Freesurfer March 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
79 discussions

intersubject registration with monkeys
by Marie Schaer 29 Mar '07

29 Mar '07

Hello everybody, Has anyone any experience with make_average_subject on monkeys brain? E.g. as it uses talairach transform, would it be biased by it, or is there any option to avoid using the talairach transform? In my experience, the resulting average surface was quite strange! And more generally, did anyone validated the traditional spherical registration on monkeys brains, does it yield an acceptable point-to- point registration? Many thanks in advance for these useful informations, Marie Schaer

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Save point (tksurfer)..go to saved point (tkmedit)
by Nandita Shetty 29 Mar '07

29 Mar '07

Hi, I have a question regarding the 'save point' and 'go to saved point' feature. I made couple of edits to the white matter (unfortunately for some strange reason, I did not fix all the defects in the inflated brain) and executed the command recon-all -autorecon2-wm -subjid pilot2 The recon was completed with no errors But, now when I try to save a point on the inflated brain and open the same in tkmedit, I get an error message saying surfer: reading canonical coordinates from surfer: /space/marvin/1/users/MRI/ACE/pilot2/surf/lh.sphere.reg mrisReadTriangleFile(/space/marvin/1/users/MRI/ACE/pilot2/surf/lh.sphere.reg): surface doesn't match /space/marvin/1/users/MRI/ACE/pilot2/surf/lh.inflated mrisReadTriangleFile failed. Is there a workaround for this? Thanks in advance for any suggestions Regards, Nandita

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ERROR: cannot find any sessions
by Alessandro Gagliardi 28 Mar '07

28 Mar '07

I'm trying to employ a FS-Fast group analysis. I worked through the individual analysis work flow up through mkanalysis-sess. My experiment involves a single scan of someone watching a video for five minutes, so averaging over conditions and defining contrasts don't make sense. (Actually, I have other scans of them watching other videos, so I could use that, but I'd rather not at this point.) So I skipped those steps and went to func2tal-sess. However, when I try to run that, I get ERROR: cannot find any sessions. I constructed the session directory structure using unpacksdcmdir and everything looks right so far as I can tell. My session is called az_45 which is also the name of the subject. My paradigm file reads: 0.0000 1 310.000 SA 310.0000 0 5.000 NULL I wasn't sure if this would work better as an "event-related" design or a "blocked" design (one event or one block depending on how you look at it) so I tried both: mkanalysis-sess -analysis video_event -TR 1.5 -paradigm video.par-designtype event-related -nconditions 1 -timewindow 310 mkanalysis-sess -analysis video_block -TR 1.5 -paradigm video.par-designtype blocked -nconditions 1 -timewindow 310 The voxels in my BOLD scan are 3.44x3.44x4 so I ran func2tal-sess -res 4 -analysis video_block -s az_45 -d az_45 and func2tal-sess -res 4 -analysis video_event -s az_45 -d az_45 but in both cases I get the same error, "cannot find any sessions". I get the same error with func2sph-sess. Any thoughts would be greatly appreciated. Thank you, -- Alessandro Gagliardi Integrative Neuroscience Program Rutgers University Mind Brain Analysis alessandro(a)gagliardi.name

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mri_glmfit bus error on mac intel
by Marie Schaer 27 Mar '07

27 Mar '07

Hello everybody, we have a problem with mri_glmfit on a mac pro (intel) with OS 10.4.8, all commands end up with bus error (see output below). It really seems to be a incompatible version of mri_glmfit (the same command work on a mac G5). Do you have any version of mri_glmfit compiled for intel processors? Thank you very much, Marie Schaer [marie-schaer-computer:freesurfer/subjects] marie% % mri_glmfit --y lh.test.10.mgh --fsgd fsgdf-test.txt --glmdir lh.test.glmdir --surf averagetest lh --C group.mat gdfReadHeader: reading fsgdf-monkeys-test.txt INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/subjects/averagetest/ surf/lh.white Number of vertices 60170 Number of faces 120336 Total area 39702.574219 AvgVtxArea 0.659840 AvgVtxDist 0.894769 StdVtxDist 0.233584 $Id: mri_glmfit.c,v 1.78.2.7 2007/01/23 21:37:47 greve Exp $ cwd /Applications/freesurfer/subjects cmdline mri_glmfit --y lh.test.10.mgh --fsgd fsgdf-test.txt --glmdir lh.test.glmdir --surf averagetest lh --C group.mat sysname Darwin hostname marie-schaer-computer.local machine i386 user marie FixVertexAreaFlag = 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/lh.test.10.mgh FSGD fsgdf-test.txt glmdir lh.test.glmdir Creating output directory lh.test.glmdir Bus error [marie-schaer-computer:freesurfer/subjects] marie%

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TBV fractions: aseg
by Juranek, Jenifer 27 Mar '07

