Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

choroid plexus
by Juranek, Jenifer 07 Aug '08

07 Aug '08

Hi, Would like to sum all CSF compartments to get a global CSF volume for each subject. Should Choroid plexus (L & R) be included in the summation? I have not seen other "non-freesurfer" apps tease out the choroid plexus. So far, I have the following 8 compartments: [Left-Lateral-Ventricle] + [Left-Inf-Lat-Vent] + [3rd-Ventricle] + [4th-Ventricle] + [Right-Lateral-Ventricle] + [Right-Inf-Lat-Vent] + [5th-Ventricle] + [CSF] Many Thanks for any advice you can provide, Jenifer ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~

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Statistics of subcortical structures
by Cibu 06 Aug '08

06 Aug '08

Hello all After running recon - all FS creates a stats folder with a bunch of data on gray volume, avg thickness etc of the various cortical structures. I was wondering if there is a similar file for subcortical structures like amygdalea etc.? And if not, is there any other way to automatically calculate the volume other than manual segmentation? Thank you Cibu Thomas Post Doctoral Research Fellow Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Harvard Medical School, Massachusetts General Hospital, 149, 13th Street, Charlestown, MA 02129 Tel: 617-726-9034

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Checking for spikes
by Brittany Cassidy 06 Aug '08

06 Aug '08

Hello all, I was looking for a general way to check for spiking from Freesurfer or the FSFast stream. Any ideas are appreciated. Thanks! -Brittany

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DTI data and FS-FAST
by muet0005＠umn.edu 06 Aug '08

06 Aug '08

Hello, I've noticed that some of the wiki tutorials/powerpoint slides hint at the potential for incorporating DTI data into an FS-FAST-like analysis. Is any documentation available on the wiki that describes how to do this? I noticed that many of the files in $FREESURFER_HOME/fsfast/bin are in csh and are readable, however I haven't been able to figure out the exact procedure for incorporating, say, an FA map instead of a BOLD map. I have registered my DTI images to the T1 using a 6DOF flirt. I believe the next step is to apply the talairach xfm, and then convert from volume to surface, but I am not exactly sure. Any advice is much appreciated! Best, Ryan

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Freesurfer Help
by Luke Tseng 05 Aug '08

05 Aug '08

To whom it may concern. We've been working with Freesurfer, under Prof. Ming Hsu at the University of Illinois at Urbana Champaign. We ran the group analysis tutorial using the provided buckner_data, but when we displayed our results visually, there were numerous discrepancies with the images provided in the visualization tutorial. Our instructor told us to rerun the precprocessing steps (recon-all) on all of the subjects in the group_analysis_tutorial data. However, these subjects lack .mgz or image files, so we can't rerun the preprocessing stream. We sent the following email to our instructor and were told to email the freesurfer mailing list. What can we do or where can we find help? Thank you for your time! Mukta Vaidya Luke Tseng Sent email: Prof. Hsu, We tried using the -no-isrunning flag, and recieved basically the same error. Then we went into the one of the subjects folders and tried to find the initial mgz or image files needed to start the entire process and could not find any (we checked in all of the subfolders). We think the problem is that no image files are present in any of the subject folders in the group analysis tutorial, which would mean that we can't "reprocess" the data using recon-all. Only the resulting files produced after preprocessing were present in the subject folder we looked at (004). Just to check if this was the case, we tried running recon-all using the same flag on another subject in the Buckner data, bert. This also exited with an error, but not with the same error. What do we do now? Mukta & Luke

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editing masks
by Daniel H Choi 05 Aug '08

05 Aug '08

Hi, I have a binary mask that I apply to my .mgz files. It allows me to block everything outside of the STG as 0 and everything inside the way it is. I was wondering though how I might go about editing the mask? I see that there are random voxels that have been left out and I would like to fill those in. Thanks Dan -- Daniel Horim Choi Northwestern University Class of 2009 dhchoi(a)u.northwestern.edu or dchoi1024(a)gmail.com

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mri_watershed regions appearing round edge, freesurfer 4.0.2
by Ian Malone 05 Aug '08

05 Aug '08

Hi, Has anyone encountered this before? I have a few volumes for which mri_watershed output volumes are fine apart from some non-zero voxels near the edges (which are not connected to the brain). The volumes are in transverse format and the most noticeable effect is some inferior slices (neck, lower jaw) which are not being masked out, though there are also some voxels close to the coronal edges. For both sets of edges there is a one or two voxel thick layer parallel to either the coronal or transverse plane. This is with Freesurfer 4.0.2, T1 images in Analyze format. Thanks for your time, Ian Malone

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segmentation errors
by Nicola Hobbs 05 Aug '08

05 Aug '08

Hello all, We've noticed some errors in the wm and pial segmentations (see t1.png) even though the wm.mgz seems to be correct (see wm.png). Could you advise us on the best way to correct these errors? Many thanks, Nicola -- Nicola Hobbs Dementia Research Centre National Hospital for Neurology and Neurosurgery Queen Square London WC1N 3BG +44 (0)845 155 5000 x723839

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NITRC website
by Nick Schmansky 05 Aug '08

05 Aug '08

Of potential interest to people on this list is the NITRC website: http://www.nitrc.org/ "The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) is funded by the National Institutes of Health Blueprint for Neuroscience Research. NITRC facilitates finding and comparing neuroimaging resources for fMRI and related structural analyses. NITRC collects and points to standardized information about tools, making the task of finding and comparing them easier than before. The site can help you find the right fMRI tool or resource and help you decide whether it can help in your research." FreeSurfer is listed in the site: http://www.nitrc.org/projects/freesurfer/

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Floating exception (core dumped)
by Juranek, Jenifer 05 Aug '08

05 Aug '08

Hi, Running fsv405 on RHEL4 (64bit) and have encountered the following error after executing recon-all -all: Floating exception (core dumped). Did not encounter this error using fsv401 on the same box. See below for the standard output to screen. Any ideas? Many Thanks, Jenifer [jjuranek@localhost subjects]$ recon-all -all -s PC_011_APO143_2mo INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rwxrwx--- 1 jjuranek root 2271789 Jul 25 07:15 /usr/local/freesurfer/subjects/ PC_011_APO143_2mo/scripts/recon-all.log Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86 _64 x86_64 x86_64 GNU/Linux Floating exception (core dumped) #-------------------------------------------- #@# MotionCor Tue Aug 5 11:38:42 CDT 2008 Found 1 runs /usr/local/freesurfer/subjects/PC_011_APO143_2mo/mri/orig/001.mgz WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /usr/local/freesurfer/subjects/PC_011_APO143_2mo/mri/orig/001.mgz /usr/local /freesurfer/subjects/PC_011_APO143_2mo/mri/rawavg.mgz /usr/local/freesurfer/subjects/PC_011_APO143_2mo mri_convert /usr/local/freesurfer/subjects/PC_011_APO143_2mo/mri/rawavg.mgz /us r/local/freesurfer/subjects/PC_011_APO143_2mo/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/PC_011_APO143_2mo/mri/rawavg.mgz /usr /local/freesurfer/subjects/PC_011_APO143_2mo/mri/orig.mgz --conform

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