Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

Re: [Freesurfer] 5.1.0 volume analysis in native space
by Douglas N Greve 03 May '12

03 May '12

If you just run selxavg3-sess, it will do the processing. If you want to run preproc-sess separately, then you can specify -per-session instead of -per-run to get things in native space. doug On 05/02/2012 02:55 PM, Maya Rosen wrote: > > Hi Doug, > Ok I see the -native flag in mkanalysis. But there is no -native flag > in preproc-sess. How do I go about preprocessing and analyzing the > data all in native volume space? > Thanks for your help, > Maya > > On Apr 26, 2012 4:39 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > There is (or should be) a -native flag to mkanalysis-sess > doug > > On 04/26/2012 11:09 AM, Maya Rosen wrote: > > Hi all, > > In v5.1.0 is there a way to do a volume analysis in native > space? I know when you do mkanalysis for the surface you can > use -surface self. But for the volume analysis the only flag I > see is -mni305. Is there some way to give it a native space > flag for the volume? > > Thanks! > > > Maya > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > The information in this e-mail is intended only for the person to > whom it is > addressed. If you believe this e-mail was sent to you in error and > the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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mri_convert error
by Kambiz Tavabi 03 May '12

03 May '12

Hello, The command mri_convert -it dicom -ot mgz 0001_9746dc8ab0544b3c8460cc2925682ba3.dcm 001.mgz gives the following output: mri_convert -it dicom -ot mgz 0001_9746dc8ab0544b3c8460cc2925682ba3.dcm 001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from 0001_9746dc8ab0544b3c8460cc2925682ba3.dcm... Starting DICOMRead2() dcmfile = /home/kambiz/data/freesurfer/ilabs/tmp/206/DICOM/0001_9746dc8ab0544b3c8460cc2925682ba3.dcm dcmdir = /home/kambiz/data/freesurfer/ilabs/tmp/206/DICOM Ref Series No = 301 Found 707 files, checking for dicoms WARNING: tag image orientation not found Found 705 dicom files in series. WARNING: tag image orientation not found First Sorting Computing Slice Direction Vs: 85.2923 -138.9 161.601 Vs: 0.371599 -0.605155 0.704061 Second Sorting Counting frames nframes = 1 nslices = 705 ndcmfiles = 705 MRIalloc(0, 0, 705): bad parm ERROR: mri alloc failed I am running freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 on RedHat 5.8 I don't understand what the problem is? Thanks in advance Kambiz -- ------------------------------------------------------------ Kambiz Tavabi PhD Institute for Learning & Brain Sciences 1715 Columbia Road N Portage Bay Building Box 357988 University of Washington Seattle, WA 98195-7988 Tel: 206-221-6415 ------------------------------------------------------------

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Freeview chrash
by Focke, Niels 03 May '12

03 May '12

Dear experts, I have experienced some problems with freeview. When loading a surface (both for my locally generated surfaces as well as for "bert" surfaces) the program exits (progress bar at approx. 10%) with this message: MatrixMultiply: m2 is null! The problem happens both for command line loading and GUI loading. Volume loading/viewing works fine. Has anyone had a similar problem? Or (even better) has a fix available? Version information: FREESURFER_HOME: /tools/freesurfer/live Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 RedHat release: CentOS release 5.7 (Final) Kernel info: Linux 2.6.18-274.el5 x86_64 Many thanks, Niels __________________________________________________________________________ Dr. Niels Focke Klinische Neurophysiologie UMG - Universitätsmedizin Göttingen

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reg-feat2anat error in Ubuntu 12.04 and a workaround
by Auer, Tibor 03 May '12

03 May '12

I have recently upgraded my Ubuntu system from 11.10 to 12.04. Before the upgrade I had no problem at all! After the upgrade the "reg-feat2anat" stopped working: it gave an error when converting the subject/mri/brainmask.mgz to featdir.feat/reg/freesurfer/tmp/refvol.fslregister.nii. However, when I do the conversion manually before the "reg-feat2anat", it works without further error. Is there any explanation for this behavior? Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Phone/Home: +49-(0)551-387-0076 Mobile: +49-(0)176-8012-7921 Mail: tauer(a)mpibpc.mpg.de

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the intensity VS the bias field
by bowang21＠mail.ustc.edu.cn 03 May '12

03 May '12

Dear all, I just want to know the difference between the intensity and the bias field.Is not the intensity indicated by the bias field? yours BOBO

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Comparing Cortical Thickness
by Jeff Sadino 03 May '12

03 May '12

Hello FreeSurfers, I want to compare cortical thickness differences between my two groups. Is this the correct pipeline? I ran make_average_subject on each group. To get the study thickness file in control space, I did this: mri_surf2surf --srcsubject study --srcsurfval study/surf/lh.thickness --trgsubject control --trgsurfval control/surf/study.thickness.mgh --hemi lh And then to calculate the differences, I used: mris_thickness_diff -out diff.mgh control/surf/pial control/surf/lh.thickness control/surf/pial control/surf/study.thickness.mgh. Is this the right way to do this? mris_thickness_diff says it should only be used on the same subject. mris_diff says it is still being tested. I also see mris_thickness_comparison. Which command is the best to use to get a thickness difference map? Thank you very much, Jeff Sadino

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osgm and correction for multiple comparisons
by Nicki Langer 03 May '12

