Freesurfer February 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
236 discussions

longitudinal processing
by Linn Mittlestein 20 Feb '13

20 Feb '13

Dear Freesurfer experts, I just tried creating the -base for longitudinal processing on two time points using recon-all -base <templateID> -tp <tp1id> -tp <tp2id> ... -all After doing this, I received no error messages and a third folder named after the template name I had given it it was present in the subjects directory, however all of these files were empty. What have I done wrong? Regards

2 1

Re: [Freesurfer] extracting hand drawn ROIs to Afni space
by Bruce Fischl 19 Feb '13

19 Feb '13

Thanks Ziad Bruce On Feb 19, 2013, at 10:42 PM, ziad <ziad.ss(a)gmail.com> wrote: > Hello Paul, > > There are a couple of ways I can think of bringing the new ROIs to AFNI land from FreeSurfer. I can suggest the following, with the assumption that you seek to dump the average time series from single-subject data using an ROI defined on the FS average surface. > > 1- Get a list from FreeSurfer of the nodes indices that constitute the ROI on the FS average surface. That list can take the form of a dataset, that we'll call ROI_dset_avg. Use GFTI/NIFTI for surface/volume exchange format between FreeSurfer and AFNI. > 2- Create a standard mesh version of the FS average surface, assuming you don't have one already. You can do that much as you would for a regular subject using @SUMA_Make_Spec_FS. > 3- Use SurfToSurf, or MapIcosahedron to map the ROI_dset_avg from the original fsaverage surface mesh onto any of the standard-mesh versions of fsaverage. We'll call that dataset ROI_dset_avg_std. > This new dataset can now be used on any of your subject's standardized meshes, as long as you use the same icosahedral mesh. > 4- Create for each subject a volumetric mask of ROI_dset_avg_std with 3dSurf2Vol > > I don't know how well you know how to use the SUMA tools I mentioned above, but if you need more detailed help let me know. > > cheers, > Ziad > > On Feb 18, 2013, at 4:39 PM, Paul Beach wrote: > >> Thank you for forwarding this. >> >> I realize I need to further clarify my issue as well. >> >> With the help of Doug Greve I've taken hand made ROIs in tksurfer, repackaged them into a new annotation, and repackaged that into a new aseg file for an average subject. Now (and this is where I'm stuck) I'm trying to take those newly minted ROIs, place them onto individual subjects' brains and THEN send them to Afni for each of those subjects (before doing seed correlation analysis). >> >> Previously I had been using mri_label2label to place the averaged subject ROI into single subjects' folders and then mri_label2vol to get them ready to send to Afni. However, this method was not producing ROIs that covered the extent of a region's gray matter. Thus, Doug's solution of re-annotating and re-segmenting. >> >> Hopefully that makes things a bit easier. >> >> >> Thanks again for your help! >> Paul >> >> >> On Mon, Feb 18, 2013 at 3:13 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Paul >> >> we usually call those labels and have an ascii label file format. Not sure how to get that into AFNI, but I'm zure Ziad (ccd) knows. >> >> cheers >> Bruce >> >> On Mon, 18 Feb 2013, Paul Beach wrote: >> >> Hi there, >> Through the help of the Freesurfer Q&A staff I've been able to get ROIs >> drawn in tksurfer into an augmented aparc+aseg file of an averaged subject. >> I need to be able to get those ROIs, which are not part of the color LUT, >> into Afni space. >> >> For ROIs that are already in the LUT, getting them to Afni is no problem, I >> simply use a 3dcalc command. However, I have the problem of needing to >> export newly parcellated and segmented ROIs that aren't in the Freesurfer >> LUT to Afni space. >> >> Is there a way to do this short of creating a new "spot" for them in our >> LUT? If not, how does one go about adding ROIs to the LUT and/or creating a >> LUT specific to my needs (since the Wiki suggests not fussing with the >> original LUT)? >> >> >> Thanks, >> Paul >> -- >> >> >> >> >> >> 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. >> >> >> >> -- >> Paul Beach >> DO/PhD candidate - Year V >> Michigan State University >> - College of Osteopathic Medicine - OMS V >> - Neuroscience Program >> - Bozoki Lab: Neurology/Radiology >> - President: American Physician Scientist Association, MSU COM Chapter >

