Freesurfer December 2007

freesurfer@nmr.mgh.harvard.edu

45 participants
74 discussions

mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm
by PKUNWAR＠nmr.mgh.harvard.edu 26 Aug '09

26 Aug '09

Hi all, I was going through the FSFAST TUTORIAL from wiki( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial?action=highlight&v…) I got the follwoing error during mri_volcluster, "NOT Adjusting threshold for 1-tailed test ERROR: you must specify a pos or neg sign with --fwhm" I have fwhm.dat file with 4. something vlaue. Command used, [galen:odd-v-0] (nmr-std-env) mri_volcluster --in tal.rfx.osgm/osgm/sig.nii --thmin 2 --fwhmdat tal.rfx.osgm/fwhm.dat --cwpvalthresh 0.1 --mask tal.rfx.osgm/mask.nii --fsaverage --sum tal.rfx.osgm/osgm/cluster.sum --cwsig tal.rfx.osgm/osgm/cwsig.cluster.nii --out tal.rfx.osgm/osgm/sig.cluster.nii --ocn tal.rfx.osgm/osgm/ocn.cluster.nii without --fwhmdat flag, it gave me another error "ERROR: need csd with --cwsig" will appreciate for help thanks pratap ----------------------------------- FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20070927 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: galen SUBJECTS_DIR: /autofs/space/galen_003/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/subjects PWD: /space/galen/3/users/carl/Tutorial/buckner_data/FsFastTutorialData/FSFTUTDIR/fb1-preproc-study/group-analysis-tut/sm-gamma-fwhm5/odd-v-0

2 1

Checking for spikes
by Brittany Cassidy 06 Aug '08

06 Aug '08

Hello all, I was looking for a general way to check for spiking from Freesurfer or the FSFast stream. Any ideas are appreciated. Thanks! -Brittany

3 3

documentation of the Freesurfer output and directory structure?
by Turner, Jessica 02 Jul '08

02 Jul '08

Hi experts-I have to document for some non-Freesurfer users what is in all the Freesurfer 3.05 subdirectories from an analysis. We have come up with a lot of it from the Wiki pages and tutorials, but there are some things that still aren't clear (what exactly is the bem directory for? What exactly is the mri_nu_correct.mni.log file? Etc.). Is it laid out clearly somewhere? I've seen the pages about which files are created by what process, etc. and it seems like it should say somewhere what these directories and files really are, I'm just missing it. Thanks, Jess ------------------------ Jessica Turner, Ph.D. Project Manager, FBIRN (www.nbirn.net) Department of Psychiatry and Human Behavior University of California, Irvine Phone: (949) 824-3331 Fax: (949) 824-3324

5 4

Matlab and Freesurfer
by Robert Baldwin 09 Mar '08

09 Mar '08

Hello- I am new to Freesurfer and Matlab. I have Matlab 7.4.0 installed on an Intel Mac. I just installed Freesurfer. Now when I start Matlab I get the following warnings: Warning: Name is nonexistent or not a directory: /matlab. In path at 110 In startup at 4 In matlabrc at 255 Warning: Name is non existent or not a directory: /toolbox. In path at 110 In startup at 11 In Matlabrc at 255 I have tried adding the freesurfer folder to these files to the path for matlab, but the error still occurs. Any suggestions on how to get this error to quit? Thanks! -Robert

2 4

Recon-all failing at CA Reg
by Caroline Chapman 25 Jan '08

25 Jan '08

Hello, I am having trouble with one subject during the recon-all process. It has failed twice at CA Reg: status file for recon-all Thu Nov 8 15:11:20 EST 2007 #@# MotionCor Thu Nov 8 15:11:20 EST 2007 #@# Nu Intensity Correction Thu Nov 8 15:18:50 EST 2007 #@# Talairach Thu Nov 8 15:21:26 EST 2007 #@# Intensity Normalization Thu Nov 8 15:23:01 EST 2007 #@# Skull Stripping Thu Nov 8 15:30:05 EST 2007 #@# EM Registration Thu Nov 8 15:33:05 EST 2007 #@# CA Normalize Thu Nov 8 15:42:54 EST 2007 #@# CA Reg Thu Nov 8 15:45:14 EST 2007 Linux node0052 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 athlon i386 GNU/Linux The brainmask, orig, and talairach look okay. Any ideas why this might be failing? Thanks! Caroline -- Caroline Chapman Research Technician Massachessetts General Hospital Geriatric Research, Education and Clinical Center VA Boston Healthcare System (857)364-2093 chapman(a)nmr.mgh.harvard.edu

