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30089 discussions

Inter-hemispheric registration issue
by Irene Altarelli 15 May '12

15 May '12

Dear all, I'm trying to use the new script for the inter-hemisphere analysis, in Fs version 5.0. I have downloaded the files as suggested (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21706.html) Surfreg seems to be running fine (surfreg --s subject --t fsaverage_sym --lh), but I have problems then with the --xhemi option. Some files appear to be missing, I get the following error messages: ERROR: cannot find /path/subject/xhemi/surf/lh.sphere ERROR: cannot find /path/subject/xhemi/surf/lh.smoothwm ERROR: cannot find /path/subject/xhemi/surf/lh.sphere ERROR: cannot find /path/subject/xhemi/label/lh.aparc.annot lh.fsaverage_sym.sphere.reg is created in $subject as it should (please find the surfreg log below). Thank you in advance, Irene Log file for surfreg samedi 12 mai 2012, 17:36:31 (UTC+0200) setenv SUBJECTS_DIR /home/ialtarelli/DATABASE/Karla5/ cd /home/ialtarelli /home/ialtarelli/freesurfer/bin/surfreg --s aa_copie --t fsaverage_sym --lh Linux lscp-iao1 2.6.32-5-amd64 #1 SMP Mon Jan 16 16:22:28 UTC 2012 x86_64 GNU/Linux #@# lh samedi 12 mai 2012, 17:36:31 (UTC+0200) #CMD# mris_register -curv -annot aparc.annot /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg using smoothwm curvature for final alignment zeroing medial wall in aparc.annot $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ $Id: mrisurf.c,v 1.678 2010/05/28 21:22:21 rpwang Exp $ reading surface from /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.sphere... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) reading template parameterization from /home/ialtarelli/DATABASE/Karla5//fsaverage_sym/lh.reg.template.tif... ripping medial wall... writing registered surface to /home/ialtarelli/DATABASE/Karla5//aa_copie/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.007, std = 0.603 curvature mean = 0.030, std = 0.806 curvature mean = 0.024, std = 0.853 curvature mean = 0.009, std = 0.826 curvature mean = 0.011, std = 0.936 curvature mean = 0.003, std = 0.836 curvature mean = 0.005, std = 0.972 curvature mean = 0.001, std = 0.837 curvature mean = 0.001, std = 0.988 curvature mean = -0.032, std = 0.312 curvature mean = 0.032, std = 0.124 curvature mean = 0.079, std = 0.315 curvature mean = 0.031, std = 0.151 curvature mean = 0.049, std = 0.489 curvature mean = 0.031, std = 0.165 curvature mean = 0.028, std = 0.631 curvature mean = 0.031, std = 0.171 curvature mean = 0.011, std = 0.749 159: 0 negative triangles surfreg-Run-Time-Hours aa_copie lh 0 0,84 samedi 12 mai 2012, 18:26:49 (UTC+0200) surfreg done -- Irene Altarelli Laboratoire de Sciences Cognitives et Psycholinguistique Ecole Normale Supérieure 29, rue d'Ulm 75230 Paris Cedex 05 tel. +33 (0)1 44 32 26 23

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Clusters size treshold question
by Antonella Kis 15 May '12

15 May '12

Dear All, I would like to know if there is a way to eliminate from my significant clusters (grf.th3.pos.sig.cluster.mgh) obtained after running mri_glmfit-sim with grf option and using mri_volcluster the clusters with a size smaller than 50 mm^3 or in other words to keep only clusters with a volume/size greater than 50 mm^3. Thank you for your time and help. Regards, Antonella

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confusion with tkregister2
by Borzello, Mia 15 May '12

15 May '12

Morning all, I ran the recon yesterday, and it says it ran without error. I am now running tkregister2, but for some reason when i compare the coronal view, things look okay on the mri, but it looks like the axial view for the CT. I'm not sure in which step this happened? Thanks, Mia

2 2

1-way ANOVA: contrast specification
by Александр Лебедев 15 May '12

15 May '12

Dear Freesurfers, I'm going to run 1-way anova, followed by post hoc pairwise comparison. My "factor-of-interest" has 4 levels and, in addition, I would like to regress out the effects of 3 continious variables. I have attached my *fsgd-file. Therefore, my first *mtx-file should contain the following: 0.5 -0.5 0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 Correct? Thank you very much beforehand! === Regards, Alexander Lebedev Stavanger University Hospital

2 1

low eff and VRF values
by Andrew Valdespino 15 May '12

15 May '12

(1) Version: optseq2.c,v 2.21.2.1 (2) Computer operating system: Mac OS X Version 10.7.3 (3) Command line: optseq2 --ntp 230 --tr 1.5 --psdwin 0 24 0.5 --ev go 7 36 --ev nogo 7 12 --nkeep 4 --o gonogo --nsearch 1000 (4) Description of the problem: This is in reference to a go/no-go paradigm. I am getting very low Eff and VRFAvg values. Is this an issue/ is common with go/no-go paradigms? If this is an issue, any recommendations for appropriate modifications. A trial in my experiment involves a countdown (duration 2 seconds) followed by the event of interest (0.5 seconds) followed by a blank screen (3.5 seconds). I set dPSD at 0.5 because this number is divisible by both the --tr and trial length (7 seconds). (5) Log and/or summary files: Searched 1000 iterations for 0.002500 hours Rate: 111.111 iterations per second INFO: 211/1000 schedules were ill-conditioned Number of iterations since last substitution 310 Cost Avg/Std: 0.0105840 0.0060667 Max Eff Encountered: 0.0154867 Max VRFAvg Encountered: 1.6717 Eff of Nominal Ideal XtX: 0.177183 Rank Cost ZCost NthIter Eff CB1Err VRFAvg VRFStd VRFMin VRFMax VRFRng IXtXErr 1 0.0155 0.808 597 0.015 0.157407 1.67 0.61 0.80 4.13 3.33 4723.04 2 0.0150 0.732 218 0.015 0.009259 1.58 0.50 0.87 3.03 2.15 4749.02 3 0.0149 0.708 82 0.015 0.009259 1.54 0.46 0.91 3.15 2.24 4882.85 4 0.0148 0.703 539 0.015 0.175926 1.56 0.52 0.94 3.86 2.91 4752.15 ____________

