Freesurfer September 2012

freesurfer@nmr.mgh.harvard.edu

89 participants
154 discussions

general questions
by Deirdre O Shea 21 Sep '12

21 Sep '12

Hi all, I'm new to FreeSurfer and so have a few questions that you may be able to anwser. My first question is ; when I am making white matter edits do I need to edit every single slice where the inaccuracy is or would every second or third slice suffice to prompt FreeSurfer to autocorrect? Secondly, in many of our FreeSurfer images, the horn of the lateral ventricles in the coronal images are being excluded from the white matter - is there a way to stop this from happening? Finally, I find that Freeview is a good way to view the images and although I know it is possible to make some edits such as filling in voxels etc., I wanted to know if it was possible to add control points like that in tkmedit? Thanks, Deirdre

2 1

Correction: cerebellum volumes
by Rachel Steinhorn 20 Sep '12

20 Sep '12

We'd like to obtain total cerebellar volumes. There are errors within the cerebellar segmentation as revealed in the aseg.mgz file. Is there a method Is there a method to manually edit the cerebellar segmentation? Thank You, Rachel Steinhorn

1 0

Editing cerebellar aseg volumes
by Rachel Steinhorn 20 Sep '12

20 Sep '12

My lab would like to look at the cerebellar parcellation volumes, but looking through the aparc+aseg.mgz, we've noticed some areas where the cerebellar segmentation includes non-cerebellar tissue. Is there any way to edit the segmentation and recalculate the volumes to exclude the incorrect voxels? Thank You, Rachel Steinhorn Washington University in St. Louis School of Medicine

1 0

mapping an set of talairach points
by Katie Bettencourt 20 Sep '12

20 Sep '12

I'm still trying to figure out a way to display an ROI made elsewhere on my freesurfer data. I can get all ROI I need in freesurfer in talairach points (ie. a list of talairach points that cover the entirety of the ROI space), but as far as I can see, I can only load one talairach point at a time (using select_talairach_point), and then the last point is lost with each subsequent call. What I really want to do is select a region on the surface that covers a set of talairach coordinates (instead of say, dilating from 1 talairach point). Is there any way to do this? Should I use something like the talairach transform file to change it into surface coordinates and load those like a label somehow, or is there some other way? Katie

5 9

recon-all 'expression syntax' error
by hhal5293＠uni.sydney.edu.au 19 Sep '12

19 Sep '12

Hello, I am relatively new to FreeSurfer, so this may be a silly question, but when i run any of the recon-all commands such as: recon-all -autorecon-pial -subjid SMART001bT1 OR recon-all -s SMART001bT1 -autorecon2 -autorecon3 OR recon-all -s SMART001bT1 I keep getting this error: if: Expression Syntax Anyone know what may be causing this? If it helps I'm running Linux (centos4-stable-pub-v5.1.0) using ubuntu 12.04 LTS. I have been using bash, but have also tired it on csh and tcsh but the same error still appears. Kind Regards, Harry

2 1

TRACULA FREEVIEW UBUNTU12 problems
by Richard Binney 19 Sep '12

19 Sep '12

Hi Anatasia and Other Freesurfers, Here is a set of frames from freeview in trying to render the merged trac file over the FA image. Hopefully you can easily see the errors I mam talking about. I have tried altering my drivers but with no improvement. do you have any ideas? R On Thu, Sep 13, 2012 at 2:01 PM, Richard Binney < binney.alerts(a)googlemail.com> wrote: > Hi Freesurfers, > > I've recently moved onto Ubuntu 12.04. The Freesurfer installation has > required me to download various libraries and create many symbolic links to > have it working. Further more I've had to set the doublebufferflag=1 > (whatever that is) in order for tkmedit and freeview to work (they > otherwise were tranparent display boxes). > > Still though I'm having some issues with freeview. It struggles with > rendering the tracts generated in dpath from TRACULA. the tracts will > disappear when the 3D box is moved and they are displayed in the wrong > colors until you change opacity or another random parameter. > > Has anyone else experienced this and had any success resolving it? Are > there any libraries or other general settings that need to be changed? > > Any help would be appreciated. > > On a side note I'm finding that freesurfer displays are also at the > forefront, meaning they block terminals and other things I'm also working > with. Any help to resolve this would be great too. > > Thanks > > Richard >

