Freesurfer January 2008

freesurfer@nmr.mgh.harvard.edu

54 participants
69 discussions

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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Memory problems
by Juergen Haenggi, Psychological Institute 03 Jan '08

03 Jan '08

Dear FS experts I tried to average the brains of 92 subjects. We used a MacPro Quad with 5 GB RAM and about 10 GB virtual memory. When running make_average_subject the following error occurred: Checking 91 /Applications/freesurfer/subjects/average/tmp/make_average_vol-tmp/seg-SNPs_Vp92.mgh nframestot = 92 Allocing output mri_concat(13587) malloc: *** vm_allocate(size=262144) failed (error code=3) mri_concat(13587) malloc: *** error: can't allocate region mri_concat(13587) malloc: *** set a breakpoint in szone_error to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 14117th slice Cannot allocate memory [Juergen-Haenggis-Computer-MacPro-Quad:/Applications/freesurfer/subjects] juergenh% Does it really mean there is too less memory or is it a similar problem occurred in other software, i.e. memory acquisition restriction by the Java Runtime Environment? Is there any possibility, beside buying more RAM, to run make_average_subject with the available 5 GB RAM? Thanks in advance and Happy New Year Best regards Juergen ------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -------------------------------------------------

3 2

focus in tkmedit
by Michael Harms 03 Jan '08

03 Jan '08

Hello, When using the "Multiple Orientations" display of tkmedit with the 'Select voxels tool' mode of operation, the centering of the images seems to "jump" around as I change the focus (i.e., green outlined quadrant) using a left click, and the cross-hair ends up at a location other than where the mouse cursor was located when the left-click was performed. Consequently, I have a hard time getting the "Multiple Orientations" view to display as I want. Is there a way around these behaviors? thanks, 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 --------------------------------------------------------------------

1 0

mri_convert
by HAMID REZA DABIRZADEH 03 Jan '08

03 Jan '08

Hi, I am very new to FMRI and would appreciate your help with my first attempt to use real data. I am trying to convert dicom images produced by a Siemens scanner to nii.gz format to be analysed by FSL FEAT. These BOLD images have 7 digit names without an extension and are in a folder on a CD which also contains a dicomdir file. Below you can see the command I have used and the output. The 001.nii.gz file has only one volume while the study consists of multiple volumes. Is there anything I should do differently. Thanks, Bahman [root@localhost Desktop]# mri_convert -i temp/45516912 -ot nii 001.nii.gz mri_convert -i temp/45516912 -ot nii 001.nii.gz $Id: mri_convert.c,v 1.146.2.1 2007/11/30 23:18:44 greve Exp $ reading from temp/45516912... Getting Series No Scanning Directory INFO: Found 723 files in temp INFO: Scanning for Series Number 80 WARNING: searching dicom file temp/dicomdir for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. WARNING: searching dicom file temp/dicomdir for Manufacturer tag 0x8, 0x70 WARNING: the result could be a mess. INFO: found 9 files in series INFO: loading series header info. INFO: sorting. RunNo = 79 INFO: (128 128 9), nframes = 1, ismosaic=0 AutoAlign matrix detected AutoAlign Matrix --------------------- 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; FileName temp/45516912 Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Symphony PatientName **** Date and time StudyDate 20070216 StudyTime 110335.484000 SeriesTime 112105.578000 AcqTime 112059.464999 Acquisition parameters PulseSeq epfid2d1_64 Protocol BOLD 1 (Dec 4) PhEncDir ROW EchoNo 0 FlipAngle 90 EchoTime 40 InversionTime -1 RepetitionTime 2000 PhEncFOV 240 ReadoutFOV 240 Image information RunNo 79 SeriesNo 80 ImageNo 1 NImageRows 128 NImageCols 128 NFrames 1 SliceArraylSize 9 IsMosaic 0 ImgPos 117.6862 129.3817 45.4824 VolRes 1.8750 1.8750 10.0000 VolDim 128 128 9 Vc -1.0000 0.0010 -0.0086 Vr -0.0000 -0.9940 -0.1097 Vs -0.0087 -0.1097 0.9939 VolCenter -2.6996 5.2827 76.0057 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2000.00, TE=40.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999962, 0.000951853, -0.00862145) j_ras = (-2.16616e-10, -0.99396, -0.109738) k_ras = (-0.00867384, -0.109734, 0.993923) writing to 001.nii.gz... _________________________________________________________________ Introducing the City @ Live! Take a tour! http://getyourliveid.ca/?icid=LIVEIDENCA006

3 2

A problem with Deflate compression of tif format
by Jiefeng Jiang 03 Jan '08

03 Jan '08

Hi, I met the problem of "Deflate compression support is not configured. TiffWrite: TIFFWriteScanline returned error" when I used mris_make_template. Currently I use libtiff4 for tiff interface and zlib1g for deflate compression. In addition, I linked libtiff.so.3 to libtiff.so.4. I also tested the two libs by opening and saving a sample tiff image and they worked well. I have no idea how to solve this, maybe I need to establish another link for deflate compression... Could somebody give me some advices? Thank you in advance! Jiefeng Jiang Medical image computing National lab of pattern recognition Institute of automation, CAS Beijing, China +86 10 62659278

2 1

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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Re: Freesurfer Digest, Vol 47, Issue 2
by Simon Rushton 02 Jan '08

02 Jan '08

I feel somewhat uneasy simply assuming that the process worked just because it didn't exit with an error. Is my concern misplaced? Should I feel happy about submitting a ms based on freesurfer analyses that have not been independently checked? If it is necessary/advisable to do some independent checking, are there a couple of simple things (later reconstructions) that can be checked that indicate whether all is fine, or whether it is necessary to go back and check systematically each of the various stages documented on the wiki pages? simon > Date: Wed, 2 Jan 2008 07:17:13 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] checking problems > To: Feng-Xian Yan <b9403208(a)stmail.cgu.edu.tw> > Cc: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <Pine.LNX.4.62.0801020716430.5653(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="big5" > > Hi, > > we don't usually stop and check anymore as things fail pretty > rarely. You > can look at the tutorial on the wiki for examples of the types of > failures > and how to fix them. > > cheers, > Bruce > > On > Wed, 2 Jan 2008, Feng-Xian Yan wrote: > >> Hi, >> I have some confusion. When I completely run the command, recon-all >> ¡Vs x249 ¡Vautorecon1, and I should stop to check for problems with >> intensity normalization, talairach transformation and skull >> stripping. >> How can I do to check these problems? And, which is I must do first? >> >> Thanks. >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >>

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checking problems
by Feng-Xian Yan 02 Jan '08

02 Jan '08

Hi, I have some confusion. When I completely run the command, recon-all –s x249 –autorecon1, and I should stop to check for problems with intensity normalization, talairach transformation and skull stripping. How can I do to check these problems? And, which is I must do first? Thanks.

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How to generate inflated.H file?
by Jiefeng Jiang 01 Jan '08

01 Jan '08

Hi, Happy New Year everybody! I met a problem when I tried to make a template using "mris_make_template", it needs ?h.inflated.H file. However, I only have ?h.inflated file. Does anyone know how to generate ?h.inflated.H file? Thank you in advance! Jiefeng Jiang Medical image computing National lab of pattern recognition Institute of automation, CAS Beijing, China +86 10 62659278

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