Freesurfer

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30089 discussions

Running recon-all fails during autorecon-2 -careg step
by Sarosh, Cyrus 09 May '12

09 May '12

I have run recon-all on multiple subjects and have had it fail at the same step every time with the same error. I am using VirtualBox with the provided Disk Image and Windows 7. 0560: dt=0.001750, rms=0.358 (0.039%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z GCAMwrite:: the popen error code is: 12 mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Tue May 8 16:45:14 EDT 2012 /home/virtualuser/freesurfer/subjects/test/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test exited with ERRORS at Tue May 8 16:45:15 EDT 2012 Has anyone had this issue and resolved this problem? Thanks for your help. - Cyrus ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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Entorhinal Ex vivo label
by Alan Francis 09 May '12

09 May '12

Hi Ruopeng: Is there a command that will allow you to extract the volumes of the EC from the Entorhinal Ex vivo label ? I need to extract this in 77 brain scans. thanks ~ Alan BIDMC/ Boston

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Reading thickness data
by Kevin Chen 09 May '12

09 May '12

Hi all, I'm new to FreeSurfer and I was wondering if there are any methods or software to read the ?h.thickness files and perhaps as a result get a list or table of all the vertices and their corresponding thickness? Also, is there a way to convert the vertex-based thickness files into voxel-based thickness data? Thanks in advance and best regards, Kevin

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Recon-all WARNING: tag image orientation not found
by Mary Ellen Koran 09 May '12

09 May '12

Hi, I'm getting the error WARNING: tag image orientation not found during the mri_convert step of recon-all. The log file is attached here. I am using version freesurfer_v.5.1.0 on Linux RHEL6. I am submitting a job to qsub (command lines in script FSscript3 attached). Any help would be greatly appreciated! Thanks!

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Error with recon-all
by Ed Gronenschild 09 May '12

09 May '12

Hi, I'm using the version of recon-all that Nick provided at April 17 to be able to run nu_correct prior to the Talairach stage. (I'm on a Mac, OSX 10.6, version v5.1.0). The command given was recon-all -autorecon-all -hippo-subfileds -no-wsgcaatlas \ -clean-tal -s subject. recon-all stopped and issued the following error: cp: ../surf/lh.orig_corrected: No such file or directory. Note that I included the option -no-wsgcaatlas to get a better skullstripping because in the default mode the skulltripping was bad. With this option it looks good. I got the above error regularly for other subjects as well and by including the -no-wsgcaatlas option recon-all finished without error, except for the present case. Cheers, Ed

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LongitudinalTutorial and long-tutorial dataset.
by Natacha Beck, Ms 08 May '12

08 May '12

Hi, I tried to run longitudinal analysis, I started by reading the LongitudinalTutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) In order to follow the tutorial, I downloaded the longitudinal tutorial dataset (long-tutorial.tar.gz) here http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Data. I uncompressed it in $FREESURFER_HOME/subjects. But I saw some symbolics links, for example: Mon May 07 user1 /Applications/freesurfer/subjects/long-tutorial =>find . -name "00*.mgz" -type l -ls 16661742 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0001_MR1/mri/orig/001.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0001_MR1/mri/orig/001.mgz 16661743 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0001_MR1/mri/orig/002.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0001_MR1/mri/orig/002.mgz ... 16678379 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0185_MR2/mri/orig/001.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0185_MR2/mri/orig/001.mgz 16678380 8 lrwxrwxrwx 1 user1 admin 74 Jun 24 2011 ./OAS2_0185_MR2/mri/orig/002.mgz -> /autofs/cluster/freesurfer/test/oasis/origs/OAS2_0185_MR2/mri/orig/002.mgz My problem is that the target files do not exist. Is it a problem in the dataset ? or have I missed a step ? Thanks. Natacha Beck

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Re: [Freesurfer] Volume to surface
by Gabriel Gonzalez Escamilla 08 May '12

08 May '12

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Volume to surface
by Gabriel Gonzalez Escamilla 08 May '12

08 May '12

2 3

Re: [Freesurfer] Volume to surface
by Gabriel Gonzalez Escamilla 08 May '12

08 May '12

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inability to pick points
by Borzello, Mia 07 May '12

07 May '12

Hi, I'm just wondering if there is something that needs to be selected using tkmedit to get electrode coordinates. I usually don't have this issue, but right now i'm unable to move my cursor to a new location. Thanks so much, Mia

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