1 0

vno-check not picking up mismatches
by Darren Gitelman 19 Sep '12

19 Sep '12

Dear List I am getting errors when running recon-all -qcache that vertices don't match. For example: Reading curvature file /projects/d20277/dek/done/analyzed/3300/surf/lh.volume ERROR: number of vertices in /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match surface (145332,147148) ERROR: reading curvature file But running recon-all -vno-check says that everything matches. What should I do at this point? Rerun recon-all -make all? The full output of the qcache run is listed below. Thanks Darren ---------------- [drg@quser01 analyzed]$ recon-all -s 3300 -qcache INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /projects/d20277/dek/done/analyzed Actual FREESURFER_HOME /projects/d20277/software/freesurfer -rwxrwxrwx 1 drg d20277 544010 Sep 19 11:56 /projects/d20277/dek/done/analyzed/3300/scripts/recon-all.log Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /projects/d20277/software/freesurfer Previous: /usr/local/freesurfer /projects/d20277/dek/done/analyzed/3300/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Wed Sep 19 13:47:32 CDT 2012 mris_preproc --s 3300 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.5628 /projects/d20277/dek/done/analyzed/3300/surf Log file is lh.thickness.fsaverage.mris_preproc.log Wed Sep 19 13:47:32 CDT 2012 setenv SUBJECTS_DIR /projects/d20277/dek/done/analyzed cd /projects/d20277/dek/done/analyzed/3300/surf /projects/d20277/software/freesurfer/bin/mris_preproc --s 3300 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.5628 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 3300 Wed Sep 19 13:47:32 CDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject 3300 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.5628/3300.1.mgh --sval /projects/d20277/dek/done/analyzed/3300/surf/lh.thickness --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 3300 srcval = /projects/d20277/dek/done/analyzed/3300/surf/lh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.5628/3300.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/3300/surf/lh.sphere.reg Loading source data Reading curvature file /projects/d20277/dek/done/analyzed/3300/surf/lh.thickness Reading target surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (147148) Reverse Loop had 31096 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 141358, nTrgMulti = 22484, MnTrgMultiHits = 2.38303 nSrc121 = 110958, nSrcLost = 0, nSrcMulti = 36190, MnSrcMultiHits = 2.32053 Saving target data Saving to ./tmp.mris_preproc.5628/3300.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.5628/3300.1.mgh --o lh.thickness.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.thickness.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.5628 Wed Sep 19 13:47:41 CDT 2012 mris_preproc done rm: No match. #-------------------------------------------- #@# Qdec Cache lh thickness fwhm0 fsaverage Wed Sep 19 13:47:41 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.thickness.fwhm0.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh thickness fwhm5 fsaverage Wed Sep 19 13:47:44 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.thickness.fwhm5.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh thickness fwhm10 fsaverage Wed Sep 19 13:47:51 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.thickness.fwhm10.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh thickness fwhm15 fsaverage Wed Sep 19 13:48:03 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.thickness.fwhm15.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh thickness fwhm20 fsaverage Wed Sep 19 13:48:18 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.thickness.fwhm20.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh thickness fwhm25 fsaverage Wed Sep 19 13:48:42 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.thickness.fsaverage.mgh --tval lh.thickness.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.thickness.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.thickness.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.thickness.fwhm25.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh area fsaverage Wed Sep 19 13:49:16 CDT 2012 mris_preproc --s 3300 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.6093 /projects/d20277/dek/done/analyzed/3300/surf Log file is lh.area.fsaverage.mris_preproc.log Wed Sep 19 13:49:17 CDT 2012 setenv SUBJECTS_DIR /projects/d20277/dek/done/analyzed cd /projects/d20277/dek/done/analyzed/3300/surf /projects/d20277/software/freesurfer/bin/mris_preproc --s 3300 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.6093 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 3300 Wed Sep 19 13:49:17 CDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject 3300 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.6093/3300.1.mgh --sval /projects/d20277/dek/done/analyzed/3300/surf/lh.area --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 3300 srcval = /projects/d20277/dek/done/analyzed/3300/surf/lh.area srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.6093/3300.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/3300/surf/lh.sphere.reg Loading source data Reading curvature file /projects/d20277/dek/done/analyzed/3300/surf/lh.area Reading target surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (147148) Reverse Loop had 31096 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 141358, nTrgMulti = 22484, MnTrgMultiHits = 2.38303 nSrc121 = 110958, nSrcLost = 0, nSrcMulti = 36190, MnSrcMultiHits = 2.32053 Saving target data Saving to ./tmp.mris_preproc.6093/3300.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.6093/3300.1.mgh --o lh.area.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.6093 Wed Sep 19 13:49:25 CDT 2012 mris_preproc done rm: No match. #-------------------------------------------- #@# Qdec Cache lh area fwhm0 fsaverage Wed Sep 19 13:49:25 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.area.fwhm0.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh area fwhm5 fsaverage Wed Sep 19 13:49:28 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.area.fwhm5.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh area fwhm10 fsaverage Wed Sep 19 13:49:34 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.area.fwhm10.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh area fwhm15 fsaverage Wed Sep 19 13:49:45 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.area.fwhm15.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh area fwhm20 fsaverage Wed Sep 19 13:50:00 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.area.fwhm20.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh area fwhm25 fsaverage Wed Sep 19 13:50:25 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.area.fsaverage.mgh --tval lh.area.