Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

wm edits
by Tetiana Dadakova 28 Mar '12

28 Mar '12

Dear FS list, After recon-all -all we had some wm missing in temporal part of the brain (fig. wm_missing1). We edited wm.mgz and re-run recon-all -autorecon2 -autorecon3. After this, the wm.mgz looks as fig. wm_missing2, but the surfaces still look as fig. wm_missing1. What can be the reason that wm.mgz edits didn't affect the surfaces? Thank you, Tanja.

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Re: [Freesurfer] Error in fast_selxavg3 (line 254) XCond = cond(XtX);
by Douglas N Greve 27 Mar '12

27 Mar '12

You will have to mri_convert all the .nii files so that they have the proper TR. On 03/27/2012 12:51 PM, Kiley Seymour wrote: > Hi Doug. I just made a dummy folder with an eccen run. It got around > the error XCond = cond(XtX) but took me back to the original error : > TR mismatch error despite me re-doing the preprocessing and re- > mri_concat-enating my SPM nii files into a 4D file for each run. > > Do you think using mri_concat with --regheader could be the problem? > Or perhaps the fact that dicoms were converted to nii files in a > program that was not freesufer? > > K > > > On Tue, Mar 27, 2012 at 6:35 PM, Kiley Seymour > <kileyseymour(a)googlemail.com> wrote: >> no I don't. >> >> On Tue, Mar 27, 2012 at 6:17 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu> wrote: >>> Do you not have any eccen runs? >>> doug >>> >>> On 03/27/2012 06:55 AM, Kiley Seymour wrote: >>>> Dear Doug, >>>> >>>> I am aware I am becoming a regular pain. But I now encounter the >>>> following problem when running selxavg3-sess -a rtopy.self.lh -s >>>> CMRU1711. I have also attached my analysis.info and Xtmp.mat files >>>> >>>> Thanks for all of your suggestions. >>>> >>>> K >>>> >>>> #@# CMRU1711 ############################### >>>> /media/sf_DATA1/RETINOTOPY/CMRU1711 >>>> ------------------------- >>>> $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ >>>> /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m >>>> /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m >>>> /home/virtualuser/freesurfer/matlab/MRIread.m >>>> ------------------------- >>>> outtop = /media/sf_DATA1/RETINOTOPY >>>> Extension format = nii.gz >>>> nruns = 3 >>>> autostimdur = >>>> >>>> >>>> outanadir = /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh >>>> Found 138599/149490 (92.7) voxels in mask >>>> Creating Design Matrix >>>> ... creation time = 0.008 sec >>>> DoMCFit = 1 >>>> ntptot = 369, nX = 33, DOF = 336 >>>> Saving X matrix to >>>> /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh/Xtmp.mat >>>> Error using svd >>>> Input to SVD must not contain NaN or Inf. >>>> >>>> Error in cond (line 39) >>>> s = svd(A); >>>> >>>> Error in fast_selxavg3 (line 254) >>>> XCond = cond(XtX); >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> -- >>> 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. >>> > -- 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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Re: [Freesurfer] Cortical Normalization Questions
by jorge luis 27 Mar '12