27 Mar '07

I'm using the aseg file located in /freesurfer/subjects/<PID>/stats folder to calculate Total Brain Volume Fractions of GM, WM, and CSF. Within the aseg file, several csf compartments are listed, including: Left-Lateral-Ventricle (segid 4) Left-Inf-Lateral-Ventricle (segid 5) 3rd-Ventricle (segid 14) 4th-Ventricle (segid 15) CSF (segid 24) Right-Lateral-Ventricle (segid 43) Right-Inf-Lateral-Ventricle (segid 44) 5th-Ventricle (segid 72) Q: SegIds 24 and 72 are unfamiliar to me. Best place to find more info? Should they be included in the SUM of CSF? Many Thanks for any info you can provide... Jenifer

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Quality control
by Paul Greenberg 26 Mar '07

26 Mar '07

Hello, I've got a question about cortical surfaces in the ventral regions below the basal ganglia and about tkregister output quality control. I'm using the latest version of freesurfer: freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.5 1) In the majority of my data sets, white matter surfaces near the basal ganglia rise dorsally to include large volumes of the basal ganglia (putamen, nucleus accumbens, both hemispheres) - attached image. This results in inaccurate cortical volumes and thickness estimates from the surface based data for these regions. How can I compensate for these surface problems in order to get the best possible estimate of total cortical volume? I've tried editing the white matter manually and this has little effect on the locations of white matter surfaces in the basal ganglia. 2) I'm having a difficult time knowing how to determine if the talairach registration is good enough for each data set, and judging the quality of my manual edits using tkregister. Could you post an additional series of tiff or jpg images (multiple parasagittal, coronal, horizontal) showing how cortical surfaces and movable volumes are supposed to align in each plane? It would help to see examples of registrations that are "perfect", "good enough not to edit", and "bad enough to require adjustment". Thanks very much!, Paul

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aseg.mgz in talairach space
by anqi 26 Mar '07

26 Mar '07

I wonder how to transform aseg.mgz into talairach space. Where is the transformation saved? Thanks! Anqi Qiu Center for Imaging Science The Johns Hopkins University

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RYGB color wheel
by Greg Appelbaum 26 Mar '07

26 Mar '07

Hello all, Does anyone have an image file of the RYGB color bar I can get access to? I am trying to visualize complex data (phase) on the cortical surface and am meeting with success except that the scale bar is not rendering correctly. I have posted on this issue recently and am told that this is a known error, and that FreeSurfer has trouble dealing with complex scale bars. In light of this I am getting wonderful activation maps and am extracting the phase angle values independently. I am therefore only lacking an RYGB scale bar for visualization. Might anyone be able to help me with this? Greg Greg Appelbaum Post-Doctoral Fellow Center for Cognitive Neuroscience Duke University Box 90999 Durham, NC 27708 Office: (919) 668-3608

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Question about mri_surfcluster
by zvalim＠gmail.com 26 Mar '07

26 Mar '07

Dear FreeSurfer Gurus I have two questions about surfcluster that I would appreciate some help with.... 1. What 'connectivity radius' is used in surfcluster? It seems to be hardwired, because I can't find a flag to specify it. By connectivity radius I do not mean the minimum cluster size that of course can be specified, but the minimum distance in mm that two vertexes can be within in order to be considered part of the same cluster on the surface. If this value is low, then clusters are probably defined as cases of adjacent vertexes (perhaps within 1 edge distance?), but I could see uses for changing this parameter so that 'adjacency' would be defined somewhat more liberally (especially in cases when smoothing is low). SUMA's surfclust has the -rad option that achieves this (["Maximum distance between an activated node and the cluster to which it belongs.Distance is measured on the surface's graph (mesh)"] and I was wondering if FreeSurfer has this option. If not, does anyone know what the hard coded value is? Knowing it will help choosing smoothing parameters on the surface. 2. When seeing the textual results of surfcluster, it is indeed very useful to see the Max T, cluster size and number of nodes in cluster. But, for purposes of some permutation algorithms, it would be extremely useful to be able to know the mean T value in each cluster. This enables calculating the *mass* of each cluster, defined roughly as the number of vertexes multiplied by the mean T value (Bullmore, 1999). This lets one normalize for T values, and define 'reliable' clusters are those that pass a certain mass, independent of their size.. Would it be possible to get the mean T value in each cluster as an output from surfcluster? Obviously one could script a utility that for each cluster, computes its mean T by cross referencing the cluster-tagged output with the T value of each vertex (pivot table by cluster), BUT, getting the mean cluster T directly from surfcluster would be a great feature. Thank you for your time and patience, Best, Uri

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aseg.stats
by Joan Fisher 25 Mar '07

25 Mar '07

It turns out that the segmentation is fine in aseg.mgz (although for some reason I am unable to view the segmentation with FreeSurferColorLUT.txt as it says it wasn't valid or wasn't found even though it is in my directory) and yet the aseg.stats table was not generated. (Doug?) How does one generate a table if the aseg.mgz file is accurate but the aseg.stats file is not? Many thanks, Joan

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Freesurfer March 2007