Freesurfer October 2010

freesurfer@nmr.mgh.harvard.edu

100 participants
129 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 79, Issue 32
by Siti Hajar 04 Oct '10

04 Oct '10

When I ran this command, " mri_segstats --seg "$fsaveragesurfpath"/"$hemi".fsaverage."$hemi"_"$roi"_"$subj".mgh --in "$hemi".thickness.fsaverage.mgh --sum segstats-"$hemi"_"$roi"_"$subj".txt, this kind of output came out "mghRead(/usr/local/freesurfer/subjects/100905lsy/surf/lh.thickness.fsaverage.mgh, -1): could not open file--> which indicated that there was no lh.thickness.fsaverage.mgh created. Well, basically, when I ran recon-all, lh.thickness.fsaverage.mgh should be created, but it wasn't. So, again with my question,is this situation happened due to the new freesurfer software that I installed or was it caused by other source? The skull strip result was ok ________________________________ From: "freesurfer-request(a)nmr.mgh.harvard.edu" <freesurfer-request(a)nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Mon, September 20, 2010 9:49:16 PM Subject: Freesurfer Digest, Vol 79, Issue 32 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: mri_label2volume issues (Michael Waskom) 2. Generating a 'non-zero' group mask (Marco Loggia, PhD) 3. Re: recon-all quality control checks on large numbers of subjects (Nick Schmansky) 4. lh.thickness.fsaverage (Siti Hajar) 5. Re: lh.thickness.fsaverage (Douglas Greve) ---------------------------------------------------------------------- Message: 1 Date: Fri, 17 Sep 2010 11:04:00 -0400 From: Michael Waskom <mwaskom(a)mit.edu> Subject: Re: [Freesurfer] mri_label2volume issues To: Freesurfer(a)nmr.mgh.harvard.edu Message-ID: <AANLkTi=5ZnihXybQu0Wwf-ysJN6oPoQk2bFuf2_iirzb(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Prapti, Basically, you just need to have a label file that you can turn into a lh.your_annot_name.annot (assuming your actual ROI is in the right hemisphere), so that mri_label2annot runs properly. The easiest thing to do would be to rename any old label you have in your subject's label directory to lh.dummy.label, and then create an annotation from that label with mri_label2annot. Then run mris_aparc2aseg as you tried to do before, which will create a volume that has 0's everywhere except in the area where your actual and dummy labels were projected. Figure out the voxel values for the ROI you want (using Freeview or tkmedit), and then run: mri_binarize --i your_annot_name+aseg.mgz --match <that voxel value> --o you_roi_name.mgz Which will have 1s where your ROI is and 0s everywhere else. Best, Mike -------Original Message------- Hi Doug, Thanks for the reply. I am sorry, I am a bit confused about what you mean by creating a dummy label. I am also not sure at which step I need to do this. As I understand it, I use mri_label2annot to transform my label into a annotation file and this will be separate for the two hemispheres. Do I then edit these files ? where exactly do I use mri_binarize? Thanks, Prapti -----Original Message----- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Friday, 17 September 2010 12:44 AM To: Prapti Gautam Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_label2volume issues Right, I see, mri_aparc2aseg is hard-coded to expect both lh and rh. The easiest thing is to make a dummy label for the other hemisphere. In the final segmentation, left hemisphere will have an index of 1000+something, the right will have 2000+something. You can then use mri_binarize with --match create a new binary volume with just your hemisphere. doug Prapti Gautam wrote: > Hi Doug, > > Thanks for the reply. I have tried using the method you've suggested, > however, I'm stuck because mri_label2annot which I use to turn my label > into a annot file only works in one hemisphere while mri_aparc2aseg > works for the whole brain. Do you know a work around for this? > > Can I merge the annot files created from each hemisphere so that I can > pass it to mri_aparc2aseg? > > > Thanks, > > Prapti > > > ------------------------------ Message: 2 Date: Fri, 17 Sep 2010 11:38:22 -0400 From: "Marco Loggia, PhD" <marco(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Generating a 'non-zero' group mask To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <5EA6CF4FA3914BC49D4CC51BD03A8618@MARCOWORK> Content-Type: text/plain; charset="us-ascii" Dear all, I am performing surface analyses on ASL CBF maps. As these maps do not cover the whole brain, and some masks have larger brain coverage than others, I would need to create a binary surface mask (in the fsaverage space) which would zero out the vertices where at least one of my subjects have a zero value. This map would then be used to spatially limit my statistical analyses in mri_glmfit. Any suggestions? Thanks a lot, Marco _____________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

