Freesurfer July 2007

freesurfer@nmr.mgh.harvard.edu

61 participants
99 discussions

mri_segstats question
by Morgan Hough 27 Jul '07

27 Jul '07

Hi , I would like to use mri_segstats with an aprac parcellation to get the mean/stddev of the norm.mgz intensities by parcel. I have tried the following usage: mri_segstats --annot con_2304 lh aparc --ctab-default --nonempty --excludeid 0 --sum con_2304.norm.aseg.sum --in $SUBJECTS_DIR/con_2304/mri/norm.mgz but I get the same output in the sum file with either the norm or orig.mgz file. Also there are certain parcellation units (PU) that have zero mean and zero standard deviation with either input. Is this usage correct for the job? Thanks in advance. Cheers, -Morgan

1 0

Orientation
by Dick, Rachel 27 Jul '07

27 Jul '07

Hello all, I have been using Freesurfer for quite some time. However, I have run into a problem. I am using a properly oriented input image (just like all others I have used before), but when I go to look at the brainmask.mgz after autorecon1, the image is flipped on the y axis. I have used mri_convert -out_orientation to change it and also the FSL tool avwswapdim to change the orientation but it doesn't make any difference. Once I open it in Freesurfer, it is always flipped along the y. Please help!! Thanks in advance. Rachel Marie Dick Research Assistant/Coordinator Brain Research and Imaging Neurosciences Dept. of Psychiatry & Behavioral Neuroscience WSU Medical School brain.wayne.edu <mailto:rcondon@med.wayne.edu> (313)577-6279 CONFIDENTIALITY NOTICE This message is confidential, intended only for the named recipient(s) and may contain information that is privileged, or exempt from disclosure under applicable law. If you are not the intended recipient(s), you are notified that the dissemination, distribution or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the e-mail address. Delete this e-mail from your computer, and destroy any copies in any form immediately. Thank you.

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recon-all error
by Andrew Ellison 27 Jul '07

27 Jul '07

Hi all, Library issues are all set, I now am having a problem getting freesurfer to recognize .img and .hdr files, [root@ebrcb-dhcp-240-47 freesurfer]# /usr/local/freesurfer/bin/recon-all -autorecon1 -subjid je001_018_4_1-001 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/je001_018_4_1-001/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 root root 16873 Jul 27 10:16 /usr/local/freesurfer/subjects/je001_018_4_1-001/freesurfer/je001_018_4_1-001/scripts/recon- all.log Linux ebrcb-dhcp-240-47.bumc.bu.edu 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux #-------------------------------------------- #@# MotionCor Fri Jul 27 10:17:12 EDT 2007 ERROR: no run data found in /usr/local/freesurfer/subjects/je001_018_4_1-001/freesurfer/je001_018_4_1-001/mri. Make sure to have a volume called 001.mgz in /usr/local/freesurfer/subjects/je001_018_4_1-001/freesurfer/je001_018_4_1-001/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux ebrcb-dhcp-240-47.bumc.bu.edu 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Fri Jul 27 10:17:12 EDT 2007 files are located where freesurfer is looking but isnt finding them, any help would be great, thanks! Andy

3 2

install in Debian/Ubuntu
by 申林 27 Jul '07

27 Jul '07

hi, I have download "freesurfer-Linux-rh9-stable-pub-v3.0.5-full.tar.gz" for Ubuntu and followed the "FreeSurfer Setup and Configuration" and "Testing your FreeSurfer installation". The first two steps( export and source ) were ok , however, tkmedit always did not work and retured "command is not found" as well as tksurfer . Is there difference between ubuntu and other linux version in installing freesurfer ? how to finish the installation in ubuntu or whether I should choose redhat ? thank you in advance ! Lin Shen 2007.7.27 -- Lin Shen, MMS, Department of Neurology, The First Affiliated Hospital, ChongQing Medical University No.1, Yixueyuan Road, ChongQing, 400016 China Phone: +86 23 13193076520 E-mail: shenlin918(a)gmail.com

