Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

white matter problem
by Matt Colvin 30 Oct '07

30 Oct '07

Dear Freesurfer gurus, Hello, my name is Matt Colvin, with the Conte Center at Washington University in St. Louis. I came across a problem with a particular brain where the wm and pial lines cut out a chunk of white and grey matter. I have not come across a problem quite like this one so I was wondering if anybody had a suggestion as to how to fix it? I believe it is in the insula of the left hemi of this brain, though I am not certain (the region gets labeled as "unknown" in the parcellation). I have attached two screen caps which show the problem area. Thanks for any help anyone could offer. --Matt Colvin

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old Mac ver.
by Kirk, Gregory 29 Oct '07

29 Oct '07

Hi, I have a radiologist that wants to do some freesurfer work, visualizing subcortical parcelations and orig and T1 volumes. The volume processing was done with freesurfer-v3.0. Can I install the current freesurfer-Darwin-tiger-stable-pub-v4.0.1-full.dmg and have it correctly visualize the volumetric parcellation data generated with 3.0 or do I need to get the PowerPC 3.0 version from you ( if possible ). thanks Greg.

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freesurfer help
by Seth Elkin-Frankston 29 Oct '07

29 Oct '07

Hello, I'm running v.4.0.1 on CentOS 5. When attempting to run autorecon1 I receive the error below. Any help is appreciated. Thanks Seth Elkin-Frankston ---- Iteration 1 Mon Oct 29 09:47:59 EDT 2007 nu_correct -clobber ./tmp.mri_nu_correct.mni.8422/nu0.mnc ./tmp.mri_nu_correct.mni.8422/nu1.mnc [NeuroBio@lr8to10-dhcp-131-112.bumc.bu.edu:/usr/local/freesurfer/subjects/Bo bFS/mri/] [2007-10-29 09:47:59] running: /usr/local/freesurfer//mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /usr/tmp/nu_correct_8477/ ./tmp.mri_nu_correct.mni.8422/nu0.mnc ./tmp.mri_nu_correct.mni.8422/nu1.imp /usr/local/freesurfer//mni/bin/volume_stats: error while loading shared libraries: libstdc++.so.5: cannot open shared object file: No such file or directory nu_estimate_np_and_em: crashed while running volume_stats (termination status=32512) nu_correct: crashed while running nu_estimate_np_and_em (termination status=32512) ERROR: nu_correct Linux lr8to10-dhcp-131-112.bumc.bu.edu 2.6.18-8.1.15.el5 #1 SMP Mon Oct 22 08:32:04 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Oct 29 09:47:59 EDT 2007

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FSfast tutorial
by McLean John (NHS Greater Glasgow & Clyde) 29 Oct '07

29 Oct '07

Hi, I am trying to work through the FSfast tutorial. When i enter the following command: tkmedit-sess -s mgh-101.1 -a sm-gamma-fwhm5 -c odd-v-0 -aparc+aseg i get the following error: INFO: Found session in: ./mgh-101.1 grep: ./mgh-101.1/session.info: No such file or directory INFO: Found session in: ./mgh-101.1 grep: ./mgh-101.1/session.info: No such file or directory -------------------------------------------------------------- tkmedit-sess logfile is /usr/local/freesurfer/fsfast/tutorialdata/fsfast-tutorial/fb1-analysis-study/log/tkmedit-sess.log -------------------------------------------------------------- setenv SUBJECTS_DIR /usr/local/freesurfer/subjects/buckner_data/tutorial_subjs ERROR: sm-gamma-fwhm5 does not exist. Try running mkanalysis-sess Does anyone have any thoughts on this? Is FS looking for a file i dont have? I have set $FSFTUTDIR correctly and i am working in fb1-analysis-study as instructed in the tutorial. Best wishes ********************************************************************** This message may contain confidential and privileged information. If you are not the intended recipient please accept our apologies. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Please inform us that this message has gone astray before deleting it. Thank you for your co-operation. NHSmail is used daily by over 100,000 staff in the NHS. Over a million messages are sent every day by the system. To find out why more and more NHS personnel are switching to this NHS Connecting for Health system please visit www.connectingforhealth.nhs.uk/nhsmail **********************************************************************

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summary-sess of FA values
by Robert Levy 27 Oct '07

27 Oct '07

Hi, Is there any way to get something like the output of roisummary-sess, but for ROI-constrained FA values instead of BOLD? What I'm actually want to use this for, is to get FA values at a single vertex for each subject in the group, so I can plot a regression line against a behavioral measure. Thanks, Rob http://nmr.mgh.harvard.edu/~levy

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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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