Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Confusing error from 'noaseg' option.
by Zhen Zonglei 08 Mar '09

08 Mar '09

Dear all: While reconstructing monkey brain with FreeSurfer, in the stage of autorecon2, I used 'noaseg' option to avoid the segmentation. The command is as follows: recon-all -s monkey_040409632 -autorecon2 -noaseg -cc-crs 128 117 123 -pons-crs 128 154 108 However, FreeSurfer finally reported me a confusing 'ERROR: cannot find aseg.mgz' and exited. In my mind, FS should know that aseg.mgz does not exist. What's this error mean? Thanks. The details of the error are as follows: #@# Cortical ribbon mask Sun Mar 8 14:22:24 CST 2009 /nfs/h1/r3/Subjects/monkey_040409632/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance monkey_040409632 SUBJECTS_DIR is /nfs/h1/r3/Subjects Exception caught while processing input files 7IoError loading input data... ERROR: cannot find /nfs/h1/r3/Subjects/monkey_040409632/mri/aseg.mgz Linux annex.cnl 2.6.9-42.ELsmp #1 SMP Tue Aug 15 10:35:26 BST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Sun Mar 8 14:22:36 CST 2009 -- Zonglei Zhen, PhD Assistant Professor of Cognitive Neuroscience BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, P.R. China

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zooming
by Sam Torrisi 08 Mar '09

08 Mar '09

hi FS peeps this seems like such a dumb question but in tkmedit can you zoom in floats? ie not just integers? thanks -Sam

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drawing ROIs in surface space
by Jeff Phillips 07 Mar '09

07 Mar '09

Hello all, I am trying to hand draw ROIs from a functional overlay. The wiki mentions a Cut Area tool in tksurfer, which sounds ideal for getting rid of the area outside my ROI, but it's nowhere to be found in the tksurfer GUI for our installation, Centos 4 x86 64 bit. Has this tool been renamed or subsumed under some other tool? If there is an easier way for me to draw ROIs? Thanks, Jeff Phillips University of Pittsburgh

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New Neuroscience Forum
by Anatoly 07 Mar '09

07 Mar '09

Hello World, Announcing a new Neuroscience Forum http://www.neuroscienceforums.com Forum Topics: . Neuroscience News . Neuroscience Podcasts . Molecular and Cellular Neuroscience . Behavioral Neuroscience . Systems Neuroscience . Developmental neuroscience . Cognitive Neuroscience . Theoretical and Computational Neuroscience . Diseases and Aging . Neural Engineering . Neurolinguistics . Neuroscience Schools & Programs . Neuroscience Jobs . Neuroscience Books . Clinical Trials in Neuroscience Please check it out at: http://www.neuroscienceforums.com Thanks for your attention and hope to see you on the forum !

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Editing results from recon-all -long.
by gmszh 06 Mar '09

06 Mar '09

Hi all, We used the longitudinal processing for our phase 2 data. For some subjects, I found very bad segmentation and surface reconstructions. Suspecting it's a registration problem, I loaded brainmask.mgz from tp1 and tp2 in tkmedit. I could see they are not aligned to each other (attached image). My questions are: 1. Is the problem due to registration? If yes, how can I fix it? 2. If we are to edit the segmentation results from "-long" processing, do we follow the same steps as what we did for tp1? Thanks, Zheng Hui

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mris_anatomical_stats with an average subject
by Rafa x 06 Mar '09

06 Mar '09

Dear FS team I would like to execute the command mris_anatomical_stats with one average subject, the problem is that the file wm.mgz is required. Is there some way to obtain the stats of one average subject?(I need the area of all the parcellations) Thank you in advance Rafa.

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tkmedit
by Siddharth Srivastava 06 Mar '09

06 Mar '09

Hi everyone, Is it possible to selectively display a few segmentation labels over an anatomical, using tkmedit? say i would just like to see label 4 (browsing by label numbers, and not names)? I am sure there is a documentation on how to do this somewhere... thanks, sid.

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LGI
by Gabriel Go.Es. 06 Mar '09

06 Mar '09

Hello i'm trying to make a local Gyrification Index (lGI), i have image Processing Toolbox instaled... and i always recibe the next error message: [root@localhost ~]$ recon-all -s s001 -localGI Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjects Actual FREESURFER_HOME /root/trabajo/freesurfer -rwxr-xr-x 1 root root 2622729 Mar 5 13:57 /root/trabajo/freesurfer/subjects/s001/scripts/recon-all.log Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux /root/trabajo/freesurfer/subjects/s001/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Mar 6 12:43:33 CET 2009 mris_compute_lgi --i lh.pial ERROR: Matlab is required to run mris_compute_lgi! Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 6 12:43:33 CET 2009 what can i do? regards Gabriel _________________________________________________________________ Chatea sin límites en Messenger con la tarifa plana de Orange http://serviciosmoviles.es.msn.com/messenger/orange.aspx

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FMRI group analysis in common surface space
by Georg Homola 06 Mar '09

06 Mar '09

Hi all, We want to perform a FMRI group analysis in common surface space. For that purpose, can we (1) run feat2surf on both cope and varcopes on first-level feat analysis (2) run higher-level feat on the output (using the transformed copes/varcopes as the inputs)? Thanks, Georg

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Voxel size smaller than 1x1x1mm?
by Falk Lüsebrink 06 Mar '09

06 Mar '09

Hi Freesurfers, I'm currently doing my bachelors thesis in medical engineering and I'm trying to measure the cortical thickness of scans acquired by a 7T MRT. A colleague of mine has used Freesurfer (v4.0.5) before and mentioned that high resolution scans with a voxel size smaller than 1x1x1mm (like .7x.7x.7mm) are converted to 1x1x1mm during a processing stage of autorecon - I think during the mri_convert process. Is it possible to keep the native size or does Freesurfer need to change the voxel size to 1mm in order to do the segmentation correctly? Regards, Falk

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