27 Mar '12

I think we must be careful about including noisy large scale measurements as global nuisance covariates in the General Linear Model (GLM). The GLM assumes that the independent variables are measured almost without error (eg. see http://en.wikipedia.org/wiki/Errors-in-variables_models) For instance, mean cortical thickness or mean global activity in fMRI (as the mean of many values) should not be as noisy as Intracranial Volume estimates (or the estimated volume of any neuroanatomical structure). -Jorge > > > >>________________________________ >> De: Anderson Winkler <andersonwinkler(a)hotmail.com> >>Para: freesurfer(a)nmr.mgh.harvard.edu >>Enviado: Lunes 26 de marzo de 2012 13:56 >>Asunto: Re: [Freesurfer] Cortical Normalization Questions >> >>Hi Jeff and all, >> >>For normalization (i.e., divide the measurement under study by some >>global measurement), I would not argue favourably, as this procedure can >>bias the results in the opposite direction if a global effect is present. >> >>Instead, include it as a covariate is not as harmful. My suggestion is, >>when there is no clear approach about using or not a global measurement >>as a nuisance, the relationships between the measurement under study, >>the independent variable, and the putative nuisance should be >>calculated, and models with and without the nuisance should be analysed >>and presented. The discussion should consider both analyses together, >>and enough information should be presented so that the final >>interpretation is left to the reader. >> >>Specifically for area, I suggest analysing and presenting two models: >>(1) without any global measurement and (2) with global area as nuisance. >> >>If brain volume (whichever way it is measured) is to be considered a >>potential nuisance for the disorder you are analysing, it can be >>included in the model #2 above, even given that they are not orthogonal >>to each other, and are related to global area. Non-orthogonality >>between the nuisance variables is not a problem as it is when effects of >>interest are involved. >> >>Hope this helps! >> >>All the best, >> >>Anderson >> >> >>On 23/03/12 11:29, Michael Harms wrote: >>> Our reply to that is here >>> http://bjp.rcpsych.org/content/196/5/414.2.long >>> >>> which reminded me of other papers that have also used a global thickness >>> measure to covary for mean cortical thickness and thereby "address whether >>> any regional thickness differences were in excess of global cortical >>> thickness differences between groups" -- see references [1,4] in our >>> Reply. >>> >>> cheers, >>> -MH >>> >>>> Hi Michael and others, >>>> >>>> maybe it's this one: >>>> >>>> http://bjp.rcpsych.org/content/196/5/414.1.long >>>> >>>> best, >>>> -joost >>>> >>>> >>>> On Fri, Mar 23, 2012 at 2:15 AM, Michael Harms >>>> <mharms(a)conte.wustl.edu>wrote: >>>> >>>>> Hi Jeff, >>>>> I personally like the idea of using average thickness as a covariate to >>>>> control for a reduction in "whole brain" thickness, and have used that >>>>> approach in a paper. If the Abstract that you mentioned indicated that >>>>> this is flawed, I'd be curious to know what the reason was... >>>>> >>>>> cheers, >>>>> -MH >>>>> >>>>> On Thu, 2012-03-22 at 21:00 -0400, Bruce Fischl wrote: >>>>>> Hi Jeff >>>>>> >>>>>> yes, I think this is still our recommendation for thickness, although >>>>>> perhaps David Salat can verify. As far as surface area, you might get >>>>>> Anderson Winkler to send you a preprint of his newly accepted paper on >>>>>> surface area comparisons and how to do them properly. I would have >>>>> said >>>>>> normalize by the 2/3 root of ICV (maybe David can comment on this as >>>>> well) >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> >>>>>> On Thu, 22 Mar 2012, Jeff Sadino wrote: >>>>>> >>>>>>> Hello, >>>>>>> For cortical thickness normalizations, Bruce said not to normalize >>>>> based on a HBM >>>>>>> abstract >>>>>>> ( >>>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06646.html) >>>>> Is >>>>>>> this still the consensus? >>>>>>> >>>>>>> For cortical volume, it is pretty standard to normalize to eTIV. >>>>>>> >>>>>>> For cortical surface area (jacobian), I couldn't find any >>>>> information >>>>> on the wiki. >>>>>>> Does anyone have any recommendations? >>>>>>> >>>>>>> Thank you, >>>>>>> Jeff >>>>>>> >>>>>>> >>>>>> _______________________________________________ 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 >>>>> >>> _______________________________________________ >>> 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 >> >> >> > >

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Re: [Freesurfer] ERROR: could not determine file fieldsign
by Douglas N Greve 27 Mar '12

