Freesurfer April 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
78 discussions

FreeSurfer & R
by Alessandro Gagliardi 03 Apr '07

03 Apr '07

Hello Emily and other FreeSurfer useRs, I'm having trouble getting data out of R and back into FreeSurfer and I was wondering how you did it. The tksurfer doesn't seem to like the .img files that the AnalyzeFMRI package produces (perhaps because it doesn't have a .mat file to go with it). I've tried to convert ascii files into Analyze and MGH files using mris_convert, but tksurfer doesn't like those either. Any help would be greatly appreciated. Thanks! -- Alessandro Gagliardi Integrative Neuroscience Program Rutgers University Mind Brain Analysis alessandro(a)gagliardi.name

2 1

Freesurfer and FSL integration
by Frederick Powell 03 Apr '07

03 Apr '07

I would like to run FSL and Freesurfer on my Linux compter. I have noticed that within Freesurfer I have a FSL directory. I have also visited the FSL website and noticed an entire downloadable version of FSL. I would like to be able to use my structural MPRAGE images that I have analyzed in Freesurfer and combine them with DTI images for ROI tractography and FA calculations. Do I need to download the version of FSL from the website? Secondly how should it be sourced so that FSL and Freesurfer are able to run together ( will I encounter any binary issues)? If you could respond with details. I am a novice to installing programs using a Linix machine. I am specifically talking about how to source the program and get it up and running. Thanks -- Frederick G. Powell

2 1

recon-all failing from script
by Martin Kavec 03 Apr '07

03 Apr '07

Hi, I am trying to further script (Bash) the autorecon1 and subcortseg. The script just sets the path to the received dicom data, gets some info from the dicom header and starts the autorecon1 followed by subcortseg. The things work well when executed from the command line, but if I execute the script from another script, I get the following error during autorecon1: mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.23434/src.mnc transforms/talairach.auto.xfm Use of uninitialized value in join or string at /opt/freesurfer/mni/bin/mritotal line 462. mritotal: Couldn't find configuration file mritotal.cfg anywhere in :/opt/freesurfer/mni/bin/../etc/mni_autoreg ERROR: mritotal failed, see transforms/talairach.log Thanks for help in advance. Martin

1 0

skull strip for monkeys
by Paul Aparicio 02 Apr '07

02 Apr '07

Hello All, I am having a very difficult time getting skullstrip to work on my monkey anatomical data set. Are there any suggestions on how to get it to work properly? Thanks in advance Paul

2 1

freesurfer & nohup
by Istvan Akos Morocz 02 Apr '07

02 Apr '07

does anybody know if FreeSurfer can be run in combination with the unix command 'nohup' like: nohup recon-all -autorecon-all -subjid fs & so that one is able to logout after beginning of the process without halting all computation ? thanks, bye, pisti ----- pisti(a)bwh.harvard.edu

2 2

autorecon1 failures
by Derin Cobia 02 Apr '07

02 Apr '07

Two questions for two different subjects during autorecon1: 1. The initial skull strip on this subject left too much extra-cerebral material. Subsequent attempts at using the wsatlas or manual adjustment of the wsthresh have resulted in this error: *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 1960516 Find the largest 110-component...mriSegmentReallocateVoxels: could not alloc 1048381 voxels for sno 8343 Cannot allocate memory done And identify it as the main brain basin...Segmentation fault Linux rainmaker 2.6.9-42.0.3.ELsmp #1 SMP Fri Oct 6 06:21:39 CDT 2006 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Apr 2 15:02:05 CDT 2007 #-------------------------------------------------------------- Are there too many voxels? I've looked, but couldn't find any information on how to fix this one. 2. This subject continues to fail with errors during intensity normalization. Here is the output: #-------------------------------------------- #@# Intensity Normalization Mon Apr 2 15:46:47 EDT 2007 /disk/conte_raid1/freesurfer/conte_mprage/021219_5734/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 0.830 -0.117 -0.004 -3.656; 0.116 0.833 -0.323 -26.577; 0.004 0.028 0.075 84.152; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize: could not find any valid peaks mri_normalize: normalization failed Linux eli 2.6.9-34.0.1.ELsmp #1 SMP Wed May 17 16:59:36 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Apr 2 15:46:49 EDT 2007 #--------------------------------------------- I've checked the talairach.xfm and it is bad. It seems I remember someone on the list saying that a -nold flag could fix this, but I couldn't find any info on the wiki about it. Any suggestions? Can I still salvage this subject? Thanks for all of your help! -Derin

3 5

control points
by lgutierrezg＠comz.org 02 Apr '07

02 Apr '07

How often do you use control points to fix white matter? Because I do not have clear when I have to use it, despite I have read the example in the website. Thanks Best Regards Leticia Gutierrez

1 0

How to edit orig surface?
by deepa preeti 02 Apr '07

02 Apr '07

Hi, I am trying to do cortical segmentation. But unfortunately during autorecon2 stage, in some of the scans the orig surface did not include some of the wm, even though these regions are included in wm.mgz and so, the pial surface failed to include them as well. How to edit in this case? ( because this region is already there in wm.mgz). I have attached the brainmask & wm.mgz. Any suggestions greatly appreciated. Thanks, Preeti Ramasamy.

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Freesurfer April 2007