Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Timecourse plots based on fsgd, not analysis?
by Adam Nitenson 04 Nov '10

04 Nov '10

Hello Freesurfers, I'm been experimenting with creating timecourses for tksurfer and tkmedit using the -hrf flag. However I've noticed that the h.nii files created provide the HDR timecourse are only based on the original analysis under which isxconcat-sess was run (in my case, error vs correct). I was wondering if there was a way to tailor the timecourse in such a way that, instead of plotting only the conditions of the analysis, it would plot lines based on subject groups (e.g. Patients and Controls from an fsgd file). Basically, is there a way that I can create an HDR timecourse plot that can separate the data by groups that I can designate depending on the type of anlaysis I wish to conduct? Thanks! Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Using another atlas besides "talaraich" (mni305)?
by Lisa F. Akiyama 04 Nov '10

04 Nov '10

Hi FreeSurfers, Is it possible to tranform a MRI to an atlas that is not "talairach" (MNI305 atlas) using the talairach_avi command or using another command in FreeSurfer? Thank you. Best, Lisa ______________________________ Lisa F. Akiyama Research Study Assistant Institute for Learning & Brain Sciences (I-LABS) University of Washington <lrisa87(a)uw.edu> P Please consider the environment before printing this e-mail.

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question about longitudinal data processing
by Sungeun Kim 04 Nov '10

04 Nov '10

Dear FreeSurfers, I have one question, related to longitudinal data processing. According to the wiki page about Longitudinal Processing, as the first step, all time points should be processed with the default workflow. All of my data, including all time points, were already processed using FreeSurfer v. 4.0.2 and I would like to process the longitudinal data using v.5.0 or later. In this case, can I use the FS results from v. 4.0.2 as the input to the second step of longitudinal processing? OR, should I re-process my data with a new version from the first step? Thank you very much for your help and answers in advance. -- Sungeun Kim

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Re: [Freesurfer] Total GM and WM volumes
by Ed Gronenschild 04 Nov '10

04 Nov '10

Dear Christian, Thanks for your suggestion. I followed the instructions to derive the GM and WM volumes. Here are the (rounded-off) results for one example: mris_volume lh.pial: 532767 mris_volume rh.pial: 536127 mris_wm_volume lh: 251139 mris_wm_volume rh: 254730 Accordingly: gm lh = 532767 - 251139 = 281628 gm rh = 536127 - 254730 = 281397 Left + right: total = 1068894 wm = 505869 gm = 563025 ------------ The aseg.stats file lists the following results: cortical wm lh: 251139 cortical wm rh: 254730 total wm: 505869 cortical gm lh: 263888 cortical gm rh: 265231 total cortical gm: 529119 subcortical gm: 181270 total gm: 710389 -------------- For wm both results are equal but for gm they are not. So now my question still exists: which wm and gm volumes should I take? Ed On 26 Oct 2010, at 20:40, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Dear Ed, > > to my knowledge, "mris_wm_volume" is the best option to determine the > white matter volume. > > See this wiki page for usage: > http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats > > Best wishes, > Christian > > > --- > Christian Scheel > Department of Psychiatry > University of Cologne > > > > > Am 26.10.2010 15:22, schrieb Ed Gronenschild: >> Hi, >> >> I post this once again because I didn't get any response. >> >> In the v5.0.0 aseg.stats file I can find the following volumes: >> >> - left/right cortical gray matter >> - subcortical gray matter >> - total cortical gray matter >> - total gray matter volume >> and >> - left/right cortical white matter >> - total cortical white matter >> >> How can I derive the total white matter volume? >> >> Ed >

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label2label result is scatter line in tksurfer
by Jin Li 04 Nov '10

04 Nov '10

Hello there, I tried mri_label2label to convert label in a subject's space into label into fsaverage's space. I used the command mri_label2label –srclabel C102/label/lh.pfc.C102.label –srcsubject C102 – trglabel fsaverage /label/lh.pfc.fsaverage.label –trgsubject fsaverage – regmethod volume The generated label was supposed to be in the same space with fsaverage, but when loaded on fsaverage's inflated surface, only scattered lines was seen. While when loaded on subjects's surface, it looks normally, but the image was exactly the same as the original label (see attached image). I tried this again and the problem exist, I also compared the command with that online, and haven't found the cause to this problem. What's wrong with my command? By the way, if I want to convert the label in a subject's space into talairach space, could the above command achieve this? The freesurfer I used was freesurfer-linux-centos4-stable-pub-v5.0.0 Any help would be greatly appreciated. Thank you in advance. Best, Jin

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Post-doctoral and data analyst positions (fMRI, MEG)
by Hasson, Uri 03 Nov '10

