Freesurfer March 2012

freesurfer@nmr.mgh.harvard.edu

137 participants
209 discussions

qdec
by Richter, Julia 08 Mar '12

08 Mar '12

Dear freesurfer experts, I am trying to run a volume analysis with qdec. One of my discrete variables has 3 three levels...Is Freesurfer capable of creating a FSGD file of a discrete variable like this? When I m running the analysis, the terminal also says "no contrasts specified" after trying to read the source surface. What is wrong here? Thank you all so much for your help, Julia

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FS 5.1 control points problem
by Tetiana Dadakova 08 Mar '12

08 Mar '12

Dear FS list, We started using FS 5.1 and encountered a problem with control points. After first recon-all some of the cortex (in occipital part) was missing, so we added control points and re-ran -autorecon2-cp -atorecon3. After that, the part of the brain with control points was removed from brainmask.mgz (Fig1). I never had this problem in 5.0, therefore I assume that something has been changed in 5.1 regarding cp. Could you please suggest what can be the problem and if it is described somewhere? Thank you, Tanja.

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Total WM and GM Vol in FS 5.0.0
by Dhinakaran Chinappen 08 Mar '12

08 Mar '12

Hi all, I am using Freesurfer 5.0.0, before the outputs for cortical and subcortical GM and WM were made available in the final output files. What is the best way to calculate total gray matter volume (cortical and subcortical)? Is it through mris_anatomical_stats or mri_segstats? Also, are there commands to calculate total cortical and total subcortical volumes of GM separately? As for total white matter, is using the sum of the volumes of Left-Cerebral-White-Matter and Right-Cerebral-White-Matter considered acceptable practice? Or should I go to the command line and use mris_wm_volume? Thanks in advance for the clarification, Dhinakaran.

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"Smart" concatenation in selxavg3-sess?
by Alex Kell 07 Mar '12

07 Mar '12

Hi Freesurfers, The selxavg3-sess's help and Freesurfer documentation say that selxavg3-sess creates a design matrix for each run, fits the glm for each run, and then combines the runs together to give summary data for the subject's whole session. Some of the fsfast 5 slides say it uses "smart" concatenation to combine each run's data -- what is "smart" concatenation? How does are the runs brought into alignment? Thanks! Alex Kanwisher Lab Manager McGovern Institute for Brain Research MIT

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aparc.a2005s+aseg.mgz
by Kern, Mark 07 Mar '12

07 Mar '12

Dear Freesurfer Mavens, After running "recon-all -all" on a set of anatomical data, I wished to used the aparc.a2005s+aseg.mgz in a connectivity analysis pipeline to create some ROI masks. I was particularly interested in the subcortical regions contained in the a2005s scheme. However, the aparc.a2005s+aseg.mgz file was not created during the recon-all processing run. Is there a way to get the a2005s segmentation data? Thanks for your help. Best, Mark Senior Research Scientist Division of Gastroenterology and Hepatology Departmernt of Medicine Medical College of Wisconsin Milwaukee, WI

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White Matter question
by Dhinakaran Chinappen 07 Mar '12

07 Mar '12

Dear all, I was wondering if you have encountered this issue before: Would you anticipate a difference between the volume calculated by Freesurfer 5.0 in Cerebral-White-Matter volume and the total volume calculated from the regions (defined by the Desikan atlas) in wmparc.stats? In one of my studies, the Cerebral-White-Matter volume is bigger than the volume obtained by summing up the regions in wmparc.stats on average and for individual patients as well. Is there an anatomical reason behind this? Which measure should be preferentially used? Help would be much appreciated. Thanks, Dhinakaran.

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recon2 error
by Jimmy Ghaziri 07 Mar '12

07 Mar '12

Dear FreeSurfer community, I am running Ubuntu 11.10 on an Intel i7 970 3.20Ghz 64bit (11 CPUs) with 12GB DDR3 RAM on a 120GB raid 0 solid state hard drives. I have ran recon-all this summer on some of my subjects and it worked perfectly in 13 hours. I'm trying to run one more analyse (a recon-all) and I keep getting this error message when it gets to recon2 : **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.789, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 26136.459 ms 0001: dt=129.472000, rms=0.731 (7.421%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 24108.512 ms and it continues this way on and on. I tried to run recon-all again on an old subject (on which it worked this summer) by renaming the files and folders of course and I got the same error message. I uninstalled and reinstalled FreeSurfer and still am getting the message. I ran one of the subject on my colleagues machine (which is slower than mine; took him 22 hours) and it worked perfectly. Can anyone tell me what could be the problem ? I will need to run more analyses in a few months and I need to fix it ASAP. Here's the command I'm using (which is the same as my colleague and as indicated on FS wiki) : recon-all -subjid a_al_t1 -i ~/Documents/T1W_3D_TFE/GHA_A-C_2234495-T1W_3D_TFE-20101207-301-1.dicom -all Thank you, Jimmy

