Freesurfer

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30132 discussions

Re: [Freesurfer] aligning functionals to anatomicals
by Douglas N Greve 07 Dec '10

07 Dec '10

And how did you reorient to run FS on the anats? Krishna Srihasam wrote: > Hi, > > Yes. We took the anatomicals with the monkey in sphinx position in a > stereotax. > > Rgds, > krsihna > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Tuesday, December 07, 2010 2:32 PM > To: Krishna Srihasam > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] aligning functionals to anatomicals > > How did you re-orient your anatomicals? Was the monkey in the sphinx > position? > > doug > > Krishna Srihasam wrote: > >> Hi, >> >> >> >> I have a question regarding overlay of functional activations on a >> freesurfer map. After much work, I flattened my monkey brain. But, I >> just realized that the input volume , which I used to generate the >> flat maps, had orientation set to LIA. I want to over lay my >> functional activations, which are in RAS orientation on them. One >> way would be to realign all functional data into LIA orientation and >> then analyze the data and then simply use spmregister-see or >> fslregister-sess to register. Is there any simpler way? >> >> >> >> My functionals are 65x85x56 for each slice. I tried using flirt to get >> the alignment matrix. But, it is failing badly.. Any ideas would be >> welcome.. >> >> >> >> Regards, >> >> krishna >> >> >> >> ---------------------------------------------------------------------- >> -- >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Partners Compliance > HelpLine at http://www.partners.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact the > sender and properly dispose of the e-mail. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Freesurfer installation on RHEL 5.4: failed to create OpenGL rendering context
by dahlia＠nmr.mgh.harvard.edu 07 Dec '10

07 Dec '10

Hi, Would really appreciate help with this insallation problem! I'm installing freesurfer on a new system, and at an initial test running "tkmedit bert.mgz" produces GLUT: Fatal Error in tkmedit.bin: failed to create OpenGL rendering context. I thought maybe updating the NVidia card would help, but when I go to their website and try to download NVidia Quadro NVS, there are only Windows options to select as OS. This is a Dell Precision T7500 preinstalled with RHEL 5.4. About a year ago I installed freesurfer on virtually identical hardware (the OS there was CentOS as a virtual machine under the Windows host), and did not run into such a problem Can you help me figure out why it's running into this problem and how to fix it? Thanks! Dahlia.

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aligning functionals to anatomicals
by Krishna Srihasam 07 Dec '10

07 Dec '10

Hi, I have a question regarding overlay of functional activations on a freesurfer map. After much work, I flattened my monkey brain. But, I just realized that the input volume , which I used to generate the flat maps, had orientation set to LIA. I want to over lay my functional activations, which are in RAS orientation on them. One way would be to realign all functional data into LIA orientation and then analyze the data and then simply use spmregister-see or fslregister-sess to register. Is there any simpler way? My functionals are 65x85x56 for each slice. I tried using flirt to get the alignment matrix. But, it is failing badly.. Any ideas would be welcome.. Regards, krishna

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analysis in v5 vs v4.5
by Katie Bettencourt 07 Dec '10

07 Dec '10

I was attempting to run an analysis that was previously done in freesurfer 4.5 in version 5 to see if I cuold switch over to the new version. However, I am getting very different results for the two versions. Below are the commands I ran in both and attached are pictures of the differences. I get much much less activation (and much less than expected) when using version 5. I assume this is because I've done something wrong with the way I set up my version 5 analysis, but I don't knwo what it is. Any help would be appreciated. version 5: mkanalysis-sess -analysis supIPS-gamma-5rh -TR 1.5 -paradigm supIPS.dat -event-related -runlistfile supIPSruns.txt -nskip 2 -nconditions 6 -gammafit 2.25 1.25 -surface self rh -fwhm 0 -refeventdur 6 mkcontrast-sess -analysis supIPS-gamma-5rh -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 selxavg3-sess -s 101103TM_supIPS -df supIPS.dir -analysis supIPS-gamma-5rh tksurfer-sess -s 101103TM_supIPS -a supIPS-gamma-5rh-c act_vs_fix -df supIPS.dir version 4.5 mkanalysis-sess -analysis supIPS-gamma -TR 1.5 -paradigm supIPS.dat -designtype event-related -funcstem fmc -motioncor -runlistfile supIPSruns.txt -inorm -tpexclude tpexclude.dat -nconditions 6 -gammafit 2.25 1.25 -noautostimdur mkcontrast-sess -analysis supIPS-gamma -contrast act_vs_fix -a 1 -a 2 -a 3 -a 4 -a 5 -c 0 tksurfer-sess -s 101103TM_supIPS -df supIPS.dir -a supIPS-gamma -c act_vs_fix -hemi rh Katie

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---regheader option in mri_label2vol
by Navid Shiee 07 Dec '10

07 Dec '10

Hi, I am trying to transform the volumetric labels from aseg.auto to the original space. As suggested on the wiki I use the command mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz --regheader aseg.mgz However, I got ERROR: Option --regheader unknown If I don't use that option at all, the image is still in coronal orientation although the header is changed to axial. Would you please help me on this? Thanks, -- Navid

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recon-all
by Yang Liu 07 Dec '10