1 0

Re: [Freesurfer] mri_ca_label problem
by paul horton 19 Feb '13

19 Feb '13

Hi Bruce, Below is the output: ############################USER=k0933235 LOGNAME=k0933235 HOME=/home/k0933235 PATH=/software/system/fsl/fsl-4.1.5//bin:/software/system/fsl/fsl-4.1.5//etc/fslconf/fsl.csh:/software/system/freesurfer/freesurfer-4.5.0//bin:/software/system/freesurfer/freesurfer-4.5.0//fsfast/bin:/software/system/fsl/fsl-4.1.8/bin:/software/system/freesurfer/freesurfer-4.5.0//mni/bin:/cns_zfs/cns_sge/bin/linux-x64:/software/local/bin:/software/system/bin:/software/system/matlab/matlab-7.8.0/bin:/software/system/fsl/fsl-4.1.8/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/software/system/mri3dX/mri3dX_v563:/software/system/surfrelax/TFI/bin:/software/system/ITK/ITK-2.0/bin:/software/local/camino/camino/bin:/software/system/minc-toolkit/20121004/bin MAIL=/var/spool/mail/k0933235 SHELL=/bin/tcsh SSH_CLIENT=137.73.249.51 51517 22 SSH_CONNECTION=137.73.249.51 51517 194.83.137.60 22 SSH_TTY=/dev/pts/21 TERM=xterm DISPLAY=localhost:28.0 SELINUX_ROLE_REQUESTED= SELINUX_LEVEL_REQUESTED= SELINUX_USE_CURRENT_RANGE= HOSTTYPE=x86_64-linux VENDOR=unknown OSTYPE=linux MACHTYPE=x86_64 SHLVL=1 PWD=/home/k0933235 GROUP=k093 HOST=cnslnx1.iop.kcl.ac.uk REMOTEHOST=pc249-51.firepass.kcl.ac.uk HOSTNAME=cnslnx1.iop.kcl.ac.uk G_BROKEN_FILENAMES=1 LANG=en_US.UTF-8 LESSOPEN=|/usr/bin/lesspipe.sh %s QTDIR=/usr/lib64/qt-3.3 QTINC=/usr/lib64/qt-3.3/include QTLIB=/usr/lib64/qt-3.3/lib PAGER=less EDITOR=vim FSLDIR=/software/system/fsl/fsl-4.1.5/ FSLOUTPUTTYPE=NIFTI_GZ FSLMULTIFILEQUIT=TRUE FSLTCLSH=/software/system/fsl/fsl-4.1.8/bin/fsltclsh FSLWISH=/software/system/fsl/fsl-4.1.8/bin/fslwish FSLLOCKDIR= FSLMACHINELIST= FSLREMOTECALL= FSLQUEUE=rhe5b FSLCONFDIR=/software/system/fsl/fsl-4.1.8/config FSLMACHTYPE=linux_64-gcc4.4 LD_LIBRARY_PATH=/cns_zfs/cns_sge/lib/linux-x64:/software/system/qwt/qwt-4.2.0/lib:/software/system/VTK/VTK-5.0.1/lib SGE_ROOT=/cns_zfs/cns_sge SGE_CELL=default SGE_CLUSTER_NAME=p3370 SGE_QMASTER_PORT=3369 SGE_EXECD_PORT=3370 MANPATH=/usr/share/man BRAINTOOLSDIR=/software/system/mri3dX/mri3dX_v563 BrainLibFont=-adobe-helvetica-medium-r-*-*-*-120-*-*-*-*-*-* TFIDIR=/software/system/surfrelax/TFI LIBGL_ALWAYS_INDIRECT=y FREESURFER_HOME=/software/system/freesurfer/freesurfer-4.5.0/ SUBJECTS_DIR=/home/k0933235/paul/PREDEP_Structural/subjects3 FUNCTIONALS_DIR=/software/system/freesurfer/freesurfer-4.5.0//sessions OS=Linux FS_OVERRIDE=0 FSFAST_HOME=/software/system/freesurfer/freesurfer-4.5.0//fsfast MINC_BIN_DIR=/software/system/freesurfer/freesurfer-4.5.0//mni/bin MNI_DIR=/software/system/freesurfer/freesurfer-4.5.0//mni MINC_LIB_DIR=/software/system/freesurfer/freesurfer-4.5.0//mni/lib MNI_DATAPATH=/software/system/freesurfer/freesurfer-4.5.0//mni/data FSL_DIR=/software/system/fsl/fsl-4.1.8 LOCAL_DIR=/software/system/freesurfer/freesurfer-4.5.0//local FSF_OUTPUT_FORMAT=nii FMRI_ANALYSIS_DIR=/software/system/freesurfer/freesurfer-4.5.0//fsfast MNI_PERL5LIB=/software/system/freesurfer/freesurfer-4.5.0//mni/lib/perl5/5.8.5 PERL5LIB=/software/system/freesurfer/freesurfer-4.5.0//mni/lib/perl5/5.8.5 FSL_BIN=/software/system/fsl/fsl-4.1.8/bin FSLDISPLAY=/usr/bin/display FSLCONVERT=/usr/bin/convert FIX_VERTEX_AREA= ############################# Thanks Paul> Date: Tue, 19 Feb 2013 17:50:05 -0500 > From: fischl(a)nmr.mgh.harvard.edu > To: horton_paul(a)hotmail.com > Subject: RE: [Freesurfer] mri_ca_label problem > > just to rule out a longshot, can you send me the output of printenv? > > > On Tue, 19 Feb 2013, paul horton wrote: > > > Hi Bruce, > > > > When I run recon -all the last thing it prints before going to the > > command prompt is > > > > 'recon-all exited with ERRORS at Mon Feb 18 19:22:12 GMT 2013' > > > > and when I run the stand alone command, i.e. mri_ca_label, the last thing it > > prints before going to the command prompt is > > > > 'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt' > > > > I hope this information helps. > > > > Thanks > > > > Paul > > > > > > > > > Date: Tue, 19 Feb 2013 17:28:52 -0500 > > > From: fischl(a)nmr.mgh.harvard.edu > > > To: horton_paul(a)hotmail.com > > > CC: freesurfer(a)nmr.mgh.harvard.edu > > > Subject: RE: [Freesurfer] mri_ca_label problem > > > > > > and that's the last thing it prints before returning to a prompt? > > > On Tue, 19 > > > Feb 2013, paul horton wrote: > > > > > > > Hi Bruce, > > > > > > > > Yes this is within recon-all. I have also tried it as a stand alone > > command > > > > but it stops at the same place, i.e. when the function outputs the > > following > > > > statement: 'saving intensity scales to > > > > aseg.auto_noCCseg.label_intensities.txt'. The file > > 'aseg.auto_noCCseg.mgz' > > > > is not saved but the file 'aseg.auto_noCCseg.label_intensities.txt' is. > > > > Yes, it is writeable and there is enough disk space. The only error > > > > messages I get refer to the functions not finding the relevant files as > > > > they were not saved. I have attached the log below: > > > > > > > > #-------------------------------------- > > > > > > > > #@# SubCort Seg Mon Feb 18 19:02:14 GMT 2013 > > > > > > > > mri_ca_label -align -nobigventricles norm.mgztransforms/talairach.m3z/software/system/freesurfer/freesurfer-4.5.0//avera > > ge/RB_all_2008-03-26.gca > > > > aseg.auto_noCCseg.mgz > > > > > > > > renormalizing sequences with structure alignment, equivalent to: > > > > > > > > -renormalize > > > > > > > > -renormalize_mean 0.500 > > > > > > > > -regularize 0.500 > > > > > > > > not handling expanded ventricles... > > > > > > > > reading 1 input volumes... > > > > > > > > reading classifier arrayfrom/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-03-26 > > .gca > > > > ... > > > > > > > > reading input volume from norm.mgz... > > > > > > > > average std[0] = 6.9 > > > > > > > > reading transform from transforms/talairach.m3z... > > > > > > > > zcat transforms/talairach.m3z > > > > > > > > Atlas used for the 3D morphwas/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-03-26. > > gca > > > > > > > > > > > > average std = 6.9 using min determinant for regularization = 4.7 > > > > > > > > 0 singular and 0 ill-conditioned covariance matrices regularized > > > > > > > > labeling volume... > > > > > > > > renormalizing by structure alignment.... > > > > > > > > renormalizing input #0 > > > > > > > > gca peak = 0.15151 (27) > > > > > > > > mri peak = 0.15062 (23) > > > > > > > > Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, > > > > overlap=0.484) > > > > > > > > Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, peak > > = > > > > 22), gca=22.3 > > > > > > > > gca peak = 0.14982 (20) > > > > > > > > mri peak = 0.16025 (24) > > > > > > > > Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 voxels, > > > > overlap=0.766) > > > > > > > > Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 voxels, > > peak = > > > > 20), gca=20.5 > > > > > > > > gca peak = 0.28003 (97) > > > > > > > > mri peak = 0.11295 (106) > > > > > > > > Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, > > overlap=0.353) > > > > > > > > Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, peak = 104), > > > > gca=104.3 > > > > > > > > gca peak = 0.18160 (96) > > > > > > > > mri peak = 0.12433 (104) > > > > > > > > Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, > > overlap=0.638) > > > > > > > > Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, peak = 101), > > > > gca=100.8 > > > > > > > > gca peak = 0.27536 (62) > > > > > > > > mri peak = 0.08252 (69) > > > > > > > > Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, > > > > overlap=0.818) > > > > > > > > Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, peak = > > 68), > > > > gca=68.2 > > > > > > > > gca peak = 0.32745 (63) > > > > > > > > mri peak = 0.07934 (66) > > > > > > > > Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, > > > > overlap=1.000) > > > > > > > > Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, peak = > > 65), > > > > gca=64.6 > > > > > > > > gca peak = 0.08597 (105) > > > > > > > > mri peak = 0.06861 (109) > > > > > > > > Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979 > > voxels, > > > > overlap=0.744) > > > > > > > > Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979 > > voxels, > > > > peak = 108), gca=107.6 > > > > > > > > gca peak = 0.09209 (106) > > > > > > > > mri peak = 0.07113 (103) > > > > > > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, > > > > overlap=0.820) > > > > > > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, > > > > peak = 106), gca=106.0 > > > > > > > > gca peak = 0.07826 (63) > > > > > > > > mri peak = 0.02785 (72) > > > > > > > > Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, > > > > overlap=0.547) > > > > > > > > Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, peak > > = > > > > 71), gca=70.9 > > > > > > > > gca peak = 0.08598 (64) > > > > > > > > mri peak = 0.02894 (68) > > > > > > > > Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels, > > > > overlap=0.642) > > > > > > > > Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels, > > peak = > > > > 69), gca=68.8 > > > > > > > > gca peak = 0.24164 (71) > > > > > > > > mri peak = 0.13663 (85) > > > > > > > > Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, > > overlap=0.000) > > > > > > > > Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, peak = 82), > > > > gca=81.7 > > > > > > > > gca peak = 0.18227 (75) > > > > > > > > mri peak = 0.14739 (80) > > > > > > > > Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, > > overlap=0.988) > > > > > > > > Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, peak = 77), > > > > gca=76.9 > > > > > > > > gca peak = 0.10629 (62) > > > > > > > > mri peak = 0.05203 (64) > > > > > > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, > > > > overlap=0.948) > > > > > > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, > > peak = > > > > 64), gca=63.5 > > > > > > > > gca peak = 0.11668 (59) > > > > > > > > mri peak = 0.05041 (65) > > > > > > > > Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 voxels, > > > > overlap=0.926) > > > > > > > > Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 voxels, > > peak > > > > = 63), gca=63.4 > > > > > > > > gca peak = 0.17849 (88) > > > > > > > > mri peak = 0.09573 (95) > > > > > > > > Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309 > > voxels, > > > > overlap=0.601) > > > > > > > > Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309 > > voxels, > > > > peak = 95), gca=94.6 > > > > > > > > gca peak = 0.16819 (86) > > > > > > > > mri peak = 0.10076 (95) > > > > > > > > Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881 > > voxels, > > > > overlap=0.590) > > > > > > > > Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881 > > voxels, > > > > peak = 92), gca=92.5 > > > > > > > > gca peak = 0.41688 (64) > > > > > > > > mri peak = 0.07820 (67) > > > > > > > > Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, > > overlap=1.000) > > > > > > > > Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, peak = 66), > > > > gca=65.6 > > > > > > > > gca peak = 0.42394 (62) > > > > > > > > mri peak = 0.10919 (71) > > > > > > > > Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, > > overlap=0.434) > > > > > > > > Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, peak = 70), > > > > gca=69.8 > > > > > > > > gca peak = 0.10041 (96) > > > > > > > > mri peak = 0.07146 (97) > > > > > > > > Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, > > > > overlap=0.910) > > > > > > > > Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, peak > > = > > > > 98), gca=98.4 > > > > > > > > gca peak = 0.13978 (88) > > > > > > > > mri peak = 0.06159 (103) > > > > > > > > Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, > > > > overlap=0.376) > > > > > > > > Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, peak > > = > > > > 99), gca=99.0 > > > > > > > > gca peak = 0.08514 (81) > > > > > > > > mri peak = 0.06222 (85) > > > > > > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, > > overlap=0.964) > > > > > > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = 81), > > > > gca=81.0 > > > > > > > > gca peak = 0.09624 (82) > > > > > > > > mri peak = 0.09383 (84) > > > > > > > > Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, > > overlap=0.815) > > > > > > > > Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, peak = 84), > > > > gca=84.0 > > > > > > > > gca peak = 0.07543 (88) > > > > > > > > mri peak = 0.05306 (86) > > > > > > > > Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, overlap=0.765) > > > > > > > > Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, peak = 92), > > > > gca=92.4 > > > > > > > > gca peak = 0.12757 (95) > > > > > > > > mri peak = 0.05862 (107) > > > > > > > > Right_VentralDC: unreasonable value (111.6/107.0), not in range [80, > > 110] - > > > > rejecting > > > > > > > > gca peak = 0.17004 (92) > > > > > > > > mri peak = 0.06574 (111) > > > > > > > > Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110] > > - > > > > rejecting > > > > > > > > gca peak = 0.21361 (36) > > > > > > > > mri peak = 0.12619 (24) > > > > > > > > Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, > > overlap=0.000) > > > > > > > > Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, peak = 25), > > > > gca=25.2 > > > > > > > > gca peak = 0.26069 (23) > > > > > > > > mri peak = 0.16285 (24) > > > > > > > > Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, > > overlap=0.640) > > > > > > > > Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, peak = > > 21), > > > > gca=20.7 > > > > > > > > gca peak Unknown = 0.94427 ( 0) > > > > > > > > gca peak Left_Inf_Lat_Vent = 0.31795 (35) > > > > > > > > gca peak CSF = 0.14367 (38) > > > > > > > > gca peak Left_Accumbens_area = 0.57033 (70) > > > > > > > > gca peak Left_VentralDC = 0.17004 (92) > > > > > > > > gca peak Left_undetermined = 1.00000 (35) > > > > > > > > gca peak Left_vessel = 0.65201 (62) > > > > > > > > gca peak Left_choroid_plexus = 0.09084 (48) > > > > > > > > gca peak Right_Inf_Lat_Vent = 0.31129 (32) > > > > > > > > gca peak Right_Accumbens_area = 0.30219 (72) > > > > > > > > gca peak Right_VentralDC = 0.12757 (95) > > > > > > > > gca peak Right_vessel = 0.83418 (60) > > > > > > > > gca peak Right_choroid_plexus = 0.10189 (48) > > > > > > > > gca peak Fifth_Ventricle = 0.72939 (42) > > > > > > > > gca peak WM_hypointensities = 0.14821 (82) > > > > > > > > gca peak non_WM_hypointensities = 0.10354 (53) > > > > > > > > gca peak Optic_Chiasm = 0.34849 (76) > > > > > > > > not using caudate to estimate GM means > > > > > > > > estimating mean gm scale to be 1.08 x + 0.0 > > > > > > > > estimating mean wm scale to be 1.01 x + 0.0 > > > > > > > > estimating mean csf scale to be 0.86 x + 0.0 > > > > > > > > Left_Pallidum too bright - rescaling by 1.007 (from 1.050) to 101.5 (was > > > > 100.8) > > > > > > > > Right_Pallidum too bright - rescaling by 0.973 (from 1.075) to 101.5 > > (was > > > > 104.3) > > > > > > > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt > > > > > > > > renormalizing by structure alignment.... > > > > > > > > renormalizing input #0 > > > > > > > > gca peak = 0.14515 (23) > > > > > > > > mri peak = 0.15062 (23) > > > > > > > > Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, > > > > overlap=0.897) > > > > > > > > Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, peak > > = > > > > 24), gca=23.6 > > > > > > > > gca peak = 0.19392 (21) > > > > > > > > mri peak = 0.16025 (24) > > > > > > > > Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 voxels, > > > > overlap=0.745) > > > > > > > > Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 voxels, > > peak = > > > > 21), gca=21.0 > > > > > > > > gca peak = 0.25607 (102) > > > > > > > > mri peak = 0.11295 (106) > > > > > > > > Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, > > overlap=1.000) > > > > > > > > Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, peak = 105), > > > > gca=104.5 > > > > > > > > gca peak = 0.17462 (103) > > > > > > > > mri peak = 0.12433 (104) > > > > > > > > Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, > > overlap=0.999) > > > > > > > > Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, peak = 103), > > > > gca=103.0 > > > > > > > > gca peak = 0.24759 (68) > > > > > > > > mri peak = 0.08252 (69) > > > > > > > > Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, > > > > overlap=0.999) > > > > > > > > Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, peak = > > 68), > > > > gca=68.0 > > > > > > > > gca peak = 0.28061 (65) > > > > > > > > mri peak = 0.07934 (66) > > > > > > > > Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, > > > > overlap=0.999) > > > > > > > > Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, peak = > > 62), > > > > gca=61.8 > > > > > > > > gca peak = 0.08360 (108) > > > > > > > > mri peak = 0.06861 (109) > > > > > > > > Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979 > > voxels, > > > > overlap=0.831) > > > > > > > > Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979 > > voxels, > > > > peak = 108), gca=108.0 > > > > > > > > gca peak = 0.09206 (106) > > > > > > > > mri peak = 0.07113 (103) > > > > > > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, > > > > overlap=0.820) > > > > > > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, > > > > peak = 106), gca=106.0 > > > > > > > > gca peak = 0.06916 (71) > > > > > > > > mri peak = 0.02785 (72) > > > > > > > > Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, > > > > overlap=0.733) > > > > > > > > Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, peak > > = > > > > 69), gca=69.2 > > > > > > > > gca peak = 0.08227 (69) > > > > > > > > mri peak = 0.02894 (68) > > > > > > > > Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels, > > > > overlap=0.734) > > > > > > > > Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels, > > peak = > > > > 69), gca=69.0 > > > > > > > > gca peak = 0.22329 (81) > > > > > > > > mri peak = 0.13663 (85) > > > > > > > > Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, > > overlap=1.000) > > > > > > > > Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, peak = 81), > > > > gca=81.0 > > > > > > > > gca peak = 0.18180 (77) > > > > > > > > mri peak = 0.14739 (80) > > > > > > > > Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, > > overlap=0.937) > > > > > > > > Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, peak = 77), > > > > gca=77.0 > > > > > > > > gca peak = 0.10419 (63) > > > > > > > > mri peak = 0.05203 (64) > > > > > > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, > > > > overlap=0.982) > > > > > > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, > > peak = > > > > 65), gca=64.6 > > > > > > > > gca peak = 0.12084 (64) > > > > > > > > mri peak = 0.05041 (65) > > > > > > > > Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 voxels, > > > > overlap=0.985) > > > > > > > > Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 voxels, > > peak > > > > = 62), gca=62.4 > > > > > > > > gca peak = 0.17137 (94) > > > > > > > > mri peak = 0.09573 (95) > > > > > > > > Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309 > > voxels, > > > > overlap=0.978) > > > > > > > > Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309 > > voxels, > > > > peak = 94), gca=94.0 > > > > > > > > gca peak = 0.15715 (93) > > > > > > > > mri peak = 0.10076 (95) > > > > > > > > Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881 > > voxels, > > > > overlap=0.983) > > > > > > > > Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881 > > voxels, > > > > peak = 93), gca=93.0 > > > > > > > > gca peak = 0.32238 (65) > > > > > > > > mri peak = 0.07820 (67) > > > > > > > > Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, > > overlap=1.000) > > > > > > > > Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, peak = 65), > > > > gca=65.0 > > > > > > > > gca peak = 0.49832 (70) > > > > > > > > mri peak = 0.10919 (71) > > > > > > > > Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, > > overlap=1.000) > > > > > > > > Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, peak = 70), > > > > gca=70.0 > > > > > > > > gca peak = 0.10606 (98) > > > > > > > > mri peak = 0.07146 (97) > > > > > > > > Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, > > > > overlap=0.901) > > > > > > > > Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, peak > > = > > > > 98), gca=98.0 > > > > > > > > gca peak = 0.12505 (99) > > > > > > > > mri peak = 0.06159 (103) > > > > > > > > Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, > > > > overlap=0.961) > > > > > > > > Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, peak > > = > > > > 99), gca=99.0 > > > > > > > > gca peak = 0.08514 (81) > > > > > > > > mri peak = 0.06222 (85) > > > > > > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, > > overlap=0.964) > > > > > > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = 81), > > > > gca=81.0 > > > > > > > > gca peak = 0.09838 (78) > > > > > > > > mri peak = 0.09383 (84) > > > > > > > > Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, > > overlap=0.982) > > > > > > > > Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, peak = 78), > > > > gca=78.0 > > > > > > > > gca peak = 0.07177 (90) > > > > > > > > mri peak = 0.05306 (86) > > > > > > > > Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, overlap=0.860) > > > > > > > > Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, peak = 92), > > > > gca=92.2 > > > > > > > > gca peak = 0.13316 (95) > > > > > > > > mri peak = 0.05862 (107) > > > > > > > > Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, > > overlap=0.010) > > > > > > > > Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, peak = > > 109), > > > > gca=109.2 > > > > > > > > gca peak = 0.16834 (92) > > > > > > > > mri peak = 0.06574 (111) > > > > > > > > Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110] > > - > > > > rejecting > > > > > > > > gca peak = 0.25342 (25) > > > > > > > > mri peak = 0.12619 (24) > > > > > > > > Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, > > overlap=0.998) > > > > > > > > Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, peak = 25), > > > > gca=25.0 > > > > > > > > gca peak = 0.20850 (21) > > > > > > > > mri peak = 0.16285 (24) > > > > > > > > Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, > > overlap=0.808) > > > > > > > > Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, peak = > > 22), > > > > gca=21.5 > > > > > > > > gca peak Unknown = 0.94427 ( 0) > > > > > > > > gca peak Left_Inf_Lat_Vent = 0.26363 (36) > > > > > > > > gca peak CSF = 0.17919 (33) > > > > > > > > gca peak Left_Accumbens_area = 0.40223 (72) > > > > > > > > gca peak Left_VentralDC = 0.16834 (92) > > > > > > > > gca peak Left_undetermined = 1.00000 (35) > > > > > > > > gca peak Left_vessel = 0.63670 (62) > > > > > > > > gca peak Left_choroid_plexus = 0.09084 (48) > > > > > > > > gca peak Right_Inf_Lat_Vent = 0.29122 (35) > > > > > > > > gca peak Right_Accumbens_area = 0.25605 (83) > > > > > > > > gca peak Right_vessel = 0.83418 (60) > > > > > > > > gca peak Right_choroid_plexus = 0.10189 (48) > > > > > > > > gca peak Fifth_Ventricle = 0.81716 (36) > > > > > > > > gca peak WM_hypointensities = 0.15216 (83) > > > > > > > > gca peak non_WM_hypointensities = 0.09346 (54) > > > > > > > > gca peak Optic_Chiasm = 0.34849 (76) > > > > > > > > mri_ca_label GCA sequential renormalization: label 28 not consistently > > > > computed. > > > > > > > > not using caudate to estimate GM means > > > > > > > > setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 > > > > > > > > estimating mean gm scale to be 0.99 x + 0.0 > > > > > > > > estimating mean wm scale to be 1.00 x + 0.0 > > > > > > > > estimating mean csf scale to be 1.01 x + 0.0 > > > > > > > > Left_Pallidum too bright - rescaling by 0.987 (from 1.000) to 101.6 (was > > > > 103.0) > > > > > > > > Right_Pallidum too bright - rescaling by 0.972 (from 1.025) to 101.6 > > (was > > > > 104.5) > > > > > > > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt > > > > > > > > mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz PREDEP40C_fsf > > > > > > > > reading input aseg from aseg.auto_noCCseg.mgz > > > > > > > > writing aseg with cc labels to aseg.auto.mgz > > > > > > > > mri_cc: could not read aseg volumefrom/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg. > > auto > > > > _noCCseg.mgz > > > > > > > > reading asegfrom/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg. > > auto > > > > _noCCseg.mgz > > > > > > > > ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg. > > auto > > > > _noCCseg.mgz > > > > > > > > No such file or directory > > > > > > > > #-------------------------------------- > > > > > > > > #@# Merge ASeg Mon Feb 18 19:22:10 GMT 2013 > > > > > > > > cp aseg.auto.mgz aseg.mgz > > > > > > > > cp: cannot stat `aseg.auto.mgz': No such file or directory > > > > > > > > #-------------------------------------------- > > > > > > > > #@# Intensity Normalization2 Mon Feb 18 19:22:10 GMT 2013 > > > > > > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri > > > > > > > > mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz > > > > > > > > using segmentation for initial intensity normalization > > > > > > > > reading from norm.mgz... > > > > > > > > mri_normalize: could not read aseg from file aseg.mgz > > > > > > > > using MR volume brainmask.mgz to mask input volume... > > > > > > > > ERROR: cannot find > > > > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.mgz > > > > > > > > No such file or directory > > > > > > > > #-------------------------------------------- > > > > > > > > #@# Mask BFS Mon Feb 18 19:22:11 GMT 2013 > > > > > > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri > > > > > > > > mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz > > > > > > > > threshold mask volume at 5 > > > > > > > > mri_mask: could not read source volume brain.mgz > > > > > > > > ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/brain > > .mgz > > > > > > > > > > > > No such file or directory > > > > > > > > #-------------------------------------------- > > > > > > > > #@# WM Segmentation Mon Feb 18 19:22:11 GMT 2013 > > > > > > > > mri_segment brain.mgz wm.seg.mgz > > > > > > > > mri_segment: could not read source volume from brain.mgz > > > > > > > > ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/brain > > .mgz > > > > > > > > > > > > No such file or directory > > > > > > > > mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz > > wm.asegedit.mgz > > > > > > > > preserving editing changes in input volume... > > > > > > > > mri_edit_wm_with_aseg: could not read wm volume from wm.seg.mgz > > > > > > > > reading wm segmentation from wm.seg.mgz... > > > > > > > > ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/wm.se > > g.mg > > > > z > > > > > > > > No such file or directory > > > > > > > > mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz > > > > > > > > mri_pretess: could not open wm.asegedit.mgz > > > > > > > > ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/wm.as > > eged > > > > it.mgz > > > > > > > > No such file or directory > > > > > > > > #-------------------------------------------- > > > > > > > > #@# Fill Mon Feb 18 19:22:11 GMT 2013 > > > > > > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri > > > > > > > > mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta > > > > -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz > > > > > > > > logging cutting plane coordinates to ../scripts/ponscc.cut.log... > > > > > > > > INFO: Using transforms/talairach.lta and its offset for Talairach volume > > ... > > > > > > > > using segmentation aseg.auto_noCCseg.mgz... > > > > > > > > reading input volume...mri_fill: could not read wm.mgz > > > > > > > > ERROR: cannot find > > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/wm.mgz > > > > > > > > No such file or directory > > > > > > > > #-------------------------------------------- > > > > > > > > #@# Tessellate lh Mon Feb 18 19:22:11 GMT 2013 > > > > > > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts > > > > > > > > mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz > > > > ../mri/filled-pretess255.mgz > > > > > > > > mri_pretess: could not open ../mri/filled.mgz > > > > > > > > ERROR: cannot find ../mri/filled.mgz > > > > > > > > No such file or directory > > > > > > > > mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix > > > > > > > > could not open ../mri/filled-pretess255.mgz > > > > > > > > ERROR: cannot find ../mri/filled-pretess255.mgz > > > > > > > > No such file or directory > > > > > > > > rm -f ../mri/filled-pretess255.mgz > > > > > > > > ? > > > > > > > > mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix > > > > > > > > MRISread(../surf/lh.orig.nofix): could not open file > > > > > > > > No such file or directory > > > > > > > > Segmentation fault > > > > > > > > #-------------------------------------------- > > > > > > > > #@# Smooth1 lh Mon Feb 18 19:22:12 GMT 2013 > > > > > > > > mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix > > ../surf/lh.smoothwm.nofix > > > > > > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts > > > > > > > > setting seed for random number generator to 1234 > > > > > > > > MRISread(../surf/lh.orig.nofix): could not open file > > > > > > > > No such file or directory > > > > > > > > mris_smooth: could not read surface file ../surf/lh.orig.nofix > > > > > > > > No such file or directory > > > > > > > > #-------------------------------------------- > > > > > > > > #@# Inflation1 lh Mon Feb 18 19:22:12 GMT 2013 > > > > > > > > mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix > > > > ../surf/lh.inflated.nofix > > > > > > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts > > > > > > > > MRISread(../surf/lh.smoothwm.nofix): could not open file > > > > > > > > Not saving sulc > > > > > > > > No such file or directory > > > > > > > > mris_inflate: could not read surface file ../surf/lh.smoothwm.nofix > > > > > > > > No such file or directory > > > > > > > > #-------------------------------------------- > > > > > > > > #@# QSphere lh Mon Feb 18 19:22:12 GMT 2013 > > > > > > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts > > > > > > > > mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix > > ../surf/lh.qsphere.nofix > > > > > > > > doing quick spherical unfolding. > > > > > > > > setting seed for random number genererator to 1234 > > > > > > > > $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ > > > > > > > > $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ > > > > > > > > MRISread(../surf/lh.inflated.nofix): could not open file > > > > > > > > No such file or directory > > > > > > > > mris_sphere: could not read surface file ../surf/lh.inflated.nofix > > > > > > > > No such file or directory > > > > > > > > #-------------------------------------------- > > > > > > > > #@# Fix Topology lh Mon Feb 18 19:22:12 GMT 2013 > > > > > > > > cp ../surf/lh.orig.nofix ../surf/lh.orig > > > > > > > > cp: cannot stat `../surf/lh.orig.nofix': No such file or directory > > > > > > > > cp ../surf/lh.inflated.nofix ../surf/lh.inflated > > > > > > > > cp: cannot stat `../surf/lh.inflated.nofix': No such file or directory > > > > > > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts > > > > > > > > mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 > > PREDEP40C_fsf lh > > > > > > > > reading spherical homeomorphism from 'qsphere.nofix' > > > > > > > > using genetic algorithm with optimized parameters > > > > > > > > setting seed for random number genererator to 1234 > > > > > > > > ************************************************************* > > > > > > > > Topology Correction Parameters > > > > > > > > retessellation mode: genetic search > > > > > > > > number of patches/generation : 10 > > > > > > > > number of generations : 10 > > > > > > > > surface mri loglikelihood coefficient : 1.0 > > > > > > > > volume mri loglikelihood coefficient : 10.0 > > > > > > > > normal dot loglikelihood coefficient : 1.0 > > > > > > > > quadratic curvature loglikelihood coefficient : 1.0 > > > > > > > > volume resolution : 2 > > > > > > > > eliminate vertices during search : 1 > > > > > > > > initial patch selection : 1 > > > > > > > > select all defect vertices : 0 > > > > > > > > ordering dependant retessellation: 0 > > > > > > > > use precomputed edge table : 0 > > > > > > > > smooth retessellated patch : 2 > > > > > > > > match retessellated patch : 1 > > > > > > > > verbose mode : 0 > > > > > > > > ************************************************************* > > > > > > > > INFO: assuming .mgz format > > > > > > > > $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ > > > > > > > > $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ > > > > > > > >MRISread(/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/surf > > > > > > /lh.qsphere.nofix): could not open file > > > > > > > > reading inputsurface/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/surf/l > > h.qsphe > > > > re.nofix... > > > > > > > > No such file or directory > > > > > > > > mris_fix_topology: could not read inputsurface/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/surf/l > > h.qsphe > > > > re.nofix > > > > > > > > No such file or directory > > > > > > > > mris_euler_number ../surf/lh.orig > > > > > > > > Linux ioplnx5.iop.kcl.ac.uk 2.6.32-279.19.1.el6.x86_64 #1 SMP Tue Dec 18 > > > > 17:22:54 CST 2012 x86_64 x86_64 x86_64 GNU/Linux > > > > > > > > recon-all exited with ERRORS at Mon Feb 18 19:22:12 GMT 2013 > > > > > > > > > > > > > Date: Tue, 19 Feb 2013 16:35:50 -0500 > > > > > From: fischl(a)nmr.mgh.harvard.edu > > > > > To: horton_paul(a)hotmail.com > > > > > CC: freesurfer(a)nmr.mgh.harvard.edu > > > > > Subject: Re: [Freesurfer] mri_ca_label problem > > > > > > > > > > Hi Paul > > > > > > > > > > is this within recon-all? Does that file exist? Can you check its > > > > > permissions to make sure it is writeable? And that you have enough > > disk > > > > > space? Are any error messages printed? > > > > > Bruce > > > > > > > > > > > > > > > On Tue, 19 Feb 2013, paul horton wrote: > > > > > > > > > > > Hi guys, > > > > > > I am wondering if you can help me. > > > > > > I have run command: mri_ca_label -align -nobigventricles norm.mgz > > > > > > transforms/talairach.m3z > > $FREESURFER_HOME/average/RB_all_2008-03-26.gca > > > > > > aseg.auto_noCCseg.mgz, on a 3T MPRAGE subject but it fails: i.e. it > > > > stops > > > > > > after the 'saving intensity scales to > > > > > > aseg.auto_noCCseg.label_intensities.txt' line and does not save the > > > > file: > > > > > > aseg.auto_noCCseg.mgz. However, it does save the file: > > > > > > aseg.auto_noCCseg.label_intensities.txt. I have tried > > > > > > it several times and it stops at the same place. I have also tried > > > > > > recon-all, where it jumps from > > > > > > 'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt' > > to > > > > the > > > > > > command 'mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz', > > where, > > > > again, > > > > > > the file: aseg.auto_noCCseg.mgz is not saved. I am using freesurfer > > > > version > > > > > > 4.5.0. > > > > > > > > > > > > So is there a way I can solve this problem. > > > > > > > > > > > > Many Thanks > > > > > > Paul > > > > > > Ps, i have attached the output log below > > > > > > ################ > > > > > > renormalizing sequences with structure alignment, equivalent to: > > > > > > -renormalize > > > > > > -renormalize_mean 0.500 > > > > > > -regularize 0.500 > > > > > > not handling expanded ventricles... > > > > > > reading 1 input volumes... > > > > > > reading classifierarrayfrom/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008- > > 03-26 > > > > .gca > > > > > > ... > > > > > > reading input volume from norm.mgz... > > > > > > average