Freesurfer

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30095 discussions

qdec matrix error
by stdp82＠virgilio.it 26 Mar '13

26 Mar '13

Hi, I'm performing qdec. This my file.dat 1 diagnosis discrete 2 1 Pathology 2 Controls2 Thickness_lh continuous 03 Thickness_rh continuous 04 NPStest continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- Thickness_lh 2.643 0.116 Thickness_rh 2.630 0.099 NPStest 0.774 1.203 Number of subjects: 31Number of factors: 4 (1 discrete, 3 continuous)Number of classes: 2Number of regressors: 8 NPStest is scored from 0 to 8. Qdec produces this error: Creating output directory /Applications/freesurfer/subjects/subject_prova/qdec/UntitledLoading y from /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/y.mghINFO: gd2mtx_method is dodsSaving design matrix to /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/Xg.datNormalized matrix condition is 1e+08Design matrix ------------------ 1.000 0.000 0.000 0.000 2.495 0.000; 1.000 0.000 0.000 0.000 2.712 0.000; 1.000 0.000 0.000 0.000 2.671 0.000; 1.000 0.000 0.000 0.000 2.728 0.000; 1.000 0.000 0.000 0.000 2.646 0.000; 1.000 0.000 0.000 0.000 2.555 0.000; 1.000 0.000 0.000 0.000 2.750 0.000; 1.000 0.000 0.000 0.000 2.555 0.000; 1.000 0.000 0.000 0.000 2.784 0.000; 1.000 0.000 0.000 0.000 2.586 0.000; 1.000 0.000 0.000 0.000 2.641 0.000; 1.000 0.000 0.000 0.000 2.561 0.000; 1.000 0.000 0.000 0.000 2.545 0.000; 1.000 0.000 0.000 0.000 2.495 0.000; 1.000 0.000 0.000 0.000 2.769 0.000; 1.000 0.000 0.000 0.000 2.740 0.000; 0.000 1.000 0.000 2.000 0.000 2.526; 0.000 1.000 0.000 2.000 0.000 2.761; 0.000 1.000 0.000 2.000 0.000 2.521; 0.000 1.000 0.000 0.000 0.000 2.592; 0.000 1.000 0.000 2.000 0.000 2.555; 0.000 1.000 0.000 2.000 0.000 2.671; 0.000 1.000 0.000 3.000 0.000 2.559; 0.000 1.000 0.000 3.000 0.000 2.469; 0.000 1.000 0.000 4.000 0.000 2.691; 0.000 1.000 0.000 2.000 0.000 2.522; 0.000 1.000 0.000 0.000 0.000 2.553; 0.000 1.000 0.000 2.000 0.000 2.702; 0.000 1.000 0.000 0.000 0.000 2.738; 0.000 1.000 0.000 0.000 0.000 2.789; 0.000 1.000 0.000 0.000 0.000 2.651;--------------------------------ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08--------------------------------Possible problem with experimental design:Check for duplicate entries and/or lack of range ofcontinuous variables within a class.If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/subject_prova/qdec/Untitled --surf fsaverage lh --label /Applications/freesurfer/subjects/subject_prova/fsaverage/label/lh.aparc.label --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-thickness-NPStest-Cor.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Cor-thickness-NPStest.mat 2. The FSGD file (if using one) 3. And the design matrix aboveError in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/subject_prova/qdec/Untitled --surf fsaverage lh --label /Applications/freesurfer/subjects/subject_prova/fsaverage/label/lh.aparc.label --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-thickness-NPStest-Cor.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Cor-thickness-NPStest.mat I don't understand what's happen? Thanks, Stefano

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error mris_anatomicalstats
by Linn Mittlestein 26 Mar '13

26 Mar '13

Dear Freesurfer experts, I have a question about trying to extract statistics from merged labels using mris_anatomical_stats. I have used the mri_annotation2label, and then the mri_merge label, however now when trying to do mris_anatomical stats, I get the error ; could not read input volume, eg Freesurfer cannot read the wm.mgz file. What step have I done wrong? Thank you very much, Kind Wishes, Linn

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Pial error (over estimation)
by Charles Malpas 25 Mar '13

