Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

wm boundries
by Amy DeLuca 06 Dec '07

06 Dec '07

Hi All, I am having difficulties with a subject and would like advice on anything else I can try. I've attached a jpeg of my issue. It appears as though the voxels are included and have white matter values but the wm boundaries seem to be dipping into the left ventrical and I've tried re-running recon with control points but it still doesn't fix the boundary lines. Thanks, ~Amy~

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qdec Table Loading Error
by James N. Porter 05 Dec '07

05 Dec '07

Hello- I'm getting a rather nondescript message of "Error loading the data table" when I try to load my qdec.table.dat into the qdec GUI. I've tried using Excel, OpenOffice Calc, OpenOffice Wordprocessor, and Kate to save my table as a tab-delimited text file. Nothing works. Any suggestions on where I can go next to get a table in the proper format for qdec to read? -- Jim Porter Graduate Student Clinical Science & Psychopathology Research University of Minnesota

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Retinotopy analysis help
by anisha narula 05 Dec '07

05 Dec '07

Dear Doug, I have attached the polar and eccentricity volume and flattened images for the same subject. I also included the fieldsign image which I previously sent you. I would really appreciate if you could take a quick look at them. Thank You! Anisha

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White matter hypointensities?
by Chris Watson 04 Dec '07

04 Dec '07

What are white matter hypointensities supposed to represent? I'm seeing this segmentation group a lot around the lateral ventricles, caudate, etc. thanks, Chris

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Re: [Freesurfer] Cluster thresholding
by Alex Fornito 04 Dec '07

04 Dec '07

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. 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

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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

2 1

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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