Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

FSPGR axial 3D WITH a slcie thickness of 2.6
by asaf achiron 12 Oct '08

12 Oct '08

Dear group, in 2009 we will change our MRI protocol. we are doing on a GE scanner 3T, T1-FSPGR axial slcies, 3D with a slice thickness of 2.6 and overlay of 50%. will it be possible to work with this data on FreeSurfer? thank you, asaf

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Question regarding pial surface correction
by John Sheppard 11 Oct '08

11 Oct '08

Hi everyone, Quick question about how you can go about manual pial surface corrections. This process is outlined at following page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Following the manual edits, user runs following bit of autorecon2 (and autorecon3 again if you want subcortical segmentation): recon-all -autorecon2-pial -autorecon3 -subjid subject3_before My questions is simply whether Freesurfer takes the user's input for pial surface verbatim (i.e. does it make the *exact* changes that user specifies). Or, does Freesurfer take the users input but then make its own judgments on where the pial surface should be, combinining user input with intensity/morphometry considerations? Kind of like the way WM control points work (in a sense). Thanks! -- John Sheppard Undergraduate Student (Class of 2010) Department of Biomedical Engineering Northwestern University Phone: (630) 957-8321 E-mail: john-sheppard(a)northwestern.edu

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Re: [Freesurfer] tksurfer display tcl error & FS training
by Derin Cobia 10 Oct '08

10 Oct '08

Nick, Here's the output: [derin@eeyore conte_mprage]$ ldd `which tkmedit.bin` linux-gate.so.1 => (0x00590000) libtix8.1.8.4.so => /pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.so (0x001c3000) libtk8.4.so => /pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtk8.4.so (0x00e8b000) libtcl8.4.so => /pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x006c6000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0x00110000) libGL.so.1 => /usr/lib/libGL.so.1 (0x06531000) libXext.so.6 => /usr/lib/libXext.so.6 (0x0088e000) libX11.so.6 => /usr/lib/libX11.so.6 (0x00789000) libXmu.so.6 => /usr/lib/libXmu.so.6 (0x00223000) libz.so.1 => /usr/lib/libz.so.1 (0x0067b000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x0713a000) libdl.so.2 => /lib/libdl.so.2 (0x0065c000) libpthread.so.0 => /lib/libpthread.so.0 (0x00662000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x07680000) libm.so.6 => /lib/libm.so.6 (0x00633000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x0763a000) libc.so.6 => /lib/libc.so.6 (0x0023a000) libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0x056f8000) libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0x00190000) libXau.so.6 => /usr/lib/libXau.so.6 (0x0077c000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00781000) libXt.so.6 => /usr/lib/libXt.so.6 (0x06e01000) /lib/ld-linux.so.2 (0x004cb000) libSM.so.6 => /usr/lib/libSM.so.6 (0x00438000) libICE.so.6 => /usr/lib/libICE.so.6 (0x0045f000) [derin@eeyore conte_mprage]$ ldd `which tksurfer.bin` linux-gate.so.1 => (0x00f6e000) libtix8.1.8.4.so => /pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.so (0x002e6000) libtk8.4.so => /pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtk8.4.so (0x003ce000) libtcl8.4.so => /pkg/brainmap/freesurfer/lib/tcltktixblt/lib/libtcl8.4.so (0x00110000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0x006f7000) libXmu.so.6 => /usr/lib/libXmu.so.6 (0x00223000) libGL.so.1 => /usr/lib/libGL.so.1 (0x06531000) libXext.so.6 => /usr/lib/libXext.so.6 (0x0088e000) libX11.so.6 => /usr/lib/libX11.so.6 (0x00789000) libz.so.1 => /usr/lib/libz.so.1 (0x0067b000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x0713a000) libdl.so.2 => /lib/libdl.so.2 (0x0065c000) libpthread.so.0 => /lib/libpthread.so.0 (0x00662000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0x07680000) libm.so.6 => /lib/libm.so.6 (0x00633000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x0763a000) libc.so.6 => /lib/libc.so.6 (0x004ee000) libXt.so.6 => /usr/lib/libXt.so.6 (0x06e01000) libGLcore.so.1 => /usr/lib/libGLcore.so.1 (0x056f8000) libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0x00259000) libXau.so.6 => /usr/lib/libXau.so.6 (0x0077c000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00781000) /lib/ld-linux.so.2 (0x004cb000) libSM.so.6 => /usr/lib/libSM.so.6 (0x001ad000) libICE.so.6 => /usr/lib/libICE.so.6 (0x001b6000) For our network: $FREESURFER_HOME=/pkg/brainmap/freesurfer Thanks, Derin On Oct 9, 2008, at 3:40 PM, Nick Schmansky wrote: Derin, Can you do this: source $FREESURFER_HOME/bin/tcl_setup then send me the output of: ldd `which tkmedit.bin` and ldd `which tksurfer.bin` I will be looking to see if the proper tcl/tk/tix/blt libs are being used (those in freesurfer/lib/tcltktixblt). Nick On Thu, 2008-10-09 at 11:15 -0500, Derin Cobia wrote: Nick, Yes, our tcltktixblt directory was intact and set correctly. The reason I thought it was a BLT lib was it came up missing when I ran fs_lib check. At any rate, the DefaultDepth is already at 24 in our xorg.conf file and the problem persists. Any other thoughts what might be occurring? Would you like me to submit my output as well? Also, any thoughts from anyone with regard to question #2 (see below)? Thanks. -Derin On Oct 8, 2008, at 5:12 PM, Nick Schmansky wrote: Derin, To answer your first question, the solution to that particular problem that you reference was not to install the BLT libs (as they are included with freesurfer in the $FREESURFER_HOME/lib/tcltktixblt directory and found by setting LD_LIBRARY_PATH in the tksurfer script), but rather by changing the 'DefaultDepth' from 16 to 24 in the 'Screen' Section in the file /etc/X11/xorg.conf file. Nick Two questions: 1. We installed the latest version of 32-bit FS on several workstations running CentOS 5.1 in our lab. However, once we ran the CentOS updates (~280 of them through up2date), tkmedit now fails to open and tksurfer exhibits behavior exactly as described in this message from the mail archive: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07570.html Having attempted to troubleshoot it I discovered that a blt lib was missing, but even with re-installation of this tksurfer continues to not display correctly. I believe it's a tcl problem, but I don't understand why performing incremental updates to CentOS would break FS. More importantly, I'm not sure which of the updates does "the breaking" so I can just avoid it. Any ideas? 2. We are in the process of training new research assistants in how to use FS. Typically we have approached this in a more qualitative way by working side-by-side with them to guide their edits and processing. I was wondering if there is a quantitative way of comparing their work that you (or others) have used when training "new recruits" in FS. Maybe something like was done in the Han et al (2006) paper, such as compare their thickness (or other) maps with someone we know does well with manual interventions? In essence, we're trying to think of a rigorous way to train new people in FS, thanks! -Derin _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Post-doc position in Geneva - Cognitive Neuroimaging of Language
by Narly A Golestani 10 Oct '08

