724/reg.init.dat: No such file or directory > tmp: Subscript out of range. > > Started at Sat May 25 19:51:17 PDT 2013 > Ended at Sat May 25 19:51:23 PDT 2013 > > fslregister Done > > To check results, run: > tkregister2 --mov ./tmp.bbregister.26724/template.nii --reg > ./tmp.bbregister.26724/reg.init.dat --surf orig > > mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg > ./tmp.bbregister.26724/reg.init.dat --out-reg > ./tmp.bbregister.26724/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 > --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 > --gm-gt-wm 0.5 > regio_read_register(): No such file or directory > Could not open ./tmp.bbregister.26724/reg.init.dat > mri_segreg --mov ./tmp.bbregister.26724/template.nii --init-reg > ./tmp.bbregister.26724/bbr.pass1.dat --out-reg register.dat --brute -0.1 > 0.1 0.1 --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 > --mincost register.dat.mincost --dof 6 --nmax 36 --param register.dat.param > --surf white --cur-reg ./tmp.bbregister.26724/reg.curopt.dat --gm-proj-frac > 0.5 --nsub 1 --gm-gt-wm 0.5 > regio_read_register(): No such file or directory > Could not open ./tmp.bbregister.26724/bbr.pass1.dat > Cleaning up > > Started at Sat May 25 19:51:15 PDT 2013 > Ended at Sat May 25 19:51:24 PDT 2013 > BBR-Run-Time-Sec 9 > > bbregister Done > To check results, run: > tkregister2 --mov QSM_906.nii.gz --reg register.dat --surf > > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >

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Re: [Freesurfer] command not found
by Louis Nicholas Vinke 28 May '13

28 May '13

Hi Clelia, That mv command is failing presumably because SetUpFreeSurfer.txt does not exist in that directory. What are you trying to do with the mv command? It does look like freesurfer was sourced successfully. Are the FreeSurfer related commands still not found? Don't forget to cc the freesurfer mailing list. -Louis On Fri, 24 May 2013, clelia pellicano wrote: > Hi Louise, > I'm now using tcsh. Here what I did > > [dyn1097-8:~] cpellica% setenv FREESURFER_HOME /Applications/freesurfer > [dyn1097-8:~] cpellica% source /Applications/freesurfer/SetUpFreesurfer.csh > -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Applications/freesurfer > FSFAST_HOME /Applications/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Applications/freesurfer/subjects > MNI_DIR /Applications/freesurfer/mni > FSL_DIR /usr/local/fsl > [dyn1097-8:~] cpellica% mv SetUpFreeSurfer.txt SetUpFreeSurfer.csh > mv: rename SetUpFreeSurfer.txt to SetUpFreeSurfer.csh: No such file or directory > > Do you have any advice? > > Thanks > > Clelia > > > > > > On Fri, May 24, 2013 at 3:04 PM, Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> wrote: > Hi Clelia, > What do you run to source FS and do you get any output in your terminal after doing so? What operating system are > you running? You might try using c-shell instead of bash. > -Louis > > On Fri, 24 May 2013, clelia pellicano wrote: > > Hi Louis, > thank you for your answer. > I sourced freesurfer again, but I still get 'command not found'. > What can I try? > Thank you, > > Clelia > > > On Thu, May 23, 2013 at 7:15 PM, Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> wrote: > Hi Clelia, > If this is in a new terminal then you'll have to source freesurfer again. See here for details: > https://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration > -Louis > > On Wed, 22 May 2013, clelia pellicano wrote: > > Hi, > I have run recon-all -s bert -all to try my installation and it worked. > Now, when I try to use other command (and also again recon-all -s bert -all) I always get > this: > > dyn1097-8:subjects cpellica$ tkmedit bert orig.mgz > -bash: tkmedit: command not found > dyn1097-8:subjects cpellica$ tkmedit -s bert orig.mgz > -bash: tkmedit: command not found > dyn1097-8:subjects cpellica$ tksurfer -s bert rh pial > -bash: tksurfer: command not found > dyn1097-8:subjects cpellica$ qdec > -bash: qdec: command not found > dyn1097-8:subjects cpellica$ recon-all help > -bash: recon-all: command not found > dyn1097-8:subjects cpellica$ recon-all -s bert -all > -bash: recon-all: command not found > > > I don't know how to do. Please, could you help me? > > Thanks > > Clelia > > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > > > >

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mri_anatomical_stats segmentation fault
by Rob Tennyson 28 May '13

28 May '13

Hi All, I'm running "mris_anatomical_stats" with a few manually defined labels. For a few of my subjects, I am getting the error: "Segmentation fault" on one of the labels. However, the other manually defined labels process without any errors on these same subjects. For example, I am running "mri_anatomical_stats" on subject 33_bay6 with a manually defined ERC label, a manually defined PHC label, and a manually defined medial frontal gyrus label. The only label that runs an error for this subject is the PHC label. This PHC label runs without any errors on the rest of my subjects. Here is what is displayed when running a label that fails: "> mris_anatomical_stats -f PHC.stats.04.txt -l lh.PHC_1.label -b 33_bay6 lh limiting computations to label lh.PHC_1.label. reading volume /Volumes/BigRaid/Rob/subjects/33_bay6/mri/wm.mgz... reading input surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... reading input pial surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.pial... reading input white surface /Volumes/BigRaid/Rob/subjects/33_bay6/surf/lh.white... Segmentation fault" Does anyone know what may be causing the Segmentation fault and what steps I should take to fix it? Thank you for your help! Rob

