Freesurfer November 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
127 discussions

fsaverage6
by Goldman, Aaron (NIH/NIMH) [C] 11 Nov '10

11 Nov '10

Hi, I had a question in reference to the following message (posted by Nick Schmansky): "1. in freesurfer v5, there are now multiple fsaverage subjects with varying number of vertices. fsaverage6 has about 40,000 vertices per hemi, so you can just include the flag: --target fsaverage6 after the -qcache flag, and it will use that as the target instead of fsaverage (producing files like 'rh.thickness.fsaverage6.mgh', which will have 40K thickness samples)." As I was also interested in trying this out, I ran the following in v5: recon-all -qcache -target fsaverage6 -s $subject However, recon-all failed to find fsaverage6, and I also couldn't manually find it in $FREESURFER_HOME. If this is included in the current distribution, where do I need to look? Thanks, Aaron

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discrepancy between p-values computed from t.nii and those stored in sig.nii
by Pablo Polosecki 11 Nov '10

11 Nov '10

Dear experts, For different reasons I found myself double checking the relationship between t-values in t.nii and p-values stored in sig.nii. If I use the following matlab code I thought that I should get the values of my_pval and stored_pval to be the same (except perhaps for the sign): cd(fullfile(basedir,session,'bold',anal,contrast)) x=load('../X.mat') t=MRIread('t.nii'); sig=MRIread('sig.nii'); test_voxel_number=4000; my_pval=-log10(2*tcdf(-(abs(t.vol(test_voxel_number))), x.DOF)) stored_pval=sig.vol(test_voxel_number) However I get: stored_pval = -0.4055 my_pval = 0.2804 Am I doing something wrong here? My FreeSurfer version is 4.5 Thank you! -- Pablo Polosecki Graduate Fellow Laboratory of Neural Systems The Rockefeller University 1230 York Avenue, Box 9 New York, NY 10065

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Re: [Freesurfer] shift in freeview
by Ruopeng Wang 10 Nov '10

10 Nov '10

Hi Alexander, Would it be possible to send me the volume file and one surface file that has this shift problem? Thanks, Ruopeng On 11/10/10 9:10 PM, Alexander Hunold wrote: > > Dear experts, > > I am perplexed how to fix the problem which is shown in the pictures. > The volume is the T1.mgz. The surfaces are computed by MNE (red -- > inner_skull, yellow -- outer_skull, green -- outer_skin). In TkMedit > the inner and outer skull are aligned to the T1.mgz, respectively. > > I used <mne_watershed_bem> and <mne_setup_forward_model> to get the > surfaces. > > I get the same shift with all surfaces I compute with > mne_write_surface, as well. > > Since I would like to visualize 3-4 surfaces with a mri volume I would > like to use freeview instead of TkMedit. > > Do you have any hint how to fix that shift problem? > > Thanks so much, > Alexander > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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shift in freeview
by Alexander Hunold 10 Nov '10

10 Nov '10

Dear experts, I am perplexed how to fix the problem which is shown in the pictures. The volume is the T1.mgz. The surfaces are computed by MNE (red - inner_skull, yellow - outer_skull, green - outer_skin). In TkMedit the inner and outer skull are aligned to the T1.mgz, respectively. I used <mne_watershed_bem> and <mne_setup_forward_model> to get the surfaces. I get the same shift with all surfaces I compute with mne_write_surface, as well. Since I would like to visualize 3-4 surfaces with a mri volume I would like to use freeview instead of TkMedit. Do you have any hint how to fix that shift problem? Thanks so much, Alexander

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Recon-all error
by Rapuano, Kristina (NIH/NIMH) [F] 10 Nov '10

10 Nov '10

Hello again, As a new freesurfer-er, I have one more question: I have another recon-all script that failed during the skull stripping step. It says it exited with errors, but does not actually specify any "ERROR" messages or even warnings. This the last thing it runs before failing: register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=9.0 skull bounding box = (48, 56, 22) --> (201, 204, 220) using (99, 105, 121) as brain centroid... mean wm in atlas = 126, using box (80,87,97) --> (117, 123,145) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Any ideas why this could be happening? Please help! Thank you very much, Kristina ---- Kristina Rapuano Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C214 10 Center Drive MSC 1366 Bethesda MD 20892-1366 Phone: (301) 402-4419 E-Mail : rapuanokm(a)mail.nih.gov

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Confused with Monte Carlo results
by Adam Nitenson 10 Nov '10

