Freesurfer February 2010

freesurfer@nmr.mgh.harvard.edu

96 participants
153 discussions

LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

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Re: [Freesurfer] Retinotopic mapping of only polar data
by f.leone＠donders.ru.nl 04 Oct '10

04 Oct '10

Hi everyone, Doug: thanks a lot for the reply, that indeed worked, I now have a polar map overlayed on my inflated brain. But something seems to be amiss, because it plots it mainly on the temporal lobe, with nothing on the most dorsal slices, while actually I only scanned the 18 most dorsal (oriented along the occipital-parietal axis), sot here shouldn't be anything in the temporal or inferior frontal lobe. How can this be/where is it going wrong? Moreover, I'm not sure on the format used by the polar map: the scale bar states it ranges from 1.18 to 1.18, but I don't see the sense in that. What will come out? Radians I pressume? kind regards, thanks a lot in advance, Frank ----- Original Message ----- From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> To: "Frank Leoné" <f.leone(a)donders.ru.nl> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Friday, January 8, 2010 4:26:21 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [Freesurfer] Retinotopic mapping of only polar data You can generate a register.dat with either fslregister-sess or spmregister-sess, or, if you have it in your version, use bbregister (note that there is not a -sess version for this yet). You can then use mri_vol2surf to resample the h.nii file to the surface, then view it in tksurfer. You can also extract certain frames with mri_convert with the --frame option. doug f.leone(a)donders.ru.nl wrote: > Hi everyone, > > Still not working fully, partly because I'm missing some info on the file formats. What I now did was a run of selfreqavg with four input polar sessions, which ran succesfully. This gives me the expected h.nii. Now I either want to > > - use this h file directly, using paint-sess (get message register.dat is missing) and sliceview-sess (get message it can't determine format h-offset, which makes sense, because it doesn't exist) > - or extract w files from the first three layers of the nii files and superimpose them in tksurfer. I don't know how I should extract them though. Can use the SPM surfrend functions, but I can't imagine that is the way, or is it? > > Hopefully someone can help me along either of the two paths, I'm really eager to see whether the retinotopic analysis worked. Thanks a lot in advance! > > kind regards, > > Frank > > ----- Original Message ----- > From: "f.leone(a)donders.ru.nl" <f.leone(a)fcdonders.ru.nl> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Monday, January 4, 2010 9:35:51 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna > Subject: Re: [Freesurfer] Retinotopic mapping of only polar data > > Hi everyone, > > I fixed it with the help of Jascha: when using the full path, e.g. /home/frank/etc.../007/f.nii it does find them. So it is now running. Thanks for the help! > > kind regards, > > Frank > > ----- Original Message ----- > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > To: "Frank Leoné" <f.leone(a)donders.ru.nl> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Tuesday, December 22, 2009 7:58:23 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna > Subject: Re: [Freesurfer] Retinotopic mapping of only polar data > > Do you have read permissions to the file? If so, can you send the log > file created by sfa-sess? > > f.leone(a)donders.ru.nl wrote: > >> Thanks a lot for the reply. I now bump into different problems though: it doesn't understand my f.nii file, see below. I run: >> >> frank@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ sfa-sess -a rtopy -s FSFAST_S1/ >> >> and I think the main error line is: >> >> ERROR: cannot determine format of 007/f >> >> >>>> ??? Attempt to reference field of non-structure array. >>>> >>>> >> 007 is my first session (is a dir) and in there is one f.nii, which includes all the scans of that run. . Previously I tried it with separate scan files, but that didn't work either. So what does it expect? And will it work with data preprocessed in SPM instead in FreeSurfer? The rest of the dir structure is setup as specified in the guide >> >> Hopefully someone can help me, thanks a lot in advance, >> >> kind regards, >> >> Frank >> >> frank@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ mkanalysis-sess.new -force -a rtopy -TR 2.12 -designtype retinotopy -paradigm rtopy.par -funcstem f -ncycles 8 >> INFO: analysis rtopy exists, but overwrite forced by user. >> Completed successfully >> frank@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ sfa-sess -a rtopy -s FSFAST_S1/ >> -------------------------------------------------------------- >> sfa-sess logfile is /home/frank/PhD/data/Exp1_Saccades_phase/log/sfa-sess-bold-rtopy-0912221252.log >> -------------------------------------------------------------- >> ------------------------------------------- >> /home/frank/PhD/data/Exp1_Saccades_phase/FSFAST_S1 >> Tue Dec 22 12:52:30 CET 2009 >> INFO (FSFAST_S1): RunList = 007 008 009 010 011 >> -------------------------------------------------- >> /home/frank/PhD/data/Exp1_Saccades_phase/FSFAST_S1/bold >> selfreqavg -TR 2.12 -o rtopy/polar/h -i 007/f -i 008/f -i 009/f -i 010/f -cfg /home/frank/PhD/data/Exp1_Saccades_phase/rtopy/analysis.cfg -parname rtopy.par >> -------------------------------------------------- >> --- Parsing Config File: /home/frank/PhD/data/Exp1_Saccades_phase/rtopy/analysis.cfg ---- >> -ncycles 8 -delay 0 -nskip 0 -fwhm 0 >> DirectionList: +1 +1 +1 -1 >> Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. >> >> < M A T L A B (R) > >> Copyright 1984-2009 The MathWorks, Inc. >> Version 7.8.0.347 (R2009a) 64-bit (glnxa64) >> February 12, 2009 >> >> >> To get started, type one of these: helpwin, helpdesk, or demo. >> For product information, visit www.mathworks.com. >> >> >> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Extension format = nii >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> hanrad = 0 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ERROR: cannot determine format of 007/f >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>> ??? Attempt to reference field of non-structure array. >>>> >>>> >> >> >> >>>> ??? Attempt to reference field of non-structure array. >>>> >>>> >> >> >> >>>> ??? Attempt to reference field of non-structure array. >>>> >>>> >> >> >> >>>>>> ??? Attempt to reference field of non-structure array. >>>>>> >>>>>> >> >> >> >>>>>> ??? Undefined function or variable 'lastslice'. >>>>>> >>>>>> >> >> >> >>>> ??? Attempt to reference field of non-structure array. >>>> >>>> >> >> >> >>>>>>>> ??? Attempt to reference field of non-structure array. >>>>>>>> >>>>>>>> >> >> >> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??? Index exceeds matrix dimensions. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> >> >> >>>>>>>>>>>> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >>>>>>>>>>>> >>>>>>>>>>>> >> >> >> >>>> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >>>> >>>> >> >> >> >>>> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >>>> >>>> >> >> >> >>>> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >>>> >>>> >> >> >> >>>> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >>>> >>>> >> >> >> >>>> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >>>> >>>> >> >> >> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Slice >> ??? Undefined function or variable 'lastslice'. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >> >> >> >>>>>>>> ??? Attempt to reference field of non-structure array. >>>>>>>> >>>>>>>> >> Error in ==> MRIwrite at 94 >> hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> >>>>>>>> ??? Attempt to reference field of non-structure array. >>>>>>>> >>>>>>>> >> Error in ==> MRIwrite at 94 >> hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> >>>>>>>> ??? Attempt to reference field of non-structure array. >>>>>>>> >>>>>>>> >> Error in ==> MRIwrite at 94 >> hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> >>>>>>>>>> Saving header to rtopy/polar/h >>>>>>>>>> >>>>>>>>>> >>>> Could not open rtopy/polar/h.sfa for writing >>>> >>>> >> quiting matlab >> selfreqavg COMPLETED >> mri_convert rtopy/polar/h.nii -o rtopy/polar/h-offset.nii --frame 10 >> mri_convert rtopy/polar/h.nii -o rtopy/polar/h-offset.nii --frame 10 >> niiRead(): error opening file rtopy/polar/h.nii >> >> ----- Original Message ----- >> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >> To: "Frank Leoné" <f.leone(a)donders.ru.nl> >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Sent: Wednesday, December 16, 2009 5:12:41 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >> >> If you run the retinotopy analysis, it will expect eccen. If it stops >> without doing the polar analysis, you can "fool" it by copying the polar >> data into the eccen directory. >> >> doug >> >> f.leone(a)donders.ru.nl wrote: >> >> >>> Dear all, >>> >>> I just started using FreeSurfer, specifically for retinotopic data, on the moment only polar data. So I followed the guide as mentioned on http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis . This does seem to work to some extend, except that it complains that I don't have eccentricity data. He is right about that, but is the analysis also doable with the eccentricity data? I really hope so, thanks a lot in advance, >>> >>> kind regards, >>> >>> Frank >>> >>> >>> >>> >> >> > > -- 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 -- Frank T.M. Leoné, MSc Graduate student | Donders Institute for Brain, Cognition and Behaviour f.leone(a)donders.ru.nl | +31 24 36 12542 / +31 24 36 68388 | Room B.1.31 / Room 1.34