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nuintensitycor and skullstrip problems
by LAOUCHEDI MAKHLOUF 28 May '13

28 May '13

hi i send you the rawavg.mgz of the subject with the massive artefact. i inform you that i proceeded differently by splitting the recon-all -all into three steps (as in freesurfer wiki) : (1) recon-all -autorecon1, (2) recon-all -autorecon2 (3) recon-all -autorecon3. i just finished with the first step which still didn't work for some subjects so i deleted then in my SUBJECTS_DIR then i run "recon-all -i" to regenerate them. after that i re-run "recon-all -autorecon1" and it worked even for the subject with the artefacted rawavg.mgz i am sending you. i noticed also that some extra cerebral structures like dura is not fully removed after the skullstripping step, and i reviewed some of my previous datasets i processed with freesurfer and i noticed that the cortical ribbon (containing the cortical parcellation) fits well the gray matter. so is a wise idea to not bother a lot about these "some" extra cerebral structures left and just go forward with the rest of the recon-all pipeline (but of course i'll take a look a posteriori). Thanks

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minor bug report
by Joseph Dien 28 May '13

28 May '13

when I run: isxconcat-sess -sf sessidlist.dat -analysis CPA.sm05.lh -all-contrasts -o secondLevel I get the error messages: secondLevel/CPA.sm05.mni305/log/isxconcat.log stat: illegal option -- c usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file ...] stat: illegal option -- c usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file ...] stat: illegal option -- c usage: stat [-FlLnqrsx] [-f format] [-t timefmt] [file …] ... I'm assuming this isn't a serious problem as it just seems to affect what goes into the log file but thought you might want to know. This is on OS X 10.8.2 with Freesurfer 5.2.0. Cheers! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//

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fix talairach transform
by LAOUCHEDI MAKHLOUF 28 May '13

28 May '13

Hi i have a problem when running "recon-all -all", so i decided to split the process into three staps : "recon-all -autorecon1", ""recon-all -autorecon2" and "recon-all -autorecon3". i have just finished with the first step (recon-all -autorecon1) and looked for misalignment in talairach transform for all subjects using "tkregister2 --mgz --s ctr1 --fstal" (i can't use "--surf orig " because i haven't the surfaces yet). so i used the small red cross in the coronal, sagittal and axial views to align as much as possible. my goal is to extract the cortical labels (cortical parcellation). is it necessary to have a precise talairach transform just for this purpose ? Thank you

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nuintensitycor and skullstrip problems
by LAOUCHEDI MAKHLOUF 28 May '13

28 May '13

hi i send you further information of the -nuintensitycor and skullstrip problem,about three control subjects. after running "recon_all -i", i decided to process my data step by step, i run "recon_all -autorecon1" for all of them and it ended with errors. i picked up three cases of the recon-all.log file : subject 1: #@# Nu Intensity Correction Mon May 27 18:08:32 CEST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home_cluster/mlaouche/freesurf_makh/ctr3/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:36 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.12456 /home_cluster/mlaouche/freesurf_makh/ctr3/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12456/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12456/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=7.05, 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 uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12456/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon May 27 18:23:46 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12456/nu0.mnc ./tmp.mri_nu_correct.mni.12456/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12456/0/ ./tmp.mri_nu_correct.mni.12456/ is a directory but not writeable [mlaouche@cn09:/home_cluster/mlaouche/freesurf_makh/ctr3/mri/] [2013-05-27 18:23:56] running: /home_cluster/amesse/software/freesurfer5.1/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.12456/0/ ./tmp.mri_nu_correct.mni.12456/nu0.mnc ./tmp.mri_nu_correct.mni.12456/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ctr3 exited with ERRORS at Mon May 27 18:47:13 CEST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting subject 2: #@# Nu Intensity Correction Mon May 27 18:08:21 CEST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home_cluster/mlaouche/freesurf_makh/ctr5/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:31 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.12252 /home_cluster/mlaouche/freesurf_makh/ctr5/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12252/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.12252/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=7.07, 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 uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.12252/nu0.mnc... tee: ./mri_nu_correct.mni.log: Input/output error -------------------------------------------------------- Iteration 1 Mon May 27 18:23:44 CEST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.12252/nu0.mnc ./tmp.mri_nu_correct.mni.12252/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.12252/0/ ./tmp.mri_nu_correct.mni.12252/ is a directory but not writeable [mlaouche@cn09:/home_cluster/mlaouche/freesurf_makh/ctr5/mri/] [2013-05-27 18:23:56] running: /home_cluster/amesse/software/freesurfer5.1/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.12252/0/ ./tmp.mri_nu_correct.mni.12252/nu0.mnc ./tmp.mri_nu_correct.mni.12252/nu1.imp Computing ranges for each class.: ............................................. Processing:.................................................................Done Fitting splines: .............................................................. Computing ranges for each class.: ............................................. Processing:.................................................................Done Computing ranges for each class.: ............................................. Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ctr5 exited with ERRORS at Mon May 27 19:13:37 CEST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting subject 3: #@# Nu Intensity Correction Mon May 27 18:08:34 CEST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home_cluster/mlaouche/freesurf_makh/ctr6/mri /home_cluster/amesse/software/freesurfer5.1/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon May 27 18:08:38 CEST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 mkdir: cannot create directory `./tmp.mri_nu_correct.mni.12552': Input/output error tee: ./mri_nu_correct.mni.log: Input/output error tmpdir is ./tmp.mri_nu_correct.mni.12552 Linux cn09 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

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