Freesurfer

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problem with c_ras in converted AFNI .BRIK
by Tom Holroyd (NIH/NIMH) [E] 21 Nov '12

21 Nov '12

If I do "3dcopy ortho+orig ortho.nii" then 3dinfo shows that the two datasets share the same coordinate system, however when I use mri_info, the results differ. For example, 3dinfo, both .BRIK and .nii: Geometry String: "MATRIX(0,0,-1,127,1,0,0,-127,0,-1,0,180):256,256,256" R-to-L extent: -128.000 [R] -to- 127.000 [L] -step- 1.000 mm [256 voxels] A-to-P extent: -127.000 [A] -to- 128.000 [P] -step- 1.000 mm [256 voxels] I-to-S extent: -75.000 {I] -to- 180.000 [S] -step- 1.000 mm [256 voxels]* mri_info ortho+orig says: voxel to ras transform: 0.0000 0.0000 1.0000 -128.5000 -1.0000 0.0000 0.0000 127.5000 0.0000 -1.0000 0.0000 75.5000 0.0000 0.0000 0.0000 1.0000 while mri_info ortho.nii produces (this is correct): voxel to ras transform: -0.0000 -0.0000 1.0000 -127.0000 -1.0000 -0.0000 -0.0000 127.0000 0.0000 -1.0000 0.0000 180.0000 0.0000 0.0000 0.0000 1.0000 in particular, the center of the volume appears to be translated. So if you run FreeSurfer on the .nii file, the surface is shifted relative to what you get when you run FreeSurfer on the .BRIK file, even though the original input was the same. Also mri_info seems to have shifted things to half-integer coordinates, while the .nii version doesn't. I'm not really sure about the half-integer thing, but it's a separate issue. I think the problem is a bug in utils/afni.c, where it calculates c_ras. I've attached a patch. The problem is that FreeSurfer wants ras coordinates, which are LPI coordinates in AFNI notation, and we're staring in dataset coordinates (here ASL). First the transform matrix is computed (correctly). Then c_ras is calculated using the AFNI DELTA and ORIGIN header fields. I'm really not sure what the old code was doing, the terms seem to be associated the wrong way. The new code correctly multiplies the ORIGIN times the DELTAs to get all negative numbers in dataset coordinates (that is, the origin). This is then added to the center, also in dataset coordinates, and then this is multiplied by the rest of the transform matrix, which is a vox2ras matrix, yielding c_ras that agrees with the result from the .nii file. Except for that half-integer thing, which boils down to the afni.c code doing (w-1)/2 and the .nii file code doing w/2. Perhaps the AFNI code shouldn't subtract 1 either ? {the relevant lines are also part of the patch, but I left in the (w-1)/2} Unfortunately it seems there is no easy way to compute the correct c_ras if you started with a .BRIK, unless you have the original .BRIK. In that case 3dcopy it to a .nii file and mri_info that. Err, I haven't actually tested the patch ... I'm fairly certain it's the .nii file results that are correct, and not the other way around. It would be nice to confirm that this happens with other datasets besides the one I tried. It's easy to check if you have an AFNI dataset sitting around. Thanks, Tom -- The white knight is talking backwards.

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Re: [Freesurfer] Pixelated DTI mask from Tracula
by Anastasia Yendiki 21 Nov '12