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Re: [Freesurfer] Cluster thresholding
by Alex Fornito 04 Jan '08

04 Jan '08

Thanks for all your help guys, but I am still having trouble (!). This time I've tried a different dataset, again just a simple 2 group comaprison with no covariates. Running this in qdec, and visualizing with a low threshold (min=1.3), I see a whole bunch of clusters (see attached). However, when I run mri_surfcluster, I only get one whole brain cluster again (see below). This time I smoothed with 15 mm in qdec, although I get the same if I smooth with 10mm. I have kept the thresholds low on purpose, because I expect that something should come out?? I did not run simulations in this instance, to cut processing time. mri_surfcluster --in qdec/MF_lh_15mm/contrasts.sig.mgh --no-adjust -- subject fsaverage/ --hemi l h --thmin 1.3 --minarea 15 --sum TestClusters thsign = abs, id = 0 version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve Exp $ hemi = lh srcid = qdec/MF_lh_15mm/contrasts.sig.mgh paint srcsubjid = fsaverage/ srcsurf = white srcframe = 0 thsign = abs thmin = 1.3 thmax = -1 fdr = -1 minarea = 15 xfmfile = talairach.xfm nth = -1 sumfile = TestClusters subjectsdir = /data/kang/work/struct/alex/freesurfer/subjects_cann FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage//mri/ transforms/t alairach.xfm 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; ---------------------------------------------------- Reading source surface /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsav erage//surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /data/kang/work/struct/alex/freesurfer/ subjects_cann/fsa verage//surf/lh.white.avg.area.mgh Done reading source surface Computing metric properties Loading source values number of voxels in search space = 163842 Done loading source values (nvtxs = 163842) overall max = 1e+10 at vertex 26 overall min = 1.75775 at vertex 126983 surface nvertices 163842 surface area 65416.985991 surface area 65416.985976 NOT Adjusting threshold for 1-tailed test Searching for Clusters ... thmin=1.300000 (1.300000), thmax=-1.000000 (-1), thsignid=0, minarea=15.000000 Found 1 clusters Max cluster size 103339.460938 INFO: fixing MNI talairach coordinates On 05/12/2007, at 4:19 AM, Doug Greve wrote: > There's really no such thing as an opt kernel size. The best size > depends on the underlying signal and can be space variant. > > doug > > Alex Fornito wrote: >> >> Yes, I selected 25 mm on qdec, based on the Lerch paper suggesting >> this was a generally 'optimal' kernel size. The 34.309.. was the >> residual output to y.fsgd. >> >> Do you recommend a smaller kernel? >> >> >> On 04/12/2007, at 5:41 PM, Pratap Kunwar wrote: >> >>> I think, one reason for getting only one big cluster is because >>> your fwhm >>> value is very high. By the way how did you get fwhm 34.309616??, >>> was it >>> produced by selecting fwhm 25 (max on Qdec)on Qdec? >>> >>> Did you try fwhm 10 or 15? >>> >>>> Thanks for your help Pratap. >>>> I've actually been trying to follow the tutorial and was running >>>> simulations initially, but when I tried to re-trace my steps I >>>> ended >>>> omitted them because I forgot they were necessary for >>>> mri_surfcluster. >>>> >>>> Either way, the results are the same- I still get one whole surface >>>> cluster as output even after running simulations. In this case, >>>> I re- >>>> ran it copying your commands, except I used perm because I have low >>>> numbers and no covariates. I also ran 