10 Oct '08

Dear users, Applications are invited for a 3-year PostDoc position at the Department of Fundamental Neuroscience at the University of Geneva in Switzerland, under the supervision of Dr. Narly Golestani. Projects will include using fMRI and EEG to better understand brain functional plasticity arising from the acquisition of language-related expertise. The laboratory is part of the Department of Fundamental Neuroscience of the medical faculty (http://medweb1.unige.ch/recherche/groupes/f/fondamentale/05.php) and the Geneva University Neuroscience Center (http://neurocenter.unige.ch/) Geneva offers a thriving international environment, with extensive cultural and outdoor activities, and a high quality of living. Applicants should have a strong interest in neuroscience and ideally also in language research. Prior experience with fMRI and EEG are highly desirable. Salary will start at 64,520 CHF or more per year (about 4,355 CHF / month net) depending on previous research experience, and will increase by about 1,467 CHF annually. Applications will be considered until the position is filled. Informal inquiries can be addressed to Narly Golestani (Narly.Golestani(a)unige.ch) Applications including a CV including list of publications, a statement of research interests, and the names and full contact details of two referees should be sent to: Narly.Golestani(a)unige.ch

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Permissions Denied (Control Points)
by Kellen Mobilia 09 Oct '08

09 Oct '08

Help- As a relatively new user to Freesurfer, I have encountered some problems none that more experienced users have been able to solve until now. Every time I try to add a control point, the message "MRIwriteColtrolPoints( <file location>): could not write file Permission denied" This may have to do with our server however even removing the read/write protections via super user didn't work. Has anyone else had this problem? If so how is it solved? Thanks

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Re: Freesurfer qdec-coord script
by Pedro Paulo de Magalhães Oliveira Junior 09 Oct '08

