Freesurfer

freesurfer@nmr.mgh.harvard.edu

13 participants
30061 discussions

unpacking anonymized data
by Doug Greve 12 Apr '06

12 Apr '06

I just wanted to give people some warning about unpacking/converting anonymized Siemens dicom files. Siemens inserts some ascii information into their dicom files (what I call the "ascii header"). This is inserted into a "private" field in the dicom header. Some anonymizers will strip this information out of the dicom file. If the dicom file contains a mosiac (eg, as with functionals), then it will not be possible to unpack it using the tools in freesurfer if the ascii header is gone. If the dicom file contains individual slice images (non-mosaics), then it is possible to unpack it correctly even if their is no ascii header. There is currently a bug in mri_convert/unpacksdcmdir that might cause a slice reversal if the ascii header is not there. If you acquired data sagitally, this would mean a left-right flip. This bug has been fixed (live in dev and stable tomorrow). Even so, be very careful when anonymizing your data. You should do some sort of check against unanonymized data to assure that nothing funny has happened. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Gnome terminal do not support OpenGL GLX extensions with freesurfer
by jorge luis 12 Apr '06

12 Apr '06

Hello all I am just starting to use freesurfer in our new laboratory of functional neuroscience. I have a Dell machine with 64 bits Intel Dual Xeon processors. I have installed the 64 bits Linux Centos 4 Operating System. Also the machine has an nVidia Quadro FX 4500 graphic card. I have installed freesurfer for x86-64 Centos 4 successfully but when I run the command: tkmedit bert orig.mgz I got this message displayed in the prompt: freeglut (tkmedit): OpenGL GLX extension not supported by display ':0.0' I was using the GNOME 2.7.3 Terminal, Copyright © 2002 Havoc Pennington I will appreciate any help to overcome this problem In advance Thank you ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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color scale bar
by anthony gallo 11 Apr '06

11 Apr '06

if you are using the overlay color display how can you configure the scale? In the paper "Measuring the thickness of the human cerebral cortex from magnetic resonance images" the images show the overlay color bar in many different scales. Thanks

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Translating labels created from aseg to DTI bfloats
by Jonathan Wisco 11 Apr '06

11 Apr '06

Hi, is there a way to translate a label created from the aseg segmentations to DTI bfloat data? I know I asked this before, but can't find the answer in my e-mails. Thanks. -- Jonathan J. Wisco, Ph.D. Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Building 149, 13th St. Charlestown, MA 02129 E-mail: jjwisco(a)nmr.mgh.harvard.edu Tel: 617-851-8492 Fax: 617-726-7422

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RE: [Freesurfer] Recommendation for Linux machine
by Durastanti, Valentina (NIH/NINDS) [F] 11 Apr '06

11 Apr '06

I used the old command (csurf) to open freesurfer and then I tried to open the volume from that! It works but don't show me the segmentation lines on the brain volume (even if it show the lines on the wm volume) thanks Valentina -----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Tuesday, April 11, 2006 2:21 PM To: Durastanti, Valentina (NIH/NINDS) [F] Cc: Bruce Fischl; Chunchun Ni; Freesurfer Mailing List Subject: RE: [Freesurfer] Recommendation for Linux machine what is the command-line that was typed? On Tue, 2006-04-11 at 15:13 -0400, Durastanti, Valentina (NIH/NINDS) [F] wrote: > > Dear Bruce, > I'm trying to open some images that I analyzed with the old version of > Freesurfer but when I charge the brain volume on tkmedit it doesn't show > me the red and green line! Have you any suggestion? > Thanks > Valentina > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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RE: [Freesurfer] Recommendation for Linux machine
by Durastanti, Valentina (NIH/NINDS) [F] 11 Apr '06

11 Apr '06

Dear Bruce, I'm trying to open some images that I analyzed with the old version of Freesurfer but when I charge the brain volume on tkmedit it doesn't show me the red and green line! Have you any suggestion? Thanks Valentina

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Converting .annot into volume
by Johannes Klein 11 Apr '06

11 Apr '06

Hi folks, I'd like to create a volume segmentation from Freesurfer's .annot output. I can get it back into volume land with something like mri_label2vol --subject sub1 --annot ../label/lh.aparc.a2005s.annot --o sub1_parcellated.mgz --hemi lh --temp norm.mgz --proj frac 0 1 0.1 The thing I'm missing, though, is the appropriate colour table - I don't know how to extract the embedded one from lh.aparc.a2005s.annot I loaded the result into tkmedit and tried the different colour tables (my best bet being surface_labels.txt) provided, but none of them gives correct anatomical labels. Thanks for your help everyone, Johannes

