Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

How to combine attached commands into one run
by Erik Lindberg 10 Feb '14

10 Feb '14

Dear Freesufers, I want to use the following commands in my recon-all to try to improve my output some difficult images: -gentle to mri_normalize and -min_border_white 85 -min_gray_at_white_border 80 So far I only managed to do this by making one step at a time. I was wondering if there is a way to combine these commands so I do not have to run it step by step.

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scuba running problem.
by Saurabh Thakur 10 Feb '14

10 Feb '14

Hello Friends, I m facing problem in freeview and scuba. can anyone help me in this matter. //==========================================================// saurabh@saurabh-Precision-WorkStation-T3500:/$ cd $FREESURFER_HOME saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ scuba -v $SUBJECTS_DIR/bert/mri/T1 Error starting scuba: File: tkUtils.tcl scuba could not be loaded because a support file was missing. Please check your installation. Make sure that the FREESURFER_HOME environment variable is set. //==========================================================// Thanks in advance. cheers Saurabh Thakur,

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Segmentation Algo
by Saurabh Thakur 10 Feb '14

10 Feb '14

Hello Freesurfer expert, I am new to freesurfer. I wanted to know which algorithm is used for segmentation in freesurfer. Thanks in advanced, cheers Saurabh Thakur,

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reporting bhvat value from lme
by Knut J Bjuland 08 Feb '14

08 Feb '14

Dear Freesurfers We are now finishing an article, where we have used linear mixed models included in FreeSurfer 5.3 for longitudinal changes between two-time points. We have used this model. Intercept(RF) + centered time+ group + group*centered time + sex(gender). Everything is clear except for one thing. When we used this contrast vector [0 1 0 1 0] to get longitudinal change for the study group, we get two bhvat values. How can we calculate these two bhvat values to one bhvat vaule in position two and four? Should we just add them together after we have been multiple them with the contrast vector, or add them as sqrt(a^2+b^2)? Best regards Knut Jørgen Bjuland NTNU

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possible to do multi planar reformats of hippocampal subfields in freeview?
by Salil Soman 07 Feb '14

07 Feb '14

Hi, I am reviewing hippocampal subfield segmentation using freeview, and was wondering if there is a way to do multiplanar reformats so I can get reorient the cor/sag/axial planes to that of the hippocampus? Thank you. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

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PET Partial volume correction
by Jonathan DuBois 07 Feb '14

07 Feb '14

Hi Freesurfer experts, I have been using freesurfer for surface-based PET analysis and was wondering if the method for voxel-based partial volume correction, used in the recent paper (Cortical surface-based analysis reduces bias and variance in kinetic modeling of brain PET data), was implemented with scripts available in the freesurfer package? If so, would you mind providing more details on what tools were used? As in the paper, I have 3T MRIs (reconstructed with FS) and BP data from controls scanned in a HRRT PET and reconstructed with a similar method. Thank you, Jonathan

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Re: [Freesurfer] kvl quantify script
by Alan Francis 07 Feb '14