10 Nov '10

Hi Freesurfers I'm a bit confused as to some recent Monte Carlo findings I've been looking at. After generating 10,000 estimations with mri_glmfit. I used mri_surfcluster to generate nii, ocn.nii, and .sum files to analyze the clusters. However I found that, when looking at the dACC, the cluster within an ROI (label) specific analysis, which almost filled the entire label, was not significant, yet the dACC region cluster in the label-free, whole brain analysis was significant. I figured that, since the whole brain (no label) monte carlo analysis compares the clusters to the entire brain and the label analysis confines the cluster to just the label, that the latter would result in a more signifcant cluster (since it fills up almost all of the space under consideration). However, I have found the opposite, and don't understand why this is. Any ideas would be greatly appreciated. I've written my commands below (Stable 4). Thanks, Adam mri_glmfit --y /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/error_vs_correct/lh.ces.005.nii --fsgd /autofs/space/ventzl_036/users/RespMon12C/fsgd_and_contrast_files/Adam_25MatchedControls_genotyped.fsgd --C /autofs/space/ventzl_036/users/RespMon12C/fsgd_and_contrast_files/CHomozyg_Minus_TCarrier.mtx --surf fsaverage lh --sim mc-full 1000 1.3 /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/Monte_Carlo_LH_error_vs_correct_6sec/LH_MCSIM1 --fwhm 16.351771 mri_surfcluster --in /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/LH_error_vs_correct_6sec/CHomozyg_Minus_TCarrier/sig.mgh --csd /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/Monte_Carlo_LH_error_vs_correct_6sec/LH_MCSIM1-CHomozyg_Minus_TCarrier.csd ....(rest of monte carlo files).... --srcsubj fsaverage --thmax infinity --annot aparc --clabel /autofs/space/ventzl_036/users/RespMon12C/subjects/fsaverage/label/lh.dACC.All56Grouplabel --sum /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_56Group_dACC.sum --o /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_56Group_dACC.nii --ocn /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_56Group_dACC.ocn.nii mri_surfcluster --in /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/LH_error_vs_correct_6sec/CHomozyg_Minus_TCarrier/sig.mgh --csd /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/Monte_Carlo_LH_error_vs_correct_6sec/LH_MCSIM1-CHomozyg_Minus_TCarrier.csd ........ --srcsubj fsaverage --thmax infinity --annot aparc --sum /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_WholeBrain.sum --o /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_WholeBrain.nii --ocn /autofs/space/ventzl_036/users/RespMon12C/group-analysis/Adam_25MatchedControls_genotyped/RM_correct_error/CC_Minus_T/MC_Findings/LH_WholeBrain.ocn.nii Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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working with labels
by swoodman＠nmr.mgh.harvard.edu 10 Nov '10

10 Nov '10

Hi All, We were wondering what is the best way to find the overlap of two label files? For example, we want to save the region where segmentation1.label and segmentation2.label files overlap. Additionaly, we also wanted to know if we could find this region for the overlap of three label files. Thanks for your help! Sandra

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Re: [Freesurfer] Problem with mri_segstats
by Douglas N Greve 10 Nov '10