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mri_convert in 4D
by Julia Hamstra 11 Apr '06

11 Apr '06

I am viewing it with tkmedit. For the timeseries, it only displayed some of it. I also tried viewing it with fslview. There it was a single dashed line in the coronal view. Here is the output: mri_convert -it dicom -ot nii i6757552.MRDC.1 run.nii.gz reading from i6757552.MRDC.1... 1260 DICOM 3.0 files in list Found 1260 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 1260. reading DICOM image... ------------------------------------------------- DICOM meta-header file name /data/Cued_Recall/CR_ds7/s6757551/i6757552.MRDC.1 Date and time study date 20050601 study time 183408 series time 190627 acquisition time 190627 Identification patient name ds060105 manufacturer GE MEDICAL SYSTEMS Dimensions number of rows 64 number of columns 64 number of frames 1260 pixel width 3.43752 pixel height 3.4375 slice thickness 7 field of view 220.001 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 30 repetition time 720 inversion time 0 echo number 1 flip angle 1.5708 bits allocated 16 Spatial information first image position -108.281 -113.295 54.3301 last image position -108.281 -60.2276 88.2841 image orientation 1 -0 0 -0 0.538953 -0.842336 ------------------------------------------------- TR=720.00, TE=30.00, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -0.538953, - 0.842336) k_ras = (0, -0.842337, 0.538951) writing to run.nii.gz... thanks ~julia On 4/8/06, Bruce Fischl < fischl(a)nmr.mgh.harvard.edu> wrote: > > how are you displaying it? And can you send the entire output? > > On Fri, 7 Apr > 2006, Julia Hamstra wrote: > > > Hi, > > I am getting two errors when creating NIFTI files from dicoms using > > mri_convert. > > The first is that the 4D images are being spatially contactonated. It > does > > not seem to be treating it as a timeseries. This is the command: > > > > mri_convert -it dicom -ot nii s6761334/i6761335.MRDC.1 run.nii.gz > > > > Additionally it is an oblique acquizition so the coronal view is not > > displaying the plane of acquizition (as intended), but an orthogonal cut > > through multiple slices. Am I missing an option or additional > information? I > > searched the options and couldn't figure out anything that helped. The > > problem applies to the co-planar oblique structural scan too. > > > > I'm guessing there is something simple that I am overlooking. What may > that > > be? > > thanks > > ~julia > > > -- Human Memory Lab 8950 Villa La Jolla Drive Suite C212 La Jolla, CA 92093 phone: (858)534-1227 fax: (858)534-1240 jhamstra(a)gmail.com

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segmentation error.
by Martin Ystad 11 Apr '06

11 Apr '06

Hi, I'm running the stable release v 3.0.1 for centos4 and I've had some problems with the segmentation. The main surface doesn't follow the wm-surface in some of the sulci, it rather 'jumps' across to the next gyri. (see picture) I've tried to edit the wm-surface and running autorecon2 again, but it doesn't work. Any ideas? Thanks, Martin Ystad University of Bergen, Norway.

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Freesurfer - autorecon1 will not write to established directory
by adam walczak 11 Apr '06

11 Apr '06

Hi, I have been having some basic problems with regard to paths. Freesurfer doesn't seem to want to write to directories that already exist. I was wondering if there is something different I need to do (I am running the reconstruction tutorial) to make this work. -------- freesurfer-Linux-rh9-stable-pub-v3.0.1 -------- SUBJECTS_DIR is /cajal/public/programs/freesurfer/subjects which: recon-all / autorecon1 pwd - /cajal/public/programs/freesurfer/subjects/13667/mri command line - recon-all -i orig.mgz -autorecon1 -s 13667 --------error--------- INFO: SUBJECTS_DIR is /cajal/public/programs/freesurfer/subjects ERROR: /cajal/public/programs/freesurfer/subjects/13667 exists I am at a loss as to why this happens. Any help would be appreciated. Adam Walczak --------------------------------- Love cheap thrills? Enjoy PC-to-Phone calls to 30+ countries for just 2¢/min with Yahoo! Messenger with Voice.

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Freesurfer