Freesurfer December 2007

freesurfer@nmr.mgh.harvard.edu

45 participants
74 discussions

retinotopy help
by anisha narula 07 Dec '07

07 Dec '07

Hello, I am carrying a retinotopy analysis and not getting good flattened images. When I view the slices using the sliceview-sess -sf sessid -df sessdir -analysis rtopy -c eccen -map h -slice h command, there is apparent activation the region desired.I then created the maps using the paint-sess command. However when I view the results on the 3D volume using the surf-sess -sf sessid -df sessdir -analysis rtopy -retinotopy eccen command, the retinotopy is messed up. There seems to be some error in the registering of the functionals to the 3D volume. Perhaps I am missing a command or a flag. I have attached my sliceview images as well as the corresponding 3D volume images. I would really appreciate if you could take a look at them. Thank You Anisha

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Question about brain masking
by Dan Dillon 06 Dec '07

06 Dec '07

Dear FreeSurfers, I'm having some trouble with my brain masks. Below I have inserted a subject's T1.mgz and brain.nii overlay (made with preproc-sess). As you can see, the mask goes well beyond the boundaries of the brain. Any ideas what could cause this-perhaps noisy functional scans? The majority of my subjects' masks look like this. Should I worry about this? My brainmask.mgz files are all fine, and I can use those to mask out voxels for visualization purposes-Do I need to be concerned if my brain.nii volumes look this way? Would I fix by running mkbrainmask-sess and tweaking the "-threshold" argument? Thanks! Dan Dillon Affective Neuroscience Lab Harvard University

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estimated total intracranial volume
by Paul Greenberg 06 Dec '07

06 Dec '07

Hi All, I'm interested in the relationship between estimated total intracranial volume (eTIV), and the volume measures generated in aseg.stats and lh/rh.aparc.stats. I have used freesurfer v3.0.3 for this data set. Here I am using the output of aseg.stats for all volumes except the cerebral cortex while using the output of aparc.stats exclusively for estimates of cortical gray matter volume. As I'm looking at this data for multiple subjects I've used asegstats2table and aparcstats2table to extract the volume data for each subject (using the "--meas volume" flag). Question: When I add these volumes generated in aseg.stats (excluding cortex), and rh,lh aparc.stats (cerebral cortex only), should the total be very close to the eTIV value found in aseg.stats? Thanks, Paul -- Paul Greenberg, Ph.D. Radiology Department, University of California, San Diego VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2903 Fax: (858) 642-3836 pgreenberg(a)ucsd.edu

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mri_convert
by Anil Roy 06 Dec '07

06 Dec '07

Hello All, I wanted to convert the brainmask volume to analyze format. I'm not very familiar with the analyze format and had two questions. 1) The wiki mentions that converting to SPM-Analyze format could involve converting to multiple or single frames. What exactly are multiple or single frames? Are they just different slices? 2) When converting, I get the message INFO: set hdr.hist.orient to 'coronal flipped'. What does that refer to? I have posted the output from mri_convert below. Thanks, Anil. ----------------------------------------------------------------------------------------------------------------------------------------------------------------- [root@slr08 freesurfer]# mri_convert -ot spm $SUBJECTS_DIR/O-06-002/mri/brainmask.mgz /root/test.img mri_convert -ot spm /mnt/win/MRI_data/MWIN4/Freesurfer//O-06-002/mri/brainmask.mgz /root/test.img $Id: mri_convert.c,v 1.146 2007/07/26 19:26:26 greve Exp $ reading from /mnt/win/MRI_data/MWIN4/Freesurfer//O-06-002/mri/brainmask.mgz... TR=2300.00, TE=3.36, TI=900.00, flip angle=9.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /root/test.img... Analyze Output Matrix -1.000 0.000 0.000 129.678; 0.000 0.000 1.000 -82.220; 0.000 -1.000 0.000 140.347; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to 'coronal flipped' [root@slr08 freesurfer]#

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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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Freesurfer December 2007