25 Mar '13

Dear Freesurfer experts, I am having a strange problem with a single brain. Freesurfer is over estimating the pial surface by a great deal. Two things are weird: (a) it occurs to the same brain scanned 6 months apart, and (b) it doesn't occur is 5.1 (I am using 5.2 now). I have attached some screen shots. Any help would be greatly appreciated! Kind regards, - Charles ***apologies if you receive this message twice, I seem to have problems posting to the list*** -- *Charles Malpas * Master of Psychology (Clinical Neuropsychology) / PhD Candidate Melbourne School of Psychological Sciences & Department of Medicine (RMH) The University of Melbourne 3010 *Melbourne Brain Centre @ RMH* Neuropsychiatry Research Group* * Level 4, Main Building, Royal Melbourne Hospital Phone: 0451 116 434 Email: c.malpas(a)student.unimelb.edu.au Skype: charles.malpas

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algorithm mris_anatomical_stats
by Valtina Pouegue 25 Mar '13

25 Mar '13

Hi, Is it possible to get the algorithm of mris_anatomicacl_Stats. Just ot know which files it uses to compute metrics ... Thanks. VP

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advice in registering a binary mask to Freesurfer space.
by Joshua Lee 25 Mar '13

25 Mar '13

Hi All, I wanted to get peoples advice on the best method of registration/interpolation to use on a manually traced segmentation (and its structural) that is not in the same space and orientation as the structurals I started Freesurfer with (although they both originally came from the same image. I want to maintain the integrity of the manual traced binary mask through this registration and reslice. For a number of reasons, I do not want to take Freesurfers output to the space of the manual segmentation. What do people think is a good technique? Flirt nearest neighbor interpolation? Something different from Freesurfer? ANTs? - Josh

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problem with registration in preprocessing
by Maryam Vaziri Pashkam 25 Mar '13