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.area.fwhm25.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh area.pial fsaverage Wed Sep 19 13:51:00 CDT 2012 mris_preproc --s 3300 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.6506 /projects/d20277/dek/done/analyzed/3300/surf Log file is lh.area.pial.fsaverage.mris_preproc.log Wed Sep 19 13:51:00 CDT 2012 setenv SUBJECTS_DIR /projects/d20277/dek/done/analyzed cd /projects/d20277/dek/done/analyzed/3300/surf /projects/d20277/software/freesurfer/bin/mris_preproc --s 3300 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.6506 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 3300 Wed Sep 19 13:51:00 CDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject 3300 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.6506/3300.1.mgh --sval /projects/d20277/dek/done/analyzed/3300/surf/lh.area.pial --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 3300 srcval = /projects/d20277/dek/done/analyzed/3300/surf/lh.area.pial srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.6506/3300.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/3300/surf/lh.sphere.reg Loading source data Reading curvature file /projects/d20277/dek/done/analyzed/3300/surf/lh.area.pial Reading target surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Done Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (147148) Reverse Loop had 31096 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 141358, nTrgMulti = 22484, MnTrgMultiHits = 2.38303 nSrc121 = 110958, nSrcLost = 0, nSrcMulti = 36190, MnSrcMultiHits = 2.32053 Saving target data Saving to ./tmp.mris_preproc.6506/3300.1.mgh ----------------------- mri_concat ./tmp.mris_preproc.6506/3300.1.mgh --o lh.area.pial.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.pial.fsaverage.mgh Cleaning up ----------------------- rm -r ./tmp.mris_preproc.6506 Wed Sep 19 13:51:09 CDT 2012 mris_preproc done rm: No match. #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm0 fsaverage Wed Sep 19 13:51:09 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 0 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm0.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm0.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Saving target data Saving to lh.area.pial.fwhm0.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm5 fsaverage Wed Sep 19 13:51:11 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 5 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm5.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm5.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 5 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 5.000000, std = 2.123305, with 18 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 18 Saving target data Saving to lh.area.pial.fwhm5.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm10 fsaverage Wed Sep 19 13:51:18 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 10 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm10.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm10.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 10 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 10.000000, std = 4.246609, with 74 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 74 Saving target data Saving to lh.area.pial.fwhm10.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm15 fsaverage Wed Sep 19 13:51:29 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 15 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm15.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm15.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 15.000000, std = 6.369914, with 165 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 165 Saving target data Saving to lh.area.pial.fwhm15.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm20 fsaverage Wed Sep 19 13:51:45 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 20 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm20.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm20.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 20 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 20.000000, std = 8.493218, with 294 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 294 Saving target data Saving to lh.area.pial.fwhm20.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh area.pial fwhm25 fsaverage Wed Sep 19 13:52:09 CDT 2012 mri_surf2surf --s fsaverage --hemi lh --fwhm 25 --sval lh.area.pial.fsaverage.mgh --tval lh.area.pial.fwhm25.fsaverage.mgh --cortex srcsubject = fsaverage srcval = lh.area.pial.fsaverage.mgh srctype = trgsubject = fsaverage trgval = lh.area.pial.fwhm25.fsaverage.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 25 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/fsaverage/surf/lh.sphere.reg Loading source data INFO: trgsubject = srcsubject Approximating gaussian smoothing of target with fwhm = 25.000000, std = 10.616523, with 460 iterations of nearest-neighbor smoothing Reading smoothing mask label lh.cortex.label NN smoothing output with n = 460 Saving target data Saving to lh.area.pial.fwhm25.fsaverage.mgh rm: No match. #-------------------------------------------- #@# Qdec Cache lh volume fsaverage Wed Sep 19 13:52:44 CDT 2012 mris_preproc --s 3300 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh nsubjects = 1 tmpdir is ./tmp.mris_preproc.6938 /projects/d20277/dek/done/analyzed/3300/surf Log file is lh.volume.fsaverage.mris_preproc.log Wed Sep 19 13:52:44 CDT 2012 setenv SUBJECTS_DIR /projects/d20277/dek/done/analyzed cd /projects/d20277/dek/done/analyzed/3300/surf /projects/d20277/software/freesurfer/bin/mris_preproc --s 3300 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.6938 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/1 3300 Wed Sep 19 13:52:44 CDT 2012 -------------- ----------------------- mri_surf2surf --srcsubject 3300 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.6938/3300.1.mgh --sval /projects/d20277/dek/done/analyzed/3300/surf/lh.volume --sfmt curv --noreshape --no-cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg srcsubject = 3300 srcval = /projects/d20277/dek/done/analyzed/3300/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.6938/3300.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = (null) label-trg = (null) OKToRevFaceOrder = 1 Reading source surface reg /projects/d20277/dek/done/analyzed/3300/surf/lh.sphere.reg Loading source data Reading curvature file /projects/d20277/dek/done/analyzed/3300/surf/lh.volume ERROR: number of vertices in /projects/d20277/dek/done/analyzed/3300/surf/lh.volume does not match surface (145332,147148) ERROR: reading curvature file Linux quser01 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3300 exited with ERRORS at Wed Sep 19 13:52:46 CDT 2012