09 Oct '08

QDEC transform your data into a common spherical space. So this file y.mgh is already in a common space. Running that script into your y.mgh (from QDEC directory) will retrieve the values of the surface stat in fsaverage space. >> mri_convert --frame $i y.mgh ../../fsaverage/surf/lh.$i.mgh This line break apart the volume of each subject. >> mris_convert -c $i.mgh ../../fsaverage/surf/lh.inflated lh.$i.asc This one convert all values to fsaverage space. Is that what you want? 2008/10/9 Mishkin Derakhshan <mishkind(a)gmail.com> > Hi Pedro, > Thanks a lot for the help. Reading through all the FreeSurfer mail > archives you are almost as helpful as Nick! > > Anyway, I just posted a msg to the list describing what it is i want > to do which is transform my own custom surface stats, into fsaverage > space. > > You can read my post for more details, but if you have any input (or > scripts) on how to do this, it would be greatly appreciated. > > thanks, > mishkin > > > > On Thu, Oct 2, 2008 at 9:08 PM, Pedro Paulo de Magalhães Oliveira > Junior <ppj(a)netfilter.com.br> wrote: > > Sure. > > > > y.mgh is the volume created by QDEC when you start a stat design. > > You'll find it usually in $SUBJECTS_DIR/qdec > > > > The other command is to export al values in asc format: > > > > x,y,z - value > > > > where value is what you studied in QDEC, for instance, thickness. > > > > If you need any other help, contact me. Maybe if you describe what you > > are trying to do I could have a script ready. > > > > Cheers, > > > > PPJ > > > > On 10/2/08, Mishkin Derakhshan <mishkind(a)gmail.com> wrote: > >> Hi Pedro, > >> I wrote to the FreeSurfer list a while ago about a problem I was having > (see > >> emails below). > >> You told me to try your qdec-coord script from the wiki: > >> > >> # Script created December 2007 by Pedro Paulo Oliveira Jr. > >> # Use with Freesurfer 4.x > >> > >> cd #your directory where qdec data are stored. > >> > >> set numsubject = 17 #your value > >> > >> for i in `seq 1 $numsubject` > >> do > >> mri_convert --frame $i y.mgh ../../fsaverage/surf/lh.$i.mgh > >> mris_convert -c $i.mgh ../../fsaverage/surf/lh.inflated > lh.$i.asc > >> done > >> > >> > >> I have a few questions as I am new to the whole qdec group analysis > thing. > >> Could you explain to me briefly what your two commads are doing, or at > the > >> least answer these two questions: > >> 1. What is y.mgh in your first command? how is it created? > >> 2. In the second command, should $i.mgh really be > >> "../../fsaverage/surf/lh.$i.mgh" ie. the output from the first command? > >> > >> thanks, > >> mishkin > >> > >> > >> On Thu, May 1, 2008 at 6:45 PM, Pedro Paulo de Magalhães Oliveira Junior > < > >> ppj(a)netfilter.com.br> wrote: > >> > >>> I think this page can give you an insight: > >>> > >>> > http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions_2fScripts_2fppau… > >>> > >>> > >>> 2008/5/1 Mishkin Derakhshan <mishkind(a)gmail.com>: > >>> > Hi, > >>> > > >>> > I know that at some point in the pipeline, the surfaces are > registered > >>> > to a common sphere, and thus I'm hopping there is a one-to-one vertex > >>> > correspondance between subjects. > >>> > > >>> > My question is, let's say I look at vertex X, on subject1, how do I > >>> > find out the corresponding vertex location on subjectN. > >>> > > >>> > thanks, > >>> > mishkin > >>> > _______________________________________________ > >>> > Freesurfer mailing list > >>> > Freesurfer(a)nmr.mgh.harvard.edu > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > > >>> > >> > > > > -- > > Sent from my mobile device > > > > ----------------------------------------------------------- > > Pedro Paulo de M. Oliveira Junior > > Diretor de Operações > > Netfilter & SpeedComm Telecom > > > -- ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom

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lh.thickness file format
by Mishkin Derakhshan 09 Oct '08