07 Dec '10

Hi, I am processing the anatomical monkey brain now. When recon-all runs, it stops at the step of "mris_fix_topology" I inserted the last part of my recon-all.log below: It stops at "CORRECTING DEFECT 0 (vertices=65691, convex hull=4296)" for more than 12 hours. Does this step take that long? Or are there some problems in the data that make freesurfer idling? Thanks, Yang #-------------------------------------------- #@# Fix Topology lh Sat Dec 4 17:01:16 EST 2010 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /home/yang/091017Castor/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 091017Castor lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ before topology correction, eno=-810 (nv=213660, nf=428940, ne=643410, g=406) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 156279 ambiguous faces found in tessellation segmenting defects... 64 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 14 into 0 -merging segment 11 into 10 -merging segment 23 into 18 -merging segment 33 into 22 -merging segment 40 into 22 -merging segment 62 into 25 -merging segment 39 into 34 -merging segment 35 into 46 56 defects to be corrected 0 vertices coincident reading input surface /home/yang/091017Castor/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -8.8048 (-4.4024) -vertex loglikelihood: -5.5855 (-2.7928) -normal dot loglikelihood: -3.4654 (-3.4654) -quad curv loglikelihood: -5.6070 (-2.8035) Total Loglikelihood : -23.4627 CORRECTING DEFECT 0 (vertices=65691, convex hull=4296)

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vertex wise ICC
by Mayuresh K 07 Dec '10

07 Dec '10

Hello freesurfer experts, I am keen on generating vertexwise intra-class correlation maps for a group of subjects with paired measurements - similar to that in Wonderlick et al in Neuroimage 2009. Reliability of MRI-derived cortical and subcortical morphometric measures: Effects of pulse sequence, voxel geometry, and parallel imaging. Any pointers how I can do this is much appreciated. regards, Mayuresh

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recon-all -make all error?
by Jeff Sadino 06 Dec '10

06 Dec '10

Hello, I am reprocessing a number of subjects from fs 4.5.0 to fs 5.0.0. I am doing this by issuing the "recon-all -make all -s subject" command. It stops right away with the message: make: Nothing to be done for `all'. There exists the wmparc.stats file from the fs450 recon, but there is no label/?h.BA*.label or label/?h.entorhinal_exvivo.label files. Looking at the recon table, it looks like these are supposed to be part of the standard recon. Is my -make all broken, or can I ignore this message? Thank you, Jeff Sadino

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RAW files
by Alan Francis 06 Dec '10

06 Dec '10

Hi FSL and FreeSurfer folk: Does anyone know how to convert *.raw files to analyze, nifti or mgz format? thanks much, Alan

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mri_convert batch conversion of ima files
by Lisa F. Akiyama 06 Dec '10

06 Dec '10

Hello, I have a large number of slice files in ima format. I would like to convert each of these ima files into either nifti or analyze format slice files. I read a past email conversation regarding batch conversion of ima files using mri_convert : https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010524.html However, when I ran the following commands, I get a single nifti/analyze file that contains all the slices for this particular subject. Is there a way to batch convert all ima slice files to individual nifti/analyze files? I read somewhere about the --sdmlist option, but that did not work. Thanks. Best, Lisa *<ima -> analyze>* > todd $ mri_convert -it ima -i 393-2-4.ima -ot nii -o kh4.nii > mri_convert -it ima -i 393-2-4.ima -ot nii -o kh4.nii > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from 393-2-4.ima... > rows = 256 > cols = 256 > TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 > i_ras = (-0, -1, -0) > j_ras = (-0, 0, -1) > k_ras = (-1, 0, 0) > writing to kh4.nii... > todd@neptune-ubuntu:/usr/local/freesurfer/subjects/kikuchi_hiromi/slices$ > mri_convert -it ima -i 393-2-4.ima -ot analyze -o kh4.img > mri_convert -it ima -i 393-2-4.ima -ot analyze -o kh4.img > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from 393-2-4.ima... > rows = 256 > cols = 256 > TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 > i_ras = (-0, -1, -0) > j_ras = (-0, 0, -1) > k_ras = (-1, 0, 0) > writing to kh4.img... > Analyze Output Matrix > -0.000 -0.000 -1.500 87.097; > -1.000 0.000 0.000 114.029; > -0.000 -1.000 0.000 118.726; > 0.000 0.000 0.000 1.000; > -------------------- > No such orientation specified in Analyze7.5. Set orient to 0 > Direction cosines for > /usr/local/freesurfer/subjects/kikuchi_hiromi/slices/393-2-4.ima are: > x_r = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r = -4.4032 > x_a = -1.0000, y_a = 0.0000, z_a = 0.0000, c_a = -14.9706 > x_s = -0.0000, y_s = -1.0000, z_s = 0.0000, c_s = -10.2740 > INFO: set hdr.hist.orient to 'transverse unflipped' > > *<ima -> nifti>* > todd $ mri_convert -it ima -i 393-2-4.ima -ot nii -o kh4.nii > mri_convert -it ima -i 393-2-4.ima -ot nii -o kh4.nii > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from 393-2-4.ima... > rows = 256 > cols = 256 > TR=11.40, TE=4.40, TI=300.00, flip angle=15.00 > i_ras = (-0, -1, -0) > j_ras = (-0, 0, -1) > k_ras = (-1, 0, 0) > writing to kh4.nii... > ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington E-mail: lrisa87(a)uw.edu P Please consider the environment before printing this e-mail.

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