Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30131 discussions

mris_preproc error for mc sim...
by Cameron Ellis 26 Oct '07

26 Oct '07

Hi, In anattempt to prepare to run a monte carlo cluster threshold simulation with a group of subjects in stable3, I run into the following error using mris_preproc: [troy:retrievalnewest] (nmr-stable3-env) mris_preproc --fsgd SM2_glm_MC_controls.fsgd --target allsubavg --hemi lh --sf sessidallsh+smvsnh --a retrievalS PMHRF_5cond_40TW --c sh+smvsnh.mat --out SM2_glm_MC_controls_sh+smvsnh.mgh ERROR: cannot find /autofs/space/troy_003/users/retrievalnewest/SM0C1/bold/retrievalSPMHRF_5cond_40TW//space/troy/3/users/retrievalnewest/MC_contrasts/single.mat/ces.bhdr I do not know why fsfast is looking for this file here or how to indicate where it is. Am I running in the wrong env? When I try dev I get this error: [troy:retrievalnewest] (nmr-std-env) mris_preproc --fsgd SM2_glm_MC_controls.fsgd --target allsubavg --hemi lh --sf sessidcontrolssh+smvsnh --a retrievalSPMHRF_5cond_40TW --c sh+smvsnh.mat --out SM2_glm_MC_controls_sh+smvsnh.mgh if: Expression Syntax. Any suggestions? Cameron

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WM volume & CSF & BPF
by Gallo, Antonio (NIH/NINDS) [F] 26 Oct '07

26 Oct '07

Dear All, We are dealing with MPRAGE data acquired at a 3.0T MRI scanner and analyzed with FS 3.0.5. Images belong to a group of Multiple Sclerosis patients. We would like to ask some questions and we apologize for the fact that we have quite a number of them :-) First, regarding measurements coming from mris_anatomical_stats: 1) What is exactly included in total WM volume? 2) Is total WM volume the sum of left and right WM hemisphere or just the WM volume from the side we specify (but if this is case, why we got the same values after running mris_anatomical_stats for lh and rh hemisphere) ? 3) Since there are many WM lesions (with many juxta-cortical lesions that need manual editing), we were wondering if total WM volume does include the WM hypointensities as well or those are just treated separately. 4) Does the total GM volume include the volume of the subcortical structures and cerebellum or just refer to the cortical GM volume? Second, some other questions on the aseg.stat file: 1) What is exactly included in CSF label? Does it comprehend the CSF in the ventricles + the sulcal CSF, or just the the sulcal CSF? 2) Does the volume of the WM hypointensities manually edited (which happens very often with MS lesions close to the cortex) end up in the WM hypointensities volume? Last, as we are interested in measuring subjects' BPF, we were wondering which would be the best way to compute it? Thanks a lot in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

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Group analysis
by deepa preeti 26 Oct '07

26 Oct '07

Hi all, Could you please tell us if the end result of GroupAnalysis on cortical thickness with mri_surfcluster command line - the coordinates in sig.cluster.sum is MNI coordinates or talairach coordinates? since I need to know Broadmann area to locate the significant region using the coordinates. 2. If I use FDR to get results at p = 0.05, where are the results stored so that I could report that a significant region for example, temporal pole 100 sq.mm has reduced to temporal pole ..70. sq.mm? Thanks Deepa.

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Aligning Mprages from different days
by Trina Kok 26 Oct '07

26 Oct '07

Hi all, We have a number of MPRAGEs acquired from the same patient from different days and would like to align them. We really want a transform matrix out of the alignment just like how spmregister aligns functional data to anatomical and gives a matrix in register.dat. I was wondering if there is a way to use spmregister for this purpose. Or is there something else for aligning two anatomical images? Thanks!! Cheers, Trina

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mris_anatomical_stats log problem
by Julien 26 Oct '07

26 Oct '07

Hi all, I'm running into a problem with log output for mris_anatomical_stats. The console output seems fine, but log files are blank. The command: ($SUBJECTS_DIR = /space/colossus/7/users/MSpect) mris_anatomical_stats -t lh.thickness \ -label lh.cortex.label \ -nsmooth 15 \ -log ${SUBJECTS_DIR}/001_MEF_A/stats/lh.anat_stats.15.log \ 001_MEF_A lh The output: outputting results to /space/colossus/7/users/MSpect/001_MEF_A/stats/lh.anat_stats.15.log... reading volume /space/colossus/7/users/MSpect/001_MEF_A/mri/wm.mgz... reading input surface /space/colossus/7/users/MSpect/001_MEF_A/surf/lh.white... reading input pial surface /space/colossus/7/users/MSpect/001_MEF_A/surf/lh.pial... reading input white surface /space/colossus/7/users/MSpect/001_MEF_A/surf/lh.white... Smooth thickness map with 15 iterations on surface Smoothing done, nsteps = 15, tsec = 0.762 structure is "lh.cortex.label" number of vertices = 150813 total surface area = 99113 mm^2 total gray matter volume = 253515 mm^3 average cortical thickness = 2.333 mm +- 0.514 mm average integrated rectified mean curvature = 0.138 average integrated rectified Gaussian curvature = 0.048 folding index = 2289 intrinsic curvature index = 297.7 using thickness file rh.thickness. limiting computations to label rh.cortex.label. Smooth thickness by 15 steps before using it The log: [colossus:MSpect] (nmr-std-env) ls -al 001_MEF_A/stats/lh.anat_stats.15.log -rw-rw-r-- 1 jswonder bnllab 0 Oct 26 11:30 001_MEF_A/stats/lh.anat_stats.15.log E.g., file exists, nothing in there. bugr output: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4_x86_64-stable-v4.0.1-20071025 RedHat release: CentOS release 4.4 (Final) Kernel info: Linux 2.6.9-42.0.3.ELsmp x86_64 NMR Center info (/space/freesurfer exists): machine: colossus SUBJECTS_DIR: /space/colossus/7/users/MSpect PWD: /space/colossus/7/users/MSpect I could just be overlooking something simple, but I don't see what it is at present. Thanks, Julien -- Julien Wonderlick Research Assistant, Behavioral Neuroscience Laboratory Department of Brain and Cognitive Sciences, MIT Building 46-5127 617.253.7437 jswonder(a)mit.edu