07 Feb '14

Hi Eugenio: The command: kvlQuantifyHippocampalSubfieldSegmentations.sh I run this in the the directory that has the processed brains. SUBJECTS_DIR /media/Alan_Francis/Freiburg FREESURFER_HOME /usr/local/freesurfer/stable5_3/ thanks so much, Alan On Fri, Feb 7, 2014 at 2:52 PM, Juan Eugenio Iglesias < iglesias(a)nmr.mgh.harvard.edu> wrote: > Hi again, Alan, > can you please send me the exact command you are running, as well as the > value of SUBJECTS_DIR, FREESURFER_HOME, and so on? > Cheers, > /E > > > On Fri, 2014-02-07 at 14:46 -0500, Alan Francis wrote: > > Hi Eugenio: > > > > > > Thanks for responding. I am running the script in the directory that > > the brains are saved not the /user/local etc. Here is the error > > message that it gives me: > > > > > > > /usr/local/freesurfer/stable5_3_0//bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: > line 22: volumeStats_left.txt: Permission denied > > failed to do > > kvlQuantifyPosteriorProbabilityImages > /usr/local/freesurfer/stable5_3_0//data/GEMS/compressionLookupTable_left.txt > posterior_Left-Hippocampus.mgz > posterior_left_presubiculum.mgz posterior_left_CA1.mgz > posterior_left_CA2_3.mgz posterior_left_fimbria.mgz > posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz > posterior_left_hippocampal_fissure.mgz > > volumeStats_left.txt > > > > > > > > > > thanks so much, > > > > > > Alan > > > > > > > > > > > > > > On Fri, Feb 7, 2014 at 1:45 PM, Juan Eugenio Iglesias > > <iglesias(a)nmr.mgh.harvard.edu> wrote: > > Hi Alan > > by default, the script saves the file in the directory you're > > on. So, > > you just need to run it from your own space, e.g., > > cd ~ > > kvlQuantify...... > > Cheers, > > /E > > PD: I assumed the problem was that you ran the script > > from /usr/local/freesurfer/stable_5_3/data > > > > > > > > On Fri, 2014-02-07 at 12:33 -0500, Alan Francis wrote: > > > Hi Eugenio; > > > > > > > > > I ran the kvl quantify script for 70 processed Asperger > > brains. > > > However, it was not able to save the output since the the > > nmr center > > > disallows folks from saving data in the pathway > > > > > > > > > /usr/local/freesurfer/stable_5_3/data > > > > > > > > > is there anyway I can modify the script to save the data > > elsewhere? > > > > > > > > > thanks so much, > > > > > > > > > Alan Francis > > > Martinos Center > > > > > > > > > > > > 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. > > > > > > >

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error in local gyrification : error in dsearchn; error in mesh_vertex_nearest; reorganize_verticeslist.....
by Wang, Guoying 07 Feb '14

07 Feb '14

Dear freesurfer expert, when I run 'recon-all -s subj -lgi' , I got the same error message for every subjects. What does that mean? I really appreciate for your hint and help! Here is the error message I got: ------------------------------------------------------------------------------------------------------------ spm@gonzo:/gdata1/freesurfer_data/subjects> recon-all -lgi -s AG01001 Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /gdata1/freesurfer_data/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-rw- 1 spm users 724920 Feb 6 20:24 /gdata1/freesurfer_data/subjects/AG01001/scripts/recon-all.log Linux gonzo 3.4.28-2.20-desktop #1 SMP PREEMPT Tue Jan 29 16:51:37 UTC 2013 (143156b) x86_64 x86_64 x86_64 GNU/Linux /gdata1/freesurfer_data/subjects/AG01001/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Feb 7 14:23:51 CET 2014 mris_compute_lgi --i lh.pial ================= rm -Rf /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components.. 67084 voxel in cpt #1: X=2 [v=67084,e=201246,f=134164] located at (-27.174467, -14.049744, 33.073147) For the whole surface: X=2 [v=67084,e=201246,f=134164] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 67084 - 201246 + 134164 = 2 --> 0 holes F =2V-4: 134164 = 134168-4 (0) 2E=3F: 402492 = 402492 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/gdata1/freesurfer_data/subjects/AG01001/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_26868_.m'); exit ================= Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.05 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.02 sec) preparing outer mesh structure ... face 5000 / 134164 face 10000 / 134164 face 15000 / 134164 face 20000 / 134164 face 25000 / 134164 face 30000 / 134164 face 35000 / 134164 face 40000 / 134164 face 45000 / 134164 face 50000 / 134164 face 55000 / 134164 face 60000 / 134164 face 65000 / 134164 face 70000 / 134164 face 75000 / 134164 face 80000 / 134164 face 85000 / 134164 face 90000 / 134164 face 95000 / 134164 .... mesh_outer = vertices: [67084x3 double] faces: [134164x3 double] facesOfVertex: [67084x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (436.29 sec). ... creating path file for vertex 1 / 67084 area file for outer ROIs saved at 1 Improper assignment with rectangular empty matrix. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully! Linux gonzo 3.4.28-2.20-desktop #1 SMP PREEMPT Tue Jan 29 16:51:37 UTC 2013 (143156b) x86_64 x86_64 x86_64 GNU/Linux recon-all -s AG01001 exited with ERRORS at Fri Feb 7 14:33:09 CET 2014 Thanks a lot for your help ! guoying