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Using peak activation voxels to determine structural areas of interest
by Nathan Dankner 01 Jun '10

01 Jun '10

Hello all. I am considering using peak activation voxels (with coordinates either in talairach or MNI space) gleaned from fmri studies in our lab to determine a priori areas of interest for examining group differences in cortical thickness. Is this something that is possible in freesurfer? In particular, I would ideally like to be able to tell freesurfer how large of an area to examine around a particular peak voxel for each subject as opposed to tracing an ROI each time. I am not particularly well versed in the technical aspects of things such as blurring kernels, but I am assuming that the amount of blurring done by freesurfer will affect the ideal circumference of any sphere around this peak voxel. Any suggestions as to how to go about this? Please let me know if any more information is necessary. Thanks, Nathan

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how to QC hippocampal measurement
by Guang Zeng 20 May '10

20 May '10

Hi, there, I have used FreeSurfer to measure the hippocampal size of 200 ADNI subjects, and now I'd like to QC the hippocampal measurement. Anyone can give me some suggestion to do this, instead of loading they one-by-one ? Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/

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MRS mask
by Lena Palaniyappan 12 May '10

12 May '10

Hi Bruce and team I have a ROI mask in analyze (img_hdr) format obtained from MR spectroscopic group analysis using a different registration (talairach based). I want to use this ROI as a label to extract thickness measures on a group of subjects. How can I do this? If I use mri_vol2surf will I be not projecting contrasts from a differently registered image set onto reconstructed freesurfer anatomical? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Re: [Freesurfer] Optseq2 - Incorporate sequential order of trials as a factor
by Gaber, Tilman 07 Apr '10