09 Oct '08

Hi, I have my own stats files that I would like to incorporate into the freesurfer stream, if possible. Ie. after running FreeSurfer, I create a ?h.mystats (containing something like image intensities for example), where the format of ?h.mystats is just an ascii file, where each line is the value at that vertex. What I ultimately want to do, is to transform ?h.mystats into fsaverage space, that way I can compare ?h.mystats across subjects. I was hoping I could use the given sphere.reg which has already been calculated to do this. I renamed ?h.mystats to ?h.thickness and tried the following which I think will work: mris_preproc --s mysubject --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh But it complains that: Reading curvature file /lab1/FreeSurfer/4.0.5/ms-mni/testing//tester/surf/lh.thickness MRISreadBinaryCurvature: incompatible vertex number in file /lab1/FreeSurfer/4.0.5/ms-mni/testing//tester/surf/lh.thickness I checked and I have the same number of lines in my file as vertices on my object so my questions are: 1. Do I have to convert my ascii ?h.mystats to a curvature (binary) file like ?h.thickness, and if so how does one do this? 2. Is this the right way to get what I ultimately want to do, or is there another method? thanks, mishkin

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Re: [Freesurfer] tksurfer display tcl error & FS training
by Derin Cobia 09 Oct '08

09 Oct '08

Nick, Yes, our tcltktixblt directory was intact and set correctly. The reason I thought it was a BLT lib was it came up missing when I ran fs_lib check. At any rate, the DefaultDepth is already at 24 in our xorg.conf file and the problem persists. Any other thoughts what might be occurring? Would you like me to submit my output as well? Also, any thoughts from anyone with regard to question #2 (see below)? Thanks. -Derin On Oct 8, 2008, at 5:12 PM, Nick Schmansky wrote: Derin, To answer your first question, the solution to that particular problem that you reference was not to install the BLT libs (as they are included with freesurfer in the $FREESURFER_HOME/lib/tcltktixblt directory and found by setting LD_LIBRARY_PATH in the tksurfer script), but rather by changing the 'DefaultDepth' from 16 to 24 in the 'Screen' Section in the file /etc/X11/xorg.conf file. Nick Two questions: 1. We installed the latest version of 32-bit FS on several workstations running CentOS 5.1 in our lab. However, once we ran the CentOS updates (~280 of them through up2date), tkmedit now fails to open and tksurfer exhibits behavior exactly as described in this message from the mail archive: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07570.html Having attempted to troubleshoot it I discovered that a blt lib was missing, but even with re-installation of this tksurfer continues to not display correctly. I believe it's a tcl problem, but I don't understand why performing incremental updates to CentOS would break FS. More importantly, I'm not sure which of the updates does "the breaking" so I can just avoid it. Any ideas? 2. We are in the process of training new research assistants in how to use FS. Typically we have approached this in a more qualitative way by working side-by-side with them to guide their edits and processing. I was wondering if there is a quantitative way of comparing their work that you (or others) have used when training "new recruits" in FS. Maybe something like was done in the Han et al (2006) paper, such as compare their thickness (or other) maps with someone we know does well with manual interventions? In essence, we're trying to think of a rigorous way to train new people in FS, thanks! -Derin _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Permissions Denied (Control Points)
by Kellen Mobilia 09 Oct '08

09 Oct '08

Help-

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FW: [Freesurfer] Talairach_with_skull.lta accuracy
by Jeff Sadino 09 Oct '08