2 1

mri_label2surf
by Alessandro Gagliardi 27 Jul '07

27 Jul '07

I've been doing all of my analysis with surface images and now I need to label my results. I can annotate the visualization in tksurfer but I can't see an automated way to, say, generate a list of all areas with voxels with a value over some threshold. I thought I might try going to the label files and using mri_label2vol followed by mri_vol2surf. I'm registering all my surfaces using the icosahedron target and outputting in analyze format so I can import it into R. I figured the best labels to use would be those from the fsaverage directory. I converted those into volume files, but in order to convert them into surfaces, I need a .reg file. I tried the sphere.regfiles in the surf subdirectory, but mri_vol2surf didn't like that. Using a .reg file for a volume registered to fsaverage seems redundant, but I see no way around it. Is there? Or am I doing this all wrong and there is a much better way to label my surfaces? Thanks, -- ,-------------------------------------------------- | Alessandro Gagliardi | Rutgers University Mind Brain Analysis | Integrative Neuroscience Program | alessandro(a)gagliardi.name `--------------------------------------------

2 1

aseg.stats detailed list
by Joan Fisher 27 Jul '07

27 Jul '07

Hello -- The aseg.stats output that I have itemizes the size of the structures up to line 86, but there are only zeros after that. For example, if I wanted to know the wm or ctx for the rh middle temporal gyrus, there's a line devoted to that, but no values. Is there an option that I should be using to get a complete listing of regional size? Many thanks, Joan Fisher U of C

2 1

OASIS freesurfer-processed dataset
by Satrajit Ghosh 27 Jul '07

27 Jul '07

Is there any documentation for the OASIS freesurfer-processed data? I'm looking for details of human intervention. For example, - were seeds inserted for any brains? - was the white matter edited - were cortical labels manually edited for correctness? Any documentation about the whole process would be much appreciated. Thanks, Satra

2 1

FS installation for FC 7 + ATI Mobility FireGL V5000 graphics card
by Gallo, Antonio (NIH/NINDS) [F] 26 Jul '07

26 Jul '07

Hi All, Does anyone have any experience with FS installation under Fedora Core 7 Linux + ATI Mobility FireGL V5000 (256K) graphics card? Which is the correct version to use? Do I need any additional patches to download or are any other configuration settings necessary? Thanks in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

2 1

freediffusion dtrecon mask
by Akram Bakkour 25 Jul '07

25 Jul '07

Hello, freesiffusion-support(a)nmr.mgh.harvard.edu doesn't seem to exist, so I'm hoping one of you can help me out. I seem to be having trouble with the -mask 0 flag in dtrecon. It doesn't apply a brainmask! I tried -mask 1 but that didn't work either. I unpacked the data properly, then ran diff-flirt -i f -o unwarp/f -tmpdir tmp for motion and eddy current correction and then ran dtrecon -i f -o maps -mask 0 but my maps/fa volume is not brain masked. Here are the logs: /space/thigpen/10/users/min/OFRR27/dti/025/unwarp/dtrecon-22259.log /space/thigpen/10/users/min/OFRR27/dti/025/unwarp/raw2tensor-22289.log /space/thigpen/10/users/min/OFRR27/dti/025/unwarp/tensor2eig-22447.log I can see where it says Calculating background fraction ... brain is 100% of volume nonbrain is 0% of volume but I still don't understand why it's not working. I even tried running dtrecon on the unpacked data without running diff-flirt, but no luck. Any and all help is highly appreciated. Thanks! Akram.

2 1

Partitioning GM/WM boundary surface
by Morgan Hough 25 Jul '07

25 Jul '07

I would like to obtain a ratio of gyral/sulcal GM/WM boundary surface area. I was wondering if the best solution would be to threshold each subject's ?h.sulc files to form a label that contains all gyral areas and then use mris_anatomical_stats -l to constrain a surface area measurement to this label? I was also wondering if there is a simple way to exclude the medial wall area from consideration in these calculations? Thanks in advance for your time. Cheers, -Morgan

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Freesurfer July 2007