21 Nov '12

Hi Alessia - So it's the FA map. Yes, this doesn't look like a correct FA map, there's no contrast between the white matter and everything else. The calculation of the FA has nothing to do with the freesurfer or tracula algorithms. It just uses your DWI data set, the gradient directions and the b-values, so these 3 things must be in disagreement if the FA doesn't come out right. I'd look into whether the subjects that have this problem were scanned with a different protocol or if the gradient directions and b-values were not extracted properly for them. Hope this helps, a.y On Wed, 21 Nov 2012, Alessia Sarica wrote: > Hi Anastasia,thanks for your fast reply. > > I mean the file named dtifit_FA.nii > > I've re-run twice recon-all and tracula both, but it doesn't change the result. > > Best regards, > Alessia. > > 2012/11/21 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Hi Alessia - I'm not sure what you're referring to as "the dti mask". Can you give me the file > name of the image that you're displaying in the screehshot? It does look like noise. > > Thanks, > a.y > > On Wed, 21 Nov 2012, Alessia Sarica wrote: > > Dear Freesurfer Users,I'm a Ph.D. Student and I'm working on tractography using > Tracula, > with the aim of conducting statistical analysis on the FA values. > > I have a cohort of 18 Amyotrophic Lateral Sclerosis Patients, and i'm doing all the > process phases, > starting from recon-all, ending to trac-all path. > > I've attached a text file with info about DTI DICOM extracted by ImageJ. > > Now, my problem is about the dti mask, as you can see on the attached image, a > pixelated one is obtained, > even if > the left and right cst tracts seem good. This problem only occurs in few patients, > not in all of them, even > if the script > is the same for all. > > This is the script i'm using: > > #Patient_name > setenv SUBJECTS_DIR $TUTORIAL_DATA/Patient_recons > set dtroot = $TUTORIAL_DATA/Patient_tracula > set subjlist = (Patient_name) > set runlist = (1) > set dcmroot = $TUTORIAL_DATA/Patient_tracula > set dcmlist = (Patient_name/orig/MR000000) > set bvalfile = > $TUTORIAL_DATA/Patient_tracula/Patient_name/bfiles/Patient_name.bval > set bvecfile = > $TUTORIAL_DATA/Patient_tracula/Patient_name/bfiles/Patient_name.bvec > set nb0 = 1 > set dob0 = 0 > set doeddy = 1 > set dorotbvecs = 1 > set usemaskanat = 0 > set thrbet = 0.3 > set doregflt = 1 > set doregbbr = 0 > set doregmni = 1 > set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz > set pathlist = (lh.cst_AS rh.cst_AS \ > lh.ilf_AS rh.ilf_AS \ > lh.unc_AS rh.unc_AS \ > fmajor_PP fminor_PP \ > lh.atr_PP rh.atr_PP \ > lh.cab_PP rh.cab_PP \ > lh.ccg_PP rh.ccg_PP \ > lh.slfp_PP rh.slfp_PP \ > lh.slft_PP rh.slft_PP) > > set ncpts = 5 > set nburnin = 200 > set usetrunc = 1 > set nkeep = 5 > set nsample = 5000 > > > I want to highlight that bval and bvec files are obtained from the tool dicom2nift, > because Tracula is not > able to extract them from DICOM header. > I will really appreciate your help. > > Best regards, > Alessia. > > > -- > Alessia Sarica > Ph.D. Student Biomedical and Informatics Engineering, > Bioinformatics Laboratory, Department of Surgical and Medical Sciences, > University "Magna Græcia" of Catanzaro, > Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY. > Phone: +3909613694193 > > > > > 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. > > > > > -- > Alessia Sarica > Ph.D. Student Biomedical and Informatics Engineering, > Bioinformatics Laboratory, Department of Surgical and Medical Sciences, > University "Magna Græcia" of Catanzaro, > Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY. > Phone: +3909613694193 > >

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freesurfer@nmr.mgh.harvard.edu
by Gabriel Gonzalez Escamilla 21 Nov '12

21 Nov '12

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Pixelated DTI mask from Tracula
by Alessia Sarica 21 Nov '12