25 Mar '13

Hi Doug, I am running fsfast preprocessing on my data and I am getting an error on one of the runs. This is the preprocessing code that I run: preproc-sess -s 130321_xu_Object4catmulti_01 -per-run -sliceorder siemens -fsd bold -fwhm 0 -mni305-2mm -surface self lhrh The error seems to happen during the fsl registration on the last run (out of 12 runs): /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 flirt.fsl -ref bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii -in bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat -init bold/018/tmp.bbregister.1228/fslregister/fslmat0.trans.mat -schedule /ncf/apps/freesurfer-5.1.0//bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort ERROR: flirt bellow is the register-sess log file. I have only included the section for the registration of the last run. I have looked at the raw data of this run and it does not look different from the other runs (all other runs are successfully registered). I am running freesurfer 5.1. Any idea how I can fix the error? Thanks, Maryam $Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $ Linux ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /ncf/apps/freesurfer-5.1.0/ mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/template.nii mri_convert bold/018/template.nii.gz bold/018/tmp.bbregister.1228/template.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/018/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998239, -0.0522464, 0.0280991) j_ras = (0.0500393, -0.995986, -0.0742193) k_ras = (0.031864, -0.0726825, 0.996846) writing to bold/018/tmp.bbregister.1228/template.nii... fslregister --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/template.nii --reg bold/018/tmp.bbregister.1228/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/fslregister --dof 6 Log file is bold/018/tmp.bbregister.1228/reg.init.dat.fslregister.log Fri Mar 22 14:42:18 EDT 2013 --s blue_street_kcb --mov bold/018/tmp.bbregister.1228/template.nii --reg bold/018/tmp.bbregister.1228/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/018/tmp.bbregister.1228/fslregister --dof 6 $Id: fslregister,v 1.34.2.1 2011/03/28 20:35:36 greve Exp $ ncfws08.rc.fas.harvard.edu Linux ncfws08.rc.fas.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -------------------------------------- /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 mri_convert /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii mri_convert /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/brainmask.mgz... TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00 i_ras = (-1, 4.47035e-08, -4.65661e-08) j_ras = (-5.58793e-08, -4.05125e-08, -1) k_ras = (-5.96046e-08, 1, 1.11759e-08) writing to bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii... -------------------------------------- /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 mri_convert bold/018/tmp.bbregister.1228/template.nii bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/018/tmp.bbregister.1228/template.nii bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from bold/018/tmp.bbregister.1228/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998239, -0.0522464, 0.0280991) j_ras = (0.0500393, -0.995986, -0.0742193) k_ras = (0.031864, -0.0726825, 0.996846) keeping frame 0 writing to bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii... Mov determinant is 35.3062 Swapping dims for pos det WARNING:: Flipping Left/Right orientation (as det < 0) tkregister_tcl /ncf/apps/freesurfer-5.1.0//tktools/tkregister2.tcl target volume bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii movable volume bold/018/tmp.bbregister.1228/template.nii reg file bold/018/tmp.bbregister.1228/fslregister/swapreg.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable bold/018/tmp.bbregister.1228/template.nii Tmov: -------------------- -3.086 0.000 0.000 108.000; 0.000 0.000 3.708 -61.182; 0.000 -3.086 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- 0.998 0.052 -0.028 3.086; 0.032 -0.073 0.997 -0.000; -0.050 0.996 0.074 -0.000; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- 0.998 0.052 -0.028 3.086; 0.032 -0.073 0.997 -0.000; -0.050 0.996 0.074 -0.000; 0.000 0.000 0.000 1.000; Determinant -1 subject = subject-unknown RegMat --------------------------- -1.000 0.000 0.000 3.086; 0.000 1.000 0.000 -0.000; -0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 tkregister2_cmdl --mov bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii --reg bold/018/tmp.bbregister.1228/fslregister/reg0.1262.dat --regheader --fslregout bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat0 --s blue_street_kcb --noedit tkregister_tcl /ncf/apps/freesurfer-5.1.0//tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii reg file bold/018/tmp.bbregister.1228/fslregister/reg0.1262.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target /ncf/vcn/Maryam/mri-space/subjects/blue_street_kcb/mri/orig.mgz Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii Tmov: -------------------- -3.086 0.000 0.000 108.000; 0.000 0.000 3.708 -61.182; 0.000 -3.086 0.000 108.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- -0.998 -0.052 0.028 3.326; 0.032 -0.073 0.997 -29.376; -0.050 0.996 0.074 29.949; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.998 -0.052 0.028 3.326; 0.032 -0.073 0.997 -29.376; -0.050 0.996 0.074 29.949; 0.000 0.000 0.000 1.000; Determinant 1 subject = blue_street_kcb RegMat --------------------------- -0.998 -0.052 0.028 3.326; 0.032 -0.073 0.997 -29.376; -0.050 0.996 0.074 29.949; 0.000 0.000 0.000 1.000; FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -35.3062, ref det = -1 Fri Mar 22 14:42:22 EDT 2013 /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 flirt.fsl -ref bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii -in bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/018/tmp.bbregister.1228/fslregister/fslmat0.trans.mat -schedule /ncf/apps/fsl-4.1.7/etc/flirtsch/xyztrans.sch -init bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat0 Fri Mar 22 14:42:30 EDT 2013 /ncf/vcn/Maryam/mri-space/studies/Obj4catmulti/unpackdata/130321_xu_Object4catmulti_01 flirt.fsl -ref bold/018/tmp.bbregister.1228/fslregister/refvol.fslregister.nii -in bold/018/tmp.bbregister.1228/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat bold/018/tmp.bbregister.1228/reg.init.dat.fsl.mat -init bold/018/tmp.bbregister.1228/fslregister/fslmat0.trans.mat -schedule /ncf/apps/freesurfer-5.1.0//bin/flirt.newdefault.20080811.sch terminate called after throwing an instance of 'NEWMAT::SingularException' Abort ERROR: flirt

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R: Re: R: Re: Problem with tracula: incomplete or lacking tracts
by stdp82＠virgilio.it 25 Mar '13

