Freesurfer February 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
126 discussions

volume changes
by Jared Price 19 Feb '09

19 Feb '09

Dear gurus, when running mri_convert -rt nearest -ot nii -rl 001.mgz seg_edited.mgz seg_edited_axial.nii to reslice from coronal to axial space we are seeing some significant volume changes in the segmentation. Anyone know why or how to fix it. Jared

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control points
by Muhammad Ayaz 19 Feb '09

19 Feb '09

Dear All, I am in phase of learning freesurfer. I added control points using tkmedit and ran recon-all -autorecon2-cp <subjid> and i get the following error. " Total Number of Modified Voxels = 854 (out of 716825: 0.119136) sh: wm.mgz: Permission denied Broken pipe Linux eesmith 2.6.9-67.ELsmp #1 SMP Fri Nov 16 12:49:06 EST 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Feb 18 14:34:54 EST 2009 " It says permission denied but I have permission to access and make changes to data. Regards Ayaz

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qdec for fMRI using categorical covariate?
by Dave Brohawn 19 Feb '09

19 Feb '09

Hello, I want to generate screenshots of group activation in an anatomical ROI on the left and right hemisphere for two different groups of subjects at a particular contrast and time point of our analysis. We want to use race as a covariate (categorical, with whites and blacks being the two racial groups), and the screenshots to reflect this covariate being taken into account. Many examples I have seen on the wiki and in freesurfer archives describe cortical thickness studies, or use covariates that are continuous (age). Is qdec the program I want to use, and how do I ensure it treats race as

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mris_anatomical_stats segmentation fault
by Diana Wotruba 19 Feb '09

19 Feb '09

Dear FS experts I divided the fsaverage parcellations (aparc.a2005s) with an area threshold of 100mm2. Now I would like to get a stats file, using the following command: mris_anatomical_stats -a aparc.a2005s_100.annot -t ?h.thickness -b -f 001/stats/?h.aparc.a2005s_100.stats 001 ?h I am getting the following error message: "Segmentation fault" (after 1374 entries are read) The same command works just fine with a parcellated .annot file I generated with a lower threshold (p.e. 150mm2). Any help would be appreciated Regards Diana

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- dt_recon and coregistration of DTI to anatomy
by Kjell Inge 19 Feb '09

19 Feb '09

I am using Freesurfer and I am having difficulties in coregistration of a DTI volume to the anatomy image. I have been running recon-all -i <anatomy1.nii> -i <anatomy2.nii> -s 2005_anatomy followed by recon-all -autorecon1 -s 2005_anatomy and then dt_recon --i dti/subj_539_dti.nii --b dti/aging_hds_2005_dti.bval dti/aging_hds_2005_dti.bvec --s 2005_anatomy --o outputdti where "dti/subj_539_dti.nii" is my DTI volume, "aging_hds_2005_dti.bval" and "dti/aging_hds_2005_dti.bvec" are my bval and bvec files and "2005_anatomy" is my subject folder. I have made an output folder inside "2005_anatomy" named "outputdti" My bval and bvec files are attached below. Everything runs smoothly with no error messages, and there is a bunch of files created in "outputdti". Now, my questions are as follow: 1. How do I see the registered DTI (for instance the FA) visualized on the anatomy? Is the finally registered FA image inside the file "FA.nii" or do you have to run a transformation on that? If so, which transformation and how is that done? There are several files containing rigid transformations, the .reg files and the register.dat file. When I check FA.nii it does NOT seem to be coregistered with my anatomical input image. What went wrong? 2. When I open the image "mask.nii" it is like a white box, no structures, is this really correct? Does this mean that the BET has not succeeded? However, when I open "brainmask.mgz" by "tkmedit" it is certainly skullstripped. 3. Does dt_recon really do a nonlinear registration? When looking through the script, I can only see that dt_recon uses flirt (inside "eddy_correct" on the "dwi.nii", producing "dwi-ec.nii" and inside "fslregister", applied to "lowb.nii") which is an affine registration tool. I hope someone can solve my problems. Erlend bvec: 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 bval: 0 0 0 0 0 -0.532213 -0.25014 0.633507 0.218922 0.41315 -0.734236 -0.93647 0.333112 -0.103315 0.92654 -0.801489 0.916837 0.537756 0.213559 0.124139 -0.27398 0.443315 -0.024171 -0.568365 -0.93093 0.825459 -0.472598 -0.504263 -0.149336 0.694717 0 0 0 0 0 0.104013 -0.721834 -0.753136 0.850393 -0.780294 -0.661804 0.054189 -0.242859 -0.991677 0.372983 0.543143 -0.261948 0.438028 -0.664684 -0.051816 0.960273 0.878048 0.368772 0.637098 -0.168158 -0.182178 -0.629557 -0.129265 0.688743 0.344412 0 0 0 0 0 -0.840197 0.64528 -0.177358 0.478441 0.469519 0.151371 0.346537 0.911074 -0.076828 -0.04907 -0.250221 0.30132 -0.720382 -0.715952 -0.990911 -0.053015 -0.180284 0.929206 0.520641 -0.324178 -0.534255 -0.616692 0.85382 -0.709459 0.631465 _________________________________________________________________ Connect to the next generation of MSN Messenger http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=…

