Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

Error encountered while running selxavg3
by Dan Dillon 03 Dec '07

03 Dec '07

Dear FreeSurfers, On my maiden voyage with selxavg3, I've encoutered an error and could use some help. After processing several subjects successfully, selxavg3 quit unexpectedly. Here is the exact message: Warning: matrix is singular to working precision > In fast_selxavg3 at 208 ntptot = 666, nX = 31, DOF = 635 ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 235 XCond = cond(XtX); Can anyone help me track down the source of this error and/or suggest a fix? Also, in the course of reviewing the error I saw the following notice: INFO: Key -timeoffset unrecognized, line 7, skipping I have the "timeoffset" argument set to half a TR in my mkanalysis step because I included slicetime correction during preprocessing. Does selxavg3 not recognize this option? Thanks in advance for any help you can provide. Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: dillon(a)wjh.harvard.edu

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Re: [Freesurfer] Cluster thresholding
by Alexander Fornito 03 Dec '07

03 Dec '07

Hi all, I was hoping someone could help me with the problem below. I'm a little stuck on my analysis. Thanks, Alex > 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 > >

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make_average_subject
by Emily Trittschuh 03 Dec '07

03 Dec '07

Dear List, Awhile back Cameron Ellis wrote to the listserv to ask about stats files for make_average_subject results. He was looking for information on the # of vertices and I believe he found another way to obtain that info. I would like to revert to his orginal question of whether there is any way to generate an ?.aparc.stats file from the make_average_subject command. I have a group of older normal controls that I want to turn into an "average" subject. They (as a mean individual) will be used for comparison with individual patients with an unusual form of dementia. It seems that as I move the cursor over the ?.avg_thickness surface it IS showing local numbers for thickness, but I can't find any stats files that will provide me with the std dev for these measurements. In addition I would love to be able to compare the results of the cortical parcellations between subjects and the average subject. Thank you! Emily Emily Trittschuh, PhD Neuropsychology Post-doctoral Fellow Cognitive Neurology and Alzheimer's Disease Center Northwestern University Feinberg School of Medicine 320 E. Superior Street, Searle 11-579 Chicago, IL 60611 phone 312/503-1155 fax 312/908-8789

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Retinotopy and MT+ localization analysis help
by anisha narula 03 Dec '07

03 Dec '07

To whom it may concern, I am a beginner at FreeSurfer and using it in my senior biomedical design project at Boston University. I have performed retinotopy and MT+ localization before on a previous subject and obtained good results. However, I have carried out retinotopy and MT+ analysis on another subject using the same commands and have not obtained significant results. I have tried the analysis using motion corrected and motion uncorrected data, and have obtained bad results both times. I have attached the fieldsign image above obtained from the retinotopy analysis. Please let me know, if you would like to see the polar, eccentricity or MT+ images as well. I appreciate your time and concern Thank You, Anisha

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sequence]
by Roberto Roiz Ssantiáñez 03 Dec '07

03 Dec '07

Hello all, Im a new user of FreeSurfer. We would like to start processing a large number of the scans. We have acquired three different sequences using a 1.5T GE scanner (a three dimensional T1-weighted SPGR sequence, and two dimensional PD and T2 sequences). We have already processed those sequences using BRAINS2, and we have obtained a segmented image. I was wondering which sequence would fit best with FreeSurfer: 1) The T1-weighted SPGR sequence. 2) The T1-weighted SPGR sequence and the PD sequence together. 3) The segmented image obtained using BRAINS2. Thanks a lot Roberto Roiz ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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after recon-all.
by Jamie Hanson 30 Nov '07

30 Nov '07

Hey Folks- So I just finished autorecon-all on a few subjects and wanted to do some prelim analyses. On the tutorial pages, there is some talk of using QDEC or FSGD... I couldn't really find a good page contrasting the two... or is there not a difference? Is FSGD just a dated version? And per the tutorial pages, I need to have pre-smoothed fsaverage surfaces using recon-all -s <subjid> -qcache. I keep getting an output of ERROR: cannot find fsaverage in /study/eemri/freesurfer, which is my subject dir. So I switched to doing mris_preproc for each subject. But I keep getting an ERROR: Cannot find fsaverage (output). So what am I doing wrong? Which target should I specify? Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53706 ***Please note my new email: jamielarshanson(a)gmail.com***

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Error message
by Juergen Haenggi 30 Nov '07