09 Oct '08

Hello, I am trying to validate the ICV value by lining up the nu_noneck image with the RB image. These are the commands I am using: mri_convert nu_noneck.mgz --apply_transform transforms/talairach_with_skull.lta nu_noneck5.mgz tkmedit -f nu_noneck5.mgz & tkmedit -f /apps/freesurfer/average/RB_all_withskull_2006-02-15.gca & When I compare these two, they don't line up. The RB image is all blurry (Maybe it's a combination of several subjects and is supposed to be like that). Any suggestions as to how to line up the noneck transformed imaged to the RB image is greatly appreciated! I also attached three files to show what's happening in my transform process. Thanks, Jeff ---------------------------------------- > Date: Fri, 5 Sep 2008 20:31:55 -0400 > From: fischl(a)nmr.mgh.harvard.edu > To: jsadino(a)hotmail.com > Subject: RE: [Freesurfer] Talairach_with_skull.lta accuracy > > can you send this to the list so others can respond? Where did you get the > tmp.reg file? If you have transformed them already you shouldn't need > tkregister2 (or a registration file in general) to compare them. > > On Fri, 5 Sep 2008, > Jeff Sadino wrote: > >> >> Thank you very much for your help. Your knowledge and quick responses are very much appreciated. >> >> I converted my image into transformed space, but it still does not match the RB image. These are the commands I used: >> >> mri_convert nu_noneck.mgz --apply_transform > transforms/talairach_with_skull.lta nu_noneckt3.mgz >> >> tkregister2 --targ > /apps/freesurfer/average/RB_all_withskull_2006-02-15.gca --reg tmp.reg > --lta /data/040002_S04_bakj/mri/transforms/talairach_with_skull.lta --mov > /data/040002_S04_bakj/mri/nu_noneckt3.mgz >> >> Again, my main goal is to verify the ICV value, so to do that I need to verify that the lta file is transforming the nu_noneck image onto the RB image...I think. >> >> What step am I missing? >> >> Thank you >> Jeff >> >> >> ---------------------------------------- >>> Date: Fri, 5 Sep 2008 13:09:21 -0400 >>> From: fischl(a)nmr.mgh.harvard.edu >>> To: jsadino(a)hotmail.com >>> CC: greve(a)nmr.mgh.harvard.edu >>> Subject: RE: [Freesurfer] Talairach_with_skull.lta accuracy >>> >>> that won't generate a transformed volume, just display it in the >>> transformed space. That is, the volumes you sent were in their native >>> space and would have no reason to be aligned. The neck removal seems to >>> have been fine in both cases. >>> On Thu, 4 Sep 2008, Jeff Sadino wrote: >>> >>>> >>>> ps, sorry, I forgot to include my command: >>>> >>>> >>>> tkregister2 --targ /apps/freesurfer/average/RB_all_withskull_2006-02-15.gca --mov /data/${file}/mri/nu_noneck.mgz --lta /data/${file}/mri/transforms/talairach_with_skull.lta --reg tmp.reg >>>> >>>> I believe this will transform the nu_neck.mgz image via the talairach matrix, so that it matches the RB image. >>>> >>>> btw, we processed the scans using freesurfer 3, but the tkregister2 that came with freesurfer 3 did not include the --lta tag, so I am using the tkregister2 from freesurfer4. >>>> >>>> Thanks! >>>> >>>> ---------------------------------------- >>>>> Date: Thu, 4 Sep 2008 21:49:27 -0400 >>>>> From: fischl(a)nmr.mgh.harvard.edu >>>>> To: jsadino(a)hotmail.com >>>>> CC: freesurfer(a)nmr.mgh.harvard.edu >>>>> Subject: Re: [Freesurfer] Talairach_with_skull.lta accuracy >>>>> >>>>> Hi Jeff, >>>>> >>>>> why do you say that one is bad? We don't resample, so neither one will be >>>>> aligned with the atlas unless you apply the transform. >>>>> >>>>> We are aware that the eTIV measures have more variability than we would >>>>> like, and we're looking into it, but don't have a good solution from only >>>>> T1 images. >>>>> >>>>> cheers, >>>>> Bruce >>>>> On Thu, 4 Sep 2008, >>>>> Jeff Sadino wrote: >>>>> >>>>>> >>>>>> Hello all, >>>>>> >>>>>> According to aseg.stats, our ICV values fluctuate on the same subject across scans, sometimes by up to 10% I have been validating the talairach_with_skull.lta accuracy by comparing the nu_neck.mgz to the RB_all_withskull_2006-02-15.gca template. I read on the boards that it is not all that necessary that the brains match, that it is more important for the skulls to match. The RB is blurred (I don't fully understand where the RB comes from, I think from 22 subjects that the freesurfers combined into one?), so am I matching up the whitest areas of the RB to the skull on the nu_neck image? I noticed also that the bottom of the brains rarely match at all to the RB image...is this normal? Are there any other parts of the image that need to be checked for validity? >>>>>> >>>>>> I attached two nu_noneck.mgz files, one was good and the other bad. Are these images typical? >>>>>> >>>>>> Thank you for your help, >>>>>> Jeff >>>>>> >>>>>> _________________________________________________________________ >>>>>> See how Windows Mobile brings your life together?at home, work, or on the go. >>>>>> http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/ >>>> >>>> _________________________________________________________________ >>>> Get more out of the Web. Learn 10 hidden secrets of Windows Live. >>>> http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!5… >>>> >>>> >>>> >> >> _________________________________________________________________ >> See how Windows connects the people, information, and fun that are part of your life. >> http://clk.atdmt.com/MRT/go/msnnkwxp1020093175mrt/direct/01/ >> >> >> _________________________________________________________________ See how Windows Mobile brings your life together—at home, work, or on the go. http://clk.atdmt.com/MRT/go/msnnkwxp1020093182mrt/direct/01/

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