1000 permutations, to get a >>>> quick initial result for testing. My commands and output are below. >>>> >>>> I would appreciate further help on this, as I'm not sure where I'm >>>> going wrong! >>>> >>>> also, I noticed that after your mri_glmfit command, you added --i >>>> divided into 5000 each. Sorry, but I'm not sure what you meant >>>> by that. >>> ---> i had split simulation (10,000 iterations)into multiple runs >>> csd1* >>> (5000 iterations) and csd2* (5000 iterations) since mc-z >>> relatively takes >>> long time comparing to permutation. >>> More on, >>> https://surfer.nmr.mgh.harvard.edu/fswiki/ >>> FsTutorial_2fGroupAnalysis?action=highlight&value=fsgd >>>> mri_glmfit --y qdec/MF_group_rh/y.mgh --fsgd qdec/MF_group_rh/ >>>> qdec.fsgd doss --surf fsaverage rh --fwhm 34.309616 --C qdec/ >>>> MF_group_rh/contrasts/Diff-1-2-Intercept.mat --sim perm 1000 2 >>>> stats/ >>>> newperm_rh/newperm_rh --glmdir stats/newperm_rh/ >>>> >>>> gdfReadHeader: reading qdec/MF_group_rh/qdec.fsgd >>>> INFO: demeaning continous variables >>>> Continuous Variable Means (all subjects) >>>> Class Means of each Continuous Variable >>>> 1 group1 >>>> 2 group2 >>>> INFO: gd2mtx_method is doss >>>> Reading source surface /data/kang/work/struct/alex/freesurfer/ >>>> subjects_cann/fsaverage/surf/rh.white >>>> reading group avg surface area 822 cm^2 from file >>>> Reading in average area /data/kang/work/struct/alex/freesurfer/ >>>> subjects_cann/fsaverage/surf/rh.white.avg.area.mgh >>>> simbase stats/newperm_rh/newperm_rh >>>> Number of vertices 163842 >>>> Number of faces 327680 >>>> Total area 65020.765625 >>>> AvgVtxArea 0.396850 >>>> AvgVtxDist 0.717994 >>>> StdVtxDist 0.193566 >>>> reading group avg surface area 822 cm^2 from file >>>> Reading in average area /data/kang/work/struct/alex/freesurfer/ >>>> subjects_cann/fsaverage/surf/rh.white.avg.area.mgh >>>> INFO: fwhm2niters: Fixing group surface area >>>> Surface smoothing by fwhm=34.309616, niters=866.000000 >>>> >>>> $Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ >>>> cwd /data/kang/work/struct/alex/freesurfer/subjects_cann >>>> cmdline mri_glmfit --y qdec/MF_group_rh/y.mgh --fsgd qdec/ >>>> MF_group_rh/ >>>> qdec.fsgd doss --surf fsaverage rh --fwhm 34.309616 --C qdec/ >>>> MF_group_rh/contrasts/Diff-1-2-Intercept.mat --sim perm 1000 2 >>>> stats/ >>>> newperm_rh/newperm_rh --glmdir stats/newperm_rh/ >>>> sysname Linux >>>> hostname kang >>>> machine i686 >>>> user alex >>>> FixVertexAreaFlag = 1 >>>> UseMaskWithSmoothing 1 >>>> fwhm 34.309616 >>>> niters 866.000000 >>>> OneSampleGroupMean 0 >>>> y /data/kang/work/struct/alex/freesurfer/subjects_cann/qdec/ >>>> MF_group_rh/y.mgh >>>> logyflag 0 >>>> usedti 0 >>>> FSGD qdec/MF_group_rh/qdec.fsgd >>>> glmdir stats/newperm_rh/ >>>> DoFFx 0 >>>> Loading y from /data/kang/work/struct/alex/freesurfer/ >>>> subjects_cann/ >>>> qdec/MF_group_rh/y.mgh >>>> Matrix condition is 1 >>>> search space = 82167.6 >>>> Smoothing input by fwhm 34.309616 >>>> Smoothing done, nsteps = 866, tsec = 1236.17 >>>> ... done >>>> DOF = 28 >>>> thresh = 2, threshadj = 2 >>>> Starting simulation sim over 1000 trials >>>> 1/1000 t=0 ------------------------------------------------ >>>> Starting fit and test >>>> 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% >>>> Diff-1-2-Intercept 0 nc=3 maxcsize=1910.81 sigmax=-3.00831 >>>> Fmax=13.551 >>>> 2/1000 t=0.0572833 ------------------------------------------------ >>>> Starting fit and test >>>> 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% >>>> Diff-1-2-Intercept 