30 Nov '07

Dear Freesurfer experts We had a problem with the preprocessing of one subject. The following error occurred: #-------------------------------------------- #@# Intensity Normalization Fri Nov 30 12:41:05 CET 2007 /Applications/freesurfer/subjects/Handball_Vp02/mri \n mri_normalize -g 1 nu.mgz T1.mgz \n using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.225 0.008 -0.123 0.315; 0.032 1.156 0.002 0.516; 0.073 0.044 1.349 -3.397; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 SPLINE_CUBIC_SET - Fatal error! The number of data points N must be at least 2. The input value is 1. Darwin juergen-haenggis-computer.local 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386 recon-all exited with ERRORS at Fri Nov 30 12:41:09 CET 2007 What does it mean? How to solve that problem? Thanks in advance 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) -----------------------------------------------------------

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problem viewing in tksurfer
by Sarah Andersen 29 Nov '07

29 Nov '07

Dear FreeSurfers, I am having a problem viewing in tksurfer: I can only see a sliver of the brain. This sliver will rotate and do everything that tksurfer is supposed to do, but I can't view any more of the brain than a tiny piece of the occipital lobe. I have tried this with several different files, and had the same issue for each of them. Tkmedit, on the other hand, works fine. I am using FreeSurfer stable release v4.0.1 on Windows Vista using a virtual machine. FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v4.0.1 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-8.1.15.el5 i686 I am working through the on-line tutorial and followed the directions to set my environment to /buckner_data/tutorial_subjs I also set SUBJECTS_DIR to $TUTORIAL_DATA . I am working in $SUBJECTS_DIR. The "which" command gives me /usr/local/freesurfer/bin/tksurfer I ran the command "tksurfer good_output lh inflated". The following is the resulting message. surfer: current subjects dir: /usr/local/freesurfer/subjects/freesurfer_tutorial/buckner_data/tutorial_sub js surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects/freesurfer_tutorial/buckner_data/tutorial_sub js surfer: Reading header info from /usr/local/freesurfer/subjects/freesurfer_tutorial/buckner_data/tutorial_sub js/good_output/mri/T1.mgz surfer: vertices=125352, faces=250700 Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... In the email archives I have seen a response that mentioned the NVidia graphics card. I checked and my machine does have an NVidia graphics card. Thanks in advance for the help! Sarah Sarah Andersen Research Specialist Dept. of Neurology Dept. of Speech, Language, and Hearing Sciences (520) 621-9878 sander(a)email.arizona.edu

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Another talairach question . . .
by Dan Dillon 29 Nov '07

29 Nov '07

Dear FreeSurfers, In the course of checking my skull-strips I discovered that one of my subjects does not have a T1.mgz because they did not pass the automatic Talairach failure detection. I checked the transformation with tkregister2 and -fstal, and it actually looks quite good; the brain is tilted, but the Talairach brain follows the tilt nicely. Nonetheless, to move things forward I made a few small edits and saved the registration. I then re-ran autorecon1 using the -notalairach option (at the end of the command line) in order to make use of my edits. However, I got the exact same error back-Talairach transformation ***FAILED***--and consequently there's no T1.mgz. I thought that by specifying -notalairach at the end of the command line while running autorecon1, I would be bypassing the Talairach detector and thus would be able to avoid this problem, but I'm obviously wrong. How do I make use of my edited Talairach and get autorecon1 to continue? Thanks in advance, Dan Dillon, Ph.D. Post-doctoral Fellow Affective Neuroscience Lab Dept. of Psychology, Harvard University Phone: (617) 495-1889 E-mail: dillon(a)wjh.harvard.edu

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Gradient Non-Linearity Distortion Correction for Allegra 3T
by Sergei Bogdanov 29 Nov '07

29 Nov '07

Dear Freesurfers, I have downloaded grad_unwarp_bash.tar.gz from the NBIRN site and am trying to follow the instructions on http://www.nbirn.net/tools/gradient_non_linearity/index.shtm and https://surfer.nmr.mgh.harvard.edu/fswiki/GradientUnwarping?action=highligh… to create the displacement table for Allegra .. I do have the spherical harmonics expansion file for Allegra .. allegra.coef .. I have done: $ perl gradient_unwarp_converter.pl allegra.coef which created grad_unwarp_tables/allegra.coef Now I am trying to run: $ ./scripts/create_displacement_table siemens allegra and I get: Table names: avanto, sonata, trio, brm, crm If you would like to use a different table name, please contact czanner(at)nmr.mgh.harvard.edu for further information Which table name I should use for Allegra 3T or are there any other options? .. I did contact Silvester but sounds like he's been off the project for a year and might not be able to help ... Thank you, Sergei Bogdanov Research Assistant Lewis Center for Neuroimaging University of Oregon sbogdano(a)uoregon.edu

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