21 Nov '12

Dear Freesurfer Users, I'm a Ph.D. Student and I'm working on tractography using Tracula, with the aim of conducting statistical analysis on the FA values. I have a cohort of 18 Amyotrophic Lateral Sclerosis Patients, and i'm doing all the process phases, starting from recon-all, ending to trac-all path. I've attached a text file with info about DTI DICOM extracted by ImageJ. Now, my problem is about the dti mask, as you can see on the attached image, a pixelated one is obtained, even if the left and right cst tracts seem good. This problem only occurs in few patients, not in all of them, even if the script is the same for all. This is the script i'm using: #Patient_name > setenv SUBJECTS_DIR $TUTORIAL_DATA/Patient_recons > set dtroot = $TUTORIAL_DATA/Patient_tracula > set subjlist = (Patient_name) > set runlist = (1) > set dcmroot = $TUTORIAL_DATA/Patient_tracula > set dcmlist = (Patient_name/orig/MR000000) > set bvalfile = $TUTORIAL_DATA/Patient_tracula/Patient_name/bfiles/ > Patient_name.bval > set bvecfile = $TUTORIAL_DATA/Patient_tracula/Patient_name/bfiles/ > Patient_name.bvec > set nb0 = 1 > set dob0 = 0 > set doeddy = 1 > set dorotbvecs = 1 > set usemaskanat = 0 > set thrbet = 0.3 > set doregflt = 1 > set doregbbr = 0 > set doregmni = 1 > set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz > set pathlist = (lh.cst_AS rh.cst_AS \ > lh.ilf_AS rh.ilf_AS \ > lh.unc_AS rh.unc_AS \ > fmajor_PP fminor_PP \ > lh.atr_PP rh.atr_PP \ > lh.cab_PP rh.cab_PP \ > lh.ccg_PP rh.ccg_PP \ > lh.slfp_PP rh.slfp_PP \ > lh.slft_PP rh.slft_PP) > > set ncpts = 5 > set nburnin = 200 > set usetrunc = 1 > set nkeep = 5 > set nsample = 5000 I want to highlight that bval and bvec files are obtained from the tool dicom2nift, because Tracula is not able to extract them from DICOM header. I will really appreciate your help. Best regards, Alessia. -- Alessia Sarica Ph.D. Student Biomedical and Informatics Engineering, Bioinformatics Laboratory, Department of Surgical and Medical Sciences, University "Magna Græcia" of Catanzaro, Viale Europa (Località Germaneto), 88100 CATANZARO, ITALY. Phone: +3909613694193

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Research Fellow/Postdoc: Functional MRI & EEG Neuroimaging in Dementia
by Direktion, Institut f. Schlaganfall- und Demenzforschung 21 Nov '12

21 Nov '12

The Institute for Stroke and Dementia Research (ISD) is looking for a Research Fellow/Postdoc: Functional MRI & EEG Neuroimaging in Dementia RESEARCH FOCUS and RESPONSIBILITIES: The research fellow/postdoc will work on multimodal imaging of human brain changes in early stages of Alzheimer's disease and cerebrovascular disease. The funded research project has a strong focus on the combined acquisition of functional MRI and high-density EEG along with other neuroimaging modalities. The establishment of the fMRI-EEG task-related paradigm and statistical analysis will be a key part of the responsibilities of research position. The fellow will work in a dynamically growing neuroimaging team and is encouraged to bring in own research ideas. REQUIREMENTS: Research experience in EEG and fMRI of brain changes is strongly encouraged. An independent work style and solid knowledge of programming and statistics is a plus. Familiarity with biological or clinical aspects of Alzheimer's disease is not a prerequisite. An enthusiastic, reliable and independent work style will provide a good fit for our team. OFFER: Our institute offers an excellent multidisciplinary environment and state-of-the-art multimodal neuroimaging equipment (3T MRI, high-density fMRI compatible EEG, molecular PET). The research fellow will have clearly defined task definitions, access to all data sets of the research project, and advanced technical support to facilitate efficient work conditions. The fellow will work in a friendly, dynamic, and highly productive team, headed by Prof. Michael Ewers, PhD. The University of Munich, Germany, and its clinics figure among Germany's premier and internationally competitive biomedical research sites funded by the government's German Universities Excellence Initiative. The Institute for Stroke and Dementia Research (ISD) is a thriving new research-dedicated institution of the University of Munich (http://www.klinikum.uni-muenchen.de/Institut-fuer-Schlaganfall-und-Demenzfo…) The ISD will be housed soon in a top-notch research facility that is currently being build and will eventually attract around 100 staff members, graduate students, scholars and foreign scholars. Salary is according to TV-L. The position is limited for two years, with a possible extension. Disabled persons will be preferentially considered in case of equal qualification. Presentation costs can unfortunately not be refunded. For more information, please contact Mr. Frühauf, Tel.: +49 (0)89 7095 7800 (E-Mail: isd(a)med.uni-muenchen.de) HOW TO APPLY: Your application - preferably in electronic form - with the usual documents indicating the earliest possible starting date should be directed to: Klinikum der Universität München, Institute for Stroke and Dementia Research Markus A. Frühauf, Managing Director ISD Heiglhofstr. 55 81377 Munich | Germany E-Mail: isd(a)med.uni-muenchen.de Viele Grüße Lilo Thomas Assistentin der Institutsleitung Institut für Schlaganfall- und Demenzforschung (ISD) Klinikum der Universität München Heiglhofstraße 55 D-81377 München Telefon: +49 (0)89 7095 - 7801 Fax: +49 (0)89 7095 - 8729 E-Mail: lilo.thomas(a)med.uni-muenchen.de<mailto:lilo.thomas@med.uni-muenchen.de> Internet: www.isd.klinikum.uni-muenchen.de<http://www.isd.klinikum.uni-muenchen.de/>

