Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

ventricles labeled as white matter in hydrocephalus brain
by Dana W. Moore 22 Apr '09

22 Apr '09

I am trying to use FreeSurfer to measure ventricular volume among patients with normal pressure hydrocephalus. I have run the first subject, whose ventricles are huge. When looking at the subcortical segmentation (aseg.mgz) in tkmedit, I saw that large portions of the ventricles are labeled as cerebral white matter or white matter hypointensities. I tried filling in the ventricles in the wm.mgz volume and then running autorecon2-wm, but this does not appear to have changed anything in the aseg.mgz segmentation nor in the aseg.stats file. Is there a way I can correct this problem, and/or prevent it when I run more NPH patients? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2823 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

4 3

3d reconstruction of the hippocampus or thalamus
by asaf achiron 22 Apr '09

22 Apr '09

hi group, Is there a way to reconstruct in 3d the hippocampus or thalamus segmentation in Freesurfer? this is for verification of the automatic process, thank you Asaf

3 2

Using a Label with Volume-based Monte Carlos
by Dave Brohawn 22 Apr '09

22 Apr '09

Hello, Here is my bugr information. FREESURFER_HOME: /usr/local/freesurfer/stable4 Build stamp: freesurfer-Linux-centos4-stable-v4.3.0-20090416 RedHat release: CentOS release 5.2 (Final) Kernel info: Linux 2.6.18-92.1.22.el5 i686 NMR Center info (/space/freesurfer exists): machine: seymour SUBJECTS_DIR: /autofs/space/ventzl_016/users/ PWD: /autofs/space/ventzl_016/users ssh seymour setenv SUBJECTS_DIR /autofs/space/ventzl_016/users/ cd /autofs/space/ventzl_016/users I am curious if it is possible to run a monte carlo analysis using volume data including a label file I generated. Here is the command I tried to run: mri_glmfit --y /autofs/space/ventzl_016/users/All-18/newEMerror-tpx/ASevASc_6s/tal.ces.nii --fsgd $SUBJECTS_DIR/fsgd/All-18.fsgd --C $SUBJECTS_DIR/fsgd/All-18.mat --label $SUBJECTS_DIR/fsaverage/label/subcortical.label --sim mc-full 1000 2 $SUBJECTS_DIR/All-18/monte_carlo_01_V/All18Vol_MCSIM1 --fwhm 13.37 This would be the first of ten monte carlo simulation commands. It returned an error message saying: gdfReadHeader: reading /autofs/space/ventzl_016/users//fsgd/All-18.fsgd INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 CC 2 T INFO: gd2mtx_method is dods simbase /autofs/space/ventzl_016/users//All-18/monte_carlo_01_V/All18Vol_MCSIM1 ERROR: need --surf with --label The subcortical label I generated from the "aseg" segmentation overlay for fsaverage includes the left and right segmentations of the following regions: Amygdala, hippocampus, DC, Putamen, Accumbens, Pallidum, Thalamus Proper, and Caudate. The brain stem label is also included. Please let me know if running a monte carlo for volume with a label is possible. Thank you, Dave Brohawn

2 1

discrepancy with mris_glmfit-sim annotation
by Devdutta W 22 Apr '09

22 Apr '09

Hi, While going through the annotation of the clusters, we noticed that the regions that the cluster summary prints out do not correspond to the actual location in the brain. For example, in the summary one of the clusters is reported to be in the isthmus of cingulate. However, when I look at the corresponding cluster on tksurfer it is quite clearly not medial (in fact it is on the temporal lobe). Has anybody encountered this problem before? If so, any idea why this is happening and how it can be fixed? I appreciate any help in this matter. Regards, Devdutta

1 0

spherical template: CMA training set
by Juranek, Jenifer 22 Apr '09

22 Apr '09

Is any information about the manually-parcellated (CMA) training set used to create the spherical template used in fsv4.*? The information reported in Cerebral Cortex (2004) 14(1):11-22 reports 36 MRI volumes from an ongoing study. Does this sound about right? Or have there been any updates to the spherical template since then? Many Thanks for any info, Jenifer

3 4

Individual thickness data extraction from plot
by Marina.Lopez＠crccorp.es 22 Apr '09

22 Apr '09

1 0

RES: [Freesurfer] Multiple Processors
by Pedro Paulo de Magalhaes Oliveira Junior 21 Apr '09

21 Apr '09

You can run 8 recon-all simultaneusly In bash recon-all -s subjid -all &> /dev/null & For each of the subjects. You should have at least one gigabyte per processor. The Darwin kernel (MacOs) will distribute the load. Sent from my Nokia phone @E71 -----Msg original----- De: Andrew Jahn Enviada: 21/04/2009 17:39:00 Para: Freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] Multiple Processors Hi, I am running Freesurfer on a Mac OS X 10.5 computer with a 2x2.8 GHz Quad-Core Intel Xeon processor. My question is, are there any subcommands to run recon-all assigning the processors to different jobs? Or is the speed of recon-all just dependent on pure processing power, no more? Thanks! -Andrew

1 0

Multiple Processors
by Andrew Jahn 21 Apr '09

21 Apr '09

Hi, I am running Freesurfer on a Mac OS X 10.5 computer with a 2x2.8 GHz Quad-Core Intel Xeon processor. My question is, are there any subcommands to run recon-all assigning the processors to different jobs? Or is the speed of recon-all just dependent on pure processing power, no more? Thanks! -Andrew

1 0

make_average_subject
by ata maroc 21 Apr '09

21 Apr '09

Dear freesurfer, i m running FS_v4.3.0 and i d like to create my own study group average subject. After finishing running make_average_subject, everything seems to work good except some files on my subjaverage/surf subdirectory that are not created at least not correctely. So instead of getting lh.curv or lh.pial all i get is a place holder indicating to or pointing to lh.avg_curv or in the other case pointing to lh.pial_avg which both files are in the same subdirectory. i ll be very gratefull for any hint _________________________________________________________________ http://redirect.gimas.net/?n=M0904xMSNMovies Filme.Gratis.Für alle. MSN Movies. Fehlt nur noch das Popcorn.

2 1

--out_orientation question using mri_convert
by Dr.med. Johannes C. Klein 21 Apr '09

21 Apr '09

Dear all, I have acquired 4D data on a Siemens machine, and I'm using mri_convert to turn the DICOMs into NIFTI files. Now, I would like to "rectify" the 4D NIFTI volume, such that the principal axes display in a standard way in fslview. I can do this for 3D files like this is, and it works a charm for all sorts of original orientations: mri_convert --out_orientation LAS input.nii rectified_output.nii However, when I'm using a 4D NIFTi file as input, only the first volume is included in the rectified output and the rest is truncated. I was wondering if this is a known limitation, and if there is another tool I could use on 4D files which would save me having to split them up before reorientation? BTW, I've tried this on Freesurfer 4.3.0 and 4.0.5. Thanks in advance for your help, Johannes

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