Freesurfer October 2013

freesurfer@nmr.mgh.harvard.edu

136 participants
244 discussions

Re: [Freesurfer] V1 Labels (fwd)
by krista kelly 09 Oct '13

09 Oct '13

Thanks Allison, So to be clear, I just need to rename talairach.auto.xfm as talairach.xfm and then rerun recon-all from the normalization step? However, I'm not sure how to run recon starting from the normalization stage. Would you be able to help with that? Also, I've been doing manual edits to the brain extraction as well as adding control points on all of my subjects and I'm wondering if this will negate any edits I've made. So I'm pretty much starting from scratch? Thanks so much for looking into this for me! Best, Krista On Mon, Oct 7, 2013 at 12:19 PM, Allison Stevens < astevens(a)nmr.mgh.harvard.edu> wrote: > Hi Krista, > I took a look at your subject and think I have determined the problem. > Because your input data was high resolution (1.0000 x 0.9375 x 0.9375), the > talairach registration step failed. If you look at the talairach.xfm, > you'll see it is way off: > tkregister2 --mgz --s BV20_2ndrun --fstal --surf orig > > But the talairach.auto.xfm is correct. You can copy the talairach.auto.xfm > to talairach.xfm and rerun from the -normalization step. > > You might also want to look at these instructions: > https://surfer.nmr.mgh.**harvard.edu/fswiki/HiResRecon<https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon> > > They might not all apply to you but could potentially. > Allison > > > > ---------- Forwarded message ---------- >> Date: Thu, 03 Oct 13 22:55:12 -0400 >> From: krista.kelly16(a)gmail.com >> To: fischl(a)nmr.mgh.harvard.edu >> Subject: V1 Labels >> >> Hey! >> >> Krista (krista.kelly16(a)gmail.com) has uploaded some files for you at >> the Martinos Center FileDrop: >> >> -> BV20_2ndrun.zip (167.53 MiB) <http://gate.nmr.mgh.harvard.** >> edu/filedrop2/?u=1079qbdf&f=**dzep9n4<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf&f=dzep9n4> >> > >> >> Also, they left this message for you: >> Hi Bruce, >> >> Here is a zipped file of one of the subjects that I'm having label >> troubles with. The lh.v1.label isn't mapping correctly. I find the same >> goes for the aparc atlas as well (I haven't checked out anything else). If >> you could help me figure out why this is happening, that would be great! >> >> Thanks, >> Krista >> >> Please be aware, your upload will expire on December 31st. If you'd like >> to download these files, feel free to use the link below: >> >> http://gate.nmr.mgh.harvard.**edu/filedrop2/?u=1079qbdf<http://gate.nmr.mgh.harvard.edu/filedrop2/?u=1079qbdf> >> >> Cheers, >> The NMR Team >> >> >> >> >> > > 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. > >

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A function to write mgh files from R
by Heath Pardoe 09 Oct '13

