Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

fsfast "selxavg-sess" error
by Paymon Hosseini 10 Apr '06

10 Apr '06

hi i am going over the fsfast tutorial. i have completed all steps up to "FsFastTutorial/905 Average session-level data by condition" https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20… when i run "selxavg-sess -sf sessid -df sesspar -analysis sem_assoc", i get the following error: " ??? Undefined function or variable 'MRIread'. Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m On line 160 ==> rstd = MRIread(instem,1); >> ??? Undefined function or variable 'r'. >> quiting matlab ------------------------------------------ ERROR: fast_selxavg() failed\n ERROR (/autofs/space/engram_012/users/pman/bert-functional): selxavg failed " can you please tell me why i am getting this error? thanks paymon hosseini

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RE: [Freesurfer] (no subject)
by Durastanti, Valentina (NIH/NINDS) [F] 10 Apr '06

10 Apr '06

Dear Nick, I tried to run recon-all -s <subjname> -skullstrip but always came out an error: read error I tried to run recon-all -subjid <subjname> -autorecon1 on the same subjects and it looks good have you any suggestion? Thanks Valentina -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Saturday, April 08, 2006 7:23 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: Bruce Fischl; Julia Hamstra; Freesurfer Mailing List Subject: Re: [Freesurfer] (no subject) Use: recon-all -s <subj> -skullstrip Also, recon-all -help will list-out most of the steps which can be run individually (see section titled STEP-WISE DIRECTIVES). On Sat, 2006-04-08 at 19:47 -0400, Durastanti, Valentina (NIH/NINDS) [F] wrote: > > Hi, > I'm using Freesurfer and I'd like to run the autorecon1 just for the > skull stripping (without intensity and spatial normalization). Is there > a command just to do that? > > Thanks > valentina > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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(no subject)
by Durastanti, Valentina (NIH/NINDS) [F] 09 Apr '06

09 Apr '06

Hi, I'm using Freesurfer and I'd like to run the autorecon1 just for the skull stripping (without intensity and spatial normalization). Is there a command just to do that? Thanks valentina

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mri_convert in 4D
by Julia Hamstra 08 Apr '06

08 Apr '06

Hi, I am getting two errors when creating NIFTI files from dicoms using mri_convert. The first is that the 4D images are being spatially contactonated. It does not seem to be treating it as a timeseries. This is the command: mri_convert -it dicom -ot nii s6761334/i6761335.MRDC.1 run.nii.gz Additionally it is an oblique acquizition so the coronal view is not displaying the plane of acquizition (as intended), but an orthogonal cut through multiple slices. Am I missing an option or additional information? I searched the options and couldn't figure out anything that helped. The problem applies to the co-planar oblique structural scan too. I'm guessing there is something simple that I am overlooking. What may that be? thanks ~julia

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Q: tkregister2 coronal/sagittal/horizontal discrepancy
by raij＠nmr.mgh.harvard.edu 07 Apr '06

07 Apr '06

Dear Fellow Surfers, After doing a reconstruction with the 3.0 Freesurfer stable version, I checked the Talairach auto-registration with tkregister2. The registration seemed fair enough. However I noticed a strange thing that has not caught my attention before - maybe this a property of the program and/or was there already earlier, maybe it is new, maybe it is a bug, or perhaps my volume is corrupt. The problem/property is observed within the original (target) volume. After launching tkregister2, if I click inside the target volume, the red cursor moves to that location and other orientations (coronal/sagittal/horizontal) slices also change accordingly (the sliders move). If I have understood correctly, the idea would be that the cursor shows the crossing in all 3 orientations. However if I look at the brain structure in the three different orientations where my cursor is, it is clearly different in all three images. For example, if I pick a mid-sagittal view and place the red cursor in the thalamus between AC and PC, and then click the "sagittal" button, the cursor is clearly higher (towards top of the head) in the interhemispheric fissure. If I click the "coronal" button, the cursor is in the frontal lobe between the hemispheres (ie much more anterior than the other views). Is this the way the program is supposed to work, or is this a bug, or is my volume plain corrupted? *** Here are the specifics: *** on machine ai source /usr/local/freesurfer/nmr-std-env setenv SUBJECTS_DIR /space/cognito/5/users/raij/subjects_mri setenv SUBJECT avml07 cd /space/cognito/5/users/raij/subjects_mri tkregister2 --mgz --s avml07 --fstal ... and there you go, click away... Thanks for your advice in advance, Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. raij(a)nmr.mgh.harvard.edu

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Buckner Data
by rhaynes＠neuro.gatech.edu 07 Apr '06

07 Apr '06

Will the Buckner data set be reprocessed with version 3.0? If it already has been, where can we get it? I can't find it in the v3.0 release. Thanks. Ryan Haynes Children's Healthcare of Atlanta

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tcl command to raise tksurfer window
by Darren Weber 07 Apr '06

07 Apr '06

Hi Kevin, how do we raise the tksurfer window into the foreground in a tcl script (in case it is obscured by other windows)? Best, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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tcl help with labl_set_color
by Darren Weber 06 Apr '06

06 Apr '06

Hi, I'm a novice with tcl, so I'm having trouble with using a variable to labl_set_color index r g b eg, set color "255 255 255" labl_set_color 0 $color gives error: Wrong # args: labl_set_color index r g b How is this done? Thanks, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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tcl command to change tksurfer background
by Darren Weber 06 Apr '06

06 Apr '06

Hi Kevin, is there a tcl command to set the tksurfer background to white? Thanks, Darren -- Darren L. Weber, Ph.D. Postdoctoral Scholar Dynamic Neuroimaging Laboratory, UCSF Department of Radiology, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA 94107, USA. Tel: +1 415 353-9444 Fax: +1 415 353-9421 www: http://dnl.ucsf.edu/users/dweber "To explicate the uses of the brain seems as difficult a task as to paint the soul, of which it is commonly said, that it understands all things but itself." Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

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recon-all problem: skull stripping asks for COR-.info files that do not exist
by Nguyen, Thang Q 06 Apr '06

06 Apr '06

Hello all, I'm not sure if this is a problem with the incorporation of the mgz format or not but when I run recon-all, the skull stripping step requests for COR-.info files. The only format that I have in the mri folder is the mgz format. Is there an override option that tells recon-all that I am using mgz format that I don't see? Thank you for your help, Thang Nguyen

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Freesurfer