Freesurfer November 2006

freesurfer@nmr.mgh.harvard.edu

41 participants
59 discussions

group level analysis
by Emily Cooper 27 Nov '06

27 Nov '06

Hi, I have functional datasets (.HEAD and .BRIK) from Afni that I'm trying to analyze in the surface domain using Freesurfer. I have Freesurfer anatomical surfaces for all my subjects, and have managed to use the tkmedit and tksurfer gui's to map my functional overlays (using the "calculate identity matrix" option) onto the volume and surface. What I'd like to do now is map the functional data onto a surface with a common number of nodes so that I can extract a matrix of beta values and do group level analysis using R. Tksurfer seems to be able to do this with the "Save plotted data to table" option (greyed over right now), however, I've read in other messages on the mail archive that the sphere.reg surface is not in common space. I've been trying to use func2sph-sess, but I seem to be missing something, getting "ERROR: cannot find any sessions." Maybe that's the wrong way to go about it? Thanks, Emily

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Partial brain statistics registered to a full brain surface-based map?
by emoulton＠mclean.harvard.edu 27 Nov '06

27 Nov '06

Can a partial brain statistical image volume be accurately registered to a whole brain surface-based map? When I try to convert a partial brain statistical file (zstat1.nii.gz, created using FSL) into an overlay for a surface-based full brain (created using FreeSurfer), the result is a statistical overlay that spreads across the entire surface of the brain. My command line looks like this: mris_preproc --out lh-zstat1.mgz target SUBJ1 --hemi lh --mean --iv zstat1.nii.gz ../../../anat/Dummy.feat/reg/freesurfer/anat2exf.register.dat My register.dat transformation matrices work fine when I use tkmedit to view the cope1.nii.gz image as an overlay of the orig.mgz file (partial brain zstats where I would expect them on the image of the full brain). Does mris_preproc adher strictly to the register.dat parameters, or is it possibly over-ridden by the target surface? Thanks, Eric Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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vertex coordinates / volume coordinates
by Roberto Toro 27 Nov '06

27 Nov '06

Hello, I have a C code that reads FS surfaces and does some processing on them. I would like to map this back to the original MRI volume. Googling around I found that vertex coordinates may correspond to coordinates in the COR volume.... but COR volumes are now deprecated....so two questions: 1. what is the relationship between vertex coordinates and volume coordinates? 2. is there a special volume where vertex coordinates just map volume coordinates? thank you very much! roberto 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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make_average problem
by bdragans＠uke.uni-hamburg.de 27 Nov '06

27 Nov '06

Dear freesurfers, running the script make_average_subject produces constantly only the rh_* files. The error message at the end is: ln: creating symbolic link `rh.sphere' to `rh.sphere.reg': Operation not supported Any suggestions why the lh_* files are missing are greatly appreciated. Running fedora core under vmware. Thanks Bogdan

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min and max voxel values in tkmedit?
by Glenn Lawyer 27 Nov '06

27 Nov '06

Hi, Ran into an odd problem with some of our scans. After processing the dicoms with recon-all autorecon2, we open the brain.mgz and T1.mgz images in tkmedit. The brain.mgz image tends to have terrible contrast. The problem seems to be the 'colorscale' for the image. The max values are around 185 (as compared to 244-254 for images acquired using a different scan protocol). Resetting the max to 254 fixes the problem. I am wondering if this indicates something went wrong in the automatic generation of the brain image? How would you go about forcing tkmedit to have the max value be 254 at startup (so the lab tech doesn't have to manually reset this each time she loads the image)? Include a tcl script on the command-line with "SetVolumeMinMax 0 254" in it? Tkmedit reads the min and max values for the volumes when it loads them, correct? Note we only see this problem on some scans, not all. Also, we have scans from several projects/magnets/protocols. It is only one magnet/protocol where we see the problem. Thanks! details: FreeSurfer v3.0.3 on FC4. The scans in question are from a Siemens machine with the following specs (output of mri_convert): Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel SonataVision Date and time StudyDate 20060429 StudyTime 093246.125000 SeriesTime 110508.984000 AcqTime 105807.800018 Acquisition parameters PulseSeq *tfl3d1_ns Protocol unknown PhEncDir ROW EchoNo 0 FlipAngle 7 EchoTime 3.93 InversionTime 1000 RepetitionTime 2730 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 12 SeriesNo 13 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 75.4460 179.1284 108.3390 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 160 Vc 0.0209 -0.9998 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -0.9998 -0.0209 0.0000 VolCenter -1.8558 49.4811 -19.6610 TransferSyntaxUID 1.2.840.10008.1.2.1 -------------------------------------- I'm only in it for the glory. > Glenn Lawyer < > +352 661 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > ><><><><><><><><><><><:)

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vertex coordinates / volume coordinates + Folding Index
by Roberto Toro 27 Nov '06

27 Nov '06

Hi, one more question: 3. can I use mris_curvature to compute the folding index only for a particular label (and not allways for the complete hemisphere)? I've been using mris_curvature path_to_mesh/lh.white, to get ICI and FI, and -min - max -w to get the min, max, gaussian and mean curvatures. thanks again! roberto 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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FS-FAST: FIR analysis baseline corrected BOLD % signal change values?
by raij＠nmr.mgh.harvard.edu 27 Nov '06

