Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

White matter volumes for Gyrus and Sulcus
by Wayne Su 27 Apr '09

27 Apr '09

Hello, Is there a way to get white matter volumes of gyrus and sulcus in Destrieux atlas? I tried to use the same method used by white matter parcellation for Desikan-Killiany atlas, but no wm volumes were reported. Or we get the total volume of the label (how?), then subtract the gray volume to get white volume? Thanks for any info. Wayne

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Comparison of cortical thickness results
by Falk Lüsebrink 27 Apr '09

27 Apr '09

Hi everyone, Id like to compare the individual cortical thickness results of Freesurfer with the results of another software. The other software measures the cortical thickness for example across the whole left parietal lobe. So I have to get the according value of the whole left parietal lobe of Freesurfers results. But I dont know exactly how to do that. Does someone have any suggestions how to get this value? At first glance I would weight the average thickness of every structure belonging to the parietal lobe given in the aparc.a2005s file by the number of vertices (or maybe the gray matter volume in case the volume had a resolution of 1mm^3?). Sum everything up and divide it by the number of vertices to get the mean average across the parietal lobe. Would that result in the value Im searching for? Thanks in advance, Falk

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Flattening marmoset cortex
by Hsin-Hao Yu 27 Apr '09

27 Apr '09

Hi, I created a triangular mesh of a marmoset cortex (layer 4) from histological slices. Although the marmoset cortex is almost flat, it does have a very deep calcarine sulcus and I need to push it out. I am hoping that it is possible to feed the mesh to FreeSurfer so that it can be flattened. I have no need for the GUI or any visualization. All I need is a flattened representation of the mesh. Can anyone provide some hints about how I should begin? The documents for mris_inflate and mris_flatten are pretty sparse. I imagine that if I can save my mesh in the format that FreeSurfer uses, I will be able to use the two command line tools to flatten. Does that seem sensible? Any other processing/commands should be involved? Thank you. Hsin-Hao Yu

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RES: [Freesurfer] Individual thickness data extraction from plot
by Pedro Paulo de Magalhaes Oliveira Junior 27 Apr '09

27 Apr '09

Check the User contribution section of the FreeSurfer wiki. I've put there a small script to do this. Sent from my Nokia phone @E71 -----Msg original----- De: Marina.Lopez(a)crccorp.es Enviada: 22/04/2009 05:43:39 Assunto: [Freesurfer] Individual thickness data extraction from plot Hello all, I have the following plot of thickness value in a specific vertex for all my subjects: My single question is: how can I take the data list of y-values (vertex thickness for all subjects) in this plot in an automatic manner (and have them in a table)? I have to extract thickness values of a lot of vertices and a quick manner will help me a lot. Thank you very much for your help, marina Av�s | Aquest correu i qualsevol fitxer adjunt existent, contenen informaci� confidencial que van dirigits �nica i exclusivament al seu destinatari. Queda totalment prohibit realitzar-ne c�pies, aix� com difondre el seu contingut a altres persones que no siguin les destin�taries. Aviso | Este correo y cualquier fichero adjunto existente, contienen informaci�n confidencial que va dirigida �nica y exclusivamente a su destinatario. Est� completamente prohibido hacer copias, as� como difundir su contenido a otras personas que no sean los destinatarios. This message and any files attached are confidential. It is intended solely for the use of the addressee(s). If you are not the intended recipient of this e-mail, please note that any review, dissemination, disclosure, alteration, printing, copying or transmission of this e-mail and/or any file transmitted with it, is prohibited and may be unlawful.

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Gradient directions of DTI data.
by Zhen Zonglei 26 Apr '09

26 Apr '09

Hi FreeSurfer and FSL Guru: We have analyzed our Siemens Trio 3T dti data with dt_recon, and hope to do TBSS and FDT analysis with FSL in the next step. However, we are not very sure that we can directly use the gradient_mgh_dtiNN.gdt in FSL. To my understanding, FSL’s default orientation is different from Freesurfer’s. Can TBSS and FDT interpret the gradient correctly? Should we adjust the gradient? Please give us some suggestions. Thanks -- Zonglei Zhen, PhD Assistant Professor of Cognitive Neuroscience BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, P.R. China

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4.3.0 macosx leopard mri_normalize segfaults
by Sebastian Moeller 24 Apr '09

24 Apr '09

Dear fellow surfers, in the process of hoisting my monkey scripts for processing of anatomical data from stable3 (3.0.5, boy some programms really expect completely different arguments now, :)) to the cutting edge 4.3.0 I am encountering some problems. On an intel mac (leopard 10.5.6) mri_normalize leads to segmentation faults, while the centos4_x86_64 version of 4.3.0 mri_normalize, happily performs the normalization using the same commandline. Here is bugr's output: --------------------------------------------------------------------- FREESURFER_HOME: /opt/freesurfer/ Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.3.0 Kernel info: Darwin 9.6.2 i386 --------------------------------------------------------------------- Please include the following additional information in your report: 1) subject name n/a, non human primate data; selfmade scripts, mri_info of nu.mgz: hms-beagle:myscripts_anat moeller$ mri_info ../mri/nu.mgz Volume information for ../mri/nu.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.0000, 1.0000, 1.0000 type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 1450.00 msec, TE: 3.05 msec, TI: 800.00 msec, flip angle: 10.00 degrees nframes: 1 ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 13.3323 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 2.5991 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 40.7345 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 141.3323 0.0000 0.0000 1.0000 -125.4009 0.0000 -1.0000 0.0000 168.7345 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 141.3323 -0.0000 -0.0000 -1.0000 168.7345 -0.0000 1.0000 -0.0000 125.4009 0.0000 0.0000 0.0000 1.0000 So to my knowledge nu.mgz looks okay, it displays okay in tkmedit 2) the entire command-line executed mri_normalize -n 1 -no1d -gentle ../mri/nu.mgz ../mri/T1.mgz adding -nosnr or removing -gentle does not solve the problem, it always segfaults with the following output 3) the error message generated performing 3d normalization 1 times disabling 1d normalization... performing kinder gentler normalization... reading from ../mri/nu.mgz... normalizing image... computing initial normalization using SNR... Segmentation fault 4) optionally include the subject's /script/recon-all.log See also: http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any idea, what I can do? -- Sebastian Moeller telephone: 626-395-6713 German GSM: 0 15 77 - 1 90 31 41 moeller(a)caltech.edu Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA

