[Freesurfer] Old FSL sourcing
Hi, I was wondering if anyone can tell me a version of FSL 3.X that I can source, I need to use an older version that is compatible with the stable3 environment. Thanks in advance! Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] cortical thickness maps
Hi, Thank you for your help before. I finished the group analysis of cortical thickness with QDEC on FreeSurfer and I would like to get the cortical thickness maps with inflated surface on Windows XP. Would you teach me how can I change the cortical thickness maps from FreeSurfer to Windows XP? Thanks in advance! Feng-Xian - Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Discrepancy between talairach coordinates entered in tool bar and time course display
Hello, I am having an issue with a discrepancy between talairach coordinates I plug into tkmedit tool bar, and what gets displayed when I generate a time course for this voxel. FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.2.0-20090128 RedHat release: CentOS release 4.6 (Final) Kernel info: Linux 2.6.9-67.ELsmp i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /space/seymour/4/users/joshdata/ PWD: /space/seymour/4/users/joshdata When I generated the time course. the overlay I loaded onto the orig volume is /space/seymour/4/users/joshdata/CC-n8_fixed/bold/EMerror/tal-ffx/ASevfix/cespct.bhdr. Registration file is: /space/seymour/4/users/joshdata/CC-n8_fixed/bold/EMerror/tal-ffx/register.dat. The voxel I want to generate a time course for has these coordinates: X -3.96 Y - -20.22 Z - -15.81 When I plug these into the tkmedit tool bar, the emerging time course graph has coordinates X- -4.00 Y - -20.00 Z- -20.00. While the X and Y coordinates are close enough, the Z is off. If I change the Z coordinate in the toolbar to -12.3, it will give me a -15. 8 value for the Z coordinate on the time course plot caption. Is this image legitimate? Which image accurately represents the original coordinates I want to use? Please write back when you can, and thank you, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Old FSL sourcing
Jake, Try using /usr/pubsw/packages/fsl/3.2b (at the NMR Center). Another option is to install an old version of freesurfer 3.0.5 locally. The distributions back then included FSL. You can get old distributions here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ Nick On Wed, 2009-01-28 at 09:36 -0500, John Kuster wrote: Hi, I was wondering if anyone can tell me a version of FSL 3.X that I can source, I need to use an older version that is compatible with the stable3 environment. Thanks in advance! Jake ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Discrepancy between talairach coordinates entered in tool bar and time course display
Dave, You may need to select View-Information-MNI, which will enable an MNI Talairach coord entry box. MNI Tal differs from Tal in the z direction to correct for differences between the mni talairach-ized brain and real tal coords. Nick On Wed, 2009-01-28 at 11:23 -0500, Dave Brohawn wrote: Hello, I am having an issue with a discrepancy between talairach coordinates I plug into tkmedit tool bar, and what gets displayed when I generate a time course for this voxel. FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.2.0-20090128 RedHat release: CentOS release 4.6 (Final) Kernel info: Linux 2.6.9-67.ELsmp i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /space/seymour/4/users/joshdata/ PWD: /space/seymour/4/users/joshdata When I generated the time course. the overlay I loaded onto the orig volume is /space/seymour/4/users/joshdata/CC-n8_fixed/bold/EMerror/tal-ffx/ASevfix/cespct.bhdr. Registration file is: /space/seymour/4/users/joshdata/CC-n8_fixed/bold/EMerror/tal-ffx/register.dat. The voxel I want to generate a time course for has these coordinates: X -3.96 Y - -20.22 Z - -15.81 When I plug these into the tkmedit tool bar, the emerging time course graph has coordinates X- -4.00 Y - -20.00 Z- -20.00. While the X and Y coordinates are close enough, the Z is off. If I change the Z coordinate in the toolbar to -12.3, it will give me a -15. 8 value for the Z coordinate on the time course plot caption. Is this image legitimate? Which image accurately represents the original coordinates I want to use? Please write back when you can, and thank you, Dave Brohawn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Extract overlay value from fsaverage ROIs
Christine, This would do it: mri_segstats --annot fsaverage lh aparc --i sig.mgh --sum out.txt where this will find the means for the 'aparc' ROI's, for the input file sig.mgh (assuming it was produced by some group analysis, like mri_glmfit or qdec), and produces output text file out.txt. Nick On Wed, 2009-01-28 at 17:29 +, Christine Ecker wrote: Hi, Just wondering whether it is possible to extract values from an overlay created on fsaverage for aparc parcellated regions e.g. the mean of a statistical test parameter for specific aparc ROIs? I know it is possible to extract values for individual subjects on the basis of fsaverage ROIs, but all I would need is the mean for individual ROIs on fsaverage. Thanks for your help! - Dr. Christine Ecker Section of Brain Maturation (PO50) Department of Psychological Medicine De Crespigny Park, Denmark Hill London SE5 8AF Phone: 0207 848 0947 Email: c.ec...@iop.kcl.ac.uk - ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] qdec ?h.sulc
Hi, Looking for a little clarification. Using qdec to look at group differences in the surface measure ?h.sulc. Large positive values in ?h.sulc indicate greater sulcal depth, right? Large negative values in ?h.sulc indicate something about gyri? Small negative values in ?h.sulc indicate transition from gyral to sulcal or sulcal to gyral? Many thanks for any additional info, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Error while registering functionals to anatomicals
Hi, I am getting an error if I try to register my functionals to anatomical image (using spmregister-sess command). It is looking for file 'subjectname'. Here are the steps I did before coming across this error. Did I miss anything? step 1 : unpacking data (unpacksdcmdir command) step 2 : run motion correction (preproc-sess command) step 3: created the paradigm file step 4: registering functional to anatomical /** spmregister-sess -s abe_090116 -- spmregister-sess logfile is /tmp/sk/FSFAST/log/spmregister-sess.19224.log -- Session: /tmp/sk/FSFAST/abe_090116 Wed Jan 28 13:27:34 EST 2009 ERROR: file 'subjectname' does not exist in /tmp/sk/FSFAST/abe_090116 /** regards, Krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Error while registering functionals to anatomicals
