Freesurfer

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21 participants
30071 discussions

Temporal derivative in mkanalysis-sess
by Dan Dillon 16 May '07

16 May '07

Dear FreeSurfers, I'd like to add a temporal derivative to my gammafit model and understand that this can be done using mkanalysis-sess. However, I can't seem to track down the relevant flag (using -help or the wiki). Can someone point me in the right direction? Thanks! Dan Dillon

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Grey matter issue.
by Kt Labadie 16 May '07

16 May '07

Hello. I have attached an image of a case I am working that I can't figure out how to fix. I have approximately 15 cases like this, so any suggestions would be helpful. You can see that some grey matter is not being included along the left and right sides. It is like this for about 30 slides. I did a few things to try and fix it, but nothing worked. I adjusted the watershed number to 30 and it just included the entire skull and did not expand the surface out. I also used the -atlas and -more commands to try and adjust the surface, but it did not shift. I also checked the Talairach registration, but it was fine. Any suggestions? Thanks KT LaBadie Research Associate The Mind Institute

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Re: [Freesurfer] Editing Segmentation Results in TkMedit
by Jared Conley 16 May '07

16 May '07

Bruce Fischl wrote: > could be. Is it set to the right place? > > > On Wed, 16 May 2007, Jared Conley wrote: > >> Bruce Fischl wrote: >>> what is the error? >>> On Wed, 16 May 2007, Jared Conley wrote: >>> >>>> I am new to FreeSurfer and am attempting to segment T1 images using >>>> the "recon-all...autorecon2" command. The segmentation results >>>> look quite accurate, but I was wondering how to best edit the >>>> results (where there is a need). I noticed on the Wiki a possible >>>> option using the TkMedit program. I have tried running the command >>>> "tkmedit subjid wm.mgz -aux T1.mgz" as directed, but it gives me an >>>> error. Could someone direct me to the correct tutorial or answer >>>> my question directly. Thanks. >>>> >>>> Jared >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >> X11 terminal says "Error: Loading volume ... couldn't read the >> anatomical volume." I am worried that perhaps it's due to my >> SUBJECTS_DIR environment variable not being properly set, as >> indicated in the Wiki. Let me know what you think. >> >> >> It is working now. Thanks for the assistance.

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Editing Segmentation Results in TkMedit
by Jared Conley 16 May '07

16 May '07

I am new to FreeSurfer and am attempting to segment T1 images using the "recon-all...autorecon2" command. The segmentation results look quite accurate, but I was wondering how to best edit the results (where there is a need). I noticed on the Wiki a possible option using the TkMedit program. I have tried running the command "tkmedit subjid wm.mgz -aux T1.mgz" as directed, but it gives me an error. Could someone direct me to the correct tutorial or answer my question directly. Thanks. Jared

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(no subject)
by Bagnato, Francesca (NIH/NINDS) [E] 16 May '07

16 May '07

Can I open images parcellated with an old version of freesurfer (the one parcellating 80 regions) with the new one (based upon the Desikan atals)? Thanks, Francesca Francesca Bagnato, MD-PhD Staff Scientist, NIB-NINDS-NIH Building 10, Room 5S205 9000 Rockville Pike Bethesda, MD, 20892-1400 MSC Phone #: (301) 594-1415 Fax #: (301) 402-0373

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(no subject)
by hankee 16 May '07

16 May '07

hi, I don't know the procedure of the FreeSurfer? Although the recon-all illustration contains lots of the steps, I don't know the meaning. So I want to know the brief step about the FreeSurfer how to deal with 3D data? Thank you very much hankee，duhanjian(a)sohu.com 2007-05-05

1 0

parcellation issues
by Bagnato, Francesca (NIH/NINDS) [E] 15 May '07

15 May '07

Dear Users: I would like to ask how to treat the data of a subject for whom segmentation worked alright but the parcellation looks like the one I am herein attaching. Thanks, Francesca Francesca Bagnato, MD-PhD Staff Scientist, NIB-NINDS-NIH Building 10, Room 5S205 9000 Rockville Pike Bethesda, MD, 20892-1400 MSC Phone #: (301) 594-1415 Fax #: (301) 402-0373

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intergroupavg-sess did not create a sig.bhdr file
by Avram Holmes 15 May '07

15 May '07

To anyone not outside enjoying the nice weather, I have recently completed running intergroupavg-sess intergroupavg-sess -analysis taumax30_stc_smooth6 -contrast Rcue_v_Ncue -group1 LowTrauma -group2 HighTrauma -intergroup LowTrauma_v_HighTrauma -space tal Only 'minsig' and 'sig' files were generated. However, no sig.bhdr files were created. I just wanted to check to see if everything is as it should be. Also, when I run tkmedit-sess in an attempt to view the data on both the between and within group (where all the normal files were created) analyses... tkmedit-sess -analysis taumax30_stc_smooth6 -s LowTrauma_v_HighTrauma -isxavg random -contrast Rcue_v_Ncue -space tal -d . I recieve the following error... -------------------------------------------------------------- tkmedit-sess logfile is /Raid/shared/exp/REfMRI/fMRI_FPPREW/functional/log/tkmedit-sess.log -------------------------------------------------------------- setenv SUBJECTS_DIR /exp/REfMRI/fMRI_FPPREW/structural/ INFO: Found session in: ./LowTrauma_v_HighTrauma INFO: LowTrauma_v_HighTrauma is a group average INFO: Found session in: ./LowTrauma_v_HighTrauma INFO: LowTrauma_v_HighTrauma is a group average INFO: subject is talairach INFO: subject is talairach ERROR: subject talairach does not exist in data base SUBJECTS_DIR: /exp/REfMRI/fMRI_FPPREW/structural/ Do I have to take any steps to add the talairach brain to my studies 'structural' folder so that I can use tkmedit-sess or is this error related to something else. Thanks in advance for any help you can offer, 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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Topological defects
by Juergen Haenggi 15 May '07

15 May '07

Dear Freesurfer users Is there any rule of thumb with respect to the size of topological defects? Sometimes large defects (involving more than 10000 or 20000 vertices) occur and the topological correction for these defects runs more than 48 hours and sometimes failed to correct them. How long should I wait? Up to which number of vertices involved in a defect I should accept it or manually edit it? Thanks a lot for help Best regards Juergen --------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) ---------------------------------------------------------------------------

2 1

binary masks: 1 output file per aseg label
by Juranek, Jenifer 14 May '07

14 May '07

I'm interested in parsing aseg.mgz into separate binary mask files for each aseg label. Is this possible? The closest topic I found was located at the following URL: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MapSegmentationsToFu nctionalSpace 2.0 Creating binary masks The segmentation for a particular structure can be extracted to create a binary mask (i.e., a volume where the voxel value is 1 if it is in the structure and 0 otherwise). To make a binary mask of the left putamen, which has been assigned label 12 (see ${FREESURFER_HOME}/FreeSurferColorLUT.txt), use the following command: avwmaths ./fbert.feat/reg/freesurfer/aparc+aseg.nii.gz \ -thr 12 -uthr 12 \ ./fbert.feat/reg/freesurfer/lh.putamen.nii.gz I checked the following for additional help...but still need some help... http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommands Many Thanks, Jenifer

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