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Re: [Freesurfer] (no subject)
by Hugh Pemberton 20 Nov '12

20 Nov '12

Hi Bruce, Just to let you know the new mris_topo_fixer worked and there was no error with the recon. I also meant to ask how I might go about including parts of the temporal lobes that have been left out of the the surfaces due to severe atrophy but where there's no white matter so control points are of no use? I have attached a jpg few screen shots as examples.. Cheers, Hugh On 16 November 2012 14:44, Hugh Pemberton <hughpemberton1(a)gmail.com> wrote: > Hi Bruce, > > I also meant to ask how I might go about including parts of the temporal > lobes that have been left out of the the surfaces due to severe atrophy but > where there's no white matter so control points are of no use? I have > attached a few screen shots as examples.. > > Cheers, > Hugh > > > On 16 November 2012 11:14, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> this is a bug in the topology fixer. Maybe Zeke or Nick can post a new >> version of it? Was it mris_topo_fixer that was runing or mris_fix_topology? >> >> On Fri, 16 Nov 2012, Hugh Pemberton wrote: >> >> Hi Bruce, >>> Thanks for getting back to me. In terminal window it says >>> "freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0" but recon-all >>> -version >>> give me "$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $" >>> >>> Hugh >>> >>> >>> On 16 November 2012 11:05, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> wrote: >>> Hi Hugh >>> This is fixed in the newest version. What version are you running? >>> Bruce >>> >>> >>> >>> On Nov 15, 2012, at 6:48 PM, Hugh Pemberton <hughpemberton1(a)gmail.com> >>> wrote: >>> >>> Hi, >>> I have just received this error after a recon-all subjid- ___ >>> all : >>> >>> ERROR: _FindFacePath: could not find path! >>> /home/hughp/freesurfer/**subjects/B______________/**scripts >>> >>> mris_remove_intersection ../surf/lh.orig ../surf/lh.orig >>> >>> intersection removal took 0.00 hours >>> removing intersecting faces >>> writing corrected surface to ../surf/lh.orig >>> >>> rm ../surf/lh.inflated >>> >>> >>> cp ../surf/lh.orig_corrected ../surf/lh.orig >>> >>> Linux naoshi-WS 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 >>> 21:33:09 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux >>> >>> recon-all -s B______________ exited with ERRORS at Thu Nov 15 >>> 11:40:44 EST 2012 >>> >>> To report a problem, see >>> http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> >>> Many thanks in advance, >>> Best, >>> Hugh >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >>> >>> >>> >>> >

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Re: [Freesurfer] error in analyze command failed: mri_concat
by Douglas N Greve 20 Nov '12