27 Mar '12

Did you run fieldsign-sess? If you don't have an eccen run you can't compute a fieldsign. doug ps. Please post emails to the list and not to me personally. Thanks! On 03/27/2012 04:07 PM, Kiley Seymour wrote: > Dear Doug, > > Thanks for all of your help today. I think I am almost there with this > retinotopy analysis. But the error below has halted me. I have > fieldsign folder, but only a fsig.nii.gz exists (i.e. no fieldsign > file) though. > > % tksurfer-sess -a rtopy.self.lh -s IFEE2211 -fieldsign > Surface self lh > Map Surface self lh > $Id: tksurfer-sess,v 1.16.2.1 2011/04/05 22:25:15 greve Exp $ > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 > UTC 2009 i686 GNU/Linux > Tue Mar 27 15:46:22 EDT 2012 > /home/virtualuser/freesurfer/tktools/tksurfer > > list fieldsign > ERROR: could not determine file for > /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/rtopy.self.lh/fieldsign/fieldsign > child process exited abnormally > > > On Tue, Mar 27, 2012 at 7:28 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu> wrote: >> You will have to mri_convert all the .nii files so that they have the proper >> TR. >> >> >> On 03/27/2012 12:51 PM, Kiley Seymour wrote: >>> Hi Doug. I just made a dummy folder with an eccen run. It got around >>> the error XCond = cond(XtX) but took me back to the original error : >>> TR mismatch error despite me re-doing the preprocessing and re- >>> mri_concat-enating my SPM nii files into a 4D file for each run. >>> >>> Do you think using mri_concat with --regheader could be the problem? >>> Or perhaps the fact that dicoms were converted to nii files in a >>> program that was not freesufer? >>> >>> K >>> >>> >>> On Tue, Mar 27, 2012 at 6:35 PM, Kiley Seymour >>> <kileyseymour(a)googlemail.com> wrote: >>>> no I don't. >>>> >>>> On Tue, Mar 27, 2012 at 6:17 PM, Douglas N Greve >>>> <greve(a)nmr.mgh.harvard.edu> wrote: >>>>> Do you not have any eccen runs? >>>>> doug >>>>> >>>>> On 03/27/2012 06:55 AM, Kiley Seymour wrote: >>>>>> Dear Doug, >>>>>> >>>>>> I am aware I am becoming a regular pain. But I now encounter the >>>>>> following problem when running selxavg3-sess -a rtopy.self.lh -s >>>>>> CMRU1711. I have also attached my analysis.info and Xtmp.mat files >>>>>> >>>>>> Thanks for all of your suggestions. >>>>>> >>>>>> K >>>>>> >>>>>> #@# CMRU1711 ############################### >>>>>> /media/sf_DATA1/RETINOTOPY/CMRU1711 >>>>>> ------------------------- >>>>>> $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ >>>>>> /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m >>>>>> /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m >>>>>> /home/virtualuser/freesurfer/matlab/MRIread.m >>>>>> ------------------------- >>>>>> outtop = /media/sf_DATA1/RETINOTOPY >>>>>> Extension format = nii.gz >>>>>> nruns = 3 >>>>>> autostimdur = >>>>>> >>>>>> >>>>>> outanadir = /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh >>>>>> Found 138599/149490 (92.7) voxels in mask >>>>>> Creating Design Matrix >>>>>> ... creation time = 0.008 sec >>>>>> DoMCFit = 1 >>>>>> ntptot = 369, nX = 33, DOF = 336 >>>>>> Saving X matrix to >>>>>> /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh/Xtmp.mat >>>>>> Error using svd >>>>>> Input to SVD must not contain NaN or Inf. >>>>>> >>>>>> Error in cond (line 39) >>>>>> s = svd(A); >>>>>> >>>>>> Error in fast_selxavg3 (line 254) >>>>>> XCond = cond(XtX); >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> -- >>>>> 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. >>>>> >> -- >> 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 >> > -- 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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Crippled fiber tracts in healthy subjects (TRACULA)
by Ansgar Furst 27 Mar '12

27 Mar '12

Dear All, Please ignore my earlier incomplete message with the same title! We are using the ADNI Acc 3D FSPGR for structurals and a 30 directional (5 B0s) dual-spin repeat sequence for DTI (on a 3T GE 750 discovery) which so far rendered really nice results. However, recently I encountered data from several healthy young subjects where the TRACULA fiber tract estimations would suggest severely "crippled" tracts which, however, is not consistent with their FA maps. The crippling is most visible when comparing left vs right cingulate gyri. In some cases either the left or right side is almost completely gone. Has anyone else experienced similar issues and found a remedy? Thanks a lot, Ansgar

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Re: [Freesurfer] Error in fast_selxavg3 (line 254) XCond = cond(XtX);
by Douglas N Greve 27 Mar '12

27 Mar '12

FSFAST assumes that you do. A silly way around this is to just replicate your polar runs and call them eccen runs. doug On 03/27/2012 12:35 PM, Kiley Seymour wrote: > no I don't. > > On Tue, Mar 27, 2012 at 6:17 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu> wrote: >> Do you not have any eccen runs? >> doug >> >> On 03/27/2012 06:55 AM, Kiley Seymour wrote: >>> Dear Doug, >>> >>> I am aware I am becoming a regular pain. But I now encounter the >>> following problem when running selxavg3-sess -a rtopy.self.lh -s >>> CMRU1711. I have also attached my analysis.info and Xtmp.mat files >>> >>> Thanks for all of your suggestions. >>> >>> K >>> >>> #@# CMRU1711 ############################### >>> /media/sf_DATA1/RETINOTOPY/CMRU1711 >>> ------------------------- >>> $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ >>> /home/virtualuser/freesurfer/fsfast/toolbox/fast_selxavg3.m >>> /home/virtualuser/freesurfer/fsfast/toolbox/fast_ldanaflac.m >>> /home/virtualuser/freesurfer/matlab/MRIread.m >>> ------------------------- >>> outtop = /media/sf_DATA1/RETINOTOPY >>> Extension format = nii.gz >>> nruns = 3 >>> autostimdur = >>> >>> >>> outanadir = /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh >>> Found 138599/149490 (92.7) voxels in mask >>> Creating Design Matrix >>> ... creation time = 0.008 sec >>> DoMCFit = 1 >>> ntptot = 369, nX = 33, DOF = 336 >>> Saving X matrix to >>> /media/sf_DATA1/RETINOTOPY/CMRU1711/bold/rtopy.self.lh/Xtmp.mat >>> Error using svd >>> Input to SVD must not contain NaN or Inf. >>> >>> Error in cond (line 39) >>> s = svd(A); >>> >>> Error in fast_selxavg3 (line 254) >>> XCond = cond(XtX); >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> 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. >> > -- 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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trac-all -prep error
by Sarina Sacco 27 Mar '12