09 Oct '13

Hi all, I've written a function that can write mgh files from R ( http://www.r-project.org/) Hopefully some of you will find it useful. It's more or less a translation of save_mgh.m. If you're looking for a function that can read mgh files into R, load.mgh.R is included in a package I wrote which can be found here: http://www.nitrc.org/frs/download.php/4629/cortex_0.1.tar.gz I recommend using load.mgh.R to read data in, only because save.mgh.R follows the same scheme within R for storing data. I'll include save.mgh.R in this package at some stage. If you run into problems with either of these let me know & I'll do my best to help. Code is pasted below between the lines below, copy this into a text file and save as "save.mgh.R" Example usage (in R): >my.surface <- load.mgh("hpardoe.lh.thickness.fsaverage.mgh") >my.surface$x <- rnorm(163842, mean = 3, sd = 0.3) # replaces thickness values with random noise >save.mgh(vol = my.surface, fname = "test.lh.mgh") you can then open "test.lh.mgh" in freeview. Best wishes Heath ---------------------------------------------- save.mgh <-function(vol,fname) { # R translation of save_mgh.m # written by Heath Pardoe, heath.pardoe(a)nyumc.org, 09/12/2013 MRI.UCHAR <- 0 MRI.INT <- 1 MRI.LONG <- 2 MRI.FLOAT <- 3 MRI.SHORT <- 4 MRI.BITMAP <- 5 MRI.TENSOR <- 6 slices <- c(1:256) fid <- file(fname,open = "wb", blocking = TRUE) width <- vol$ndim1 height <- vol$ndim2 depth <- vol$ndim3 writeBin(as.integer(1),fid,size = 4, endian = "big") writeBin(as.integer(width),fid,size = 4, endian = "big") writeBin(as.integer(height),fid,size = 4, endian = "big") writeBin(as.integer(depth),fid,size = 4, endian = "big") writeBin(as.integer(1),fid,size = 4, endian = "big") # HP note: I've ignored all the diffusion tensor stuff writeBin(as.integer(MRI.FLOAT),fid,size = 4, endian = "big") writeBin(as.integer(1),fid,size = 4, endian = "big") # dof = fread(fid, 1, 'int'); ## HP note: ignored ^this line^ from save_mgh.m UNUSED.SPACE.SIZE <- 256 USED.SPACE.SIZE <- (3*4+4*3*4) # space for ras transform unused.space.size <- UNUSED.SPACE.SIZE - 2 # ignored all the stuff about "M" - could probably do it if necessary so let me know #if (nargin > 2) ## fwrite(fid, 1, 'short') # ras.good.flag <- 0 # writeBin(1,fid,size = 2, endian = "big") # unused.space.size <- unused.space.size - USED.SPACE.SIZE ## fwrite(fid, sizes(1), 'float32') # xsize ## fwrite(fid, sizes(2), 'float32') # ysize ## fwrite(fid, sizes(3), 'float32') # zsize # # fwrite(fid, M(1,1), 'float32') # x.r # fwrite(fid, M(2,1), 'float32') # x.a # fwrite(fid, M(3,1), 'float32') # x.s # fwrite(fid, M(1,2), 'float32') # y.r # fwrite(fid, M(2,2), 'float32') # y.a # fwrite(fid, M(3,2), 'float32') # y.s # fwrite(fid, M(1,3), 'float32') # z.r # fwrite(fid, M(2,3), 'float32') # z.a # fwrite(fid, M(3,3), 'float32') # z.s # fwrite(fid, M(1,4), 'float32') # c.r # fwrite(fid, M(2,4), 'float32') # c.a # fwrite(fid, M(3,4), 'float32') # c.s #else # fwrite(fid, 0, 'short') # ras.good.flag <- 0 writeBin(as.integer(0),fid,size = 2, endian = "big") # } # writeBin(as.integer(rep.int(0,unused.space.size)),fid,size = 1) bpv <- 4 # bytes/voxel nelts <- width * height # bytes per slice writeBin(vol$x,fid, size = 4, endian = "big") close(fid) } --------------------------------------------- -- Heath Pardoe, PhD Research Scientist School of Medicine New York University 223 East 34th Street New York, NY 10016 Office: +1-646-754-5320 Cell: +1-347-285-1126 Skype: hpardoe https://sites.google.com/site/hpardoe/

1 0

Freesurfer Confidence Index
by Daniel Moadel 09 Oct '13

09 Oct '13

Dear Freesurfer friends, I am wondering if there is a confidence value or correction index for the volumetric data in aseg.stats. Thanks for your help! Daniel Moadel

2 3

Repost: pcc maps and mri_glmfit
by Caspar M. Schwiedrzik 09 Oct '13

09 Oct '13

Hi Doug, it would be great if you could give me some further advise on the group analysis of functional connectivity maps. Specifically, I am trying to get PCC maps for certain seeds, and am not planning any comparison between groups. Following your previous advise, I am running isxconcat-sess with -m pcc to get the PCC maps. I would then run mri_glmfit \ --surf averagesubject hemisphere \ --y pcc.nii \ --no-cortex \ --osgm \ --glmdir analysisname *Could you please provide some more detail on what kind of analysis is performed when I provide pcc.nii as an input for mri_glmfit? Is it a t-test of the Fisher-transformed r-values against 0? *Is the average r-value or z-value saved somewhere? *Do you take the autocorrelation into account (as in Vincent JL et al., 2007. Intrinsic functional architecture in the anaesthetized monkey brain. Nature. 447:83-86)? I'd also be happy to look this up but I'd need to know where I can find this information. Thanks, Caspar

2 18

sim ocn clusters mean effect size
by Kayle Sawyer 09 Oct '13

09 Oct '13

Hi, Using FS 5.3, I ran a group analysis with mri_glmfit-sim to identify clusters where my two groups differed (along with many other analyses, e.g. age slope for each group). For each cluster, I would like to see what the mean group difference is, in mm. So, I used this command: mri_segstats --i gamma.mgh --sum group_effectsize_clusters.txt --annot fsaverage rh ./mc-z.th1.3.pos.sig.ocn.annot Unfortunately, mri_segstats looks in the wrong place for the annot file, prepending "$SUBJECTS_DIR/fsaverage/label/rh." instead of looking in my present GLM directory that I typed the command from. In comparison, if I manually create a label for one of the clusters from the ocn.annot, and use the label, mri_segstats works: mri_segstats --i gamma.mgh --sum group_effectsize_clusters.txt --slabel fsaverage rh ./label.th1.3.neg/rh.cluster-001.label This time, it doesn't try to look under fsaverage, but uses the present GLM directory. Is there a way to override the SUBJECTS_DIR issue with --annot? I tried without the "./", and with specifying the absolute path, but it still pre-pended the "$SUBJECTS_DIR/fsaverage/label/rh." before the path. Or, should I just create labels for each analysis, run mris_segstats for each cluster, and then combine them all back together with grep? Thanks, -Kayle

