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30132 discussions

cortical thickness values in a specified gyrus...
by Gonzalo Rojas Costa 30 Nov '11

30 Nov '11

Hi: In rh.aparc.a2009s.stats file, appears the average cortical thickness (ThickAvg) value for frontal middle gyrus (G_front_middle): how can I get the values of the cortical thickness in that gyrus (for example), not the average value ?... Sincerely, Gonzalo Rojas Costa

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persistent bvecs error
by Alexander Lebedev 30 Nov '11

30 Nov '11

Dear Freesurfer users and developers, I decided to run Tracula with our DTI data and eventually got bvecs error. I tried different solutions without any results: added decimals after zeros, shortened all decimal points to 3, modified my locale - nothing helped. I'm providing you my trac-all log, original (with shortened and long decimal points: MMADI_C* ) and output bvecs- and bvals-, parameter file and my locale as well. [Workstation: CentOS 5.6 x86_64] Any advises and suggestions are very welcome... Thank you beforehand. --- Best Regards, Alex Lebedev Stavanger University Hospital, Norway P.S.: And one short question... I was just thinking that it might make sense to perform some of the preprocessing steps in FSL (considering that FS and FSL share these algorithms and the preprocessing for TBSS ran perfectly), but I didn't find any solution on this. Is there such an opportunity? *** LOCALE: LANG=en_US.UTF-8 LC_CTYPE="en_US" LC_NUMERIC="en_US" LC_TIME="en_US" LC_COLLATE="en_US" LC_MONETARY="en_US" LC_MESSAGES="en_US" LC_PAPER="en_US" LC_NAME="en_US" LC_ADDRESS="en_US" LC_TELEPHONE="en_US" LC_MEASUREMENT="en_US" LC_IDENTIFICATION="en_US" LC_ALL=en_US

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Re: [Freesurfer] FSGD file with two set of regressors adding up to 1
by Douglas N Greve 30 Nov '11

30 Nov '11

Hi Orjan, it looks like there are some errors in your design. The "Variables" function is only for continuous variables (covariates) such as Age. Sex and diagnosis are discrete variables and they should be coded as part of the class (eg, if you only wanted to add sex, then you'd have 4 classes Q1-Q4 for males and the same for females). doug Ørjan Bergmann wrote: > Dear Dr. Greve, > > I have been working with FreeSurfer for a while now, amongst others in > collaboration with my colleague Dr. Lars-Morten Rimol here in Oslo. We > have contected you on issues relating to FreeSurfer before, and hope > you have some insights as to how to deal with a particular problem > we've come across. > > We have a set of subjects divided into four groups, depending on how > they score on a particular test; the first group are those scoring in > the lower 25% (i.e. Q1), those scoring from 25-50% (Q2), etc. Each of > these groups additionally belong to one of 3 diagnostic groups; Scz, > BD and NOS. > > We have formulated this as a FSGD file: > Class Q1 > Class Q2 > Class Q3 > Class Q4 > Variables Age Sex Scz BD NOS > > We are interested in seeing if, when correcting for the age, sex and > diagnosis, there are differences between the groups. E.g. a contrast > vector would be [1 -1 0 0 0 0 0 0 0]. > > The problem is of course that the resulting design matrix resulting > from this FSGD file becomes singular since its first 4 colums and its > 3 columns each add up to 1. Clearly this design matrix is singular. > > In the context of FSGD-files, do you know of any other way to solve > this problem? > > --- > Mvh > Ørjan Bergmann, PhD > Post. Doc. > TOP-prosjektet > Universitetet i Oslo > -- 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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Problem with mri_glmfit-sim cache option in freesurfer 4.5.0
by ALEXA HUBER 30 Nov '11