1 nc=0 maxcsize=0 sigmax=1.36036 Fmax=4.46612 >>>> 3/1000 t=0.0994333 ------------------------------------------------ >>>> >>>> ... and so on... then >>>> >>>> mri_surfcluster --src qdec/MF_group_lh/contrasts.sig.mgh --csd >>>> stats/ >>>> newperm_lh/newperm_lh-Diff-1-2-Intercept.csd --sum stats/ >>>> newperm_lh/ >>>> newperm_lh --ocp stats/newperm_lh/newperm_lh.mgh >>>> >>>> thsign = abs, id = 0 >>>> version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve >>>> Exp $ >>>> hemi = rh >>>> srcid = qdec/MF_group_lh/contrasts.sig.mgh paint >>>> srcsubjid = fsaverage >>>> srcsurf = white >>>> srcframe = 0 >>>> thsign = abs >>>> thmin = 2 >>>> thmax = -1 >>>> fdr = -1 >>>> minarea = 0 >>>> xfmfile = talairach.xfm >>>> nth = -1 >>>> sumfile = stats/newperm_lh/newperm_lh >>>> subjectsdir = /data/kang/work/struct/alex/freesurfer/ >>>> subjects_cann >>>> FixMNI = 1 >>>> ------------- XFM matrix (RAS2RAS) --------------- >>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/mri/ >>>> transforms/talairach.xfm >>>> 1.000 0.000 0.000 0.000; >>>> 0.000 1.000 0.000 0.000; >>>> 0.000 0.000 1.000 0.000; >>>> 0.000 0.000 0.000 1.000; >>>> ---------------------------------------------------- >>>> Reading source surface /data/kang/work/struct/alex/freesurfer/ >>>> subjects_cann/fsaverage/surf/rh.white >>>> reading group avg surface area 822 cm^2 from file >>>> Reading in average area /data/kang/work/struct/alex/freesurfer/ >>>> subjects_cann/fsaverage/surf/rh.white.avg.area.mgh >>>> Done reading source surface >>>> Computing metric properties >>>> Loading source values >>>> number of voxels in search space = 163842 >>>> Done loading source values (nvtxs = 163842) >>>> overall max = 43.1907 at vertex 101931 >>>> overall min = 7.66111 at vertex 28089 >>>> surface nvertices 163842 >>>> surface area 65020.838384 >>>> surface area 65020.838382 >>>> NOT Adjusting threshold for 1-tailed test >>>> Searching for Clusters ... >>>> thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, >>>> minarea=0.000000 >>>> Found 1 clusters >>>> Max cluster size 103836.125000 >>>> INFO: fixing MNI talairach coordinates >>>> Saving cluster pval stats/newperm_lh/newperm_lh.mgh >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 04/12/2007, at 11:30 AM, Pratap Kunwar wrote: >>>> >>>>> Alex, >>>>> >>>>> You have to do simulations using mri_glmfit before youdo >>>>> mri_surfcluster, >>>>> >>>>> [more info in this link at >>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/ >>>>> FsTutorial_2fGroupAnalysis?action=highlight&value=fsgd >>>>> go down to [4.0 Using mri_glmfit to correct for multiple >>>>> comparisons: ] >>>>> >>>>> USAGE: ./mri_glmfit >>>>> >>>>> --glmdir dir : save outputs to dir >>>>> >>>>> --y inputfile **y.mgh >>>>> --fsgd FSGDF <gd2mtx> : freesurfer descriptor file **qdec.fsgd >>>>> --C contrast1.mat <--C contrast2.mat ...> >>>>> --fwhm fwhm : smooth input by fwhm ** your smoothing value >>>>> from " >>>>> fwhm.dat" >>>>> --surf subject hemi <surfname> : needed for some flags (uses >>>>> white by >>>>> default) **lh or rh >>>>> --sim nulltype nsim thresh csdbasename : simulation perm, mc- >>>>> full, mc-z >>>>> **mc-z (i used) is faster than mc-full, minimum threshold value >>>>> ( i.e. >>>>> 1.3 for 0.05), >>>>> >>>>> My command was more like this, >>>>> >>>>> mri_glmfit --y y.mgh --fsgd qdec.fsgd doss --surf fsaverage rh -- >>>>> fwhm < ?? >>>>>> --C contrast/contrastname.mat --sim mc-z 5000 1.3 f11/csd1 -- >>>>>> glmdir f11 >>>>> >>>>> >>>>> mri_glmfit --y y.mgh --fsgd qdec.fsgd doss --surf fsaverage rh >>>>> --fwhm >>>>> 14.504073 --C contrast/contrastname.mat --sim mc-z 5000 1.3 f11/ >>>>> csd2 >>>>> --glmdir f11 >>>>> >>>>> --i divided into 5000 each >>>>> >>>>> from above mri_glmfit, i got two files starting with csd1* .csd >>>>> and >>>>> csd2*.csd. >>>>> >>>>> Next one is >>>>> >>>>> mri_surfcluster, >>>>> mri_surfcluster --src contrastname/sig.mgh --csd csd1* .csd --csd >>>>> csd2* >>>>> ..csd --sum <text summary file --sum <*.sum> --ocp <*.mgh> >>>>> >>>>> the output file *.sum can be opened in text editor and *.mgh can >>>>> be seen >>>>> using tksurfer. Check the link above link for more details (i just >>>>> followed that link when i did last month). >>>>> >>>>> let me know if you get into more problems. >>>>> >>>>> pratap >>>>>> >>>>>>> On 11/28/2007 07:43 PM, Alex Fornito wrote: >>>>>>>> Hi, >>>>>>>> I have run qdec for a simple contrast comparing thickness >>>>>>>> across >>>>>>>> the >>>>>>>> cortical surface between a patient and control group. Not much >>>>>>>> survives vertex-wise FDR correction, and I would like to try >>>>>>>> cluster-based thresholding. I would like to make sure I >>>>>>>> understand the >>>>>>>> inputs to the command. Am I correct on the following? >>>>>>>> >>>>>>>> --in = the signifcance values (i.e., contrast_name.sig.mgh >>>>>>>> file) >>>>>>>> --thmin = the vertexwise threshold for determining clusters, >>>>>>>> where 2 >>>>>>>> corresponds to p=.01 >>>>>>>> --minarea = the cluster extent threshold - Am I correct in >>>>>>>> assuming >>>>>>>> this should not be smaller than the smoothing kernel? >>>>>>>> >>>>>>>> When I run the command below, I get the following output. >>>>>>>> Only one >>>>>>>> (whole hemi) cluster is identified. I'm not sure if its a >>>>>>>> problem in >>>>>>>> my command line, or with my data. Also, I seem to have the -- >>>>>>>> cwsig >>>>>>>> flag wrong, but can't figure out the error (appending .w >>>>>>>> or .label to >>>>>>>> the end of the output filename does not change the error). >>>>>>>> >>>>>>>> I greatly appreciate your help. >>>>>>>> >>>>>>>> >>>>>>>> mri_surfcluster --in qdec/MF_group_lh/contrasts.sig.mgh -- >>>>>>>> subject >>>>>>>> fsaverage --hemi lh --surf white --annot aparc --sign abs -- >>>>>>>> thmin 2 >>>>>>>> --minarea 25 --sum stats/qdec_run/cluster/summary.txt --o >>>>>>>> stats/qdec_run/cluster/cluster_output --cwsig >>>>>>>> stats/qdec_run/cluster/cwsig --olab >>>>>>>> stats/qdec_run/cluster/MF_group_lh_thk >>>>>>>> >>>>>>>> thsign = abs, id = 0 >>>>>>>> version $Id: mri_surfcluster.c,v 1.39 2007/07/31 00:34:19 greve >>>>>>>> Exp $ >>>>>>>> hemi = lh >>>>>>>> srcid = qdec/MF_group_lh/contrasts.sig.mgh paint >>>>>>>> srcsubjid = fsaverage >>>>>>>> srcsurf = white >>>>>>>> srcframe = 0 >>>>>>>> thsign = abs >>>>>>>> thmin = 2 >>>>>>>> thmax = -1 >>>>>>>> fdr = -1 >>>>>>>> minarea = 25 >>>>>>>> xfmfile = talairach.xfm >>>>>>>> nth = -1 >>>>>>>> outid = stats/qdec_run/cluster/cluster_output paint >>>>>>>> sumfile = stats/run2/cluster/summary.txt >>>>>>>> subjectsdir = /data/kang/work/struct/alex/freesurfer/ >>>>>>>> subjects_cann >>>>>>>> FixMNI = 1 >>>>>>>> ------------- XFM matrix (RAS2RAS) --------------- >>>>>>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/ >>>>>>>> mri/transforms/talairach.xfm >>>>>>>> 1.000 0.000 0.000 0.000; >>>>>>>> 0.000 1.000 0.000 0.000; >>>>>>>> 0.000 0.000 1.000 0.000; >>>>>>>> 0.000 0.000 0.000 1.000; >>>>>>>> ---------------------------------------------------- >>>>>>>> Reading source surface >>>>>>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/ >>>>>>>> surf/lh.white >>>>>>>> reading group avg surface area 822 cm^2 from file >>>>>>>> Reading in average area >>>>>>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/ >>>>>>>> surf/lh.white.avg.area.mgh >>>>>>>> Done reading source surface >>>>>>>> Reading annotation >>>>>>>> /data/kang/work/struct/alex/freesurfer/subjects_cann/fsaverage/ >>>>>>>> label/lh.aparc.annot >>>>>>>> reading colortable from annotation file... >>>>>>>> colortable with 35 entries read (originally >>>>>>>> /space/amaebi/26/users/buckner_cortical_atlas/scripts/ >>>>>>>> colortable_final.txt) >>>>>>>> Computing metric properties >>>>>>>> Loading source values >>>>>>>> number of voxels in search space = 163842 >>>>>>>> Done loading source values (nvtxs = 163842) >>>>>>>> overall max = 43.1907 at vertex 101931 >>>>>>>> overall min = 7.66111 at vertex 28089 >>>>>>>> surface nvertices 163842 >>>>>>>> surface area 65416.985991 >>>>>>>> surface area 65416.985976 >>>>>>>> NOT Adjusting threshold for 1-tailed test >>>>>>>> Searching for Clusters ... >>>>>>>> thmin=2.000000 (2.000000), thmax=-1.000000 (-1), thsignid=0, >>>>>>>> minarea=25.000000 >>>>>>>> Found 1 clusters >>>>>>>> Max cluster size 103339.460938 >>>>>>>> INFO: fixing MNI talairach coordinates >>>>>>>> Saving thresholded output to stats/qdec_run/cluster/ >>>>>>>> cluster_output >>>>>>>> avg = 35.029, stdev = 4.669, min = 7.661, max = 43.191 >>>>>>>> Saving cluster pval stats/qdec_run/cluster/cwsig >>>>>>>> unknown file type for file (stats/qdec_run/cluster/cwsig) >>>>>>>> LabelWrite: saving to stats/qdec_run/cluster/ >>>>>>>> MF_group_lh_thk-0001.label >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Alex Fornito >>>>>>>> JN Peters Research Fellow >>>>>>>> Melbourne Neuropsychiatry Centre >>>>>>>> Department of Psychiatry >>>>>>>> The University of Melbourne >>>>>>>> >>>>>>>> Postal address: >>>>>>>> Melbourne Neuropsychiatry Centre >>>>>>>> National Neuroscience Facility >>>>>>>> Levels 2 & 3, 161 Barry St >>>>>>>> Carlton South Vic 3053 Australia >>>>>>>> >>>>>>>> Ph: +61 3 8344 1861 >>>>>>>> Fax: +61 3 9348 0469 >>>>>>>> >>>>>>>> fornitoa(a)unimelb.edu.au <mailto:fornitoa@unimelb.edu.au> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> --------------------------------------------------------------- >>>>>>>> ---- >>>>>>>> ----- >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>> >>>> >>>> Alex Fornito >>>> JN Peters Research Fellow >>>> Melbourne Neuropsychiatry Centre >>>> Department of Psychiatry >>>> The University of Melbourne >>>> >>>> Postal address: >>>> Melbourne Neuropsychiatry Centre >>>> National Neuroscience Facility >>>> Levels 2 & 3, 161 Barry St >>>> Carlton South Vic 3053 Australia >>>> >>>> Ph: +61 3 8344 1861 >>>> Fax: +61 3 9348 0469 >>>> >>>> fornitoa(a)unimelb.edu.au >>>> >>>> >>>> >>>> >>>> >>> >> >> Alex Fornito >> JN Peters Research Fellow >> Melbourne Neuropsychiatry Centre >> Department of Psychiatry >> The University of Melbourne >> >> Postal address: >> Melbourne Neuropsychiatry Centre >> National Neuroscience Facility >> Levels 2 & 3, 161 Barry St >> Carlton South Vic 3053 Australia >> >> Ph: +61 3 8344 1861 >> Fax: +61 3 9348 0469 >> >> fornitoa(a)unimelb.edu.au >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre Department of Psychiatry The University of Melbourne Postal address: Melbourne Neuropsychiatry Centre National Neuroscience Facility Levels 2 & 3, 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 fornitoa(a)unimelb.edu.au

