Freesurfer January 2010

freesurfer@nmr.mgh.harvard.edu

78 participants
123 discussions

ICV/brain volume
by Xiangchuan Chen 08 Jan '10

08 Jan '10

Dear FreeSurfer experts, After searching on FreeSurfer wiki and mailing list, I know that the ICV reported in aseg.stats is an estimated value based on talairach transformation. So, if the talairach transformation for a subject's head is not good, the ICV for this subject is not accurate, am I right? If this is the case, it may not be suitable to use ICV to adjust the volumetric data in aseg.stats and ?h.aparc.stats for some special subjects. I am thinking of using "brain volume" for this purpose. Here are the steps to get it: 1. Get the surface-based volume of cerebral white matter (aseg.stats). 2. Add up the volumes of all cortical regions to get the surface-based volume of cerebral cortex (aparc.stats). 3. Add up the above volumes (including both hemispheres) and the volumes of all other regions listed in aseg.stats (except for cerebral white matter and cerebral cortex) to get the brain volume. Is this a suitable way to obtain more accurate brain volume? Thanks in advance and any suggestions are greatly appreciated, Xiangchuan Chen

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Lose Keyboard
by Oya, Hiroyuki 08 Jan '10

08 Jan '10

Dear all, I am running freesurfer 4.5 on Ubuntu9.10(64bit). Is anybody experiencing " lost keyboard " problem? I cannot put any number in tkmedit and tksurfer using keyboard. Thank you. Hiroyuki

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Ubuntu FreeSurf VirtualBox root password
by Vadim Axel 08 Jan '10

08 Jan '10

Hi all and Pedro Paulo Oliveira, I have installed Ubuntu VirtualBox on Windows. I would like to thank Pedro Paulo Oliveira for for making this convenient solution for Windows OS. What I am missing is the root password (without root password it's impossible to install guest additions, make shared folders etc). Thanks, Vadim

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help - gm segmentation problem
by johanna feiler 08 Jan '10

08 Jan '10

Dear freesurfer experts, After running the autorecon2 process the pial surface (red line) fails to catch up pieces of gm in the insula region. I gained little improvement with setting control points, but the problem still occurs, lasting about five slices. As an illustration, I attached a screenshot. How can I solve this problem? Thanks for your help! Johanna Feiler ___________________________________________________________ Preisknaller: WEB.DE DSL Flatrate für nur 16,99 Euro/mtl.! http://produkte.web.de/go/02/

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annot to label to gm thickness map
by Ritobrato Datta 08 Jan '10

08 Jan '10

Hello All, I want to create a gm thickness map from central sulcus and precentral gyrus. I plotted the lh.aparc.a2005s.annot on the inflated surface and I see the sulci and gyri. Is there a way to create a binary label of the central sulcus and precentral gyrus ? Can that label be then used to create a thickness map ? Please let me know ? Thanks Rito

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Re: [Freesurfer] Retinotopic mapping of only polar data
by f.leone＠donders.ru.nl 08 Jan '10

08 Jan '10

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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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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erroneous segmentation of white matter and cortical thickness...
by Gonzalo Rojas Costa 08 Jan '10

08 Jan '10

Hi: In the temporal lobe I got a white matter "erroneous" segmentation (that I know that I could correct it using control points)... In the aseg.auto.mgz file the white matter appears as cerebral cortex... The cortical thickness computation is related to that segmentation ?... Or the segmentation and cortical thickness are computed in a independent way ?... Sincerely, Gonzalo Rojas Costa

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question about mris_ca_train
by Guang Zeng 07 Jan '10

07 Jan '10

Hi, there, I have created our own template and am creating our own atlas now. I have annotation files for each subject in my training set, and my mris_ca_train command line is: mris_ca_train -n 2 -t /home/freesurfer-install/freesurfer/ATLASColorLUT.txt lh sphere.reg myatalas.annot custom_1 custom_2 custom_3 custom_4 lh_myatlas.gcs my question is here, I should use the lh.sphere.reg file which register the sphere to the FS default template or the registration file which register the sphere to my own template? Thanks! Guang _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/196390707/direct/01/

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tkmedit : Functional RAS to Functional index
by Oya, Hiroyuki 07 Jan '10

07 Jan '10

Hello Experts, Transformation from Volume RAS to Functional RAS is done with anat2exf.reg.dat. But how does tkmedit calculate Functional index from Functional RAS ? Thank you in advance. Hiroyuki

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Re: [Freesurfer] --bg option for mri_glmfit-sim
by Douglas N Greve 07 Jan '10

07 Jan '10

You can only run it on one node. The problem is going to be that you can't submit it to a scheduler. You'd have to ssh into the node and run it from the cmd line. doug Xiangchuan Chen wrote: > Dear FreeSurfer experts, > > Our cluster has 8 nodes. Each node has 8 cpu cores sharing 8GB ram. So, if I > want to apply --bg option when running mri_glmfit-sim on this cluster, which > value I can set for it: <8 or <64? > > Thanks in advance, > > Xiangchuan Chen > > > _______________________________________________ > 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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Freesurfer January 2010