Freesurfer

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21 participants
30070 discussions

breaking up dti data set
by Dennis Jen 27 Sep '06

27 Sep '06

Hi, I have a DTI dataset of size 128 x 128 x 60 x 9. I'd like to convert it into 9 volumes of size 128 x 128 x 60. Is there a utility I can use for this? Thanks, Dennis

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suse 10.1 / CentOS 4 v3.0.3 / tksurfer Problems
by Lei.Zhang＠uniklinik-freiburg.de 27 Sep '06

27 Sep '06

Hi, Dear FreeSurfers, I am running freesurfer (centos 4 / v3.0.3 under SuSE 10.1). I got the following Error while trying to run surf-sess: surfer: ### GL window already open: can't open second % freeglut ERROR: Function <glutBitmapCharacter> called without first calling 'glitInit'. I found the same problems in the mailing list which is http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg03266.html , but I’m sorry that I can’t use the new tksurfer on ftp://surfer.nmr.mgh.harvard.edu/pub/dist because that is special for an x86_64 system. Please help me and thanks in advance! Lei Zhang

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Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

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tksurfer time course script help
by raij＠nmr.mgh.harvard.edu 26 Sep '06

26 Sep '06

Dear Freesurfers, We are trying to write a tksurfer tcl script that would save FIR analysis hemodynamic waveform time course windows in postscript format (rgb or tiff are not sufficient as we need to do a lot of editing on the figures with Adobe Illustrator to get publishable figures. No, not THAT kind of editing :)). The script loads a label, loads a hemodynamic waveform, calculates the mean value across the label, and plots the curves. Most of the stuff is working already, thanks to Kevin Teich, but a few pieces are missing. The functions we are looking for exist in the GUI, but we could not find the corresponding script commands in the wiki or archive. Could you tell us the tcl script commands for: 1. Save the time course window in /<path>/<filename-timecourse>.ps 2. Select only some of the contrasts for display (e.g., we have contrasts 0-7 and only want to display 1, 2, and 3) 3. Setting "subtract pre-stim average" on, i.e. forcing the pre-stimulus time window mean values to zero on the y-axis ("baseline correction"). I will add the script to the wiki when we have it working. Very convenient when you have multiple contrasts in multiple experimental conditions and many ROIs in many subjects - just edit the list of ROIs/labels and time courses to be loaded, and let the computer do the rest! Thanks! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. raij(a)nmr.mgh.harvard.edu

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cotical surface labeling...
by Shahabuddin Ansari 26 Sep '06

26 Sep '06

Hi, I can extract subcorical objects from freesurfer segmentation, since each object is lableled with normalized intesity value. I was wondering if I can extract different cortical regions in the same fashion. I can, though, view the labeled cotical surface in tksurfer. Thanks Shahab --------------------------------- Get your email and more, right on the new Yahoo.com

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processing steps
by claudia wheeler-kingshott 25 Sep '06

25 Sep '06

Hi, I have just started to look at freesurfer and decided to run each step to try to understand what recon-all does. Well, after a bit of teething to put the data in the right orientation, we managed to start, but we have a few questions :-) First of all, our SPGR data is 1.2x1.2x1.2mm^3 and it is acquired coronally. I used mri_convert to get the data resampled to 1x1x1mm^3. 1) When I run the mri_nu_correct command to generate the nu file I get a lot of "Not yet installed" errors. Do I have to generate this file at all? It seems redundant. 2) When I get to the generation of the T1 file and then the brainmask, this last file is not compatible with the original data or the nu data because of a different voxel size. This causes me the first problem with the mri_em_register command, which fails if I use the --mask option with my brainmask image and the nu data, giving me a segmentation fault. If I use the T1 data, then the command runs fine! Is there a reason why we can't use the T1 file instead of the nu or orig file? 3) We also have a problem with the commands that use the $FREESURFER_HOME/average/RB40_talairach_2005-12-30.gca file because it is not in the directory. Can we use the RB_all_2006-02-15.gca file instead? What is the difference between these two files? 4) Has anybody got a feeling on how freesurfer works on brains with MS lesions? 5) Is there any way to find descriptions and info on commands that do not have an official page? Sorry for the basic questions and I hope to hear from you soon. Claudia

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Getting PET statistics using the subcortical segmentation
by jorge luis 25 Sep '06

25 Sep '06

Hello all I have PET images corregistered in spm with their corresponding MRI images obtained by converting brain.mgz to analyze. I have created in freesurfer the file register.dat for each one of them, so i can use tksurfer and tkmedit. Now I would like to compute for each PET image the average value of the pixels intensities in several regions resulting from the subcortical segmentation (for example hippocampus) and others manually painted. Also I would like to produce an average region from all the individuals for each one of these selected regions (the average subject does not have a subcortical segmentation and it could be used as a mask in spm analysis). Any tip is welcome 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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anonymizing dicom files
by Najmeh Khalili M. 25 Sep '06

25 Sep '06

sorry about nonstop posting! I'm trying to remove the patient names from dicom files. I was advised to use dcm_modify_elements but it fails on DCM_Openfile. Is there a straight forward way of doing this? Thanks Naj P.S. Doug, I am still looking for the graddir tags :)

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Performance
by Raksha Urs 25 Sep '06

25 Sep '06

Hello We are running freesurfer on a Power Mac G4 with a 1.25 GHz processor and 1 GB Ram. The subcortical segmentation procedure recon-all subcortseg -s <subjid> ran for 49 hours. The rest of autorecon2 (recon-all -autorecon2-cp -s <subjid>) has been running for 6 days and is still working on the left hemisphere. Is this normal? Do you have any recommendations to speed up this process? Thank you Raksha Urs Research Associate Wien Center for Alzheimer's Disease and Memory Disorders Mount Sinai Medical Center, Miami Beach FL

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surface and volume measurements
by pgreenberg＠ucsd.edu 22 Sep '06

22 Sep '06

Hi, 1) I'm interested in the relationship between voxels labeled within the aseg.mgz file and those bounded by the white matter and pial surfaces. In regions such as the hippocampus, the pial surface (red) may cut through the middle of the gray matter designated as hippocampus in the aseg volume overlay. It therefore looks like some of the hippocampus fits between the white/pial boundary and some lies outside the pial boundary. If I wanted to know hippocampal volume, would the value in the aseg stats file be correct, or would regions of the hippocampus outside the pial boundary not be included? 2) Ignoring the hippocampus and looking at the neocortex only, there again seems to be a difference between the volume of tissue found between the white/pial boundaries and that designated as either R or L hemisphere cerebral cortex in the aseg volume overlay. Specifically, in some of our data sets there is unlabeled gray matter to be found between the white/pial surfaces. If a voxel doesn't have an "aseg" label will it be counted toward the total volume in the aseg stats file? If that same voxel lies within the white/pial surfaces will it be counted as gray matter in a different stats file? Which output will provide the most accurate determination of neocortical gray matter volume? Thanks very much, Paul

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