10 Nov '10

Hi Elizabeth, I'm cc'ing the list so that others may benefit from the answer: The labels that you are referencing are defined in the aparc.a2009s atlas, but the wmparc is generated from the aparc atlas. To generate a wmparc using the a2009s, run the following: cd $SUBJECTS_DIR/subject mri_aparc2aseg --s subject --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.a2009s.mgz --ctxseg aparc.a2009s+aseg.mgz --a2009s Then reference wmparc.a2009s.mgz instead of wmparc.mgz in the mri_segstats cmd doug Elizabeth Gutierrez wrote: > Hi Douglas, > Thank you for directing me towards reporting form. > Here is more information: > > FREESURFER_HOME: /software/Freesurfer/5.0.0 > > Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 > > Debian version: squeeze/sid > > Kernel info: Linux 2.6.31-22-generic x86_64 > > 1) subject name - s120 > SUBJECTS_DIR - /mindhive/gablab/memory/sourcemem/fsdata_REM > > 2) the entire command-line executed > > *Successful -* mri_segstats --seg > /mindhive/gablab/memory/sourcemem/fsdata_REM/s120/mri/wmparc.mgz > --ctab-default --id 3001 --in fa.anat.mgh --sum fa.stats > > *Unsuccessful* - mri_segstats --seg > /mindhive/gablab/memory/sourcemem/fsdata_REM/s120/mri/wmparc.mgz > --ctab-default --id 3101 --in fa.anat.mgh --sum fa.stats > > also unsuccessful for other 30 ids from aparc2009 > -id 13112 --id 14112 --id 13113 --id 14113 --id 13114 --id 14114 --id > 13118 --id 14118 --id 13115 --id 14115 --id 13116 --id 14116 --id > 13123 --id 14123 --id 13137 --id 13138 --id 14138 --id 13148 --id > 14148 --id 13150 --id 14150 --id 13163 --id 14163 --id 13153 --id > 14153 --id 13154 --id 14154 --id 13155 --id 14155 > > > 3) the error message generated > Reporting on 0 segmentations > > > More on fa.stats file : > > > sysname Linux > # hostname ba6 > # machine x86_64 > # user eguti > # anatomy_type volume > # > # SegVolFile > /mindhive/gablab/memory/sourcemem/fsdata_REM/s120/mri/wmparc.mgz > # SegVolFileTimeStamp 2010/06/02 15:09:42 > # ColorTable /software/Freesurfer/5.0.0/FreeSurferColorLUT.txt > # ColorTableTimeStamp 2010/08/13 20:56:24 > # InVolFile fa.anat.mgh > # InVolFileTimeStamp 2010/11/05 17:09:14 > # InVolFrame 0 > # Only reporting non-empty segmentations > # VoxelVolume_mm3 1 > > > > On Wed, Nov 10, 2010 at 10:45 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > Hi Elizabeth, > > we'll need more info to track down the problem. Please take a look > at surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> for the > kinds of things we need. > > thanks > > doug > Elizabeth Gutierrez wrote: > > Hi, > > I've been trying to use mri_segstats on a FA map with a white > matter parcellation file (wmparc.mgz) but there might be a > problem in the program. When I open the fa.stats output file, > all the values (std.dev, etc) are 0.0000 for the 2009 table > parcellation ids. However, when I use the label id 251 (corpus > collosum) from the first few labels on the list, I get a > value. When I use the corpus collosum id for more current > labels like the aparc 2005 and 2009, I get 0.0000 again. > > Could there be a bug in the program? > > > -- > Elizabeth C. Gutierrez > Graduate Student > Department of Brain and Cognitive Sciences > Massachusetts Institute of Technology > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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. > > > > > -- > Elizabeth C. Gutierrez > Graduate Student > Department of Brain and Cognitive Sciences > Massachusetts Institute of Technology -- 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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Talairach transform error
by Rapuano, Kristina (NIH/NIMH) [F] 10 Nov '10

10 Nov '10

Hello, I am fairly new to freesurfer, and recently encountered an error while running recon-all (-autorecon1 -autorecon2) during Talairach Failure Detection: talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***Fp=0.0001, pval=0.0000 < threshold=0.0050) I have looked at the tutorial on "fixing bad output from the talairach registration," however, when I open up the image with tkregister2, there are no green lines. It seems to me that I should be using those lines to align various anatomical points. I tried using the 's' key to turn the lines "on," but nothing seems to happen (and yes, the fmov box is set to 1.0). I appreciate any help you can give me, thanks! Kristina ---- Kristina Rapuano Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C214 10 Center Drive MSC 1366 Bethesda MD 20892-1366 Phone: (301) 402-4419 E-Mail : rapuanokm(a)mail.nih.gov

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Core dump during imgreg_4dfp
by Freesurfer Local Archive 10 Nov '10

10 Nov '10

Freesurfers, I am running freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 on a Linux 2.6.18-164.11.1.el5_lustre.1.8.3 cluster and I have a group of subjects that consistently crash during the talairach transform with the following message in the recon-all.log: ERROR: mpr2mni305 failed, see transforms/talairach_avi.log The talairach_avi.log indicates that imgreg_4dfp abnormally terminates with a core dump: Reading image: /lustre/scratch/jjoncaja/freesurfer/average/711-2C_as_mni_average_305.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 talsrcimg_g11.4dfp.img 256 256 256 1 1.000000 1.000000 1.000000 orientation T byte_order littleendian Reading image: talsrcimg_g11.4dfp.img dimensions: 256 256 256 mmppix: 1.0000 -1.0000 -1.0000 center: 128.0000 -129.0000 -129.0000 Abort (core dumped) ERROR: 'imgreg_4dfp /lustre/scratch/jjoncaja/freesurfer/average/711-2C_as_mni_average_305 none talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 4355' failed! status=134 ERROR: mpr2mni305 execution aborted This problem was replicated on FS 4.2, 4.3, and 5.0. While datasets I am analyzing were not exactly optimized for use with Freesurfer (screen shots attached), most of my subject either process okay or return error message identifying the problem. Before dropping the "core dump" subjects from the analysis I wanted to see what I can do to save them. If needed I can drop a tarball containing a single problematic subject into the filedrop or email the 001.mgz whichever is more convenient. Thank you in advance for all your help. Greetings, Jacek Jonca-Jasinski ღ >^..^< Jacek Jonca-Jasinski Texas Tech University As we act, let us not become the evil that we deplore. --Barbara Lee

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Freesurfer November 2010