Freesurfer May 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

asegstats2table error
by Rashmi Singh 15 May '12

15 May '12

Hello, I am trying to get the asegmentation information after the recon-all run in the table form, but I am continuously getting the following error asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume --tablefile asegstats.txt SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files ERROR: The stats file /opt/freesurfer/subjects/AA262.G1/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files I did try to use the skip option , but then , it skips all the files giving the same error. When I individually open the aseg files from the stats folder, those look fine to me. Please advise. Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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mri_segstats for T2-relaxation time data?
by Carl Anderson 15 May '12

15 May '12

Dear Freesurfer Folks, I have returned to the problem of trying to extract T2 values from a T2-map using aseg & mri_segstats. When I attempt mri_segstats it only returns a small subset of the regions from aseg (see attached file). I would like to attach the T2 map but the file exceeds the 25mb limit for gmail (could I drop the file somewhere?) Could the T2 values need to be in a special format? Thanks very much for your help. Carl On Thu, Dec 30, 2010 at 6:06 PM, Nick Schmansky <nicks(a)nmr.mgh.harvard.edu <mailto:nicks@nmr.mgh.harvard.edu>> wrote: mri_segstats, for example: mri_segstats --seg aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --i T1.mgz \ --sum T1.stats produces a text file 'T1.stats' which has stats on each aseg struct as taken from the vol T1.mgz. n. On Thu, 2010-12-30 at 17:52 -0500, Carl Anderson wrote: > Dear Freesurfer, > > > I have co-registered a map of whole brain T2-relaxation time values to > the corresponding aseg.mgz for this subject (see attached jpegs). > Does a tool exist in freesurfer to enable regional sampling of T2 > values from the T2-relaxation time map based on aseg? > > > Thanks for any thoughts. > -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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average lGI for each subject's hemipshere
by Inês Violante 15 May '12

15 May '12

Dear all, How can I obtain an average lGI for each subject's hemipshere? I've tried: mris_anatomical_stats -mgz -f lh.lgi.stats -b -a ../label/lh.aparc.annot -c ../label/ lgi.annot.ctab -t pial_lgi $SUBJECT lh but I had the following error: ERROR: stating file .../label/lh.aparc.annot It calculates the lgi for each gyri label but it does not give average values for the hemisphere. Thanks a lot. ines

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mri_robust_template
by Arman Eshaghi 15 May '12

15 May '12

Dear all, For a longitudinal analysis I need to have within subject templates. After some preprocessing that included FSL's BET, and linear registration of all time points to time-point 1, I fed images to mri_robust_template: mri_robust_template --mov tp1 tp2 tp3 --template <template_address> --satit It runs fine for some subjects, however I get the following error for some others: ERROR: All entries are zero! Images do not overlap (anymore?). This can have several reasons (i.e. different modalities, different intensity scales, large non-linearities, too diff. voxel sizes ...) Maybe use --transform <init.lta> with an approx. alignment obtained from tkregister or another registration program. Or do some prior intensity correction? I have rechecked data, they are bias corrected, and coregistered. Any thoughts of what could possibly go wrong here? All the best, Arman

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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

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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

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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

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Freesurfer May 2012