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problem with tksurfer display
by 昌明 04 Oct '10

04 Oct '10

Dear Freesurfers： When I display and edit surfaces with tksurfer, the image can be loaded correctly, but whenever i rotate it, load curvatures, or load patches, it always freezes after my first operation and can't continue with the next operations. The freesurfer version i use is FS 4.5.0 under Fedora core 12, and the woking momory of computer is 4 Gigabytes with 4 processors, also enough hard disk space is available. can someone tell my what the problem is, and how i can fix it? thank you very much! changming

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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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Making a surface from the skull?
by Mark J. Pearrow 04 Oct '10

04 Oct '10

Hi all, I know this is slightly outside the normal bounds, but I am wondering if there is a way to create a surface from the skull? One of our folks is looking to create some custom-fitted recording chambers for nonhuman primates based on the individual skull. I seem to recall that FS has a way of generating STL files, which would be perfect for submitting to a rapid prototyping machine. Here's what the user says: " In brief, I would like to shape the bottom-side of my recording chambers (elliptical/circular cylinder) so that they form-fit to the curvature of the primate skull. Ideally, this will involve segmenting and extracting a 3D portion of the skull and converting it into an STL file to use for machining the implant." Best, mjp

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Are cortical thickness and surface area independent of each other?
by Jürgen Hänggi 04 Oct '10

04 Oct '10

Dear FS experts I would like to know whether cortical thickness and cortical surface area as computed by FS are independent of each other. My guess is that they are not independent, isn't it? Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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squashed ascii coordinates of flattened patch
by Eyal Dechter 03 Oct '10

03 Oct '10

Hi, I'm trying to get the coordinates of vertices on a flattened patch that I've cut out of an inflated surface using tksurfer in fs 4.5.0. I save the patch, use mris_flatten, and then mris_convert -p. However, the coordinates I'm getting render the patch somewhat distorted and I'm wondering how I can recover the original geometry. Loading the ascii file back into tksurfer results in the correct geometry, so is there some distortion that tksurfer accounts for when loading up a patch. At the link below I've put a screen shot of the ascii coordinates plotted (ignore the black line) and the flat patch as it looks in tksurfer. I've also put the patch files I'm using. Note how the patch seems squashed. http://web.mit.edu/~edechter/Public/ After saving the patch I run: mris_flatten -w 10 patch_file patch_file.flat mris_convert -p patch_file.flat patch_file.flat.asc Also, there are a number of extraneous random vertices that show up in the ascii files. They are speckled around the patch in the left hand plot. What are these? And how do I get rid of them? Thanks, Eyal Dechter -------------------------- edechter(a)mit.edu Kanwisher Lab MIT

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connot complete setup (Mac OS X snow leopard)
by Tomita Satoshi 02 Oct '10

02 Oct '10

Hi, I cannot proceed setup using tkmedit ! Fatal Error in tkmedit.bin: could not open display freesurfer ver 4.5.0 Mac OS X snow leopard (MacPro) please give me help...

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correcting segmentation errors near the cerebellum
by Mehul Sampat 01 Oct '10

01 Oct '10

Hi Folks, One of my colleagues has a case which has a strange artifcfact near the cerebellum; it seems like it recognizes the tentorium as part of brain This bright artifact (?) throws off the segmentation and also the main surface. To correct this artifact should he just make manual edits to the wm.mgz ? Thanks Mehul

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Motion correction
by hakon.grydeland＠psykologi.uio.no 01 Oct '10

01 Oct '10

Dear all, we are currently processing a dataset using FreeSurfer 5.0 and in a (very) few subjects (3 of 450) the output is distorted. However, when rerunning the 3 subjects adding the -flirt-motioncor flag to the recon-all -all command, the output is fine (please see http://folk.uio.no/haakongr/files/inflated444.jpg for an example, left side is the -flirt-motioncor version). Any ideas as how to solve this problem without mixing procedures (or rerunning all subjects) would be highly appreciated! Thanks, Håkon Grydeland --- FREESURFER_HOME: /psyklab/local/freesurfer.5.0.0 Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 RedHat release: Red Hat Enterprise Linux Client release 5.5 (Tikanga) Kernel info: Linux 2.6.18-194.11.4.el5.usit_CVE_2010_3081 x86_64

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Freesurfer October 2010