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lGI differences without variation in other cortical morphometric variables
by Inês Violante 15 May '12

15 May '12

Dear all, I am comparing a group of patients with controls. I extracted: cortical volume, surface area, cortical thickness and gyrification index for each subject's lobe. Comparisons between this variables with Total Intracranial Volume as a covariate indicated a difference in frontal and temporal lobes lGI. However, differences were not significant for any of the other variables. I can´t understand these results from a biological perspective. I was expecting that if a difference exist in lGI it would also manifest in surface area or volume. Can someone help me with an explanation for this? Thank you. ines

2 2

Problem creating longitudinal template file
by Corinna Bauer 15 May '12

15 May '12

Hello all, I am trying to create a template for longitudinal processing and am running into some problems generating the file. I have many subjects so I am running a batch script. I am using version 5.1.0 Any suggestions? Thanks! Corinna Here is my script: #!/bin/tcsh setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh setenv SUBJECTS_DIR /Applications/freesurfer/subjects/corinna/ADNI/template set subjects=`cat $1` foreach subject ($subjects) echo "-------------------- Processing $subject -------------------------" set subj_dir=/Applications/freesurfer/subjects/corinna/ADNI/ set template=/Applications/freesurfer/subjects/corinna/ADNI/template/${subject}_template/mri set tp_BLmos=/Applications/freesurfer/subjects/corinna/ADNI/BL/${subject}/mri/norm.mgz set tp_12mos=/Applications/freesurfer/subjects/corinna/ADNI/12mos/${subject}/mri/norm.mgz set tp_24mos=/Applications/freesurfer/subjects/corinna/ADNI/24mos/${subject}/mri/norm.mgz set tp_36mos=/Applications/freesurfer/subjects/corinna/ADNI/36mos/${subject}/mri/norm.mgz #set nu_mgz=${subj_dir}/mri/nu.mgz recon-all -base ${subject}_template -tp ${tp_BLmos} -tp ${tp_12mos} -tp ${tp_24mos} -tp ${tp_36mos} -all end Here is my output: -------------------- Processing 137_S_0631 ------------------------- Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/corinna/ADNI/template Actual FREESURFER_HOME /Applications/freesurfer Darwin ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel Version 10.4.2: Tue Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64 #-------------------------------------------- #@# Longitudinal Base Subject Creation Mon May 14 18:21:23 EDT 2012 /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template \n mri_robust_template --mov /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz --lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/transforms/norm.mgz_to_137_S_0631_template.lta --template /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz --average 1 --sat 4.685 \n $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume. --mov: Using /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz as movable/source volume. Total: 4 input volumes --lta: Will output LTA transforms --template: Using /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/mri/norm_template.mgz as template output volume. --average: Using method 1 for template computation. --sat: Using saturation 4.685 in M-estimator! reading source '/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz'... mghRead(/Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz, -1): could not open file MultiRegistration::loadMovables: could not open input volume /Applications/freesurfer/subjects/corinna/ADNI/template/norm.mgz/mri/norm.mgz. Darwin ebrcb-dhcp-240-126.bumc.bu.edu 10.4.2 Darwin Kernel Version 10.4.2: Tue Jul 27 21:17:17 PDT 2010; root:xnu-1504.7.60~1/RELEASE_X86_64 x86_64 recon-all -s 137_S_0631_template exited with ERRORS at Mon May 14 18:21:23 EDT 2012 For more details, see the log file /Applications/freesurfer/subjects/corinna/ADNI/template/137_S_0631_template/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 3

recon-all exiting with errors
by Richter, Julia 15 May '12

15 May '12

Dear FreeSurfer experts, I am trying to recon-all T1 images with the command recon-all -s <subjectname> -i /path/to/subject/directory/subject.nii.gz. This command used to work with several images, but one of my images is always exiting with errrors, in my opinion without a reason. Any suggestions what is going on? I am attaching the recon-all.log of my data. Thanks for your help, Julia

2 1

Need some materials
by bowang21＠mail.ustc.edu.cn 15 May '12

15 May '12

Dear Freesurfer Experts, I am a senior, and I am going to finish my graduation thesis which is about the use of freesurfer.So I need some written materials,such as the development history of Freesurfer, the achievement of Freesurfer and so on. But I don't know. Can you help me? Or give me some wed pages. Thanks in advance. Yours Bobo

2 1

"cannot allocate memory" issue
by Borzello, Mia 14 May '12

14 May '12

Hi all, I was wondering if you could help me figure out why the recon isn't running to completion. I've attached the log file (recon-all.log), but it's unclear to me what I should do to fix this problem. I tried to compute the lh.pial, but I guess it was never made in the recon. Thanks so much, Mia

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