07 Apr '10

Thank you for your quick response. Initially I had the same idea. Unfortunately, this easy solution does not work. All trials are successor of the previous and predecessor of the following trial. Therefore we can't just randomly distribute pairs of trials. The whole chain of trials has to be in proper order. ([A-B-A-A-B-B-B-A-...] = [AB BA AA AB BB BA ...]) My thinking was to somehow add these restrictions to the initial part of optseq2 algorithm and fix for null event interuptions afterwards... Tilman --------------------------------------------------------------------------------- Tilman J. Gaber, Dipl.Psych. Translational Neuroscience in Psychiatry and Neurology Dpt. of Child and Adolescent Psychiatry and Psychotherapy RWTH Aachen University Neuenhofer Weg 21 52074 Aachen Germany PHONE: +49-(0)241-80.85347 FAX: +49-(0)241-80.3335070 Email: tgaber(a)ukaachen.de ________________________________________ Von: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Gesendet: Freitag, 26. Februar 2010 18:56 An: Gaber, Tilman Cc: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Optseq2 - Incorporate sequential order of trials as a factor You can specify that there are 4 trial types (AA, AB, BA, BB), and give the duration twice that of the individual. doug Gaber, Tilman wrote: > Dear mailinglist recipients, > > I am currently planning an optimized experiment using optseq2 and a 2x2 factors behavioral response task (Simon-task). > The task consists of a pseudo-randomized series of two kinds of trials (congruent and incongruent). > In addition there is a sequential factor, i.e. it is of interest whether a trial follows a trial of the same or the opposite kind. In other words there are (2x2) four different conditions where trials relate to precedent trials (AA,AB,BB,BA). > Would it be possible to incorporate this sequential factor into the optseq2? > I am aware that null events will fall between trials and thus interrupt trial sequences. Trials following null events would therefore be treated separately (i.e. for data analysis). In order to obtain an equal number of trials per condition, this would require increasing the number of trials depending on the number and order of null events. > Currently I am able to produce a randomized order of equally balanced trials regarding trial type and sequential order (AA,AB,BB,BA). > Any thoughts or suggestions are more than welcome! > > Best, > Tilman > _______________________________________________ > 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

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modification made to longitudinal results
by Guang Zeng 16 Mar '10

16 Mar '10

Hi, there, I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should I use? recon-all -s subj.long.baseid .... or recon-all -long subj baseid .... Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/

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How to verify cerebellum segmentation
by Gergely Orsi 04 Mar '10

04 Mar '10

Hi all! We have processed 100 subjects with autorecon. I'd like to know how to check the cerebellum segmentation on the subjects. It would be crucial, because the images are a bit dimmer at the lower areas (it's far from the isocenter) and despite the intensity normalisation it still has lower intensity compared to the dorsal part of the cerebellum. After the skull-strip the cerebellum is still intact (the whole cerebellum exists on the images), but I'd like to know wether freesurfer recognised the lower intensity parts or not. Unfortunatly BET in FSL simply cut off these areas, thus our VBM results (showing significan changes at the ventral cerebellum) are compromised. We have measured significant group differences in total cerebellar volume using freesurfer, but we should check the segmentation first, and believe the results later. Could anyone help us in this? And if the segmentation failed, is there any manual method to correct it (by hand), because the whole cerebellum is on the images (despite of the different intensity). And one last question, is it possible to carry out VBM in freesurfer (after checking/correcting the cerebellum if needed, although the intensity difference will still be a big problem in VBM ). Thank you very much. Gergely Orsi

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ICV Error fs 4.3.1
by Jeff Sadino 01 Mar '10

01 Mar '10

Hello, I reconed 149 subjects using freesurfer 4.3.1 automatically using our cluster. When I did asegstats2table, all 149 subjects had the exact same icv: # Measure IntraCranialVol, ICV, Intracranial Volume, 1948106.000000, mm^3 Running mri_segstats manually, here is the beginning of the output: mri_segstats --seg mri/aseg.mgz --sum stats/aseg2.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --ctab $FREESURFER_HOME/ASegStatsLUT.txt --subject 040002_S04 atlas_icv (eTIV) = 1948106 mm^3 (det: 1.000000 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 246101 rh white matter volume 251160 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1766623 # brainmaskvolume 1766623.0 # nbrainsegvoxels 1310448 # brainsegvolume 1310448.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 1 2 Left-Cerebral-White-Matter 247216 247216 Looking at the log files for several other subjects, they all have a determinant of 1. However, all of the other numbers - brainmask, brain seg volume, individual regions - are all unique and correct. It is just the icv. Can anyone point me in the right direction of how to investigate the determinant value? Here is the mri_segstats version: # cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp $ Thanks! Jeff Sadino

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Destrieux boundaries Insular cortex
by Lena Palaniyappan 28 Feb '10

28 Feb '10

Is there any reference available for tracking the boundaries of 5 parcellations within insula as given by Destrieux a2009s? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Freesurfer February 2010