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Registration file conversion
by John Kuster 24 Apr '09

24 Apr '09

Dear Freesurfers, I was wondering if anyone can tell me if there is a command to convert an existing register.dat file from to .mat format for FSL, and vice versa. Thank you! Jake

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Registration matrices
by John Kuster 24 Apr '09

24 Apr '09

Hello! I was just wondering if anyone can tell me about any issues in converting registration matrices from register.dat to register.mat for FSL. Does conversion change the orientation of the matrix for the two images? Do the matrices contain orientation data, or just translational data? Thanks!! Jake

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error running 'fast'
by Dominique Jennings 24 Apr '09

24 Apr '09

Hi, I have been getting a new error when using 'fast', FMRIB's automated segmentation tool. I can run 'fast -t2' on my T2-weighted images without errors (the result is expected segmentation of CSF, WM and GM). However, isolating the number of tissue classes using the command 'fast -c 2' inevitably results in an error, even when I run this command on data I have successfully segmented in the past. Error reads: [aura[129]:] (nmr-std-env) fast -c 2 temp FAST - FMRIB's Automated Segmentation Tool Version 3.53 Image: /tmp/fsl_3bA3BQ_temp AVWReader: Warning, /tmp/fsl_3bA3BQ_temp -- Can not read header file! Can not open file /tmp/fsl_3bA3BQ_temp.hdr! If anyone is familiar with 'fast', any advice would be greatly appreciated. Thank you in advance. Nicki

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Tal QA log outputs
by carl＠nmr.mgh.harvard.edu 24 Apr '09

24 Apr '09

Nick, Could you please help me reconcile your reply to Zhen below with Avis note below about the tal_QC_AZS script? Below we have pasted a sample of our recon all log. Is the talAviQA in the default log the same as the eta term that Avi describes as output of the tal_QC_AZS script below in his note to Zhen? What does the z refer to in the recon all log? It appears that the default tal check does not generate the atlas_transform_error term, correct? ( I also dont see any term less than 15). Does one need to run Avis tal_QC_AZS script to generate the atlas_transform_error term ? While it looks like tal check not not automatically output the value of the atlas_transform_error term, Is the z score that DOES appear (automatically) in the log file the same z score that Avi mentions below, that compares the atlas_transform_error term to the training set? Thanks! Carl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------------------------------------------------------------------------------------------------------ Mon Apr 13 15:14:55 CST 2009 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Apr 13 15:14:56 CST 2009 /nfs/h2/r6/subjects/A39/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8116, pval=0.8469 >= threshold=0.0050) awk -f /nfs/h1/r1/jliu/new_soft_test/freesurfer/bin/extract_talairach_avi_QA.awk /nfs/h2/r6/subjects/A39/mri/transforms/talairach_avi.log TalAviQA: 0.97187 z-score: -1 #------------------------------------------- On 4/22/09 4:04 PM, "Nick Schmansky" <nicks(a)nmr.mgh.harvard.edu> wrote: Zhen, The -tal-check flag included with recon-all will perform the QA check that Avi mentions, with the addition of creating a z-score comparing the subject's QA score to a set of QA scores of known-good talairach alignments. The -tal-check flag runs by default in recon-all (in -all and -autorecon1), and will error exit if the alignment is below threshold. Nick >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, 2009-04-21 at 19:02 +0800, Zhen Zonglei wrote: > Dear Avi: > > Thanks for your kind and the script.I will use it to check tal QC of > all my data . > > Zognlei > > > 2009/4/21 Avi Snyder <avi(a)npg.wustl.edu> > Zonglei, > > 1. Re: how to detemine Talairach transform success from the > logfile: > Attached is a simple csh script (tal_QC_AZS) and a required > awk script. > tal_QC_AZS reads the log file and writes out two numbers. > The first number (eta) is the spatial correlation between the > (blurred) input > image and the atlas representative target image. eta values > less than 0.96 are highly > suspect. The second number ("atlas_transform_error") is > computed on the basis of > registration objective function curvature in parameter space. > The 12 present numbers > are compared to values derived from a training set. > atlas_transform_error values > less than ~15 are good. > > > Avi > ----------------------------------------------------------------------- > >Date: Tue, 21 Apr 2009 12:52:45 +0800 > >Subject: Re: [Freesurfer] t4_read error (fwd) > >From: Zhen Zonglei <zonglei.fsl(a)gmail.com> > >To: Avi Snyder <avi(a)npg.wustl.edu> > > >Cc: freesurfer(a)nmr.mgh.harvard.edu, > fischl(a)nmr.mgh.harvard.edu, nicks(a)nmr.mgh.harvard.edu > > > > Hi avi: > > > >Thanks for your help. Still have two questions. > > > >1) How to determine whether the Talairach transform is > reasonable > >based on recon-all.log?

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