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qdec for fMRI analysis with categorical covariate? (continued)
by Dave Brohawn 19 Feb '09

19 Feb '09

as a categorical covariate? Thank you, Dave Brohawn

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recon-all error: libexpat.so.0
by Narly A Golestani 19 Feb '09

19 Feb '09

Dear all, I installed freesurfer_Linux_centos4_x86_64-stable-pub-v4.2.0-full on SuSE Enterprise (SLED 10.2), and ran recon-all. The process ran until near the end, and then terminated with the following error: ***************** ..... Reporting on 49 segmentations #-------------------------------------------- #@# Cortical ribbon mask Fri Feb 13 15:31:16 CET 2009 /home/narly/data/freesurfer/subjects/2_Lena/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance 2_Lena mris_volmask.bin: error while loading shared libraries: libexpat.so.0: cannot open shared object file: No such file or directory ************************** but I'm able to visualise the labels on the 3D volume using tksurfer (i.e. the output looks ok). Do I still need to install libexpat.so.0, and if so, how? thanks in advance, Narly.

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getting vertex numbers
by Lars M. Rimol 19 Feb '09

19 Feb '09

Hi, I've done a glm model fit comparing cortical thickness between two groups, and have certain areas ("blobs") on the cortical surface that are above sig. threshold. I'd like to get a list of the vertex numbers for each of these significant areas, which do not correspond to the parcellations in FS. In other words, I'm not trying to combine the already excisting ROI's. I've tried drawing labels (on fsaverage) and saving them, but without success. I clicked on 'Make path' and tried to mark vertices around the area, then I tried 'Custom fill' with various options, and 'Mark label', 'New label from marked' and 'save label'. But I only manage to save one or at most 3-4 vertices. I'm using FS v 4.0.5. Any tip on how to do this would be appreciated! Thank you! -- yours, LMR

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graph average ROI
by Juranek, Jenifer 18 Feb '09

18 Feb '09

Hi, I'm running fsv420 on RHEL4. Within the qdec module (v1.2) menu options, View, Graph the ROI --> generates average +/- SD or SE? Many Thanks, Jenifer

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Group Cortical Thickness
by Jeff Sadino 18 Feb '09

18 Feb '09

Hello, I want to run group statistics on the cortical thickness for a study with 3 groups, each with about 30 subjects. To do this, I need to create an average cort thickness map for each group. We are interested in basic statistics, so nothing too advanced. I am wondering what would be the most efficient way to go about this. From what I can tell, FsFast is the program used to do group analysis. Would it be fastest to learn FsFast to process all my group data, or I am thinking since we only need basic stats, it may be faster and easier to register each subject's ?h.thickness file to an average sphere and then load the registered thickness file into matlab to do the stats? I think I would need to modify the commands from auto-recon stage 3 to use the thickness file, for example: mris_sphere ?h.thickness ?h.thickness.sphere mris_register -curv ?h.sphere $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif ?h.thickness.sphere.reg mris_jacobian ?h.white ?h.thickness.sphere.reg ?h.jacobian_white mrisp_paint -a 5 $FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif#6 ?h.thickness.sphere.reg ?h.thickness.avg_curvWe have a cluster, so the processing could be done fairly quickly. Thank you in advance for your advice! Jeff Sadino _________________________________________________________________ Stay up to date on your PC, the Web, and your mobile phone with Windows Live. http://clk.atdmt.com/MRT/go/msnnkwxp1020093185mrt/direct/01/

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Freesurfer February 2009