20 Nov '12

I don't think it should be as long as you are consistent. It might be worth trying to track down this problem just so that you don't have to mix versions. doug On 11/20/2012 03:37 PM, Berg, S.F. van den wrote: > Hi Doug, > > Thanks for respons. We also install the dev version of freesurfer. We do the recon-all with the stable version. But smoothing with the dev version. Qdec is till now on correctly running with the dev version. > > Running qDEC with the dev version. Is that a problem? > > Thanks, > > Stan > ________________________________________ > From: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: 20 November 2012 21:04 > To: Berg, S.F. van den > Subject: Re: [Freesurfer] error in analyze command failed: mri_concat > > If you change the order or leave one out, does it still crash? > > On 11/19/2012 11:21 AM, Berg, S.F. van den wrote: >> Hi Doug, >> >> I try the mri_concat command with the --debug flag. Output is also in the text file >> >> Thanks. >> >> Stan >> >> -------- freesurfer-Linux-centos5_x86_64-dev-20110315 -------- >> SUBJECTS_DIR /data1/projects/ysbrand-vumc/pddatabase-freesurfer >> guest@somerenserver:~$ mri_concat --debug /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh11 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh >> 10 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh >> 9 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh >> 8 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh >> 7 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh >> 6 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh >> 5 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh >> 4 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh >> 3 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh >> 2 --o >> ninputs = 9 >> Checking inputs >> Checking 0 /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh >> reading MRI_FRAME structure from file... >> Segmentation fault >> >> >> ________________________________________ >> From: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >> Sent: 19 November 2012 16:50 >> To: Berg, S.F. van den >> Subject: Re: [Freesurfer] error in analyze command failed: mri_concat >> >> Hi Stan, can you run it again this time with --debug as the first >> argument and send me the result? >> thanks >> doug >> >> On 11/19/2012 08:00 AM, Berg, S.F. van den wrote: >>> Hi Doug, >>> >>> Like you said. I run the command in the terminal. >>> >>> I run the mri_concat command with 9 subjects in the command line. for the LH thickness and volume. A segmentation fault is the problem. >>> >>> What do i have to do in this case? >>> >>> Many thanks, >>> Stan >>> >>> -------- freesurfer-Linux-centos5_x86_64-dev-20110315 -------- >>> SUBJECTS_DIR /data1/projects/ysbrand-vumc/pddatabase-freesurfer >>> guest@somerenserver:~$ mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh >>> ninputs = 9 >>> Checking inputs >>> reading MRI_FRAME structure from file... >>> Segmentation fault >>> guest@somerenserver:~$ mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.thickness.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.thickness.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/caudalmiddlefrontal_curv/y.mgh >>> ninputs = 9 >>> Checking inputs >>> reading MRI_FRAME structure from file... >>> Segmentation fault >>> guest@somerenserver:~$ >>> >>> >>> ________________________________________ >>> From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >>> Sent: 13 November 2012 17:32 >>> To: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] error in analyze command failed: mri_concat >>> >>> Hi Stan, can you run that mri_concat command from the terminal command line and send me the resulting terminal output? I've put the command below >>> >>> doug >>> >>> mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh >>> >>> >>> >>> On 11/13/2012 06:53 AM, Berg, S.F. van den wrote: >>>> mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh >>> -- >>> 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 >>> >>> >>> >>> _______________________________________________ >>> 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. >>> >>> -------------------------------------------------------------------------------------------------------------- >>> >>> Mail 13 november 2012: >>> >>> Hello Freesurfer experts, >>> I have got some problems with qdec. For testing my data i make an design with age, sexe and right and left hippocampus. The same design as the tutorial on the freesurfer wiki. When starting analyze i get an Error in Analyze: command failed: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh. >>> surf is the map with the smoothings. The correct smoothings file. In this design is 10 is correctly presented in the map surf. >>> Thanks, >>> Stan >>> >>> lh-Avg-Intercept-volume ----------------------- >>> Does the average volume differ from zero? >>> 1.000 1.000 0.000 0.000; >>> lh-Avg-volume-Left-Hippocampus-Cor ----------------------- >>> Does the correlation between volume and Left-Hippocampus, accounting for gender, differ from zero? >>> 0.000 0.000 1.000 1.000; >>> lh-Diff-male-female-Intercept-volume ----------------------- >>> Does the average volume differ between male and female? >>> 1.000 -1.000 0.000 0.000; >>> lh-Diff-male-female-Cor-volume-Left-Hippocampus ----------------------- >>> Does the volume--Left-Hippocampus correlation differ between male and female? >>> 0.000 0.000 1.000 -1.000; >>> ninputs = 9 >>> Checking inputs >>> reading MRI_FRAME structure from file... >>> Error in Analyze: command failed: mri_concat /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh --o /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh >>> >>> >> -- >> 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 >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > -- > 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 > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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bbregister
by MCLAREN, Donald 20 Nov '12