2 1

Error with bbregister (using T2 to refine pial surface)
by Sophie Maingault 09 Oct '13

09 Oct '13

Dear FS experts, I'm trying to use T2 weighted image to refine the pail surface. I have this error message : ERROR: you must have the FSLDIR environment variable defined and pointing to the FSL installation In release notes, I saw that in "known issues" : fslregister (and so bbregister with --init-fsl) requires that FSL be installed. This has been fixed. The fix will be in the next version. Ask for a patch if you need it before then. Could you send me this "patch" to perform my analyzes ? Thank you by advance. Sophie

2 1

Missing geometry information when converting lh.white using mris_convert
by Clive Wong 09 Oct '13

09 Oct '13

Dear Surfers, I am trying to create a ROI in freesurfer, and export surface ROI for FSL/ProbtrackX. I have successfully created label in the template, and use mri_label2label to map the label to different subjects. As suggested by FSL, I use mris_convert to convert the lh.white to Gifti mris_convert lh.white lh.white.gii echo LMOG.label > listOfAreas.txt label2surf -s lh.white.gii -o lh.LMOG.gii -l listOfAreas.txt After I failed to do ProbtrackX, I tried to visualize the gii surface in freesurfer, and it tells me: "Did not find any volume geometry information in the surface" So, I tried to check the mailing list and tried: mris_convert -t subj1 lh.white lh.white2.gii However, it's even worse... [image: Inline image 2] Red: original lh.white Green: mris_convert -t subj1 lh.white lh.white2.gii Blue: mris_convert lh.white lh.white2.gii Does anyone successfully used freesurfer surface to do FSL/ProbtrackX？ Any suggestions? Thanks, Clive

1 0

recon -all exited with errors
by Boric, Katica A. 08 Oct '13

08 Oct '13

Dear freesurfer experts: I am trying to process an MRI using recon-all -autorecon1 -autorecon2 -autorecon3 and exited with errors. Apparently the encoded image data is not supported (below you can see the recon-all.log) Is there a way to process this study? Thank you very much for your help, Katica Here is the recon-all.log: Tue Oct 8 14:06:54 PDT 2013 /home/spaz/Cat/subjects/MGH020_SurferOutput /usr/local/freesurfer/bin/recon-all -autorecon1 -autorecon2 -autorecon3 -subject MGH020_SurferOutput -i /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm subjid MGH020_SurferOutput setenv SUBJECTS_DIR /home/spaz/Cat/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 1012544 931236 81308 0 42064 556144 -/+ buffers/cache: 333028 679516 Swap: 2030588 126356 1904232 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:54-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:55-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:56-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:57-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:57-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/10/08-21:06:57-GMT BuildTimeStamp: May 13 2013 18:45:07 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: spaz Machine: localhost.localdomain Platform: Linux PlatformVersion: 3.6.11-4.fc16.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/spaz/Cat/subjects/MGH020_SurferOutput mri_convert /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm /home/spaz/Cat/subjects/MGH020_SurferOutput/mri/orig/001.mgz mri_convert /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm /home/spaz/Cat/subjects/MGH020_SurferOutput/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm... Starting DICOMRead2() dcmfile = /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3/IM-0003-0001.dcm dcmdir = /home/spaz/Cat/subjects/MGH020/Mribrnwo/SAG_FSPGR_3D_3 ERROR: RLL-encoded image data not supported! (Transfer Syntax UID: 1.2.840.10008.1.2.5) Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 20:57:42 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s MGH020_SurferOutput exited with ERRORS at Tue Oct 8 14:06:57 PDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

1 0

mri_vol2surf clarification
by Satrajit Ghosh 08 Oct '13

08 Oct '13

hi folks, i'm using mri_vol2surf to map functional time series into fsaverage3/4. my assumption is that each vertex time series will be the mean over an icosahedral patch corresponding to the vertex on fsaverage. is that how the resampling is done? also is the resampling done with a single interpolation? if it's a single step, is there a way to project the interpolation kernel corresponding to a vertex in fsaverage3 on the subject's own surface? cheers, satra

2 2

Cluster Annotation file and mris_anatomical_stats
by Tara Ann Miskovich 08 Oct '13

08 Oct '13

Hi Everyone, I am having trouble running mris_anatomical_stats on an annotation file produced from my group analysis in qdec. This is my code, but it seems to want to pull the annotation file from the subject/label directory. Should I just make a copy into everyone's label file? mris_anatomical_stats -a qdec/lh_5FWHM_trait_anxiety/lh-Avg-pial_lgi-Cor/mc-z.abs.th13.sig.ocn.annot -t ${subject}/surf/lh.pial_lgi -f ${subject}/stats/lh.parietal_lgi.stats ${subject} lh Thank you! Tara

2 13

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Freesurfer October 2013