25 Mar '13

Hi Anastasia,now I have correct the nodif mask and run again trac-all. Is normal "WARN: Could not find satisfactory control point fit - try 83Finding center streamline" during -prior? Stefano ----Messaggio originale---- Da: ayendiki(a)nmr.mgh.harvard.edu Data: 25-mar-2013 18.02 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts I also remember that your brain masks had some big chunks of brain missing. Was whatever caused that fixed as well? On Mon, 25 Mar 2013, stdp82(a)virgilio.it wrote: > Yes, I fix them. I'm attacking the maps after the last trac-all. > > Stefano > > > ----Messaggio originale---- > Da: ayendiki(a)nmr.mgh.harvard.edu > Data: 25-mar-2013 17.26 > A: <stdp82(a)virgilio.it> > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: Problem with tracula: incomplete or lacking tracts > > > Hi Stefano - As I recall, we established that your bvecs were wrong. Did > you fix them? > > a.y > > On Mon, 25 Mar 2013, stdp82(a)virgilio.it wrote: > > > Hi Anastasia, > > > > I ran again trac-all, after checking all bvecs. Some tract are incomplete. Is possible that it depends from > > an error in my configuration file? > > > > I'm using to create bvecs file DTI TABLE CREATOR. Do you advice mi another one? > > > > Thanks, > > > > > > Stefano > > > > > > > > On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > Thank you Anastasia. > > > I'm checking bvecs/bvals. I obtain it by DTI table creator > > > (http://godzilla.kennedykrieger.org/~jfarrell/OTHERphilips/GUI.html) > > > > > > bvecs/bvals should be done. > > > > > > Gradients can be the unique responsable? > > > > > > > > > Stefano > > > > > > > > > > > > > > > ----Messaggio originale---- > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > Data: 22-mar-2013 17.07 > > > A: <stdp82(a)virgilio.it> > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts > > > > > > > > > Your gradient table is wrong. See where I've marked the corpus callosum in > > > your screenshot. The eigenvectors are not pointing along the corpus > > > callosum, but perpendicular to it. So they're off by 90 degrees, which > > > means the same is true about the vectors in your gradient table. > > > > > > On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > Hi Anastasia - I attacked the screenshots. > > > > Thanks, > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > Data: 22-mar-2013 1.39 > > > > A: <stdp82(a)virgilio.it> > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > Ogg: Re: [Freesurfer] R: Re: R: Re: R: R: Re: Problem with tracula: incomplete or lacking tracts > > > > > > > > > > > > Hi Stefano - There's nothing in these screenshots that tells you that the > > > > eigenvectors are correct. These are vectors, so the way to check them is > > > > to display them as lines. You display dtifit_V1 as lines, overlaid on > > > > dtifit_FA. Then you see if the lines point in the right direction. > > > > > > > > a.y > > > > > > > > On Fri, 22 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > Here they are attacked. > > > > > Thanks, > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > Data: 21-mar-2013 21.50 > > > > > A: <stdp82(a)virgilio.it> > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > Ogg: Re: R: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or > > > > > lacking tracts > > > > > > > > > > > > > > > Can you send a screenshot that shows dtifit_V1 and dtifit_FA? > > > > > > > > > > On Thu, 21 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > I have checked the gradient directions. How can I resolve the brain mask > > > > > > problem. > > > > > > Can I send you my files of this subject? > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > Data: 20-mar-2013 22.46 > > > > > > A: <stdp82(a)virgilio.it> > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > Ogg: Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or > > > > > lacking > > > > > > tracts > > > > > > > > > > > > > > > > > > There are chunks of the brain missing from the brain mask. This may cause > > > > > > some tracts to be incomplete or missing. > > > > > > > > > > > > But you should still check that the gradient directions are correct, so > > > > > > you know if you have multiple problems or just one. The FA map can't tell > > > > > > you if the gradient table was correct, you have to check the eigenvectors > > > > > > in dtifit_V1 for that. > > > > > > > > > > > > > > > > > > On Wed, 20 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > File attacked > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > Da: stdp82(a)virgilio.it > > > > > > > Data: 20-mar-2013 22.34 > > > > > > > A: <ayendiki(a)nmr.mgh.harvard.edu> > > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking > > > > > > tracts > > > > > > > > > > > > > > Thank you Anastasia. I'm checking gradient table but I would like > > > > > > underline that I'm noting some holes in > > > > > > > dti_FA.nii.gz and not in dwi.nii.gz (I have attacked the relative > > > > > > images). > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > > Data: 20-mar-2013 16.40 > > > > > > > A: <stdp82(a)virgilio.it> > > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts > > > > > > > > > > > > > > > > > > > > > Hi