27 Nov '06

Hi, We are measuring BOLD % signal change levels (from cespct maps) across separate analyses and the issue of whether the cespct values are pre-stimulus baseline corrected - or not - obviously would be expected to effect the results. We use a FIR group analysis of a rapid event-related design with a - mkanalysis-sess -prestim = 2 TRs - mkcontrast-sess -rmprestim We then use a tcl script to plot the numerical values in a table - here we use set gbPreStimOffset 1 func_print_timecourse_selection $lpath/<table-of-time-course-values>.txt Visually, when we use tksurfer to view the time course results from the bold/<analysisname>/h-lh.bhdr file, then all contrasts included in the analysis are showed at the same time (nice) and the two prestimulus values are included in the display. So far so good. However there is no option to view the results as BOLD % signal change (cespct). A minor annoyance is that the time courses are not baseline corrected despite that we used the -rmprestim option as explained above (they change to be baseline corrected only after we push the View/Configure/Time Course putton Remove prestim). The only way we have found to visually view (or plot with the tcl script) the cespct values is to look at the time course results inside the folders for specific contrasts (e.g., bold/<analysisname>/A-REST/cespct-lh.bhdr). However here we never see any prestimulus values (otherwise the same full analysis time window as above is shown), so we do not know if the mean of the two prestim points has been subtracted from the amplitudes (= baseline correction). Below please find the detailed commands for looking at the h-lh.bhdr and cespct curves. We would appreciate any advice how to get the pre-stim values visible even for cespct and/or double check that the cespct values (when plotted using the tcl script) are baseline corrected. Thanks!!! -Tommi Details: On machine cuzco nmr-dev-env (or nmr-std-env, does not seem to make a difference in this case) cd /space/cuzco/7/users/raij/avml_fmri_mctogether setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT fsaverage Load the h-lh.bhdr curves (prestim baseline are visible, no cespct option): tksurfer fsaverage lh inflated -timecourse fegroup/bold/group_ISI1TR_BERT_ERFIRsm5pf5tpefsub/sphsm10-ffx/h-lh.bhdr Load the cespct-lh.bhdr curves, no prestim baseline data points visible: tksurfer fsaverage lh inflated -timecourse fegroup/bold/group_ISI1TR_BERT_ERFIRsm5pf5tpefsub/sphsm10-ffx/A-REST/cespct-lh.bhdr --- Tommi Raij, MD., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

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3.0.4: some remarks
by Sebastian Moeller 25 Nov '06

25 Nov '06

Hi List, Hi Developers, a few days ago I switched our lab over to 3.0.4 from 3.0.3 (both Freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.N-full versions, running on SuSE 10.1, x86_64). Here are my impressions: 1) Scuba and tksurfer now work out of the box, cool! (my system had freeglut problems) 2) fslview is missing; this script called fslview_exe (which is still around in the new version) this small script made sure the right libraries are accessible for flview_exe; I copied it over from v3.0.3 and everything is fine. See below for a copy of the script. (I use fslview to fine tune bet). And another fsl related observation, the fsl version shipped is the 32bit one, maybe thr 64bit build might seem abetter fit for the 64bit freesurfer version. 3) the nice modification Doug made for mri_nu_correct.mni did not make it to 3.0.4. That is my download of 3.0.4 contains mir_nu_correct.mni v 1.3 2005/12/08 01:27:21, instead of v 1.5 2006/11/03 19:59:55. I just copied the modified version from 3.0.3 over; it works fine and looks better with my single channel surface coil recons. 4) it is a really great tool, thanks for all the work and especially the support on this list. aloha Sebastian ----- cut me ----- #!/bin/sh LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${FSLDIR}/lib export LD_LIBRARY_PATH $FSLDIR/bin/fslview_exe $@ ------ cut me ----- -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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Re: [Freesurfer] command for aseg stats to export to spreadsheet(excel)
by Chacko Cherian 22 Nov '06

22 Nov '06

Thank you Jenni. How do i use asegstats2table?What is the command?Is it a tcl script file?If so,could you also mention where it is located. Regards Chacko. ----- Original Message ---- From: Jenni Pacheco <jpacheco(a)nmr.mgh.harvard.edu> To: Chacko Cherian <chacko_cherian(a)yahoo.com>; Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Sent: Wednesday, November 22, 2006 3:04:28 PM Subject: RE: [Freesurfer] command for aseg stats to export to spreadsheet(excel) You can use asegstats2table. Jenni Pacheco, M.A. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 jpacheco(a)nmr.mgh.harvard.edu -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Chacko Cherian Sent: Wednesday, November 22, 2006 5:02 PM To: Freesurfer Subject: [Freesurfer] command for aseg stats to export to spreadsheet(excel) Hello Users, I wanted to know if there is a command to directly export the aseg-stats table to a spreadsheet rather than cuttting and pasting. And wishing all of you a very happy Thanksgiving and a great weekend!! Regards Chacko. ____________________________________________________________________________ ________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ____________________________________________________________________________________ Cheap talk? Check out Yahoo! Messenger's low PC-to-Phone call rates. http://voice.yahoo.com

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command for aseg stats to export to spreadsheet(excel)
by Chacko Cherian 22 Nov '06

22 Nov '06

Hello Users, I wanted to know if there is a command to directly export the aseg-stats table to a spreadsheet rather than cuttting and pasting. And wishing all of you a very happy Thanksgiving and a great weekend!! Regards Chacko. ____________________________________________________________________________________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited

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Freesurfer November 2006