Freesurfer July 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
140 discussions

Freesurfer file
by wen miao 08 Jul '10

08 Jul '10

Hello, Freesurfer experts I'v got a work with the freesurfer files. As we all know, there are many files in the freesurfer subject directory, and each file has its usage. My question is, what's the particular usage for each of these files and how can I read these files using Matlab or any other softwares rather than the freesurfer tools? Is there a list for this? Thanks in advance. -- Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA

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probabilistic white matter mask
by Mehul Sampat 08 Jul '10

08 Jul '10

Hi Folks, I believe that I can create a binary white matter mask using "mri_wmfilter". I was wondering if there is a way to create a probabilistic white matter mask ? (for each voxel, I would like to obtain the probability of it being white matter) I did a search on the mailing list and found the following related message: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11786.html The message suggests to use "-write_probs" flag with the mri_ca_label command but I dont see this flag as on option in the usage instructions for mri_ca_label. If this is the right way, should i just add "-write_probs wm.mgz" to mri_ca_label to get a probablistic white matter mask ? Thanks Mehul

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ERROR selxavg-sess
by 卯野賢太 07 Jul '10

07 Jul '10

Hi,Freesurfers I'm going to analyze the functional data. By now I finished reconstruction of anatomical data and maiking hierarchy, mc-sess,spatialsmooth-sess,inorm-sess,mkanalysis-sess and fslregister. But selxavg-sess output following ERROR. please tell me about -ipr. Keta kenta@localhost[retino1] % mkanalysis-sess.new -analysis retino -TR 2 -paradigm para.para -designtype blocked -funcstem fmcs -nconditions 4 -timewindow 34 -motioncor -inorm -gammafit 2.25 1.25 -polyfit 2 -mcextreg -force Completed successfully kenta@localhost[retino1] % selxavg-sess -analysis retino -s sekiguchi001 -df sessdirfile -noomnibus INFO: WhitenFlag = 0 -------------------------------------------------------------- selxavg-sess logfile is /home/kenta/data/sessions/retino1/log/selxavg-sess-bold-retino-100708112251.log -------------------------------------------------------------- ------------------------------------------- /home/kenta/data/sessions/retino1/sekiguchi001 2010年 7月 8日木曜日 11:22:51 JST INFO (sekiguchi001): RunList = 001 002 003 004 -------------------------------------------------------- /home/kenta/data/sessions/retino1/sekiguchi001/bold selxavg2 -TR 2 -parname para.para -o retino/h -i 001/fmcs -i 002/fmcs -i 003/fmcs -i 004/fmcs -cfg /home/kenta/data/sessions/retino1/retino/analysis.cfg -ipr -------------------------------------------------------- here --- Parsing Config File: /home/kenta/data/sessions/retino1/retino/analysis.cfg ---- -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 ERROR: flag -ipr requires one argument ERROR (/home/kenta/data/sessions/retino1/sekiguchi001): selxavg failed

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editing labels in tksurfer
by Keefe, Helen L 07 Jul '10

07 Jul '10

Hi Everyone, I remember a post in March when Allison referred someone to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit and I think this will be really helpful for me if I can figure out how to make it work. I have a scan with corpus callosum bleeding into the caudalanteriorcingulate. When I try to change the label, I am able to select the region by clicking on it. However, when I try to "Draw a complete outline path that encloses the desired "incursion"", every time I click to draw the path, the image refreshes. Here are the instructions: "Create outline path: * Possibly start with Edit > Unmark all vertices * Make a series of clicks along the desired outline path. tksurfer shows marked vertices." Is "create outline path" the same as "Make Path" on the TkSurfer tools box? What would make the decision between "Possibly start with Edit > Unmark all vertices" and not doing that? I succeeded once in getting the path drawn, but have no luck replicating that. Also, when I tried to relabel the part inside the path, I was able to turn it into label = "None" or turn 90% of the brain into caudalanteriorcingulate. I'm missing something really simple here - help, please. Also - can this be done also on the pial surface using this command? I can see the boundaries better on this view than on the inflated tksurfer $i lh pial -annotation aparc Thanks for any help - let me know if you need more information Helen Keefe

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entorhinal surface and wm intensity
by Derin Cobia 07 Jul '10