std[0] = 6.9 > > > > > > reading transform from transforms/talairach.m3z... > > > > > > zcat transforms/talairach.m3z > > > > > > Atlas used for the 3Dmorphwas/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-0 > > 3-26. > > > > gca > > > > > > > > > > > > average std = 6.9 using min determinant for regularization = 4.7 > > > > > > 0 singular and 0 ill-conditioned covariance matrices regularized > > > > > > labeling volume... > > > > > > renormalizing by structure alignment.... > > > > > > renormalizing input #0 > > > > > > gca peak = 0.15151 (27) > > > > > > mri peak = 0.15062 (23) > > > > > > Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, > > > > > > overlap=0.484) > > > > > > Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, > > peak > > > > = > > > > > > 22), gca=22.3 > > > > > > gca peak = 0.14982 (20) > > > > > > mri peak = 0.16025 (24) > > > > > > Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 > > voxels, > > > > > > overlap=0.766) > > > > > > Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 > > voxels, > > > > peak = > > > > > > 20), gca=20.5 > > > > > > gca peak = 0.28003 (97) > > > > > > mri peak = 0.11295 (106) > > > > > > Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, > > > > overlap=0.353) > > > > > > Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, peak = > > 104), > > > > > > gca=104.3 > > > > > > gca peak = 0.18160 (96) > > > > > > mri peak = 0.12433 (104) > > > > > > Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, > > > > overlap=0.638) > > > > > > Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, peak = > > 101), > > > > > > gca=100.8 > > > > > > gca peak = 0.27536 (62) > > > > > > mri peak = 0.08252 (69) > > > > > > Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, > > > > > > overlap=0.818) > > > > > > Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, peak > > = > > > > 68), > > > > > > gca=68.2 > > > > > > gca peak = 0.32745 (63) > > > > > > mri peak = 0.07934 (66) > > > > > > Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, > > > > > > overlap=1.000) > > > > > > Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, peak > > = > > > > 65), > > > > > > gca=64.6 > > > > > > gca peak = 0.08597 (105) > > > > > > mri peak = 0.06861 (109) > > > > > > Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979 > > > > voxels, > > > > > > overlap=0.744) > > > > > > Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979 > > > > voxels, > > > > > > peak = 108), gca=107.6 > > > > > > gca peak = 0.09209 (106) > > > > > > mri peak = 0.07113 (103) > > > > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 > > voxels, > > > > > > overlap=0.820) > > > > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 > > voxels, > > > > > > peak = 106), gca=106.0 > > > > > > gca peak = 0.07826 (63) > > > > > > mri peak = 0.02785 (72) > > > > > > Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, > > > > > > overlap=0.547) > > > > > > Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, > > peak > > > > = > > > > > > 71), gca=70.9 > > > > > > gca peak = 0.08598 (64) > > > > > > mri peak = 0.02894 (68) > > > > > > Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels, > > > > > > overlap=0.642) > > > > > > Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels, > > > > peak = > > > > > > 69), gca=68.8 > > > > > > gca peak = 0.24164 (71) > > > > > > mri peak = 0.13663 (85) > > > > > > Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, > > > > overlap=0.000) > > > > > > Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, peak = > > 82), > > > > > > gca=81.7 > > > > > > gca peak = 0.18227 (75) > > > > > > mri peak = 0.14739 (80) > > > > > > Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, > > > > overlap=0.988) > > > > > > Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, peak = > > 77), > > > > > > gca=76.9 > > > > > > gca peak = 0.10629 (62) > > > > > > mri peak = 0.05203 (64) > > > > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, > > > > > > overlap=0.948) > > > > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, > > > > peak = > > > > > > 64), gca=63.5 > > > > > > gca peak = 0.11668 (59) > > > > > > mri peak = 0.05041 (65) > > > > > > Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 > > voxels, > > > > > > overlap=0.926) > > > > > > Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 > > voxels, > > > > peak > > > > > > = 63), gca=63.4 > > > > > > gca peak = 0.17849 (88) > > > > > > mri peak = 0.09573 (95) > > > > > > Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309 > > > > voxels, > > > > > > overlap=0.601) > > > > > > Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309 > > > > voxels, > > > > > > peak = 95), gca=94.6 > > > > > > gca peak = 0.16819 (86) > > > > > > mri peak = 0.10076 (95) > > > > > > Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881 > > > > voxels, > > > > > > overlap=0.590) > > > > > > Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881 > > > > voxels, > > > > > > peak = 92), gca=92.5 > > > > > > gca peak = 0.41688 (64) > > > > > > mri peak = 0.07820 (67) > > > > > > Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, > > > > overlap=1.000) > > > > > > Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, peak = > > 66), > > > > > > gca=65.6 > > > > > > gca peak = 0.42394 (62) > > > > > > mri peak = 0.10919 (71) > > > > > > Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, > > > > overlap=0.434) > > > > > > Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, peak = > > 70), > > > > > > gca=69.8 > > > > > > gca peak = 0.10041 (96) > > > > > > mri peak = 0.07146 (97) > > > > > > Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, > > > > > > overlap=0.910) > > > > > > Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, > > peak > > > > = > > > > > > 98), gca=98.4 > > > > > > gca peak = 0.13978 (88) > > > > > > mri peak = 0.06159 (103) > > > > > > Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, > > > > > > overlap=0.376) > > > > > > Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, > > peak > > > > = > > > > > > 99), gca=99.0 > > > > > > gca peak = 0.08514 (81) > > > > > > mri peak = 0.06222 (85) > > > > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, > > > > overlap=0.964) > > > > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = > > 81), > > > > > > gca=81.0 > > > > > > gca peak = 0.09624 (82) > > > > > > mri peak = 0.09383 (84) > > > > > > Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, > > > > overlap=0.815) > > > > > > Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, peak = > > 84), > > > > > > gca=84.0 > > > > > > gca peak = 0.07543 (88) > > > > > > mri peak = 0.05306 (86) > > > > > > Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, > > overlap=0.765) > > > > > > Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, peak = > > 92), > > > > > > gca=92.4 > > > > > > gca peak = 0.12757 (95) > > > > > > mri peak = 0.05862 (107) > > > > > > Right_VentralDC: unreasonable value (111.6/107.0), not in range [80, > > > > 110] - > > > > > > rejecting > > > > > > gca peak = 0.17004 (92) > > > > > > mri peak = 0.06574 (111) > > > > > > Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, > > 110] > > > > - > > > > > > rejecting > > > > > > gca peak = 0.21361 (36) > > > > > > mri peak = 0.12619 (24) > > > > > > Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, > > > > overlap=0.000) > > > > > > Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, peak = > > 25), > > > > > > gca=25.2 > > > > > > gca peak = 0.26069 (23) > > > > > > mri peak = 0.16285 (24) > > > > > > Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, > > > > overlap=0.640) > > > > > > Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, peak = > > > > 21), > > > > > > gca=20.7 > > > > > > gca peak Unknown = 0.94427 ( 0) > > > > > > gca peak Left_Inf_Lat_Vent = 0.31795 (35) > > > > > > gca peak CSF = 0.14367 (38) > > > > > > gca peak Left_Accumbens_area = 0.57033 (70) > > > > > > gca peak Left_VentralDC = 0.17004 (92) > > > > > > gca peak Left_undetermined = 1.00000 (35) > > > > > > gca peak Left_vessel = 0.65201 (62) > > > > > > gca peak Left_choroid_plexus = 0.09084 (48) > > > > > > gca peak Right_Inf_Lat_Vent = 0.31129 (32) > > > > > > gca peak Right_Accumbens_area = 0.30219 (72) > > > > > > gca peak Right_VentralDC = 0.12757 (95) > > > > > > gca peak Right_vessel = 0.83418 (60) > > > > > > gca peak Right_choroid_plexus = 0.10189 (48) > > > > > > gca peak Fifth_Ventricle = 0.72939 (42) > > > > > > gca peak WM_hypointensities = 0.14821 (82) > > > > > > gca peak non_WM_hypointensities = 0.10354 (53) > > > > > > gca peak Optic_Chiasm = 0.34849 (76) > > > > > > not using caudate to estimate GM means > > > > > > estimating mean gm scale to be 1.08 x + 0.0 > > > > > > estimating mean wm scale to be 1.01 x + 0.0 > > > > > > estimating mean csf scale to be 0.86 x + 0.0 > > > > > > Left_Pallidum too bright - rescaling by 1.007 (from 1.050) to 101.5 > > (was > > > > > > 100.8) > > > > > > Right_Pallidum too bright - rescaling by 0.973 (from 1.075) to 101.5 > > > > (was > > > > > > 104.3) > > > > > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt > > > > > > renormalizing by structure alignment.... > > > > > > renormalizing input #0 > > > > > > gca peak = 0.14515 (23) > > > > > > mri peak = 0.15062 (23) > > > > > > Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, > > > > > > overlap=0.897) > > > > > > Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, > > peak > > > > = > > > > > > 24), gca=23.6 > > > > > > gca peak = 0.19392 (21) > > > > > > mri peak = 0.16025 (24) > > > > > > Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 > > voxels, > > > > > > overlap=0.745) > > > > > > Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 > > voxels, > > > > peak = > > > > > > 21), gca=21.0 > > > > > > gca peak = 0.25607 (102) > > > > > > mri peak = 0.11295 (106) > > > > > > Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, > > > > overlap=1.000) > > > > > > Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, peak = > > 105), > > > > > > gca=104.5 > > > > > > gca peak = 0.17462 (103) > > > > > > mri peak = 0.12433 (104) > > > > > > Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, > > > > overlap=0.999) > > > > > > Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, peak = > > 103), > > > > > > gca=103.0 > > > > > > gca peak = 0.24759 (68) > > > > > > mri peak = 0.08252 (69) > > > > > > Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, > > > > > > overlap=0.999) > > > > > > Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, peak > > = > > > > 68), > > > > > > gca=68.0 > > > > > > gca peak = 0.28061 (65) > > > > > > mri peak = 0.07934 (66) > > > > > > Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, > > > > > > overlap=0.999) > > > > > > Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, peak > > = > > > > 62), > > > > > > gca=61.8 > > > > > > gca peak = 0.08360 (108) > > > > > > mri peak = 0.06861 (109) > > > > > > Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979 > > > > voxels, > > > > > > overlap=0.831) > > > > > > Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979 > > > > voxels, > > > > > > peak = 108), gca=108.0 > > > > > > gca peak = 0.09206 (106) > > > > > > mri peak = 0.07113 (103) > > > > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 > > voxels, > > > > > > overlap=0.820) > > > > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 > > voxels, > > > > > > peak = 106), gca=106.0 > > > > > > gca peak = 0.06916 (71) > > > > > > mri peak = 0.02785 (72) > > > > > > Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, > > > > > > overlap=0.733) > > > > > > Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, > > peak > > > > = > > > > > > 69), gca=69.2 > > > > > > gca peak = 0.08227 (69) > > > > > > mri peak = 0.02894 (68) > > > > > > Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels, > > > > > > overlap=0.734) > > > > > > Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels, > > > > peak = > > > > > > 69), gca=69.0 > > > > > > gca peak = 0.22329 (81) > > > > > > mri peak = 0.13663 (85) > > > > > > Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, > > > > overlap=1.000) > > > > > > Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, peak = > > 81), > > > > > > gca=81.0 > > > > > > gca peak = 0.18180 (77) > > > > > > mri peak = 0.14739 (80) > > > > > > Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, > > > > overlap=0.937) > > > > > > Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, peak = > > 77), > > > > > > gca=77.0 > > > > > > gca peak = 0.10419 (63) > > > > > > mri peak = 0.05203 (64) > > > > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, > > > > > > overlap=0.982) > > > > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, > > > > peak = > > > > > > 65), gca=64.6 > > > > > > gca peak = 0.12084 (64) > > > > > > mri peak = 0.05041 (65) > > > > > > Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 > > voxels, > > > > > > overlap=0.985) > > > > > > Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 > > voxels, > > > > peak > > > > > > = 62), gca=62.4 > > > > > > gca peak = 0.17137 (94) > > > > > > mri peak = 0.09573 (95) > > > > > > Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309 > > > > voxels, > > > > > > overlap=0.978) > > > > > > Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309 > > > > voxels, > > > > > > peak = 94), gca=94.0 > > > > > > gca peak = 0.15715 (93) > > > > > > mri peak = 0.10076 (95) > > > > > > Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881 > > > > voxels, > > > > > > overlap=0.983) > > > > > > Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881 > > > > voxels, > > > > > > peak = 93), gca=93.0 > > > > > > gca peak = 0.32238 (65) > > > > > > mri peak = 0.07820 (67) > > > > > > Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, > > > > overlap=1.000) > > > > > > Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, peak = > > 65), > > > > > > gca=65.0 > > > > > > gca peak = 0.49832 (70) > > > > > > mri peak = 0.10919 (71) > > > > > > Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, > > > > overlap=1.000) > > > > > > Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, peak = > > 70), > > > > > > gca=70.0 > > > > > > gca peak = 0.10606 (98) > > > > > > mri peak = 0.07146 (97) > > > > > > Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, > > > > > > overlap=0.901) > > > > > > Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, > > peak > > > > = > > > > > > 98), gca=98.0 > > > > > > gca peak = 0.12505 (99) > > > > > > mri peak = 0.06159 (103) > > > > > > Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, > > > > > > overlap=0.961) > > > > > > Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, > > peak > > > > = > > > > > > 99), gca=99.0 > > > > > > gca peak = 0.08514 (81) > > > > > > mri peak = 0.06222 (85) > > > > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, > > > > overlap=0.964) > > > > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = > > 81), > > > > > > gca=81.0 > > > > > > gca peak = 0.09838 (78) > > > > > > mri peak = 0.09383 (84) > > > > > > Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, > > > > overlap=0.982) > > > > > > Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, peak = > > 78), > > > > > > gca=78.0 > > > > > > gca peak = 0.07177 (90) > > > > > > mri peak = 0.05306 (86) > > > > > > Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, > > overlap=0.860) > > > > > > Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, peak = > > 92), > > > > > > gca=92.2 > > > > > > gca peak = 0.13316 (95) > > > > > > mri peak = 0.05862 (107) > > > > > > Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, > > > > overlap=0.010) > > > > > > Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, peak = > > > > 109), > > > > > > gca=109.2 > > > > > > gca peak = 0.16834 (92) > > > > > > mri peak = 0.06574 (111) > > > > > > Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, > > 110] > > > > - > > > > > > rejecting > > > > > > gca peak = 0.25342 (25) > > > > > > mri peak = 0.12619 (24) > > > > > > Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, > > > > overlap=0.998) > > > > > > Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, peak = > > 25), > > > > > > gca=25.0 > > > > > > gca peak = 0.20850 (21) > > > > > > mri peak = 0.16285 (24) > > > > > > Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, > > > > overlap=0.808) > > > > > > Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, peak = > > > > 22), > > > > > > gca=21.5 > > > > > > gca peak Unknown = 0.94427 ( 0) > > > > > > gca peak Left_Inf_Lat_Vent = 0.26363 (36) > > > > > > gca peak CSF = 0.17919 (33) > > > > > > gca peak Left_Accumbens_area = 0.40223 (72) > > > > > > gca peak Left_VentralDC = 0.16834 (92) > > > > > > gca peak Left_undetermined = 1.00000 (35) > > > > > > gca peak Left_vessel = 0.63670 (62) > > > > > > gca peak Left_choroid_plexus = 0.09084 (48) > > > > > > gca peak Right_Inf_Lat_Vent = 0.29122 (35) > > > > > > gca peak Right_Accumbens_area = 0.25605 (83) > > > > > > gca peak Right_vessel = 0.83418 (60) > > > > > > gca peak Right_choroid_plexus = 0.10189 (48) > > > > > > gca peak Fifth_Ventricle = 0.81716 (36) > > > > > > gca peak WM_hypointensities = 0.15216 (83) > > > > > > gca peak non_WM_hypointensities = 0.09346 (54) > > > > > > gca peak Optic_Chiasm = 0.34849 (76) > > > > > > not using caudate to estimate GM means > > > > > > setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 > > > > > > estimating mean gm scale to be 0.99 x + 0.0 > > > > > > estimating mean wm scale to be 1.00 x + 0.0 > > > > > > estimating mean csf scale to be 1.01 x + 0.0 > > > > > > Left_Pallidum too bright - rescaling by 0.987 (from 1.000) to 101.6 > > (was > > > > > > 103.0) > > > > > > Right_Pallidum too bright - rescaling by 0.972 (from 1.025) to 101.6 > > > > (was > > > > > > 104.5) > > > > > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > >

1 0

mri_ca_label problem
by paul horton 19 Feb '13

19 Feb '13

Hi guys,I am wondering if you can help me.I have run command: mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z $FREESURFER_HOME/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz, on a 3T MPRAGE subject but it fails: i.e. it stops after the 'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt' line and does not save the file: aseg.auto_noCCseg.mgz. However, it does save the file: aseg.auto_noCCseg.label_intensities.txt. I have tried it several times and it stops at the same place. I have also tried recon-all, where it jumps from 'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt' to the command 'mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz', where, again, the file: aseg.auto_noCCseg.mgz is not saved. I am using freesurfer version 4.5.0. So is there a way I can solve this problem. Many ThanksPaulPs, i have attached the output log below################renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.15062 (23) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, overlap=0.484) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, peak = 22), gca=22.3 gca peak = 0.14982 (20) mri peak = 0.16025 (24) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 voxels, overlap=0.766) Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 voxels, peak = 20), gca=20.5 gca peak = 0.28003 (97) mri peak = 0.11295 (106) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, overlap=0.353) Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, peak = 104), gca=104.3 gca peak = 0.18160 (96) mri peak = 0.12433 (104) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, overlap=0.638) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, peak = 101), gca=100.8 gca peak = 0.27536 (62) mri peak = 0.08252 (69) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, overlap=0.818) Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, peak = 68), gca=68.2 gca peak = 0.32745 (63) mri peak = 0.07934 (66) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, peak = 65), gca=64.6 gca peak = 0.08597 (105) mri peak = 0.06861 (109) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979 voxels, overlap=0.744) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.07113 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, overlap=0.820) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, peak = 106), gca=106.0 gca peak = 0.07826 (63) mri peak = 0.02785 (72) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, overlap=0.547) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, peak = 71), gca=70.9 gca peak = 0.08598 (64) mri peak = 0.02894 (68) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels, overlap=0.642) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels, peak = 69), gca=68.8 gca peak = 0.24164 (71) mri peak = 0.13663 (85) Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, overlap=0.000) Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, peak = 82), gca=81.7 gca peak = 0.18227 (75) mri peak = 0.14739 (80) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, overlap=0.988) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, peak = 77), gca=76.9 gca peak = 0.10629 (62) mri peak = 0.05203 (64) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, overlap=0.948) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, peak = 64), gca=63.5 gca peak = 0.11668 (59) mri peak = 0.05041 (65) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 voxels, overlap=0.926) Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 voxels, peak = 63), gca=63.4 gca peak = 0.17849 (88) mri peak = 0.09573 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309 voxels, overlap=0.601) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309 voxels, peak = 95), gca=94.6 gca peak = 0.16819 (86) mri peak = 0.10076 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881 voxels, overlap=0.590) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881 voxels, peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.07820 (67) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, peak = 66), gca=65.6 gca peak = 0.42394 (62) mri peak = 0.10919 (71) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, overlap=0.434) Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, peak = 70), gca=69.8 gca peak = 0.10041 (96) mri peak = 0.07146 (97) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, overlap=0.910) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, peak = 98), gca=98.4 gca peak = 0.13978 (88) mri peak = 0.06159 (103) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, overlap=0.376) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, peak = 99), gca=99.0 gca peak = 0.08514 (81) mri peak = 0.06222 (85) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, overlap=0.964) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = 81), gca=81.0 gca peak = 0.09624 (82) mri peak = 0.09383 (84) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, overlap=0.815) Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, peak = 84), gca=84.0 gca peak = 0.07543 (88) mri peak = 0.05306 (86) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.05862 (107) Right_VentralDC: unreasonable value (111.6/107.0), not in range [80, 110] - rejecting gca peak = 0.17004 (92) mri peak = 0.06574 (111) Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110] - rejecting gca peak = 0.21361 (36) mri peak = 0.12619 (24) Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, overlap=0.000) Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, peak = 25), gca=25.2 gca peak = 0.26069 (23) mri peak = 0.16285 (24) Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, overlap=0.640) Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, peak = 21), gca=20.7 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_VentralDC = 0.17004 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_VentralDC = 0.12757 (95) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.08 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.86 x + 0.0 Left_Pallidum too bright - rescaling by 1.007 (from 1.050) to 101.5 (was 100.8) Right_Pallidum too bright - rescaling by 0.973 (from 1.075) to 101.5 (was 104.3) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14515 (23) mri peak = 0.15062 (23) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, overlap=0.897) Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, peak = 24), gca=23.6 gca peak = 0.19392 (21) mri peak = 0.16025 (24) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 voxels, overlap=0.745) Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 voxels, peak = 21), gca=21.0 gca peak = 0.25607 (102) mri peak = 0.11295 (106) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, overlap=1.000) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, peak = 105), gca=104.5 gca peak = 0.17462 (103) mri peak = 0.12433 (104) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, overlap=0.999) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, peak = 103), gca=103.0 gca peak = 0.24759 (68) mri peak = 0.08252 (69) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, peak = 68), gca=68.0 gca peak = 0.28061 (65) mri peak = 0.07934 (66) Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, overlap=0.999) Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, peak = 62), gca=61.8 gca peak = 0.08360 (108) mri peak = 0.06861 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979 voxels, overlap=0.831) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979 voxels, peak = 108), gca=108.0 gca peak = 0.09206 (106) mri peak = 0.07113 (103) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, overlap=0.820) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels, peak = 106), gca=106.0 gca peak = 0.06916 (71) mri peak = 0.02785 (72) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, overlap=0.733) Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, peak = 69), gca=69.2 gca peak = 0.08227 (69) mri peak = 0.02894 (68) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels, overlap=0.734) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels, peak = 69), gca=69.0 gca peak = 0.22329 (81) mri peak = 0.13663 (85) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, peak = 81), gca=81.0 gca peak = 0.18180 (77) mri peak = 0.14739 (80) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, overlap=0.937) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, peak = 77), gca=77.0 gca peak = 0.10419 (63) mri peak = 0.05203 (64) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, overlap=0.982) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels, peak = 65), gca=64.6 gca peak = 0.12084 (64) mri peak = 0.05041 (65) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 voxels, overlap=0.985) Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 voxels, peak = 62), gca=62.4 gca peak = 0.17137 (94) mri peak = 0.09573 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309 voxels, overlap=0.978) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309 voxels, peak = 94), gca=94.0 gca peak = 0.15715 (93) mri peak = 0.10076 (95) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881 voxels, overlap=0.983) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881 voxels, peak = 93), gca=93.0 gca peak = 0.32238 (65) mri peak = 0.07820 (67) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, peak = 65), gca=65.0 gca peak = 0.49832 (70) mri peak = 0.10919 (71) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, overlap=1.000) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, peak = 70), gca=70.0 gca peak = 0.10606 (98) mri peak = 0.07146 (97) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, overlap=0.901) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, peak = 98), gca=98.0 gca peak = 0.12505 (99) mri peak = 0.06159 (103) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, overlap=0.961) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, peak = 99), gca=99.0 gca peak = 0.08514 (81) mri peak = 0.06222 (85) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, overlap=0.964) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = 81), gca=81.0 gca peak = 0.09838 (78) mri peak = 0.09383 (84) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, overlap=0.982) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, peak = 78), gca=78.0 gca peak = 0.07177 (90) mri peak = 0.05306 (86) Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, overlap=0.860) Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, peak = 92), gca=92.2 gca peak = 0.13316 (95) mri peak = 0.05862 (107) Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, overlap=0.010) Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, peak = 109), gca=109.2 gca peak = 0.16834 (92) mri peak = 0.06574 (111) Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110] - rejecting gca peak = 0.25342 (25) mri peak = 0.12619 (24) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, overlap=0.998) Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, peak = 25), gca=25.0 gca peak = 0.20850 (21) mri peak = 0.16285 (24) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, overlap=0.808) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, peak = 22), gca=21.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26363 (36) gca peak CSF = 0.17919 (33) gca peak Left_Accumbens_area = 0.40223 (72) gca peak Left_VentralDC = 0.16834 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63670 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.29122 (35) gca peak Right_Accumbens_area = 0.25605 (83) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.81716 (36) gca peak WM_hypointensities = 0.15216 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.01 x + 0.0 Left_Pallidum too bright - rescaling by 0.987 (from 1.000) to 101.6 (was 103.0) Right_Pallidum too bright - rescaling by 0.972 (from 1.025) to 101.6 (was 104.5) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt

2 4

gray matter surface
by Eric Cunningham 19 Feb '13

19 Feb '13

hello freesurfer experts, attached is an image drawn from the tutorial page. http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits i have circled 3 examples of what i am asking about sometimes the gray matter surface (the red line) appears to include an area of membrane or something else that isn't brain. will this adversely affect the any of the measures in the region? what, if anything, should be done about it? thank you, -eric cunningham

2 3

make_average_subject error
by Kristina Nalbandian 19 Feb '13

19 Feb '13

Hello, I am trying to run Surface Group Analysis with Qdec, but am stuck on the "make_average_subject" step. I have run this command on four subjects in my virtual machine and everything is fine. However, I have 13 subjects and there is not enough room in the virtual machine for them. I have moved my subjects to the C drive after running all the appropriate commands. I set the environment to the C drive from the virtual machine, but the make_average_subject does not complete. This is the error: writing update template with 13 subjects to lh.reg.template.tif... TIFFLinkDirectory: Error fetching directory count. TIFFWriteScanLine: lh.reg.template.tif: In place update to compressed TIFF images not supported.. TIFFWrite: TiffWriteScanLine returned error curvature mean = 0.003, std = 0.572 curvature mean = -0.081, std = 1.818 Protocol error Segmentation fault Error:make_average_surface In addition, since I am out of space, is there any way to increase the size of virtual machine disk image? We are using the Xubuntu Virtual Box as recommended on the FreeSurfer installation webpage. Thank you in advance, Kristina

1 0

Re: [Freesurfer] Freesurfer Digest, Vol 108, Issue 12
by Rashmi Singh 19 Feb '13

19 Feb '13

Hi Melonee, Please record my off Campus work hrs this morning at OU. IN 9:30 AM and out 1:10 PM. I have logged into LIBR when I entered so that should be in records. Let me know if you may have any question. Thanks, Rashmi On 2/11/13 8:39 AM, "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: >Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > >To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > >You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Freesurfer digest..." > > >Today's Topics: > > 1. A question regarding a "nii-read" error I get when running a > script for FA values output (Rotem Saar) > 2. re conversion (Linn Mittlestein) > 3. LME matlab toolbox - smooth error (Yolanda Vives) > 4. thickness and area in aparc.stats and mri_glmfit (Wolff Schlotz) > 5. trac-all -path error (stdp82(a)virgilio.it) > 6. R: trac-all -path error (stdp82(a)virgilio.it) > 7. Re: re conversion (Bruce Fischl) > 8. Antw: Re: thickness and area in aparc.stats and mri_glmfit > (Wolff Schlotz) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Mon, 11 Feb 2013 11:50:15 +0200 >From: Rotem Saar <saar.rotem(a)gmail.com> >Subject: [Freesurfer] A question regarding a "nii-read" error I get > when running a script for FA values output >To: freesurfer(a)nmr.mgh.harvard.edu >Message-ID: > <CAMjFEmY3_B2G7VVqeGTcptYmS4cdAAdgbka6UTR=-1W_p=G7JQ(a)mail.gmail.com> >Content-Type: text/plain; charset="iso-8859-1" > >Hi, > >My name is Rotem, I'm a PhD. student and recently started to work with >freesurfer software (freesurfer-Linux-centos4-stable-pub-v5.1.0). QUESTION >For several weeks, I have been trying to operate a script for FA values, >with no success, and would really appreciate your help with shading some >light regarding the problem and it's solution. >I have a data set, after an anatomical segmentation (file is attached, >named "Anatomical segmentation for fs", this is the script I'm using for >brain anatomical segmentation). What I'm trying to run now is the DTI >script, in which I run commands that at least for my understanding spouse >to give me at the end a table with all the FA values for each brain region >(ROI). The script I'm using to do this is attached and called >"DTI_RUN_NEW_FOR_FS". >*After running phase 5*, in which a mask file should be created (indeed I >have checked and the file is created in the same folder it should be): > >fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_mask >/usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii >/usr/local/freesurfer/subjects/FOLDER_NAME/mri/brainmask.mgz >/usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii >DoAbs = 0 >Found 16777216 voxels in mask >Writing masked volume to >/usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii...d >one. > >*I run phase 6, and then get the following error message:* > >fmri4-P67A-D3-B3:/usr/local/freesurfer/subjects> mri_segstats --seg >/usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab >$FREESURFER_HOME/FreeSurferColorLUT.txt --i >usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii >--sum >/usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME > >$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ >cwd >cmdline mri_segstats --seg >/usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz --ctab >/usr/local/freesurfer/FreeSurferColorLUT.txt --i >usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.nii --sum >/usr/local/freesurfer/subjects/FOLDER_NAME/stats/all_stats_fa_FOLDER_NAME >sysname Linux >hostname fmri4-P67A-D3-B3 >machine i686 >user fmri4 >Loading /usr/local/freesurfer/subjects/FOLDER_NAME/mri/wmparc.mgz >Loading >usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii >niiRead(): error opening file >usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii >ERROR: loading >usr/local/freesurfer/subjects/FOLDER_NAME/DTI/fa_FOLDER_NAME.mask.nii > >I think the problem is between phase 5 and 6, and is related to file >format >(.nii) but don't have a hint regarding what can I do to solve this:( Can >someone please write me the correct code line ? > >I would really appreciate your kind help since I run out of ideas for >solutions. > >Thanks in advance, > >Rotem >

1 0

extracting hippocampus volume using asegstats2table
by Mojdeh Zamyadi 19 Feb '13

19 Feb '13

Hi all, I have a question about the volume of the hippocampus. I want to know why when I convert the left and right hippocampus from mgz to nii (after extracting the labels from aseg.mgz) the number of voxels in the masks don't match the number I get from the asegstats2table (using --segno 17 and 53)? below are some examples numbers, the first column is the hippocampal volume using asegstats2table, and 2nd column is the volume as extracted from aseg.mgz and then converted to nii: 5157 5368 4821 4968 4858 5075 5678 5716 4970 5068

2 1

badly generated surfaces
by Deirdre O Shea 19 Feb '13

19 Feb '13

Dear FreeSurfer community, After running FreeSurfer on almost a hundred subjects, I have encountered just two that have strange surface reconstructions. I have re-ran them from scratch hoping it would rectify this problem but to no avail. I have not done anything different with these subjects and the rest turned out okay. I have attached an image to show you what I mean. Any suggestions about why this happens and how it can be fixed would be great! Thanks in advance, Deirdre

3 3

Re: [Freesurfer] Fwd: trac-all problem
by ayendiki＠nmr.mgh.harvard.edu 18 Feb '13