Stefano - Have you checked that your gradient table is correct by > > > > > > > looking at the output of the tensor fit? > > > > > > > > > > > > > > a.y > > > > > > > > > > > > > > On Wed, 20 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > > > Hi list and Anastasia, > > > > > > > > if you remember the last week I had same problems with tracula output: > > > > > > the final tract are lacking or > > > > > > > > incomplete for same subjects. Some of these are less wrong (only > > > > > forceps > > > > > > major), other have more evident > > > > > > > > error (you can see this in picture that I have attacked). > > > > > > > > > > > > > > > > To resolve this issue I have: > > > > > > > > > > > > > > > > 1-checked the correct overlap of dwi and dwi_mask > > > > > > > > 2-rerun data with new version 5.2 > > > > > > > > 3-rerun new registration using bbregister (fsl/spm option): for > > > > > example, > > > > > > in the subject of the picture > > > > > > > > attacked, the .mincost file now contains as first value 0.87 (previous > > > > > > it was 1.1) > > > > > > > > > > > > > > > > Please, give me an advise > > > > > > > > > > > > > > > > Thanks > > > > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > > Da: stdp82(a)virgilio.it > > > > > > > > Data: 12-mar-2013 17.47 > > > > > > > > A: <ayendiki(a)nmr.mgh.harvard.edu> > > > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > > Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap > > > > > > > > > > > > > > > > I got it from mri directory but I'm understanding that this directory > > > > > > isn't ok.I'm attacking the image > > > > > > > > from dlabel/diff/aparc+aseg.bbr.nii > > > > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > > > Data: 12-mar-2013 17.19 > > > > > > > > A: <stdp82(a)virgilio.it> > > > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > > Ogg: Re: [Freesurfer] R: Re: Question on tracula and dwi-T1 overlap > > > > > > > > > > > > > > > > > > > > > > > > Can you please answer my question? I can't really tell if the issue is > > > > > > due > > > > > > > > poor dwi-aseg overlap unless you tell me where you got that aseg > > > > > volume > > > > > > > > from. > > > > > > > > > > > > > > > > On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > > > > > Thank you Anastasia. What do you think about the issue in the file > > > > > > attacked > > > > > > > > > (I'm noting that same subjects are lacking of same > > > > > > > > > tracts or same tracts are incomplete) > > > > > > > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > ----Messaggio originale---- > > > > > > > > > Da: ayendiki(a)nmr.mgh.harvard.edu > > > > > > > > > Data: 12-mar-2013 17.02 > > > > > > > > > A: <stdp82(a)virgilio.it> > > > > > > > > > Cc: <freesurfer(a)nmr.mgh.harvard.edu> > > > > > > > > > Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap > > > > > > > > > > > > > > > > > > > > > > > > > > > Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's > > > > > > in > > > > > > > > > the dlabel/diff/ directory has been mapped to the same space as the > > > > > > DWI, > > > > > > > > > so those are the volumes that can be compared directly to > > > > > dwi.nii.gz. > > > > > > > > > > > > > > > > > > a.y > > > > > > > > > > > > > > > > > > On Tue, 12 Mar 2013, stdp82(a)virgilio.it wrote: > > > > > > > > > > > > > > > > > > > Hi list, > > > > > > > > > > > > > > > > > > > > I have two questions, please. > > > > > > > > > > > > > > > > > > > > I'm using version 5.1 to complete my analysis. > > > > > > > > > > > > > > > > > > > > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of > > > > > the > > > > > > same > > > > > > > > > > subject (figure 1 and 3). You can note the dwi do not overlap to > > > > > the > > > > > > aseg. > > > > > > > > > > How can I resolve this issue? > > > > > > > > > > > > > > > > > > > > 2-After TRACULA analysis, I'm noting that same subjects are > > > > > lacking > > > > > > of > > > > > > > > > same > > > > > > > > > > tracts or same tracts are incomplete (figure 3). > > > > > > > > > > > > > > > > > > > > Could it depends from the issue in question 1? I'm thinking to > > > > > rerun > > > > > > all > > > > > > > > > > using version 5.2 but before starting new analyses, I'd like to > > > > > ask > > > > > > you > > > > > > > > > > which is the possible error. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > > > > Freesurfer mailing list > > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > > > Freesurfer mailing list > > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > > Freesurfer mailing list > > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > > > Freesurfer mailing list > > > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > >_______________________________________________ > > > > Freesurfer mailing list > > > > Freesurfer(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > >_______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > 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. > > > > > > > > > > > >_______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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. > > > > > > > > > > >_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.