Hi Krishna, this link should help http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastLinkAnatData Hi, I am getting an error if I try to register my functionals to anatomical image (using spmregister-sess command). It is looking for file 'subjectname'. Here are the steps I did before coming across this error. Did I miss anything? step 1 : unpacking data (unpacksdcmdir command) step 2 : run motion correction (preproc-sess command) step 3: created the paradigm file step 4: registering functional to anatomical /** spmregister-sess -s abe_090116 -- spmregister-sess logfile is /tmp/sk/FSFAST/log/spmregister-sess.19224.log -- Session: /tmp/sk/FSFAST/abe_090116 Wed Jan 28 13:27:34 EST 2009 ERROR: file 'subjectname' does not exist in /tmp/sk/FSFAST/abe_090116 /** regards, Krishna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec ?h.sulc
Jenifer, I've attached a picture from one the slides showing what is stored in .sulc (except ignore the 'thickness' bit, that is stored in .thickness). You are correct in your interpretation of values. Nick On Wed, 2009-01-28 at 12:28 -0600, Juranek, Jenifer wrote: Hi, Looking for a little clarification. Using qdec to look at group differences in the surface measure ?h.sulc. Large positive values in ?h.sulc indicate greater sulcal depth, right? Large negative values in ?h.sulc indicate something about gyri? Small negative values in ?h.sulc indicate transition from gyral to sulcal or sulcal to gyral? Many thanks for any additional info, Jenifer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer attachment: sulc.jpg___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] --fsgd file
Hi everyone, I was wondering if it is possible to flag missing entries in the covariates corresponding to subjects, in the construction of the file passed through --fsgd to mri_glmfit ? Not all my subjects completed all the tasks, and i need to code them in the file, somehow. thanks, sid. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdec ?h.sulc
Hi Jenifer - On Wednesday 28 January 2009 15:16:20 Juranek, Jenifer wrote: So does the info in ?h.sulc contain sulcal depth information wrt the mean cortical surface? How does this differ from the positive values contained in the ?h.curv file? The 'sulc' and 'curv' overlays do tend to look similar sometimes, but they in fact measure quite different things. You are correct that the 'sulc' conveys information on how far removed a particular vertex point on a surface is from a hypothetical mid-surface that exists between the gyri and sulci. This surface is chosen so that the mean of all these displacements is zero. The 'sulc' gives a indication then of linear distance and displacements: how deep and how high are brain folds In FreeSurfer, gyri have negative 'sulc' values, are colored green, and indicate how far down a point has to travel to reach this mid-surface. Sulci have positive 'sulc' values, are colored red, and indicate how far up a point needs to travel to reach the mid-surface. The 'curv' conveys information on the curvature (not distance) at a specific vertex point. The color conveys the sign, and is just an arbitrary choice. The sharper the curve, the higher the value (positive or negative). Areas with positive curvature, are colored red, and correspond to curvatures in sulci, i.e. curving up. Areas with negative curvature are colored green, and correspond to curves pointing down, i.e. gyri. So, in a nutshell, the difference is that the 'curv' files contain information about curvatures, and the 'sulc' files contain information about displacement. HTH -=R -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Calculate corticol thickness
Hello all,
Real basic question: How do I calculate the thickness of the cortex, preferably
at each vertex/face? I have tried read_curv.m, but get this error:
[thickness, f] = read_curv('lh.thickness')
??? Undefined function or method 'fread3' for input arguments of type 'double'.
Error in == read_curv at 21
vnum = fread3(fid) ;
This should be simple, but the discussion board starts one step after me I
think :) Any help would be appreciate!
Second, when I try to load it in freesurfer, I get an error:
[fsu...@cluster ~]$ tksurfer 050080_S01 lh thickness
surfer: current subjects dir: /share/apps/freesurfer/subjects
surfer: not in scripts dir == using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /export/home/FSuser
Talairach transform
/home/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm does not
exist ...
Loading tal xfm file
/share/apps/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm
surfer: Reading header info from
/share/apps/freesurfer/subjects/050080_S01/mri/T1.mgz
I tried loading the inflated first, then loading the thickness, which works,
but the surface just turns all red. Are the minimum thicknesses maxing out my
color map? This seems unlikely. Can anybody help me?
[fsu...@cluster ~]$ tksurfer 050080_S01 lh inflated
surfer: current subjects dir: /share/apps/freesurfer/subjects
surfer: not in scripts dir == using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /export/home/FSuser
Talairach transform
/home/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm does not
exist ...
Loading tal xfm file
/share/apps/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm
surfer: Reading header info from
/share/apps/freesurfer/subjects/050080_S01/mri/T1.mgz
surfer: vertices=144686, faces=289368
Talairach transform
/home/freesurfer/subjects/050080_S01/mri/transforms/talairach.xfm does not
exist ...
Loading tal xfm file
/share/apps/freesurfer/subjects/050080_S01/surf/../mri/transforms/talairach.xfm
surfer: single buffered window
libGL error: open DRM failed (Operation not permitted)
libGL error: reverting to (slow) indirect rendering
surfer: using interface /share/apps/freesurfer/lib/tcl/tksurfer.tcl
Reading /share/apps/freesurfer/lib/tcl/tkm_common.tcl
Reading /share/apps/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /share/apps/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /share/apps/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
(And then File - Load Curvature - lh.thickness)
% surfer: curvature read: min=0.226951 max=5.00
Thanks you very much,
Jeff Sadino
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