Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30076 discussions

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.

2 1

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.

2 1

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

2 3

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 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

2 3

cerebellum not segmented well
by deepa preeti 30 Mar '07

30 Mar '07

Hi Bruce, I checked the skullstripping, the image is good with intact cerebellum. I have attached the skull stripping image as well. I wonder why the inferior regions of the cerebellum looks very bright and they are not included in subcortical segmentation resulting in failed segmentation. Any suggestions greatly appreciated. Thanks, Deepa.

2 1

cerebellum not segmented well
by deepa preeti 30 Mar '07

30 Mar '07

Hi, I am trying to segment a few scans with freesurfer. Unfortunately, they failed during autorecon2 - the cerebellum not well segmented and the inferior portion looks very bright. I have attached the images below. I appreciate your suggestions as how to proceed. Thanks, Deepa. --

2 1

intersubject registration with monkeys
by Marie Schaer 29 Mar '07

29 Mar '07

Hello everybody, Has anyone any experience with make_average_subject on monkeys brain? E.g. as it uses talairach transform, would it be biased by it, or is there any option to avoid using the talairach transform? In my experience, the resulting average surface was quite strange! And more generally, did anyone validated the traditional spherical registration on monkeys brains, does it yield an acceptable point-to- point registration? Many thanks in advance for these useful informations, Marie Schaer

2 1

Save point (tksurfer)..go to saved point (tkmedit)
by Nandita Shetty 29 Mar '07

29 Mar '07

Hi, I have a question regarding the 'save point' and 'go to saved point' feature. I made couple of edits to the white matter (unfortunately for some strange reason, I did not fix all the defects in the inflated brain) and executed the command recon-all -autorecon2-wm -subjid pilot2 The recon was completed with no errors But, now when I try to save a point on the inflated brain and open the same in tkmedit, I get an error message saying surfer: reading canonical coordinates from surfer: /space/marvin/1/users/MRI/ACE/pilot2/surf/lh.sphere.reg mrisReadTriangleFile(/space/marvin/1/users/MRI/ACE/pilot2/surf/lh.sphere.reg): surface doesn't match /space/marvin/1/users/MRI/ACE/pilot2/surf/lh.inflated mrisReadTriangleFile failed. Is there a workaround for this? Thanks in advance for any suggestions Regards, Nandita

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