Freesurfer April 2006

freesurfer@nmr.mgh.harvard.edu

50 participants
83 discussions

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

06 Apr '06

Forgot to include the message: Skull Stripping Thu Apr 6 10:09:25 PDT 2006 /subject12/mri mri_mask -xform /subject1/mri/transforms/Subject1_to_Subject12.lta T1 /subject1/mri/brain brain transform file name is /subject1/mri/transforms/Subject1_to_Subject12.lta corRead(): can't open file /subject1/mri/brain/COR-.info mri_mask: could not read mask volume T1 --------------------------------------------- Segmentation Thu Apr 6 10:09:28 PDT 2006 ERROR: cannot find brain/COR-.info recon-all exited with errors at Thu Apr 6 10:09:28 PDT 2006 -----Original Message----- From: Nguyen, Thang Q Sent: Thursday, April 06, 2006 10:27 AM To: 'freesurfer(a)nmr.mgh.harvard.edu' Subject: recon-all problem: skull stripping asks for COR-.info files that do not exist 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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recon-all -subjid < > -autorecon2
by anthony gallo 06 Apr '06

06 Apr '06

I have tried to run this command 2 times and it does not seem to finish the command. The log file just says: Em registration (date/time) CA Normalization (date/time) CA Reg (date/time) The log file ends each time with Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4319 voxels, overlap= 0.599) aligning Right_Thalamus_Proper... source mean =83.5658, std = 26.5322 X:99-132; Y:128-155; Z:103-141 gca peak = 0.06253 (102\n\n then that is it. No formal error presents but there is nonprogression. Any ideas? Thanks (again...and again)

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Freesurfer April 2006