Freesurfer

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30132 discussions

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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Re: [Freesurfer] pwd: permission denied
by Marcel Zwiers 07 Mar '12

07 Mar '12

Hi Michael, Thanks for your help and suggestions! > I'd have to try to recreate the error, but I have an idea of what it > could be (assuming > /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness/BIG1026_1 > is a directory). Actually not yet, /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness is a directory but BIG1026_1 is supposed to be created by recon-all (but wasn't as a consequence of the error). > While you may have read, write, and execute permissions to your > colleague's directory, you must make sure that these permissions have > been recursively added to the contents of that directory (child > directories, child directory files, and directory files). There are only *.nii.gz files in that directory plus a few extra files and (symbolic links to) folders that I assume should have nothing to do with the error? The content looks like this (ls -al): drwxrwxr-x 2 marhoo big 352256 Mar 6 09:51 ./ drwxrwx--x 15 marhoo big 4096 Feb 29 15:49 ../ -rw------- 1 marzwi big 12219623 Mar 2 16:06 BIG1026_1.nii.gz [..] -rw------- 1 marzwi big 12219623 Mar 2 16:06 BIG4025_1.nii.gz -rw-rwxr-- 1 marhoo big 75806 Feb 27 10:54 BIG_aseg_stats.log* lrwxrwxrwx 1 marhoo big 34 Feb 19 09:12 fsaverage -> /opt/freesurfer/subjects/fsaverage/ lrwxrwxrwx 1 marhoo big 38 Feb 19 09:12 lh.EC_average -> /opt/freesurfer/subjects/lh.EC_average/ lrwxrwxrwx 1 marhoo big 38 Feb 19 09:12 rh.EC_average -> /opt/freesurfer/subjects/rh.EC_average/ -rw-rwxr-- 1 marhoo big 18200 Sep 27 10:39 v5.0.txt* -rw-rwxr-- 1 marhoo big 3220 Sep 27 10:39 v5.1.txt* -rw-rwxrw- 1 marhoo big 523 Feb 24 10:07 .xdebug_tkmedit* > I believe that your problem is that the file BIG1026_1.nii.gz > (however, from my experience this file should not simply be in the > BIG1026_1 folder but in the orig directory of the mri folder) has not > inherited the specified permissions from its parent directory. My username is marzwi, I am member of the big group and I have rw permissions of all the files and directories (see listing above) . > If this does not correct the error, set the environmental SUBJECTS_DIR > variable to the directory housing the subject directories (making sure > that your colleague gives you sufficient access to this directory), > lose the -sd path in the command, and make sure that you have read, > write, execute permissions recursively added to the directories and > files that you will be working with. I did that but the error message remains. Here's the full message, started from a newly opened bash terminal: -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /opt/freesurfer FSFAST_HOME /opt/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /opt/freesurfer/subjects MNI_DIR /opt/freesurfer/mni FSL_DIR /opt/fsl mentat002:$ export SUBJECTS_DIR=/home/mrphys/marzwi/BIG/Freesurfer_CorticalThickness mentat002:$ recon-all -subject BIG1026_1 -i BIG1026_1.nii.gz -autorecon1 /bin/pwd: cannot open directory `../..': Permission denied mkdir: cannot create directory `/BIG1026_1': Permission denied mkdir: cannot create directory `/BIG1026_1': Permission denied cp: cannot create regular file `/BIG1026_1/scripts/build-stamp.txt': No such file or directory cat: /BIG1026_1/scripts/build-stamp.txt: No such file or directory INFO: FreeSurfer build stamps do not match Subject Stamp: Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is Actual FREESURFER_HOME /opt/freesurfer-v5.1 /BIG1026_1: No such file or directory. > Another option would be if your colleague set up a "subjects > directory" within his parent directory and add each subject's folder > to this directory and then setting this as your SUBJECTS_DIR variable > (ensuring you have read, write, execute permissions). I created a subfolder, copied the BIG1026_1.nii.gz file into it and ran recon-all using this subfolder as SUBJECTS_DIR but I kept getting permission denied errors. > I hope this helps; however, not knowing the version of free surfer > that you are running nor the operating system makes it difficult to > trou bleshoot your problem. Let me know if you arrive at a solution or > require further assistance. > Thanks, > Michael Nowak I hope the info above can help troubleshooting my problem. Thanks a lot Michael! Cheers, Marcel On Mon, Mar 5, 2012 at 9:55 PM, Marcel Zwiers < m.zwiers(a)fcdonders.ru.nl > wrote: > Hi, > > I am new to FS and have encountered a weird problem that I do not know how to solve and did not find any earlier > postings on. When I run recon-all on a file in my own home directory everything works normally: > > recon-all -subject BIG1026_1 -sd /home/mrphys/marzwi/test -i BIG1026_1.nii.gz > -autorecon1 > [..] > > However, if I run the same command on the same file, except that this file is now located in a directory of a > colleague of mine that I certainly have full access to (+r+w+x), I immediately get a 'permission denied' error: > recon-all -subject BIG1026_1 -sd /home/control/marhoo/Projects > /BIG/Freesurfer_CorticalThickness -i BIG1026_1.nii.gz -autorecon1 > pwd: cannot open directory `../..': Permission denied > /bin/pwd: cannot open directory `../..': Permission denied > mkdir: cannot create directory `/BIG1026_1': Permission denied > [..] > > From the error message it seems to me as if FS is trying to access the parent directory (of which I do not have > full rights but only -r-w+x)? As this does not make a lot of sense to me I suspect there must be another cause > and hope you have any ideas here. > > Cheers, > Marcel -- Marcel Zwiers www.ru.nl/donders MR techniques +31-(0)24-3668495 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands

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