Freesurfer February 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
126 discussions

Missing some parcellations
by Jürgen Hänggi 07 Feb '09

07 Feb '09

Dear FS experts There are 94 surface labels listed in the surface_labels.txt file in the FS home directory. However, when using aparcstats2table with the --parc option aparc.a2005s there are only 78 parcellated areas per subject reported in the list. Why? Thanks Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division 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[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Fwd: transforms/talairach.xfm ***FAILED***
by roberto toro 07 Feb '09

07 Feb '09

Dear Freesurfers, I haven't been able to run recon-all in a set of subjects. All them stop at the point of the talairach transform verification. I uploaded one of the files here (5.3MB): http://dl.getdropbox.com/u/74925/20070404.nii.zip For that volume, the transform.xfm file looked indeed odd (m22=7.2??): 1.39488649 0.08332049 0.01164643 3.51684260 -0.14383204 7.20834160 -2.21084833 11.16247082 -0.16614650 1.02134335 1.85208952 -45.74753189 Using flirt (flirt -in 20070404.nii -ref MNI152_T1_1mm -out 20070404trans.nii -omat 20070404trans.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear), the transformation was: 1.05366 -0.050378 0.0606504 4.05766 0.0446432 1.09476 0.1321 -28.652 -0.058117 -0.180136 1.09158 31.7066 0 0 0 1 The voxel size of the volume is 1.17x1.17x1.2, so it shouldn't be a problem of resolution. When I converted the volume to mgz (mri_convert 20070404.nii mri/orig/001.mgz), the orientation was wrong; but changing it using the Volume Tools in tkmedit did not alter the outcome... Finally, I also used the --notal-check switch in recon-all, but then the script failed before completing skull stripping... thank you very much in advance for your help! roberto

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ventricles in wm.mgz volume
by Derin Cobia 07 Feb '09

07 Feb '09

We're experiencing some difficulties with editing several of our control subjects' wm.mgz volumes. For many of them the ventricle space was not filled during the recon-all process (some subjs have enlarged ventricles, while others do not). Re-running with the - bigventricles flag did not correct the problem, and we subsequently filled the space manually by added new voxels (255 value) in the wm.mgz volume. After running them again under -autorecon2-wm, we discovered that the wm.mgz volumes now appear without any of our edits (as if they had been run with a -clean-wm flag). We edited and reran again, but with the exact same result for a second time, but only for a subset of the original (edits worked on some, didn't on others). Any thoughts as to why this is occurring? We are pretty confident that the volumes are saved each time edits are made, and we are not running with any -clean flags. If all else fails, is it permissible to using the subjects as is (see attached pics) if the surfaces being affected are only the 'unknown' regions? FS 4.1.0 is the version that is being used, thanks. -Derin

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SPM Register Issues
by Dave Brohawn 06 Feb '09

06 Feb '09

Hello, I am having issues with SPM Register-Sess and I am not sure why. The command I am entering and the response I receive are spmregister-sess -s FB11059A -------------------------------------------------------------- spmregister-sess logfile is /autofs/space/seymour_001/users/folate_subjects/log/spmregister-sess.11485.log -------------------------------------------------------------- Session: /autofs/space/seymour_001/users/folate_subjects/FB11059A ---------------- Fri Feb 6 11:43:07 EST 2009 Detected format at nii Log file is /autofs/space/seymour_001/users/folate_subjects/FB11059A/bold/011/spmregister.log Fri Feb 6 11:43:07 EST 2009 --s FB110059A --mov /autofs/space/seymour_001/users/folate_subjects/FB11059A/bold/011/f.nii --reg bold/register.dat --fsvol brainmask $Id: spmregister,v 1.21.2.3 2008/07/07 13:53:49 greve Exp $ matlab matlab ERROR: /space/seymour/1/users/folate_subjects/FB110059A/mri/brainmask.mgz not found in either COR or MGZ formats ERROR: spmregister failed The pre-proc command worked, and brainmask construction was completed successfully. In fact, I can go into this subjects mri folder, and see the brainmask.mgz file. Here is the bugr information: FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.2.0-20090203 RedHat release: CentOS release 4.6 (Final) Kernel info: Linux 2.6.9-67.ELsmp i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /space/seymour/1/users/folate_subjects PWD: /space/seymour/1/users/folate_subjects Thank you, Dave Brohawn

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labels for atlas
by amyr＠nmr.mgh.harvard.edu 06 Feb '09

06 Feb '09

Hi All, I have created labels (and annotation files) for just the ventro-medial pre-frontal cortex. I would like to create an atlas based on my manual labels. Do I need to create another label "other", that includes the rest of the surface, before I can create the atlas? Thanks for your help. Amy Raudenbush

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bug: tkmedit - image view
by Flavio Seixas 06 Feb '09

06 Feb '09

Hi all, I'm Flavio, doctorate student at Fluminense University from Brazil. I would like to report a bug with tkmedit. I'm using Ubuntu distribution, kernel release 2.6.27.11 (32-bits). I have installed FreeSurfer version freesurfer-Linux-centos4-stable-pub-v4.2.0. My video card is a ATI Radeon 9600Pro. I'm using ATI/AMD FGLRX device driver on Linux. When I start tkmedit (eg. tkmedit bert orig.mgz), the coronal session image is displayed. But, when I move the mouse (eg. to select the sagittal view on tkmedit menu), the image disappear. The display window may be minimized and I can't view the image anymore. When I try maximizing image window, the image is displayed until I move the mouse. Then, it is disappeared again. Does anyone have a doubt? I would appreciate any help. Thank you, Flavio.

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aparcstats2table new version (-parc)
by Diana Wotruba 06 Feb '09

06 Feb '09

Hi Krish Thanks again for your quick help! I tried out the new version, it seams to work fine. Nevertheless, I created a new parcellation with mris_anatomical_stats getting a .stat file I called aparc.a2005s_300. Only now I get the following error message (Which was not the case in the former version): aparcstats2table: error: option --parc: invalid choice: 'aparc.a2005s_300' (choose from 'aparc', 'aparc.a2005s') How can I force the -parc option to read my own parcellations? Diana

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white matter defect
by karlkarl 06 Feb '09

06 Feb '09

Hello, experts One quick question of editing the white matter. I attached one figure after autorecon2. In the middle of right hemisphere, there is a one small enclosed area. I would like to fill that area using the brainmask as a guide, but there is nothing between the brainmask mgz and wm.mgz in that area; so I can’t paint in anything. Is this a minor defect to neglect or any other way to fix it. Thanks a lot Karl _________________________________________________________________ 一点即聊，MSN推出新功能“点我！” http://im.live.cn/click/

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aparcstats2table bug
by Diana Wotruba 05 Feb '09

05 Feb '09

Dear experts If some of the subjects in a group have missing values of a certain label, aparcstats2table fails to designate a 0 for them. According to the freesurfers website, this bug will be fixed in the next release. Is it already known when this can be expected? Thanks in advance Diana

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Rutvik Desai sent you a Friend Request on Yaari
by Rutvik Desai 05 Feb '09

05 Feb '09

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Freesurfer February 2009