18 Feb '13

The memory error was in the -path part, that's what you should try rerunning. What you downloaded will have no effect on bedpostx itself. > i just downloaded dmri_5.1_snow_leopard.tar.gz: from that web page and > installed the new version of the dmri file in the freessurfer /boin > directory > I'm rerunning trac-all -bedp > thanks for your help > Jon > > ----- Original Message ----- > From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > To: "Jon Wieser" <wieser(a)uwm.edu> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Monday, February 18, 2013 5:07:38 PM > Subject: Re: [Freesurfer] Fwd: trac-all problem > > > Hi Jon - There was an updated build of the tracula executables > specifically for macos users that was posted a while back. See the tracula > wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula > > Better yet, wait for 5.2 to be released later this week! > > a.y > > On Mon, 18 Feb 2013, Jon Wieser wrote: > >> >> I'm using freesurfer 5.1 >> >> Jon >> >> ----- Original Message ----- >> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >> To: "Jon Wieser" <wieser(a)uwm.edu> >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Sent: Monday, February 18, 2013 4:41:15 PM >> Subject: Re: [Freesurfer] Fwd: trac-all problem >> >> >> Hi Jon - So the files are there but there's to be a memory allocation >> problem. Are you using the updated mac build from the tracula wiki page >> or >> the one that was originally released with freesurfer 5.1? >> >> a.y >> >> On Mon, 18 Feb 2013, Jon Wieser wrote: >> >>> Hi , >>> >>> i have the following files in my dmri.bedpostX directory >>> >>> >>> bvals dyads2.nii.gz >>> mean_f2samples.nii.gz merged_f1samples.nii.gz >>> merged_th2samples.nii.gz >>> bvecs dyads2_dispersion.nii.gz >>> mean_ph1samples.nii.gz merged_f2samples.nii.gz monitor >>> commands.txt logs >>> mean_ph2samples.nii.gz merged_ph1samples.nii.gz >>> nodif_brain_mask.nii.gz >>> dyads1.nii.gz mean_dsamples.nii.gz >>> mean_th1samples.nii.gz merged_ph2samples.nii.gz xfms >>> dyads1_dispersion.nii.gz mean_f1samples.nii.gz >>> mean_th2samples.nii.gz merged_th1samples.nii.gz >>> >>> Jon >>> >>> >>> ----- Original Message ----- >>> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>> To: "Jon Wieser" <wieser(a)uwm.edu> >>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>> Sent: Monday, February 18, 2013 3:51:40 PM >>> Subject: Re: [Freesurfer] Fwd: trac-all problem >>> >>> >>> Hi Jon - There's a list of all bedpostx output files here: >>> http://fsl.fmrib.ox.ac.uk/fsl/fsl4.0/fdt/fdt_bedpostx.html >>> >>> Do you see these files in the dmri.bedpostX directory? >>> >>> a.y >>> >>> On Mon, 18 Feb 2013, Jon Wieser wrote: >>> >>>> >>>> >>>> >>>> >>>> I ran trac-all -bedp -c /Studies/MJMRI/DTI/dmrirc_single_subject >>>> the end of the output was: >>>> >>>> >>>> 52 slices processed >>>> 52 slices processed >>>> 53 slices processed >>>> 53 slices processed >>>> 54 slices processed >>>> 54 slices processed >>>> 55 slices processed >>>> 55 slices processed >>>> 56 slices processed >>>> 57 slices processed >>>> 58 slices processed >>>> Queuing post processing stage >>>> 60 slices processed >>>> All slices processed >>>> /Applications/freesurfer/bin/bedpostx_seychelles: line 281: kill: >>>> (35687) - No such process >>>> >>>> >>>> >>>> is this normal? >>>> >>>> >>>> >>>> then I ran trac-all -path -c /Studies/MJMRI/DTI/dmrirc_single_subject >>>> >>>> it ended in an error >>>> >>>> Here's the last part of the trac-all -path output: >>>> >>>> Neighbor aseg label ID list: >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cst_AS_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cst_AS_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ilf_AS_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.unc_AS_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.unc_AS_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fmajor_PP_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fminor_PP_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.atr_PP_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.atr_PP_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cab_PP_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cab_PP_avg23_mni_flt_fsnnids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/l > h >> . >>> ccg_PP_avg23_mni_flt_fsnnids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ccg_PP_avg23_mni_flt_fsnnids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.slfp_PP_avg23_mni_flt_fsnnids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.slfp_PP_avg23_mni_flt_fsnnids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.slft_PP_avg23_mni_flt_fsnnids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.slft_PP_avg23_mni_flt_fsnnids >>>> Local aseg prior: >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cst_AS_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cst_AS_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ilf_AS_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.unc_AS_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.unc_AS_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fmajor_PP_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fminor_PP_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.atr_PP_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.atr_PP_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cab_PP_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cab_PP_avg23_mni_flt_fsprior >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.ccg_PP_av > g >> 2 >>> 3_mni_flt_fsprior >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ccg_PP_avg23_mni_flt_fsprior >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.slfp_PP_avg23_mni_flt_fsprior >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.slfp_PP_avg23_mni_flt_fsprior >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.slft_PP_avg23_mni_flt_fsprior >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.slft_PP_avg23_mni_flt_fsprior >>>> Local aseg label ID list: >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cst_AS_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cst_AS_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.ilf_AS_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ilf_AS_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.unc_AS_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.unc_AS_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fmajor_PP_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/fminor_PP_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.atr_PP_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.atr_PP_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.cab_PP_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.cab_PP_avg23_mni_flt_fsids >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.ccg_PP_avg23_mni_flt_fsid > s >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.ccg_PP_avg23_mni_flt_fsids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.slfp_PP_avg23_mni_flt_fsids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.slfp_PP_avg23_mni_flt_fsids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lh.slft_PP_avg23_mni_flt_fsids >>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/rh.slft_PP_avg23_mni_flt_fsids >>>> Segmentation map: >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/aparc+aseg.nii.gz >>>> Type of aseg prior: 0 >>>> DWI-to-atlas affine registration: >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/xfms/diff2mni.flt.mat >>>> Number of burn-in samples: 200 >>>> Number of post-burn-in samples: 5000 >>>> Keep every: 5-th sample >>>> Update proposal every: 0-th sample >>>> Loading spline control points from >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/lh.cst_AS_avg23_mni_flt_cpts_5.txt >>>> Loading spline mask from >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/aparc+aseg_mask.bbr.nii.gz >>>> Creating output directory >>>> /Studies/MJMRI/MJ0012/freesurfer/dpath/5cpts/priormni/seg14/initmni/regflt/lh.cst_AS_avg23_mni_flt >>>> Loading DWIs from /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz >>>> Loading mask from >>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/aparc+aseg_mask.bbr.nii.gz >>>> Loading BEDPOST parameter samples from >>>> /Studies/MJMRI/MJ0012/freesurfer/dmri.bedpostX >>>> dmri_paths(38479) malloc: *** mmap(size=262144) failed (error code=12) >>>> *** error: can't allocate region >>>> *** set a breakpoint in malloc_error_break to debug >>>> MRIalloc(256, 256, 60): could not allocate 262144 bytes for 1193th >>>> slice >>>> >>>> Cannot allocate memory >>>> Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version >>>> 10.8.0: Tue Jun 7 16:32:41 PDT 2011; >>>> root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 >>>> >>>> trac-paths exited with ERRORS at Mon Feb 18 09:14:48 CST 2013 >>>> >>>> >>>> >>>> >>>> how can I fix this? >>>> Jon >>>> >>>> >>>> >>>> >>>> ----- Original Message ----- >>>> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>> Sent: Thursday, February 14, 2013 1:22:02 PM >>>> Subject: Re: [Freesurfer] trac-all problem >>>> >>>> >>>> Great! >>>> >>>> On Thu, 14 Feb 2013, Jon Wieser wrote: >>>> >>>>> Hi Anastasia, >>>>> >>>>> update on my processing. >>>>> I finished recon-all -autorecon1 ,-autorecon2, and -autorecon3 . >>>>> I finished trac -prep with No errors! >>>>> moving on the Trac-all -bedp >>>>> >>>>> >>>>> thanks! >>>>> Jon >>>>> >>>>> >>>>> ----- Original Message ----- >>>>> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>> Sent: Tuesday, February 12, 2013 3:44:59 PM >>>>> Subject: Re: [Freesurfer] trac-all problem >>>>> >>>>> >>>>> Hi Jon - You'll the aparc+aseg.mgz (cortical parcellation + >>>>> subcortical >>>>> segmentation). The basis of TRACULA is that it uses the underlying >>>>> anatomy >>>>> to reconstruct the tracts. >>>>> >>>>> a.y >>>>> >>>>> On Tue, 12 Feb 2013, Jon Wieser wrote: >>>>> >>>>>> no i have not run recon-all yet on this dataset, >>>>>> do i need to run recon-all with -autorecon1 ,-autorecon2, and >>>>>> -autorecon3 before i analyze the dti data? >>>>>> >>>>>> thanks >>>>>> Jon >>>>>> >>>>>> ----- Original Message ----- >>>>>> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>> Sent: Tuesday, February 12, 2013 3:34:19 PM >>>>>> Subject: Re: [Freesurfer] trac-all problem >>>>>> >>>>>> >>>>>> Hi Jon - Have you run freesurfer (recon-all) on your T1 data? >>>>>> >>>>>> a.y >>>>>> >>>>>> On Tue, 12 Feb 2013, Jon Wieser wrote: >>>>>> >>>>>>> i got past the problem with the bvesc, and bvals, >>>>>>> >>>>>>> >>>>>>> my current output has a new problem: >>>>>>> here's the last part of the output. >>>>>>> >>>>>>> >>>>>>> >>>>>>> #@# Tensor fit Tue Feb 12 15:24:51 CST 2013 >>>>>>> dtifit -k /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz -m >>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/diff/lowb_brain_mask.nii.gz >>>>>>> -r /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs -b >>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals -o >>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dtifit >>>>>>> 0 256 0 256 0 60 >>>>>>> 0 slices processed >>>>>>> 1 slices processed >>>>>>> 2 slices processed >>>>>>> 3 slices processed >>>>>>> 4 slices processed >>>>>>> 5 slices processed >>>>>>> 6 slices processed >>>>>>> 7 slices processed >>>>>>> 8 slices processed >>>>>>> 9 slices processed >>>>>>> 10 slices processed >>>>>>> 11 slices processed >>>>>>> 12 slices processed >>>>>>> 13 slices processed >>>>>>> 14 slices processed >>>>>>> 15 slices processed >>>>>>> 16 slices processed >>>>>>> 17 slices processed >>>>>>> 18 slices processed >>>>>>> 19 slices processed >>>>>>> 20 slices processed >>>>>>> 21 slices processed >>>>>>> 22 slices processed >>>>>>> 23 slices processed >>>>>>> 24 slices processed >>>>>>> 25 slices processed >>>>>>> 26 slices processed >>>>>>> 27 slices processed >>>>>>> 28 slices processed >>>>>>> 29 slices processed >>>>>>> 30 slices processed >>>>>>> 31 slices processed >>>>>>> 32 slices processed >>>>>>> 33 slices processed >>>>>>> 34 slices processed >>>>>>> 35 slices processed >>>>>>> 36 slices processed >>>>>>> 37 slices processed >>>>>>> 38 slices processed >>>>>>> 39 slices processed >>>>>>> 40 slices processed >>>>>>> 41 slices processed >>>>>>> 42 slices processed >>>>>>> 43 slices processed >>>>>>> 44 slices processed >>>>>>> 45 slices processed >>>>>>> 46 slices processed >>>>>>> 47 slices processed >>>>>>> 48 slices processed >>>>>>> 49 slices processed >>>>>>> 50 slices processed >>>>>>> 51 slices processed >>>>>>> 52 slices processed >>>>>>> 53 slices processed >>>>>>> 54 slices processed >>>>>>> 55 slices processed >>>>>>> 56 slices processed >>>>>>> 57 slices processed >>>>>>> 58 slices processed >>>>>>> 59 slices processed >>>>>>> #------------------------------------- >>>>>>> #@# Priors Tue Feb 12 15:26:36 CST 2013 >>>>>>> /Applications/freesurfer/bin/dmri_train --outdir >>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni --out >>>>>>> lh.cst_AS_avg23_mni_flt rh.cst_AS_avg23_mni_flt >>>>>>> lh.ilf_AS_avg23_mni_flt rh.ilf_AS_avg23_mni_flt >>>>>>> lh.unc_AS_avg23_mni_flt rh.unc_AS_avg23_mni_flt >>>>>>> fmajor_PP_avg23_mni_flt fminor_PP_avg23_mni_flt >>>>>>> lh.atr_PP_avg23_mni_flt rh.atr_PP_avg23_mni_flt >>>>>>> lh.cab_PP_avg23_mni_flt rh.cab_PP_avg23_mni_flt >>>>>>> lh.ccg_PP_avg23_mni_flt rh.ccg_PP_avg23_mni_flt >>>>>>> lh.slfp_PP_avg23_mni_flt rh.slfp_PP_avg23_mni_flt >>>>>>> lh.slft_PP_avg23_mni_flt rh.slft_PP_avg23_mni_flt --slist >>>>>>> /tmp/subj23.freesurfer.92196.txt --trk dlabel/mni/lh.cst_AS.flt.trk >>>>>>> dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk >>>>>>> dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk >>>>>>> dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk >>>>>>> dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk >>>>>>> dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk >>>>>>> dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk >>>>>>> dlabel/mni/rh.ccg_PP.flt > . >> t >>> r >>>> k >>>>>> dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk >>>>>> dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg >>>>>> dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz >>>>>> --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois >>>>>> dlabel/mni/lh.cst_AS_roi1.flt.nii.gz >>>>>> dlabel/mni/lh.cst_AS_roi2.flt.nii.gz >>>>>> dlabel/mni/rh.cst_AS_roi1.flt.nii.gz >>>>>> dlabel/mni/rh.cst_AS_roi2.flt.nii.gz >>>>>> dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz >>>>>> dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz >>>>>> dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz >>>>>> dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz >>>>>> dlabel/mni/lh.unc_AS_roi1.flt.nii.gz >>>>>> dlabel/mni/lh.unc_AS_roi2.flt.nii.gz >>>>>> dlabel/mni/rh.unc_AS_roi1.flt.nii.gz >>>>>> dlabel/mni/rh.unc_AS_roi2.flt.nii.gz >>>>>> dlabel/mni/fmajor_PP_roi1.flt.nii.gz >>>>>> dlabel/mni/fmajor_PP_roi2.flt.nii.gz >>>>>> dlabel/mni/fminor_PP_roi1.flt.nii.gz >>>>>> dlabel/mni/fminor_PP_roi2.flt.nii.gz >>>>>> dlabel/mni/lh.atr_PP_roi1.flt.nii.gz >>>>>> dlabel/mni/lh.atr_PP_roi2.flt.nii.gz >>>>>> dlabel/mni/rh.atr_PP_roi1.flt.nii.gz >>>>>> dlabel/mni/rh.atr_PP_roi2.flt.nii. > g >> z >>>> d >>>>> l >>>>>> abel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2! >>>>>> .flt.nii >>>>>> .gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz >>>>>> dlabel/mni/rh.cab_PP_roi2.flt.nii.gz >>>>>> dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz >>>>>> dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz >>>>>> dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz >>>>>> dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz >>>>>> dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz >>>>>> dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz >>>>>> dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz >>>>>> dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz >>>>>> dlabel/mni/lh.slft_PP_roi1.flt.nii.gz >>>>>> dlabel/mni/lh.slft_PP_roi2.flt.nii.gz >>>>>> dlabel/mni/rh.slft_PP_roi1.flt.nii.gz >>>>>> dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask >>>>>> /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni/lowb_brain_mask.flt.nii.gz >>>>>> --fa /Studies/MJMRI/MJ0012/freesurfer/dmri/mni/dtifit_FA.flt.nii.gz >>>>>> --ncpts 5 --debug >>>>>>> ERROR: fio_pushd: /Studies/MJMRI/MJ0012/freesurfer/dlabel/mni >>>>>>> ERROR: must specify brain mask volume for output subject >>>>>>> Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version >>>>>>> 10.8.0: Tue Jun 7 16:32:41 PDT 2011; >>>>>>> root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 >>>>>>> >>>>>>> trac-preproc exited with ERRORS at Tue Feb 12 15:26:36 CST 2013 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> what is the brainmask volume that it is looking for? >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ----- Original Message ----- >>>>>>> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>>> Sent: Tuesday, February 12, 2013 1:26:55 PM >>>>>>> Subject: Re: [Freesurfer] trac-all problem >>>>>>> >>>>>>> >>>>>>> Hi Jon - This is the same issue. The reading from the dicom part >>>>>>> will work >>>>>>> for the Siemens dicoms that we have here but is not guaranteed to >>>>>>> work >>>>>>> with other dicoms. You'll have to define bvecfile, bvalfile, and >>>>>>> nb0. (The >>>>>>> first two should be in columns, not rows.) >>>>>>> >>>>>>> Let me know if you run into any other problems, >>>>>>> a.y >>>>>>> >>>>>>> On Tue, 12 Feb 2013, Jon Wieser wrote: >>>>>>> >>>>>>>> i ran the program with the nb0 set to 2 >>>>>>>> >>>>>>>> i got the following error: it's not finding a bvec files. the >>>>>>>> document says that the bevecs are read from the DICOM headers. >>>>>>>> here's the output of the run >>>>>>>> >>>>>>>> >>>>>>>> : >>>>>>>> INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 >>>>>>>> INFO: Diffusion root is /Studies/MJMRI/MJ0012 >>>>>>>> Actual FREESURFER_HOME /Applications/freesurfer >>>>>>>> trac-preproc -c >>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log >>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd >>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd >>>>>>>> #------------------------------------- >>>>>>>> /Applications/freesurfer/bin/trac-preproc >>>>>>>> #------------------------------------- >>>>>>>> #@# Image corrections Tue Feb 12 13:00:35 CST 2013 >>>>>>>> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >>>>>>>> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >>>>>>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >>>>>>>> reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... >>>>>>>> Starting DICOMRead2() >>>>>>>> dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >>>>>>>> dcmdir = /Studies/MJMRI/MJ0012//s780 >>>>>>>> Ref Series No = 13 >>>>>>>> Found 3304 files, checking for dicoms >>>>>>>> Found 3300 dicom files in series. >>>>>>>> First Sorting >>>>>>>> Computing Slice Direction >>>>>>>> Vs: 0 0 2 >>>>>>>> Vs: 0 0 1 >>>>>>>> Second Sorting >>>>>>>> Counting frames >>>>>>>> nframes = 55 >>>>>>>> nslices = 60 >>>>>>>> ndcmfiles = 3300 >>>>>>>> PE Dir = COL (dicom read) >>>>>>>> TransferSyntaxUID: --1.2.840.10008.1.2.1-- >>>>>>>> jpegUID: --1.2.840.10008.1.2.4-- >>>>>>>> Loading pixel data >>>>>>>> TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 >>>>>>>> i_ras = (-1, 0, 0) >>>>>>>> j_ras = (0, -1, 0) >>>>>>>> k_ras = (-0, -0, 1) >>>>>>>> writing to >>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... >>>>>>>> mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 > >>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat >>>>>>>> flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>>>>>> INFO: input image orientation is LPS >>>>>>>> INFO: input image determinant is 2 >>>>>>>> fslswapdim /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x >>>>>>>> -y z /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>>>>>> INFO: left-right orientation was flipped by fslswapdim >>>>>>>> fslorient -forceradiological >>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>>>>>> mv -f >>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs >>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >>>>>>>> mv: rename >>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs >>>>>>>> to /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs: No such file or >>>>>>>> directory >>>>>>>> Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version >>>>>>>> 10.8.0: Tue Jun 7 16:32:41 PDT 2011; >>>>>>>> root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 >>>>>>>> >>>>>>>> trac-preproc exited with ERRORS at Tue Feb 12 13:05:29 CST 2013 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ----- Original Message ----- >>>>>>>> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>>> Sent: Tuesday, February 12, 2013 11:24:56 AM >>>>>>>> Subject: Re: [Freesurfer] trac-all problem >>>>>>>> >>>>>>>> >>>>>>>> Yeah, the tutorial should say "Siemens dicoms" instead of >>>>>>>> "dicoms". In any >>>>>>>> case in the next version this won't be a problem b/c it'll >>>>>>>> determine the >>>>>>>> nb0 from the bvals file. >>>>>>>> >>>>>>>> On Tue, 12 Feb 2013, Jon Wieser wrote: >>>>>>>> >>>>>>>>> hi >>>>>>>>> our scanner is a GE >>>>>>>>> Jon >>>>>>>>> >>>>>>>>> ----- Original Message ----- >>>>>>>>> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>> Sent: Tuesday, February 12, 2013 11:14:42 AM >>>>>>>>> Subject: Re: [Freesurfer] trac-all problem >>>>>>>>> >>>>>>>>> >>>>>>>>> Sorry, reading stuff from the dicom header will not work for all >>>>>>>>> dicom >>>>>>>>> versions. It should work for Siemens dicoms though. >>>>>>>>> >>>>>>>>> On Tue, 12 Feb 2013, Jon Wieser wrote: >>>>>>>>> >>>>>>>>>> according to the >>>>>>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula >>>>>>>>>> >>>>>>>>>> nb0 does not need to be specified when using original dicoms. >>>>>>>>>> , but i'll try defining the nb0 variable >>>>>>>>>> thanks >>>>>>>>>> Jon >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ----- Original Message ----- >>>>>>>>>> From: "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> >>>>>>>>>> To: "Jon Wieser" <wieser(a)uwm.edu> >>>>>>>>>> Cc: "freesurfer" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>>> Sent: Tuesday, February 12, 2013 10:49:18 AM >>>>>>>>>> Subject: Re: [Freesurfer] trac-all problem >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Hi Jon - My guess is you didn't define the nb0 variable in your >>>>>>>>>> configuration file, see here: >>>>>>>>>> http://www.freesurfer.net/fswiki/dmrirc >>>>>>>>>> >>>>>>>>>> The new version, which will come out in a few days, will be able >>>>>>>>>> to figure >>>>>>>>>> it out without you having to specify it but with the current >>>>>>>>>> version you >>>>>>>>>> have to. >>>>>>>>>> >>>>>>>>>> Hope this helps, >>>>>>>>>> a.y >>>>>>>>>> >>>>>>>>>> On Tue, 12 Feb 2013, Jon Wieser wrote: >>>>>>>>>> >>>>>>>>>>> hello >>>>>>>>>>> >>>>>>>>>>> i am trying to process the dti data with trac-all. I am new >>>>>>>>>>> to tracula >>>>>>>>>>> my input images are 3300 dicoms, 60 slices and 55 dti >>>>>>>>>>> diffusions >>>>>>>>>>> i have attached my dmrirc_single_subject file >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> i did the following command: >>>>>>>>>>> >>>>>>>>>>> trac-all -prep -c /Studies/MJMRI/DTI/dmrirc_single_subject >>>>>>>>>>> >>>>>>>>>>> and got the result: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> INFO: SUBJECTS_DIR is /Studies/MJMRI/MJ0012 >>>>>>>>>>> INFO: Diffusion root is /Studies/MJMRI/MJ0012 >>>>>>>>>>> Actual FREESURFER_HOME /Applications/freesurfer >>>>>>>>>>> trac-preproc -c >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/scripts/dmrirc.local -log >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.log -cmd >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/scripts/trac-all.cmd >>>>>>>>>>> #------------------------------------- >>>>>>>>>>> /Applications/freesurfer/bin/trac-preproc >>>>>>>>>>> #------------------------------------- >>>>>>>>>>> #@# Image corrections Mon Feb 11 12:41:04 CST 2013 >>>>>>>>>>> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >>>>>>>>>>> mri_convert /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >>>>>>>>>>> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ >>>>>>>>>>> reading from /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1... >>>>>>>>>>> Starting DICOMRead2() >>>>>>>>>>> dcmfile = /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >>>>>>>>>>> dcmdir = /Studies/MJMRI/MJ0012//s780 >>>>>>>>>>> Ref Series No = 13 >>>>>>>>>>> Found 3304 files, checking for dicoms >>>>>>>>>>> Found 3300 dicom files in series. >>>>>>>>>>> First Sorting >>>>>>>>>>> Computing Slice Direction >>>>>>>>>>> Vs: 0 0 2 >>>>>>>>>>> Vs: 0 0 1 >>>>>>>>>>> Second Sorting >>>>>>>>>>> Counting frames >>>>>>>>>>> nframes = 55 >>>>>>>>>>> nslices = 60 >>>>>>>>>>> ndcmfiles = 3300 >>>>>>>>>>> PE Dir = COL (dicom read) >>>>>>>>>>> TransferSyntaxUID: --1.2.840.10008.1.2.1-- >>>>>>>>>>> jpegUID: --1.2.840.10008.1.2.4-- >>>>>>>>>>> Loading pixel data >>>>>>>>>>> TR=9300.00, TE=76.20, TI=0.00, flip angle=90.00 >>>>>>>>>>> i_ras = (-1, 0, 0) >>>>>>>>>>> j_ras = (0, -1, 0) >>>>>>>>>>> k_ras = (-0, -0, 1) >>>>>>>>>>> writing to >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz... >>>>>>>>>>> mri_probedicom --i /Studies/MJMRI/MJ0012//s780/i1735678.MRDC.1 >>>>>>>>>>> > /Studies/MJMRI/MJ0012/freesurfer/dmri/dcminfo.dat >>>>>>>>>>> flip4fsl /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>> INFO: input image orientation is LPS >>>>>>>>>>> INFO: input image determinant is 2 >>>>>>>>>>> fslswapdim >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.nii.gz x -y z >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>> INFO: left-right orientation was flipped by fslswapdim >>>>>>>>>>> fslorient -forceradiological >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>> INFO: found >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvals, >>>>>>>>>>> converting to FSL format >>>>>>>>>>> INFO: found >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig.mghdti.bvecs, >>>>>>>>>>> converting to FSL format >>>>>>>>>>> mv -f >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvecs >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >>>>>>>>>>> mv -f >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.mghdti.bvals >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvals >>>>>>>>>>> eddy_correct >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_orig_flip.nii.gz >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz 0 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0000 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0001 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0002 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0003 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0004 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0005 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0006 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0007 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0008 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0009 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0010 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0011 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0012 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0013 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0014 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0015 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0016 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0017 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0018 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0019 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0020 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0021 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0022 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0023 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0024 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0025 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0026 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0027 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0028 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0029 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0030 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0031 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0032 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0033 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0034 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0035 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0036 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0037 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0038 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0039 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0040 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0041 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0042 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0043 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0044 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0045 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0046 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0047 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0048 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0049 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0050 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0051 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0052 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0053 >>>>>>>>>>> processing /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi_tmp0054 >>>>>>>>>>> mv -f /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot >>>>>>>>>>> xfmrot /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.ecclog >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs.norot >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/bvecs >>>>>>>>>>> fslroi /Studies/MJMRI/MJ0012/freesurfer/dmri/dwi.nii.gz >>>>>>>>>>> /Studies/MJMRI/MJ0012/freesurfer/dmri/lowb.nii.gz 0 >>>>>>>>>>> >>>>>>>>>>> Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> >>>>>>>>>>> <zmin> <zsize> >>>>>>>>>>> fslroi <input> <output> <tmin> <tsize> >>>>>>>>>>> >>>>>>>>>>> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> >>>>>>>>>>> <zmin> <zsize> <tmin> <tsize> >>>>>>>>>>> Note: indexing (in both time and space) starts with 0 not 1! >>>>>>>>>>> Darwin psy-cerebellum.uits.uwm.edu 10.8.0 Darwin Kernel Version >>>>>>>>>>> 10.8.0: Tue Jun 7 16:32:41 PDT 2011; >>>>>>>>>>> root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 >>>>>>>>>>> >>>>>>>>>>> trac-preproc exited with ERRORS at Mon Feb 11 13:25:16 CST 2013 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> can you tell me how to fix this? >>>>>>>>>>> Thanks >>>>>>>>>>> Jon Wieser >>>>>>>>>>> UW-Milwaukee >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> 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. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>> >>> >>> >> >> >> > > >

1 0

← Newer
1
...
8
9
10
11
12
13
14
...
24
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer February 2013