2 1

surf2vol
by Daniel Lumsden 25 Mar '13

25 Mar '13

Dear All Apologies for what I'm sure is a very basic question. I'm new to using freesurfer, and would like to generate cortical parcellations for running in probtrakx. I have followed the instructions from various sources and have managed to generate the parcellations from recon-all, extract the label files from the parcellation, then use mri_mergelabels and label2surf to generate the the .gii files needed for probtrakx. I'd like to be able to display the surface files for illustrative purposes, but I'm struggling to apply the surf2vol command. >From the terminal window I can see that the commands required are: surf2vol <surf> <refvol> <outvol> <convention> I presume that <surf> is the .gii file I'm trying to visualise, and <outvol> is to specify the name of the output volume the command will generate, but what should I be using as the <refvol>? I would be very grateful for any guidance. Please accept my apologies if I've missed a very obvious online explanation for this and thank you in advance. Dan Lumsden Clinical Research Fellow

2 1

-clean-* flags
by obregon＠nmr.mgh.harvard.edu 25 Mar '13

25 Mar '13

Hi, I was wondering if the -clean-* flags should only be used when you've performed manual edits on your volumes, or if they are also necessary when you re-process your subjects? For instance, let's say I edit the Talairach transform and run the entire recon-all process (using the -all flag) on a subject I had previously processed using the previous release of Freesurfer. If I had done no other manual edits on volumes such as brainmask.mgz, wm.mgz, etc., will these volumes be automatically overwritten when I run the latest version of recon-all, or do I need to specify the corresponding -clean-* flags in order for this to take place? Thanks, Gabriel

2 1

QDEC issues
by Tudor Popescu 25 Mar '13

25 Mar '13

Hello everyone, I created a qdec.table.dat for my design (a simple group analysis, with gender as categorical factor and age as continuous factor), and created a gender.levels file containing the values that are found in qdec.table.dat, spellt in exactly the same way (all files attached). However, when loading the file in QDEC, I get the error: *ERROR: Subject C01 has an invalid level 'controls' in the group column INFO: If 'group' is a discrete factor, then create a file named 'group.levels' containing the valid factor names one per line. Error loading the data table. * The strings under the fsid column (subject ID) correspond to those that I used after the –subjid xxx, in my previous call to recon-all (e.g. "C01, C02, M01, M02.."). The qdec.table.dat was created in Excel and saved as a tab-delimited txt file. Replacing the tabs with spaces/commas does not change the error message. What could be the problem? I also have a few more questions, if I may: - how much more accurate are the results of a QDEC analysis if an average subject is computed from the subjects of the sample, with make_average_subject, as opposed to using FS's default average subject, fsaverage? - the qdec.table.dat in the tutorial <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis>contains more than just "demographical information", for instance it contains the volumes of the left and right hippocampi; are these types of informations normally brought in from previous analyses (that may have been done in a package other than FS), or does one first have to obtain any such relevant predictors in FreeSurfer, before starting the QDEC analysis? - the QDEC tutorial seems to be for whole-brain analyses; the ROI analysis tutorial <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI>mentions nothing of QDEC, however; can ROI analyses not also be done in QDEC? - in the Group Analysis (non-QDEC) tutorial<http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>, the design matrix (Xg.dat) is in the form MembershipF| MembershipM|AgeF|AgeM, while the values in the contrast are said to correspond to the 4 parameters (intercept for F,M; slope for F,M). Either way, how can the contrast vector be interpreted to give the correlation between thickness and age? - in the same tutorial, why is the value 0 being given to the first two elements in the matrix, when it should only be given to nuisance variables? Many thanks in advance for any help! Tudor

2 1

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