27 Mar '12

quando avvio il trac-all (relase FS5.1) mi crea questo errore: /opt/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Mar 27 11:17:27 CEST 2012 mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz mri_convert /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm... Starting DICOMRead2() dcmfile = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm dcmdir = /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig Ref Series No = 7 Found 2242 files, checking for dicoms Found 2240 dicom files in series. First Sorting Computing Slice Direction Vs: 0.029 0.321 1.9739 Vs: 0.0144997 0.160497 0.98693 Second Sorting Counting frames nframes = 28 nslices = 80 ndcmfiles = 2240 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=10050.00, TE=87.10, TI=0.00, flip angle=90.00 i_ras = (-0.999859, -0.0058291, -0.0157782) j_ras = (0.00830111, -0.987041, -0.160255) k_ras = (-0.0144997, -0.160497, 0.98693) writing to /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz... mri_probedicom --i /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./orig/1.2.840.113619.2.260.6945.224896.29441.1274773115.263.dcm > /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dcminfo.dat flip4fsl /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig.nii.gz x -y z /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.nii.gz fslorient: Command not found. mv -f /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs /opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/bvecs mv: cannot stat `/opt/freesurfer/subjects/subjects_trac_all/Diff001_F.B./dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Linux thunder 2.6.38-8-generic #42-Ubuntu SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Mar 27 11:18:21 CEST 2012 Non riesco a capire perchè,da cosa può dipendere?

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Re: [Freesurfer] volume mapping
by Johnson 27 Mar '12

27 Mar '12

OK T1 space is the space acquired from the machine, original anatomical space regards JG On 03/26/2012 2:25 PM, Bruce Fischl wrote: > can you post to the list so others can answer? And can you clarify > what you mean by "T1" space? > > On Mon, 26 Mar 2012, Johnson wrote: > >> Hi >> well, I had to transfer the fiber tracts coordinates from DWI space >> to T1 space, I used the b0 and the T1 for the registration process, I >> got the transformation matrix and applied it onto the tracts and they >> fit very well. >> Now I want to transform the tracts from T1 space to the freesurfer >> space, I need to know the transformation matrix that was used during >> the processing if it was saved in any of the logs >> thanks >> Johnson >> On 03/26/2012 2:09 PM, Bruce Fischl wrote: >>> Hi Johnson >>> >>> what T1 did you register to? Most of the ones we generate (T1.mgz, >>> brainmask.mgz, ...) are in a common coordinate system and you shouldn't >>> have to transform from one to another. >>> cheers >>> Bruce >>> >>> >>> On Mon, 26 Mar 2012, Johnson wrote: >>> >>>> Hi >>>> Let me re-phrase my question: >>>> I already did registration from DWI to T1, this step is OK. >>>> Now I want to go from T1 to FreeSurfer space (aparc+aseg.mgz file not >>>> the aparc+aseg-in-rawavg file). I know I have two choices: >>>> 1) do registration using bbregister >>>> 2) since Freesurfer during processing have already done this step, the >>>> transformation matrix is there somewhere, the question is where to >>>> find >>>> it? which log or which file? this choice is better since it is more >>>> accurate. >>>> >>>> Thanks >>>> JG >>>> >>>> On 03/26/2012 12:41 PM, Anastasia Yendiki wrote: >>>>> If you want to register your DWI to T1, you should register to >>>>> mri/brain.mgz. You can do this with bbregister, or with any affine >>>>> registration tool of your choice. >>>>> >>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>> >>>>>> Hi >>>>>> I found it in a 256x256x256 space while the T1 we use is in >>>>>> different >>>>>> space, I found this page on the registration step: >>>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat >>>>>> I wish to know how this script work? >>>>>> >>>>>> mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o >>>>>> aseg-in-rawavg.mgz >>>>>> --regheader aseg.mgz >>>>>> >>>>>> what is the transformation used ? >>>>>> JG >>>>>> >>>>>> >>>>>> On 03/26/2012 12:24 PM, Anastasia Yendiki wrote: >>>>>>> Hi Johnson - The aparc+aseg.mgz is in the same space as the T1 >>>>>>> used as >>>>>>> input to freesurfer. >>>>>>> >>>>>>> a.y >>>>>>> >>>>>>> On Mon, 26 Mar 2012, Johnson wrote: >>>>>>> >>>>>>>> Hi FS expert >>>>>>>> I need to know the transformation matrix itself since I will do >>>>>>> the> transformation in matlab. >>>>>>>> I successfully transformed white matter fibers coordinates to T1 >>>>>>> using> AIR 5.0 from LONI lab. >>>>>>>> They provide a transformation matrix. >>>>>>>> Now I want to transform the coordinates from T1 to Freesurfer >>>>>>> space, so >>>>>>>> my question is: what is the transformation matrix that relates >>>>>>> the T1 >>>>>>>> which FS have used for parcellation and segmentation with the> >>>>>>> aparc+aseg.mgz file? >>>>>>>> I searched the logs but couldn't find such matrix. >>>>>>>> I don't want to do a registration step since it will be less >>>>>>> accurate> than the one that was generated during the segmentation >>>>>>> process. >>>>>>>> Also is it just one transformation or a combination of >>>>>>> transformations? >>>>>>>>> thanks >>>>>>>>> >>>>>>> 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 >>> >> >> >> > -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2(a)uic.edu