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Cerebellum Segmentation
by Pedro Paulo Oliveira Jr 26 Oct '07

26 Oct '07

Yesterday I gave a course on FreeSurfer basics + usage for our Radiology department in São Paulo University. Two questions that I was not able to answer was: 1) When will the source code of FreeSurfer be released? 2) Is there some plan to include the cerebellum in the automatic parcellation/segmentation? I think last question about this in this list was in 2005. Thanks Pedro Paulo Jr.

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skull strip problem
by Michael Harms 25 Oct '07

25 Oct '07

Hello, We have a subject processed in V4 for which T1.mgz looks fine (white matter ~ 110; no obvious artifacts), but the brainmask.mgz is basically all zeros (except for a section of the background in slices 200-255 of the coronal view). The recon-all.log file is attached. I don't know if the problem is with the derivation of talairach_with_skull.lta that is used in 'mri_watershed' in V4, or if the issue occurs in 'mri_watershed' itself. (NB: There are a lot of "ambiguous basin" messages as part of the 'mri_watershed' output). How do you check the accuracy of talairach_with_skull.lta? Any other suggestions (particular options to change for the watershed...)? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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talairach failure detection
by Michael Harms 25 Oct '07

25 Oct '07

Hello, Thought that this might be of interest: We've found a case for which the talairach.xfm is grossly wrong (checked using tkregister2) but the automatic-failure detection of version 4.0.1 indicated no problems. #-------------------------------------------- #@# Talairach Failure Detection Thu Oct 25 12:29:08 CDT 2007 /disk/conte_raid1/freesurfer/HASD_mprage_NOTDONE/010502_61774/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.2262, pval=0.0169 >= threshold=0.0050) #------------------------------------------ Is this something that anyone else has noticed so far? thanks, Mike H. -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6615 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Re: [Freesurfer]thickness difference map
by Nick Schmansky 25 Oct '07

25 Oct '07

Support for the curv format as a target was added to mri_surf2surf in freesurfer v4.0. For your version, you can just exclude the -tfmt curv parameter. On Wed, 2007-10-24 at 21:19 -0400, Wang, Xin wrote: > ERROR: Cannot select curv as target format. > > Thank you, Nick. > > Xin Wang > > > ______________________________________________________________________ > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > Sent: 2007-10-24 (星期三) 21:16 > To: Wang, Xin > Cc: Doug Greve; Freesurfer Mailing List > Subject: Re: {Spam?} 答复: [Freesurfer]thickness difference map > > > > Can you send along the output text that shows the error? > > On Wed, 2007-10-24 at 21:10 -0400, Wang, Xin wrote: > > Thank you for your response, Doug. I attached all the commends I > > modified from Han's note. I worked through step1 & 2. But the step3 > is > > the problem now. step4 hasn't been tried. I look forward to hearing > > your suggestions. > > > > Thank you again, > > > > Xin > > > > > > > ______________________________________________________________________ > > From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] > > Sent: 2007-10-24 (星期三) 19:12 > > To: Wang, Xin > > Cc: Nick Schmansky; Freesurfer Mailing List > > Subject: RE: [Freesurfer] thickness difference map > > > > > > > > > > > > What is your cmd line and what is the terminal output? > > > > > > > > On Wed, 24 Oct 2007, Wang, Xin wrote: > > > > > Thank you very much, Nick. I ran into a problem when I ran the > step > > 3 of Han's note of thickness repeatability. The --tfmt of > > mri_surf2surf is curv. The step can not be completed. > > > > > > Please help me. > > > > > > Thank you again, > > > > > > Xin > > > > > > ________________________________ > > > > > > From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] > > > Sent: Sat 10/20/2007 5:34 PM > > > To: Wang, Xin > > > Cc: Freesurfer Mailing List > > > Subject: Re: [Freesurfer] thickness difference map > > > > > > > > > > > > Xin, > > > > > > Have a look at this wiki page written by Xiao (the author of the > > paper): > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility > > > > > > It describes the procedure for how Figure 2 was created. > > > > > > Nick > > > > > > On Fri, 2007-10-19 at 15:42 -0400, Wang, Xin wrote: > > >> Hello, Group, > > >> > > >> We want to make a figure as Fig2 in Han X et al. 2006 reliability > > >> paper. Does anyone kindly share his/her way to make a map of > > >> difference in average thickness between two groups? > > >> > > >> Thank you in advance, > > >> > > >> Xin Wang > > >> _______________________________________________ > > >> 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 > > > > In order to help us help you, please follow the steps in: > > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > > > > >

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stats for average subject...
by Cameron Ellis 25 Oct '07

25 Oct '07

Hi, Does anyone know if it is possible to generate an aparc.stats file for an average subject? mris_anatomical stats does not seem like it will work because it requires wm.mgz which is not generated in the make_average_subject process. I would like to find the number of vertices and the surface area of each hemisphere. I think the average surface area can be found in the make_average_subject log file but I cannot find the number of vertices there. Any suggestions? Thanks, Cameron

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