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Qdec Error in analyze: command failed
by Laura Tully 07 Mar '12

07 Mar '12

Hi, I'm getting an error in analyze: command failed: mri_concat notification when trying to run qdec on a within subjects analysis (N=29, looking at thickness and social functioning whilst controlling for ICV). I'm not sure what this means. See the output below. Thanks! Laura. Data table loading completed successfully. SUBJECTS_DIR is '/ncf/snp/04/SCORE/freesurfer_analysis' lh-Avg-Intercept-thickness ----------------------- Does the average thickness differ from zero? Nuisance factors: ICV_Mean_Centered 1.000 0.000 0.000; lh-Avg-thickness-Social_Fx-Cor ----------------------- Does the correlation between thickness and Social_Fx differ from zero? Nuisance factors: ICV_Mean_Centered 0.000 1.000 0.000; sh: ICV/y.mgh: No such file or directory ninputs = 29 Checking inputs nframestot = 29 Allocing output Done allocing nframes = 29 Writing to /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx unknown file type for file (/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx) Error in Analyze: command failed: mri_concat /ncf/snp/04/SCORE/freesurfer_analysis/27119/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27120/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27121/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27122/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27125/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27127/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27131/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27140/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27145/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27160/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27164/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27191/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27193/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27194/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27195/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27196/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27199/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27201/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27203/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27204/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27205/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27206/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27208/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27210/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27211/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27212/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27213/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27216/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27218/surf/lh.thickness.fwhm10.fsaverage.mgh --o /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx&ICV/y.mgh -- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully(a)fas.harvard.edu

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FreeSurfer Course in Amsterdam!
by Allison Player 07 Mar '12

07 Mar '12

Hi everyone, The Department of Radiology at VU University Medical Center in Amsterdam, Netherlands is hosting a FreeSurfer Course on June 27th through June 29th. Registration is now open. You can find details about course as well as the registration form on the following website: http://www.freesurfercourseamsterdam.nl/ Questions about the Amsterdam course should go to Veronica Popescu (info(a)freesurfercourseamsterdam.nl) Hope to see you there, Allison

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freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable
by Ian Charest 07 Mar '12

07 Mar '12

Hi When running recon-all I get the following error: ERROR: mpr2mni305 failed, see transforms/talairach_avi.log I called recon-all like so: recon-all -i /imaging/ic01/mridata/subject01/structurals/subject01.MR.SEQUENCE.0014.0001.2011.12.16.57.613319.8231038.IMA -all -subjid subject01 I checked the talairach_avi.log file (see the full report below), and the mistake happens at the call to mpr2mni305 MPR2MNI305_TARGET: Undefined variable. I searched the mailing list for similar errors and saw a similar post here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018445.html<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-May/018445.html> but in this user's case there seemed to be a problem with the MPRAGE image itself (the brain seemed "squashed") I checked the dimensions of my orig.mgz and they are ok (1x1x1). I had a look at my orig.mgz in tkmedit and all seems fine. Any Idea what could be going wrong? Best Wishes Ian Charest ====== talairach_avi.log: /imaging/ic01/subjects/subject01/mri /imaging/local/software/freesurfer/5.1.0/i686//bin/talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ Linux l34 2.6.9-89.0.25.ELsmp #1 SMP Mon Apr 19 06:05:15 EDT 2010 i686 i686 i386 GNU/Linux Wed Mar 7 16:56:30 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mri_convert orig.mgz talsrcimg.img $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-1, 4.65661e-08, -4.09782e-08) j_ras = (-2.23517e-08, -3.72529e-09, -1) k_ras = (3.81842e-08, 1, -6.98492e-10) writing to talsrcimg.img... Analyze Output Matrix -1.000 -0.000 0.000 132.161; 0.000 -0.000 1.000 -103.886; -0.000 -1.000 -0.000 97.205; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 mpr2mni305 talsrcimg Wed Mar 7 16:56:34 GMT 2012 /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mpr2mni305 talsrcimg $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ MPR2MNI305_TARGET: Undefined variable.

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Freesurfer March 2012