2 1

mkbrainmask-sess
by Kiley Seymour 27 Mar '12

27 Mar '12

Dear Freesurfers, I am currently trying to do some retinotopic mapping. I have been successful in running the reconstruction commands and setting everything up for the analysis, but I have run into problems when using the selxavg3-sess command. i.e. selxavg3-sess -a rtopy.self.lh -s IFEE2211 -no-preproc ( -no-preproc since I have co-registered and motion corrected my files in SPM). I was unable to run this command as freesurfer could not find /media/sf_DATA1/RETINOTOPY/IFEE2211/bold/001/global.meanval.dat So I ran mktemplate - sess, which was successfully completed. And then I ran mkbrainmask-sess (see below). Any help with this would be much appreciated. Thanks Kiley FreeSurfer:~/data1/RETINOTOPY> mkbrainmask-sess -s IFEE2211 -d ~/data1/RETINOTOPY ------------------------------------------------ /media/sf_DATA1/RETINOTOPY/IFEE2211 Fri Mar 23 09:42:26 EDT 2012 mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 FSLMATHSfslmaths.fsl Scratch Dir is /tmp/mkbrainmask_7930 /media/sf_DATA1/RETINOTOPY/IFEE2211/bold mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii mri_convert template.nii.gz /tmp/mkbrainmask_7930/in.nii $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ reading from template.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998558, -0.0534653, -0.00482299) j_ras = (-0.0536701, 0.992375, 0.110955) k_ras = (0.00114604, -0.111054, 0.993814) writing to /tmp/mkbrainmask_7930/in.nii... # ---------- Using FSL's BET to Extract Brain------------------ # /media/sf_DATA1/RETINOTOPY/IFEE2211/bold bet.fsl /tmp/mkbrainmask_7930/in.nii /tmp/mkbrainmask_7930/brain -m -f 0.1 /home/virtualuser/freesurfer/bin/bet.fsl: 150: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 151: /bin/remove_ext: not found /home/virtualuser/freesurfer/bin/bet.fsl: 158: /bin/imtest: not found [: 158: =: unexpected operator /home/virtualuser/freesurfer/bin/bet.fsl: 380: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_7930/brain_mask.nii $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /media/sf_DATA1/RETINOTOPY/IFEE2211/bold cmdlinemri_binarize --i /tmp/mkbrainmask_7930/brain_mask.nii --min .01 --o /tmp/mkbrainmask_7930/brain_mask.nii sysname Linux hostnameFreeSurfer machine i686 user virtualuser input /tmp/mkbrainmask_7930/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_7930/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0

3 6

Failure to convert DICOM files
by Ed Gronenschild 27 Mar '12

27 Mar '12

Hi, I got an error during the first step in recon-all (Mac OS 10.6.8, FreeSurfer v5.1.0). The eror message in the log file is: WARNING: file ...../MR.1.3.12.2.1107.5.2.18.41016.201008031106017688438785.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header. This is strange because it is no mosaic file and all the files can be converted without any problems with e.g., dcm2nii and viewed with OSIRIX. Cheers, Ed

2 1

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