Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

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

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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

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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

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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

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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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control points and voxel segmentation stats
by Trina Kok 30 Mar '07

30 Mar '07

Hi, I understand that it is possible to use control points to fix intensity normalization, so that volumes which were not selected as white matter can be manually selected as white matter. Is it possible to "de-select" volumes which were determined as white matter in freesurfer, even though it is not (these volumes are part of the cortex). In general, is it possible to manually select certain volumes and assign them a segmentation label/value that seems more correct? Is there a way to obtain an output (.txt or .xls?) file that gives the segmentation label/value of each voxel on top of mousing over the voxel in tkmedit to obtain the segmentation label? Thanks! Regards, Trina Kok

2 1

QDEC
by Chacko Cherian 30 Mar '07

30 Mar '07

Hello developers, How can I get access to QDEC? Regards Chacko. ____________________________________________________________________________________ Need Mail bonding? Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=list&sid=396546091

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optseq help
by Mithra 30 Mar '07

30 Mar '07

Hello, I am trying to use the optseq command for 2 conditions of 30 trials each with TR = 2 optseq -ntp 120 -TR 2 -npercond 30 30 -tpercond 3 3 -nsessions 3 -label critical independent -o TestFile I get the following result: -0.000 1 3.000 critical 4.000 1 3.000 critical 8.000 0 2.000 independent The program adds an extra 1 second at the end of each trial. I want each trial dureation as 3 seconds. This is the true even when when I don't give the option -TR. ( I am assuming the default TR is taken as 2 by the program). I guess the program tries to start to each trial at mutiples of TR. Is this true? I want my trials not to have any intervals between trials. I get my desired results by "lying" to the program that the TR is 1. "optseq -ntp 180 -TR 1 -npercond 30 30 -tpercond 3 3 -nsessions 3 -label critical independent -o TestFile" gives the results as: -0.000 1 3.000 critical 3.000 1 3.000 critical 6.000 1 3.000 independent Is this the right way to go? Thanks. Mithra.

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fsaverage and mni305
by roberto toro 30 Mar '07

30 Mar '07

Hi, I'm trying to figure out how to go from a coordinate in mni305 space to a vertex index in fsaverage. In the README file that comes with fsaverage it's stated that surface coordinates are in talairach space, so they align with the MNI305 volume (and the talairach.xfm is the identity). But when I select a vertex in fsaverage (using tksurfer) I have three different coordinates. For example, vertex 62176 gives 1. the actual 3d coordinate of the vertex in the mesh -2.4876, -5.1338, 10.0494 2. the RAS coordinate -1.97, -4.48, 10.51 3. the Talairach coordinate (which I suppose are in fact MNI305 coordinates..) -1.95, -3.85, 9.87 this doesn't seem to be just a translation because when I compare actual 3d and talairach, the difference between the x coord (for example) of different vertices is not the same... how does tksurfer convert to talairach coordinates? thanks in advance! roberto

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stc-sess -fsd error
by Avram Holmes 30 Mar '07

30 Mar '07

FSFast folks, I am setting up an analysis stream and I am having an issue with stc-sess. If I leave my funcs in a folder called 'bold' the script works. stc-sess -i fmc -o fmcstc -so siemens -s c01 -d . However, we have multiple studies for each participant and I would like to use the '-fsd' flag. When I do so I get the following error... stc-sess -i fmc -o fmcstc -so siemens -s c01 -d . -fsd Flanker ERROR: Flag -fsd unrecognized. -i fmc -o fmcstc -so siemens -s c01 -d . -fsd Flanker Any advice would be appreciated. Thanks, Avram ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Avram Holmes Department of Psychology Harvard University 1210 William James Hall Phone:(617) 495-0790 33 Kirkland Street Fax:(617) 495-3728 Cambridge, MA 02138, USA Email: holmes(a)fas.harvard.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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