20 Nov '12

Doug, I received this question from a colleague, "Exactly which segmentation file from "recon -all" is being used in the "bbregister" command?" Thanks, Donald

3 4

Training Comparison
by Ryan 20 Nov '12

20 Nov '12

Hello all, I'm doing a training comparison (training type A vs. type B), and I created thickness difference files (the rate files from the long_mris_slopes command) for each subject. How can I conduct an FSGD analysis with these thickness difference files? I tried replacing all of the lh.thickness and rh.thickness files with the lh.long.thickness-rate files, but it gives me the following error: MRISreadBinaryCurvature: incompatible vertex number in file /Applications/freesurfer/subjects/7107-60_base/surf/lh.thickness ERROR: reading curvature file -- -Ryan

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Re: [Freesurfer] Vertex wise analysis and area/pial area/volume interpretation
by S.E. Mous 20 Nov '12

20 Nov '12

Dear FreeSurfers, I didn't notice a resolution to this thread. I'm experiencing the same 'problem'; When I run Qdec and perform a Monte Carlo correction of 1.3, the terminal window output gives me the following clusters and values (during the MC correction I used the 'abs' option): # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 -4.665 132680 2413.29 -41.5 2.8 24.3 0.00010 0.00000 0.00020 4785 precentral 2 -3.915 4012 1620.38 -30.7 -26.1 61.8 0.00010 0.00000 0.00020 3811 postcentral 3 -3.257 53060 1559.53 -51.7 -0.2 -23.9 0.00010 0.00000 0.00020 2447 middletemporal 4 -2.846 100336 1266.09 -17.0 30.2 44.1 0.00240 0.00180 0.00300 2203 superiorfrontal 5 -2.676 4834 855.91 -19.3 30.5 -14.5 0.03440 0.03210 0.03670 1194 lateralorbitofrontal But when (after performing MC correction) I hit the button 'Find Clusters and Goto Max' I get different (less) clusters and different Max and coordinate values: ============================================================ Generating cluster stats using min threshold of 2... Found 4 clusters Contrast: 'lh-Avg-thickness-sumD_adh_5_add1_SQRT-Cor', 10fwhm, DOF: 360 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -4.0000 0 2413.29 -36.8 -18.3 64.5 4785 precentral 2 -4.0000 17 1620.38 -21.0 -34.8 68.6 3811 postcentral 3 -4.0000 39 1559.53 -53.5 -20.2 -25.5 2447 middletemporal 4 -2.6198 21 1266.09 -6.6 33.8 49.8 2203 superiorfrontal ============================================================ Could you please explain this difference in output and why the Max and coordinate values differ? Thank you very much for your help! Best, Sabine Mous -- Sabine Mous, MSc Department of Child & Adolescent Psychiatry/Psychology PhD student, Generation R Study Erasmus MC, room AE-005 P.O.Box 2040 3000 CA Rotterdam The Netherlands Phone: (+31) 10 7038019 E-mail: s.mous(a)erasmusmc.nl http://www.erasmusmc.nl/kinderenjeugdpsychiatrie http://www.generationr.nl/

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