30 Nov '11

Hi all, I am a new freesurfer user and am trying to use mri_glmfit-sim with --cache option from my freesurfer 4.5.0 installation. I followed the instructions on this page: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg14415.html but as the files are not available for download any more from the link indicated on that page, I instead downloaded the newest freesurfer version (v5.1.0) and took the files from there. I copied the "mult-comp-cor" directory into $FREESURFER_HOME/average/. and replaced the "mri_glmfit-sim" file in $FREESURFER_HOME/bin/. as suggested. I then ran the simulation on a previously done glm analysis like this: mri_glmfit-sim --glmdir n49.lh.ZM11_2age_oldf2.thick.glmdir --cache 2 pos The programme stops with error and gives me feedback as shown below. Does anybody know what I did wrong? I prefer not to switch to the newest freesurfer version as I heard this is not a good idea during an analysis (is that right?). Many thanks for any help! Alexa Here is the feedback: cmdline mri_glmfit --y n49.lh.M11_2age_oldf2.thick.10.mgh --fsgd n49_ZM11_2grp_2age_oldf2.fsgd doss --C M11_C01_C-P_000_doss.mtx --C M11_C02_00aCaP0_doss.mtx --C M11_C03_00aP-aC0_doss.mtx --C M11_C04_0000oldf2_doss.mtx --surf fsaverage lh --cortex --glmdir n49.lh.ZM11_2age_oldf2.thick.glmdir WARNING: unrecognized mri_glmfit cmd option doss SURFACE: fsaverage lh log file is n49.lh.ZM11_2age_oldf2.thick.glmdir/cache.mri_glmfit-sim.log cd /STORAGES/storage2/dati/FREESURFER/glm /usr/local/freesurfer-4.5.0/bin/mri_glmfit-sim --glmdir n49.lh.ZM11_2age_oldf2.thick.glmdir --cache 2 pos $Id: mri_glmfit-sim,v 1.36.2.1 2011/03/28 15:46:10 greve Exp $ Wed Nov 23 18:37:40 CET 2011 Linux fisiologia24 2.6.37.6-0.5-default #1 SMP 2011-04-25 21:48:33 +0200 x86_64 x86_64 x86_64 GNU/Linux neuroscienze setenv SUBJECTS_DIR /STORAGES/img800/home/neuroscienze/subjects FREESURFER_HOME /usr/local/freesurfer-4.5.0 Original mri_glmfit command line: cmdline mri_glmfit --y n49.lh.M11_2age_oldf2.thick.10.mgh --fsgd n49_ZM11_2grp_2age_oldf2.fsgd doss --C M11_C01_C-P_000_doss.mtx --C M11_C02_00aCaP0_doss.mtx --C M11_C03_00aP-aC0_doss.mtx --C M11_C04_0000oldf2_doss.mtx --surf fsaverage lh --cortex --glmdir n49.lh.ZM11_2age_oldf2.thick.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = doss fwhm = 14.676053 CSD /usr/local/freesurfer-4.5.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th20/mc-z.csd fname2ext: Command not found. mri_surfcluster --in n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/sig.mgh --csd /usr/local/freesurfer-4.5.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th20/mc-z.csd --mask n49.lh.ZM11_2age_oldf2.thick.glmdir/mask.mgh --cwsig n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.cluster. --vwsig n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.voxel. --sum n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.cluster.summary --ocn n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.ocn. --oannot n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.ocn.annot --annot aparc --csdpdf n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.pdf.dat --cwpvalthresh .05 --o n49.lh.ZM11_2age_oldf2.thick.glmdir/M11_C01_C-P_000_doss/cache.th20.pos.sig.masked. --no-fixmni --surf white ERROR: Option --no-fixmni unknown -- Dipartimento di Scienze Biomediche Università degli Studi di Modena e Reggio Emilia Via G. Campi, 287 41125 Modena, Italia Tel: +39-059 205 5684

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mri_glmfit-sim error with v5.0
by yukoyy 30 Nov '11

30 Nov '11

Hello I'm having a trouble with mri_glmfit-sim with v5.0, which is locally installed on Mac 10.6.8. Whan I ran: mri_glmfit-sim --glmdir MPglm.wls --cache 3.0 pos --cwpvalthresh .0166 I got: ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm15/pos/th30/mc-z.csd I have /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th30/mc-z.csd in my directory. It looks like I need to somehow tell freesurfer "/fsaverage/lh/", but how? Before mri_glmfit-sim, I did the followings: isxconcat-sess -df sessdirfile -sf sessidlist -analysis PreL -hemi lh -c 16vs4 -o MPgroup mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz % ------------------------------------------------------------------------- Also, when I did: mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite I got several warnings and errors (full error message pasted at the end of this email): > cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz > WARNING: unrecognized mri_glmfit cmd option --surface > WARNING: unrecognized mri_glmfit cmd option fsaverage > WARNING: unrecognized mri_glmfit cmd option lh > WARNING: unrecognized mri_glmfit cmd option --nii.gz .... > mri_glmfit --y /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii --C > MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz --sim mc-z 100 2 MPglm.wls/csd > /mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls /Users/kawabata/Documents/freesurfer > /sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii > Bus error I don't understand why mri_glmfit-sim calls mri_glmfit, and gives warnings? When I paste "mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz" in the command line, it works without any error. Thanks in advance! Yuko Yotsumoto % full error message regarding the second question ------------------------------------------- cmdline mri_glmfit --y ces.008.nii --wls cesvar.008.nii --osgm --surface fsaverage lh --glmdir MPglm.wls --nii.gz WARNING: unrecognized mri_glmfit cmd option --surface WARNING: unrecognized mri_glmfit cmd option fsaverage WARNING: unrecognized mri_glmfit cmd option lh WARNING: unrecognized mri_glmfit cmd option --nii.gz log file is MPglm.wls/mc-z.abs.2.mri_glmfit-sim.log cd /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4 /Applications/freesurfer/bin/mri_glmfit-sim --glmdir MPglm.wls --sim mc-z 100 2 mc-z.abs.2 --sim-sign abs --overwrite $Id: mri_glmfit-sim,v 1.24.2.5 2010/07/27 22:49:00 greve Exp $ Wed Nov 23 13:55:01 JST 2011 Darwin Hideaki-Kawabata-no-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64 kawabata setenv SUBJECTS_DIR /Users/kawabata/Documents/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 15.248189 nSimPerJob = 100 1/1 Wed Nov 23 13:55:01 JST 2011 mri_glmfit --y /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/ces.008.nii --C MPglm.wls/tmp.mri_glmfit-sim-6456/osgm.mtx --mask MPglm.wls/mask.nii.gz --sim mc-z 100 2 MPglm.wls/csd/mc-z.abs.2.j001 --sim-sign abs --fwhm 15.248189 --X MPglm.wls/Xg.dat --wls /Users/kawabata/Documents/freesurfer/sessions/MP/MEAN/MPgroup/PreL/16vs4/cesvar.008.nii Bus error