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Re: [Freesurfer] kvl quantify script
by Alan Francis 07 Feb '14

07 Feb '14

Hi Eugenio: Thanks for responding. I am running the script in the directory that the brains are saved not the /user/local etc. Here is the error message that it gives me: /usr/local/freesurfer/stable5_3_0//bin/kvlQuantifyHippocampalSubfieldSegmentations.sh: line 22: volumeStats_left.txt: Permission denied failed to do kvlQuantifyPosteriorProbabilityImages /usr/local/freesurfer/stable5_3_0//data/GEMS/compressionLookupTable_left.txt posterior_Left-Hippocampus.mgz posterior_left_presubiculum.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_fimbria.mgz posterior_left_subiculum.mgz posterior_left_CA4_DG.mgz posterior_left_hippocampal_fissure.mgz > volumeStats_left.txt thanks so much, Alan On Fri, Feb 7, 2014 at 1:45 PM, Juan Eugenio Iglesias < iglesias(a)nmr.mgh.harvard.edu> wrote: > Hi Alan > by default, the script saves the file in the directory you're on. So, > you just need to run it from your own space, e.g., > cd ~ > kvlQuantify...... > Cheers, > /E > PD: I assumed the problem was that you ran the script > from /usr/local/freesurfer/stable_5_3/data > > > > On Fri, 2014-02-07 at 12:33 -0500, Alan Francis wrote: > > Hi Eugenio; > > > > > > I ran the kvl quantify script for 70 processed Asperger brains. > > However, it was not able to save the output since the the nmr center > > disallows folks from saving data in the pathway > > > > > > /usr/local/freesurfer/stable_5_3/data > > > > > > is there anyway I can modify the script to save the data elsewhere? > > > > > > thanks so much, > > > > > > Alan Francis > > Martinos Center > > > > > 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. >

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Autorecon2 Pipeline Problem
by Johnson, Chad P 07 Feb '14

07 Feb '14

Good morning, I am new to the e-mail list and would like to request help with a problem that has arisen when running recon-all. As such, I apologize if this question has been posed previously. We are running Freesurfer version 5.3.0 on Red Hat Enterprise Linux Release 6.3 using the freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 stable release of Freesurfer. Following white matter edits, the invocation "recon-all -autorecon2-wm -s <subjid>" begins at the Normalization 2 step, rather than the Fill step as stated in the processing stages pipeline. This is problematic as the following segmentation step overwrites the edited wm.mgz file with new automated information. Review of the output also indicates that the wm.mgz is being regressed back to the pre-edited state. A check of the recon-all lib file revealed the following. recon-all lib file source code from version 5.3.0 (lines 5465 through 5482): case "-autorecon2-cp": case "-autorecon2-noaseg": case "-autorecon2-wm": set DoNormalization2 = 1; set DoSegmentation = 1; set DoFill = 1; set DoTessellate = 1; set DoSmooth1 = 1; set DoInflate1 = 1; set DoQSphere = 1; set DoFix = 1; set DoMaskBFS = 1; set DoWhiteSurfs = 1; set DoSmooth2 = 1; set DoInflate2 = 1; set DoSegStats = 1; set DoCurvStats = 1; breaksw Where it appears that -cp, -noaseg, and -wm are all aliases of the same command. This differs significantly from the previous release we used in the lab of 5.1.0. recon-all lib file source code from version 5.1.0 (lines 4806 through 4819): case "-autorecon2-wm": set DoFill = 1; set DoTessellate = 1; set DoSmooth1 = 1; set DoInflate1 = 1; set DoQSphere = 1; set DoFix = 1; set DoMaskBFS = 1; set DoWhiteSurfs = 1; set DoSmooth2 = 1; set DoInflate2 = 1; set DoSegStats = 1; set DoCurvStats = 1; breaksw I assume that I can modify my pipeline with some -no commands to keep the DoNormalization2 and DoSegmentation steps from running but I was wondering if there was a reason for the change between versions which would argue against starting at the fill stage following white matter edits. I can provide any additional information if needed to help solve this problem and any information that can be provided regarding this would be most helpful. Thanks. Chad P. Johnson, Ph.D. Postdoctoral Fellow University of Texas Health Science Center

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