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error message with crStateSetCurrentPointers() in your SPU
by Dana Wagshal 18 Sep '12

18 Sep '12

Hi Everyone, I installed Freeview on Ubuntu 10.04 and the program kind of works but I get this error message when I'm running the program. OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU What happens is that when I try and load a file, it disappears behind the black box viewer and I have to move the gui to see the file tab. Is there a solution? And the same thing happens in FSL... -Dana

1 0

Re: [Freesurfer] Testing Freesurfer Installation- Errors
by Melissa Lancaster 18 Sep '12

18 Sep '12

> Dr. Fischl, > > Thanks so much. Unfortunately, I had closed the window. But here is what > happened: > > I set the environment: setenv FREESURFER_HOME /Applications/freesufer > > However, after typing the next command: source > $FREESURFER_HOME/SetUpFreeSurfer.csh I got the following error: > > FREESURFER_HOME: Undefined variable. > > I found an old post on the listserv with a similar problem, and directly > copied the setenv command you had sent back to that user. I then got the > source command to work, and the output was in line with what the > installation website said I should get. Of note, at that time, I used a r > *egular terminal window*, I believe. > > A friend told me to 'echo $FREESURFER_HOME' to see what the path is > currently set at. When I do that, I get a blank space. > > Thanks so much for the help!!! > > -Missy > > > > On Thu, Sep 13, 2012 at 8:12 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> Hi Missy, >> >> yes, that sounds like at least part of your problem. What trouble did you >> have sourcing our env file? Can you send us the screen output? >> >> >> Bruce >> On Wed, 12 Sep 2012, Melissa Lancaster wrote: >> >> Hi again- >>> >>> I should have added that I am using Mountain Lion. I have downloaded >>> Quartz >>> and when I work from an X11 window I get: >>> tkmedit: command not found >>> >>> I had difficulty with the source command when setting up the >>> FREESURFER_HOME >>> directory but eventually got it to work...not sure if this could have >>> something to do with it. >>> >>> Thanks again!!! >>> -Missy >>> >>> On Wed, Sep 12, 2012 at 10:46 PM, Melissa Lancaster >>> <melissa.lancaster(a)my.rfums.**org <melissa.lancaster(a)my.rfums.org>> >>> wrote: >>> Hi, >>> >>> It seemed I had successful installed Freesufer, but when I went to run >>> the tests I got errors with both tkmedit and tksurfer. >>> >>> when typing <tkmedit bert orig.mgz> I got the following error: >>> >>> Couldn't create output file .xdebug_tkmeditGLUT: Fatal Error in >>> tkmedit.bin: could not open display: >>> >>> when typing <tksurfer bert rh pial> I got the following error: >>> GLUT: Fatal Error in tksurfer.bin: could not open display: >>> >>> >>> Any advice? >>> >>> Thanks, >>> Melissa >>> >>> >>> >>> >>> >> >> 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<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. >> > > > > -- > Melissa A. Lancaster, M.S. > Clinical Psychology Doctoral Student > Rosalind Franklin University of Medicine and Science > > -- Melissa A. Lancaster, M.S. Clinical Psychology Doctoral Student Rosalind Franklin University of Medicine and Science

2 2

AR1 issues
by Skyler Gabriel Shollenbarger 17 Sep '12

17 Sep '12

Hello, After running -autorecon1, there were issues with finding the best water threshold for skull stripping (one value would leave excess anatomy and the next lowest value would leave regions in the cerebellum missing). FS appears to differentiate brain matter from extraneous anatomy quite well. Do you recommend going with the value that results in remaining anatomy or the value with missing cerebellar regions? Thanks in advance, Skyler -- Skyler G. Shollenbarger Graduate Student - UWM Brain Lab Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee

2 1

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Freesurfer September 2012