03 May '12

Dear Freesurfer experts, I've calculated a I used the mri_glmfit for a one-sample group means (osgm) analysis: mri_glmfit --y Tatool_lh_thickness.15.mgh --fsgd FSGD.txt --glmdir Tatool_Thickness_LH.glmdir --surf average lh --osgm --cortex with following FSGD file: GroupDescriptorFile 1 Title Tatool working_memory_group_young MeasurementName external Tessellation surface PlotFile /Applications/freesurfer/subjects/average_tatool/stats/ glm_wm_young/Tatool_lh_thickness.15.mgh DesignMatFile X.mat dods DeMeanFlag -1 ReScaleFlag 0 ResidualFWHM 21.999092 LogY 0 Class working_memory_group_young Input 20969474.long.20969474_base working_memory_group_young Input 20969474_T2.long.20969474_base working_memory_group_young Input 23912784.long.23912784_base working_memory_group_young Input 23912784_T2.long.23912784_base working_memory_group_young Input 25579161.long.25579161_base working_memory_group_young Input 25579161_T2.long.25579161_base working_memory_group_young Input 25793236.long.25793236_base working_memory_group_young Input 25793236_T2.long.25793236_base working_memory_group_young Input 27363346.long.27363346_base working_memory_group_young Input 27363346_T2.long.27363346_base working_memory_group_young Input 29378587.long.29378587_base working_memory_group_young Input 29378587_T2.long.29378587_base working_memory_group_young Input 29572758.long.29572758_base working_memory_group_young Input 29572758_T2.long.29572758_base working_memory_group_young Input 41282970.long.41282970_base working_memory_group_young Input 41282970_T2.long.41282970_base working_memory_group_young Input 45220481.long.45220481_base working_memory_group_young Input 45220481_T2.long.45220481_base working_memory_group_young Input 49925500.long.49925500_base working_memory_group_young Input 49925500_T2.long.49925500_base working_memory_group_young Input 52695504.long.52695504_base working_memory_group_young Input 52695504_T2.long.52695504_base working_memory_group_young Input 56064196.long.56064196_base working_memory_group_young Input 56064196_T2.long.56064196_base working_memory_group_young Input 56403386.long.56403386_base working_memory_group_young Input 56403386_T2.long.56403386_base working_memory_group_young Input 60241875.long.60241875_base working_memory_group_young Input 60241875_T2.long.60241875_base working_memory_group_young Input 75765433.long.75765433_base working_memory_group_young Input 75765433_T2.long.75765433_base working_memory_group_young Input 76596439.long.76596439_base working_memory_group_young Input 76596439_T2.long.76596439_base working_memory_group_young Creator mri_glmfit SUBJECTS_DIR /Applications/freesurfer/subjects SynthSeed 1315181525 In a second step, I tried to correct for mulitple comparisons by using the glmfit_sim: mri_glmfit-sim --glmdir Tatool_Thickness_LH.glmdir --sim mc-z 5000 1.3 lh_mc-z.abs --sim-sign abs --overwrite But there was the following errormessage: ERROR: dimension mismatch between y and X. y has 16 inputs, X has 32 rows. Has anybody solved this problem before? (When I delete 16 rows of the FSGD file the simulation works, but then I don't trust the output anymore) Thanks for your help. Best, Nicolas Nicolas Langer MSc.UZH (lic. phil.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, 8050 Zurich, Switzerland 0041 44 635 73 96 (phone office) 0041 76 422 46 45 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) n.langer(a)psychologie.uzh.ch (email) nicolas.langer[at]uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website)

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Freeview scripting
by Auer, Tibor 03 May '12

03 May '12

Hi, I am looking for an option to script freeview as I could tksurfer via TCL. I checked the command-line options, and there is a "-cmd Load freeview commands from a text file", but I could not find any documentation about the language/syntax/commands. Could someone tell me, where can I find a reference about it? Thanks, Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Phone/Home: +49-(0)551-387-0076 Mobile: +49-(0)176-8012-7921 Mail: tauer(a)mpibpc.mpg.de

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Vertex correspondence between brains
by "Thomas W. Mühleisen" 03 May '12

03 May '12

Dear all, We have processed two individual datasets using the whole pipeline. We have recognized that the absolute number of generated vertices differs between the two brains (130k per hemisphere vs. 155k per hemisphere). Our question is how do the vertices from one brain correspond to those from the other brain? What happens to the 25k vertices which differ between both brains? Many thanks in advance for your answer! Best Regards, Thomas -- Dr. rer. nat. Thomas W. Muehleisen Postdoctoral Scientist Institute of Human Genetics Department of Genomics Life & Brain Center University of Bonn Sigmund-Freud-Strasse 25 D-53127 Bonn Germany Phone: +49 (0)228 6885 434 Cell phone: +49 (0)176 57001211 Fax: +49 (0)228 6885 401 Email: thomas.muehleisen(a)uni-bonn.de

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Freeview-FSL
by Auer, Tibor 03 May '12

03 May '12

Hi, a bit connecting to my previous mail: How can I overlay an FSL activation map onto the surface in FreeView? The solution working in tksurfer (i.e. overlay) is not working here. I can load the data as a volume, but then it is not projected to the surface. Thanks, Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Phone/Home: +49-(0)551-387-0076 Mobile: +49-(0)176-8012-7921 Mail: tauer(a)mpibpc.mpg.de

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Freesurfer May 2012