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qdec error
by Michael Harms 03 Jan '08

03 Jan '08

Hello, First, ... Happy New Year! When trying to run a basic qdec analysis between two groups (using qdec from FS v4.0.2), I get an error in a pop-up window, which I've screen- captured and attached as a gif. This is a Linux-centos4 installation, and it doesn't have a /usr/pubsw directory, so I'm at a bit of a loss for how to interpret the error message. Do I need to install some other library? The output in the terminal at the point of the error window reads: -------- ... gdfReadHeader: reading /disk/conte_raid1/freesurfer/conte_mprage/qdec/Untitled/y.fsgd INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 classificationProband 2 classificationControl WARNING: Marker for class classificationProband was invalid. WARNING: Color for class classificationProband was invalid. WARNING: Marker for class classificationControl was invalid. WARNING: Color for class classificationControl was invalid. --------- If I click 'Ok', the popup goes away momentarily, and then the same popup window reappears. If I click 'Ok' a second time, I get an inflated surface with p-values in the qdec display, but the popup error message continually re-occurs as I select different analyses under the "Scalars" box. I tried "setenv XLIB_SKIP_ARGB_VISUALS 1" wondering if that might be related, but this had no effect. thanks for any insight, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Status of the Source ?
by Ivan Blagoev Topolsky 30 Dec '07

30 Dec '07

Hello, I wanted to ask about what's hapenning with the source code, will it be release anytime soon ? The webpages say that it will be available any moment now, but in fact the message has remained such for quite some time : my last question about it on this list was back in summer 2006. Did some unexpected problem arise ? Or will actually the source code be available soon ? Also, another question : Are there developers trying to use GPGPU techniques to accelerate the processing speed ? (using nvidia's CUDA, ATI's Brook or similar technologies ?) Thank you for your help. - Ivan -

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mri_convert --out_orientation with inhomogeneous volumes
by Ray Fix 23 Dec '07

23 Dec '07

Dear FS Listers, mri_convert isn't giving me quite what I expected when I use it to reorient an inhomogeneous volume. I apologize in advance if it is my misunderstanding or something that has been covered before. These orientation issues make my head spin (as they do the subject data ;-). Consider the following example: > % mri_info volume.mgz > : > dimensions: 256 x 256 x 128 > voxel sizes: 1.0000, 1.0000, 1.3300 > : > Orientation : PIL > Primary Slice Direction: sagittal > : > I take this volume and reorient it with mri_convert to LIA orientation. > % mri_convert --out_orientation LIA volume.mgz volume_LIA.mgz But what it gives me back is unexpected. > % mri_info volume_LIA.mgh > : > dimensions: 256 x 256 x 128 > voxel sizes: 1.0000, 1.0000, 1.3300 > : > Orientation : LIA > Primary Slice Direction: coronal I was first surprised first that mri_convert was resorting to trilinear interpolation. It seems like this kind of transformation could be done with 100% fidelity using nearest neighbor. But the bigger concern is I would have also expected the output dimensions to be 128x256x256 with the voxel sizes 1.33, 1.00, 1.00. It seems like if you reorient a non cubic volume with mri_convert, it arbitrarily cuts some of the data out from the posterior and anterior. tkmedit display seems to confirm this. To put it another way, I would expect: > mri_convert --out_orientation PIL volume_LIA.mgz volume_PIL.mgz to generate at volume_PIL.mgz file that was voxel identical to the original volume.mgz. Thanks for your time. Ray

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where is the patient information in the mgz files
by Wang, Xin 23 Dec '07

23 Dec '07

Hello, Group, I have a problem to read patient information in the .mgz files. this information was stored in the header files of dicom files. Could sb. tell me how to read this information from the .mgz files? Thank you in advance, Xin Wang

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