07 Jul '10

I have questions regarding two issues we've run into processing dementia and age-matched healthy subjects: 1. For several of our subjects, we've noticed that an isolated region of the entorhinal pial surface becomes 'indented' towards the white surface (see in RH in attached pics- P5b*). Not sure what's going, I've tried to correct it by removing any extraneous neighboring voxels or other 'anomalies' (no voxel gaps in the wm volumes from lesions, etc). It almost reminds me of the insula 'spike' a few versions back. Thoughts? 2. After re-running a subject for cp and wm edits, the resulting white (and consequently pial) surface has become inaccurate for large portions of the anterior temporal and frontal lobes, but just in the LH (attached pics- P8b*). To clarify, this was not the case after the data's initial run, only once edits were made and incorporated. We've run into this before, but only after editing a subject multiple times (3-4x, thus more recons), or 'updating' subjects to a new FS version (e.g., re-running v4.1.0 data with v4.5.0). Are edits changing the intensity threshold? It's odd that it's asymmetric. Any help/thoughts would be appreciated, thanks. -Derin

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Help on QDEC: Obtainign mean, sd and p-values from glm result
by Fernanda Palhano 07 Jul '10

07 Jul '10

Hello, I've just started using freesurfer. I've reading the mail list wich helps me a lot, but I can't find how I can obtain a table with the values of my glm analysis. For exemple, in the Qdec's tutorial I have a surface that answer the question "Does the correlation between thickness and age differ from zero?" It's possible to see this data like a table: region mean sd p-value precentral xx x xxxx Or at least obtain those values individually? thank you very much in advance, Fernanda

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manual corregistration...
by Gonzalo Rojas 07 Jul '10

07 Jul '10

Hi: How can I do a manual corresistration with freesurfer ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Re: [Freesurfer] subcortical segmentation
by Bruce Fischl 07 Jul '10

07 Jul '10

Hi Salem, yes, you can run any individual options in recon-all. See the -help output and run it through step 11 if you want. Note that we do use the surfaces to improve the aseg accuracy at the very end, so you'll be giving that up. cheers Bruce On Wed, 7 Jul 2010, Hannoun wrote: > > > Hi, > > I am a new user of freesurfer. Is it possible to do just the volumetric > processing stages without the surface processing stages? > > In fact what I want is to segment the subcortical structures. > > Is there a command line for this purpose only or should we run all the > recon-all steps? > > Thank you for your help > > Salem > > > > > >

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Qdec - problem with the Generate Stats Data Import button.
by Gaëlle Leroux 07 Jul '10

07 Jul '10

Dear FS, I'm basically stocked with a problem when I press the "Generate Stats Data Import" in the Qdec GUI. I got the following error message as in the attached file. I'm running FS using a python 2.6 version. It seems that I do have a problem with the asegstat2table command line but I don't understand why... Any advice, please? Many thanks in advance for your help. Sincerely, Gaëlle Leroux.

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RV: FREESURFER
by SANTIAGO GONZALEZ CALERO 07 Jul '10

07 Jul '10

> Good morning,I am working on brain segmentation using freesurfer program. > I wonder if it is possible to turn an initial image with some tool freesurfer. Because my problem is that when I start to perform segmentation in freesurfer, I get an error and I think that is because dicom image format is a little crooked. If you can not rotate with tkmedit or similar tool. > The error I get is as follows: > > ERROR > cp transforms/talairach.auto.xfm transforms/talairach.xfm > > #-------------------------------------------- > #@# > Talairach Failure Detection Tue Jun 22 04:45:20 EDT 2010 > /usr/local/freesurfer/subjects/ome/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** > (p=0.0063, pval=0.0000 < threshold=0.0050) > > I have tested the segmentation with another patient and gives me the following error. > > ERROR > > ********FINAL ITERATIVE TEMPLATE DEFORMATION******** > Compute Local values csf/gray > Fine Segmentation...44 iterations > mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/francia/mri/T1.mgz',frame -1, errno 12 > > mri_strip_skull: done peeling brain > > Brain Size = 1260141 voxels, voxel volume = 1.000 mm3 > = 1260141 mmm3 = 1260.141 cm3 > > mri_watershed Error: read failed > > Linux freesurfer-virtual 2.6.28-19-generic #61-Ubuntu SMP Wed May 26 23:35:15 UTC 2010 i686 GNU/Linux > > recon-all exited with ERRORS at Tue Jun 22 08:27:59 EDT 2010 > > Do not know if these errors can be solved with some kind of tool or if on the contrary are due to initial images of patients are slightly slanted, and if the same could reorient vertically. > Thank you very much. A greeting. > Attentively

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Freesurfer July 2010