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Tkmedit Talairach coordinates
by Tanner,Jared J 30 Nov '11

30 Nov '11

Hi, I just wanted to verify what the Talaiarch coordinates reported in tkmedit actually are. Are they based on Matthew Brett's 10/8/98 non-linear transform from MNI305 space or are they actually MNI305 coordinates? See screenshot. I would like to get coordinates of voxels within subcortical structures for some fMRI work and need MNI coordinates rather than "true" Talaiarch. I'm trying to minimize the number of transformations. Thank you, Jared Tanner Doctoral Candidate Clinical and Health Psychology University of Florida

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extracting ROIs from the freesurfer atlases in Qdec
by Catherine Wan 30 Nov '11

30 Nov '11

Dear list, I would like to use specific regions from either the Destrieux Atlas (aparc.a2009s.annot), Desikan-Killiany Atlas (aparc.annot) for an ROI analysis. Is there a way to use these ROIs in Qdec (similar to WFUpicktlas)? If we need to trace them manually based on these atlases, what do we need to do within qdec to load the annot files? Many thanks, Catherine

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Students for position (fwd)
by Bruce Fischl 29 Nov '11

29 Nov '11

FYI ---------- Forwarded message ---------- Date: Tue, 29 Nov 2011 14:26:21 -0500 From: Thomas Talavage <tmt(a)purdue.edu> To: "Sutton, Brad" <bsutton(a)illinois.edu>, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>, Noam Harel <noam(a)cmrr.umn.edu>, dnoll(a)umich.edu, Peter A. Bandettini <bandettini(a)nih.gov>, xhu3(a)emory.edu, Steve Wright <smwright(a)tamu.edu> Subject: Students for position Hey folks --- If you could do one last ping of folks, anyone who wishes to apply for a position in BME here at Purdue should do so in the next few days (letters not needed immediately). We anticipate doing a first review of the imaging-related apps in the next week or so. https://engineering.purdue.edu/BME/AboutUs/FacultyPositions Thanks immensely! Tom

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TAL-to-avg35
by Antonella Kis 29 Nov '11

29 Nov '11

Dear experts, I would appreciate if you can provide me with the TAL-to-avg35 template. Thank you very much! ANtonella

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How to display the dtrecon results
by Antonella Kis 29 Nov '11

29 Nov '11

Dear Lilla, Sorry I am bother you one more time with a question: I was trying to display the dtrecon result smore exactly the GLM group analysis results. After I did the mri_concat */fa-tal.nii --o group-fa-tal.nii I created a mask: mri_concat */mask-tal.nii --o group-masksum-tal.nii --mean mri_binarize --i group-masksum-tal.nii --min .999 --o group-mask-tal.nii then I ran the GLM Fit: mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\ --fsgd your.fsgd --C contrast --glmdir group_analysis.glmdir My questions are: 1) How I can display the uncorrected significance map values for the group analysis? What files should I use? I checked the DTI basic tutorial and I was trying the following: freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group-masksum-tal.nii \ /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/sig.mgh:colormap=heat Is this right? Or I should use the mask.mgh 2) If my contrast is C = +1.00000 -1.00000 (I am not accounting for age nor for gender) the what the colours represents and how I can get the p values for the forming clusters? THANK YOU VERY MUCH! Antonella

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