03 Nov '10

Applications are invited for two postdoctoral positions and one data analyst position funded by an ERC (European Research Council) Starting Grant. The research program examines the cognitive mechanisms and neural systems by which the human brain codes the recent past and predicts the immediate future. It uses neuroimaging, behavioral studies, and eye tracking methods. The ideal candidates for all positions are highlymotivated and creative individuals, capable of working independently and ingroups, who will thrive in a dynamic startup-like work environment. Prior experience with computational modeling of complex systems would be helpful. The research takes place at the Center for Mind/Brain Sciences at the University of Trento, Italy. Salaries are comparable to those offered by research institutions in the US and Europe, include benefits and health insurance, and are commensurate with training and experience. Expected starting date for all positions is Feb 1st, 2011. Interested candidates should Email a CV and a description of research interests to: Dr. Uri Hasson uri.hasson(a)unitn.it<mailto:uri.hasson@unitn.it> Center for Mind/Brain Sciences via delle Regole, 101 I-38060 Mattarello (TN) Italy Positions offered: a. Post-doctoral position (2-4 years) for fMRI research. The person will beresponsible for the design of several fMRI studies, conducting data analysis and leading the write-up of scientific work. The person will have access to the center’s onsite 4T fMRI scanner. REQUIREMENTS: expertise with fMRI design and analysis methods and a solid background in cognitive neuroscience. HELPFUL:knowledge of functional connectivity methods including those applicable to resting state data, analysis of perfusion (ASL) data, R/Matlab programming,good understanding of UNIX. Interest in MEG methods. b. Post-doctoral position (2-4 years) for Magnetoencephalography (MEG) research. The person will be responsible for the design of several MEG studies, conducting data analysis and leading the write-up of scientific work. The person will have access to the center’s onsite MEG apparatus and 4T fMRI scanner. REQUIREMENTS: expertise with MEG techniques and a solid background in cognitive neuroscience. HELPFUL: Knowledge of coherence analysis and pattern classifier methods; knowledge of fMRI analysis techniques and the integration of fMRI and MEG data. c. Data Analyst (2 years): The data analyst will be responsible for analysis of fMRI datasets, algorithm development, programming and conducting fMRI studies, and monitoring computer hardware. This position is ideal for college graduates who are technically inclined and are considering future graduate studies in cognitive neuroscience. REQUIREMENTS: Prior experience with fMRI analysis. HELPFUL: a bachelor's degree in psychology, computer science, math, cognitive science, neuroscience, or computer science, knowledge of Italian. Experience with diverse computing environments (Linux/OSX/Windows), programming (python/perl/shell scripting, or R) and relational databases.

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read data mri_vol2surf
by Oya, Hiroyuki (UI Health Care) 03 Nov '10

03 Nov '10

Hello Is it possible to load the outputs of mri_vol2surf with matlab? Thank you. Hiroyuki

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selxavg3-sess question
by Eyal Dechter 03 Nov '10

03 Nov '10

Hi, I'm analyzing fMRI data using freesurfer 5.0.0. I run into the following error when running selxavg3-sess. Any suggestions? Thanks, Eyal ************************************************************************************************************************************************* edechter@ba7:~/projects/stability/analysis$ selxavg3-sess -s tower001 -d ../data/ -analysis tower_allruns -c unstable-stable -no-preproc -------------------------------------------------------------- selxavg3-sess logfile is /u2/edechter/projects/stability/analysis/log/selxavg3-sess-bold-tower_allruns-101103112400.log -------------------------------------------------------------- ------------------------------------------- /u2/edechter/projects/stability/data/tower001 Wed Nov 3 11:24:01 EDT 2010 anadir = /u2/edechter/projects/stability/data/tower001/bold/tower_allruns DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 ------------------------------------------ ------- matlab output -------------------- Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B > Copyright 1984-2007 The MathWorks, Inc. Version 7.5.0.338 (R2007b) August 9, 2007 Warning: Duplicate directory name: /u2/edechter/matlab. To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> /software/Freesurfer/current/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> $Id: fast_selxavg3.m,v 1.55.2.8 2009/04/17 20:09:46 greve Exp $ outtop = /u2/edechter/projects/stability/data Extension format = nii ??? Undefined function or variable 'UseFloat'. Error in ==> fast_selxavg3 at 82 fprintf('UseFloat = %d\n',UseFloat); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n edechter@ba7:~/projects/stability/analysis$

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Re: [Freesurfer] Total GM and WM volumes
by bell0368＠umn.edu 03 Nov '10

03 Nov '10

I had a question about gray matter and white matter volumes in FreeSurfer version 4.5. Sorry, we have too many subjects to rerun easily through 5.0. There is no gray matter listed in aseg.stats in 4.5. The two options I see are using mris_volume or summing the aparc gray matter structures, are there pros/cons to this? More specifically, should the sum of the aparc gm regions equal the surface-based gm volume from mris_volume or will they be different? The aseg.stats also produces surface-based wm volumes, which I presume need the subcortical structures subtracted away, is there a command to do this with mri_segstats or do I just need to run a loop for every subcortical structure to get these corrected wm volumes? One last question. The mri_segstats says BrainSeg is computed WITHOUT partial volume correction. My understanding was in the aseg pipeline every voxel got assigned to a specific structure in aseg.mgz. So, I don't undestand how partial voluming comes into play? In BrainSeg are some voxels counted twice as being part of two different structures, and then this is fixed when the volume of each structure is reported in the aseg table? Also, it would be nice to be able to directly compare BrainSeg (no partial volume correction) with BrainSegNotVent (partial volume correction), is this possible? Thanks! Chris Bell University of Minnesota

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Talairach failure detection error
by Rapuano, Kristina (NIH/NIMH) [F] 03 Nov '10

03 Nov '10

Hello there, I am fairly new to freesurfer, and received an error message that I am not sure how to handle. I was running recon-all (-autorecon1 and -autorecon2) which then quit with this error: cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Oct 29 15:05:25 EDT 2010 /misc/data30/kyle/obesity_study/freesurfer/o_s307/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***Fp=0.0001, pval=0.0000 < threshold=0.0050) Linux thalamos 2.6.18-194.17.4.el5 #1 SMP Mon Oct 25 15:50:53 EDT 2010 x64 x86_64 GNU/Linux Please let me know if you have any idea what should be done about this. Thank you! Kristina ---- Kristina Rapuano Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C214 10 Center Drive MSC 1366 Bethesda MD 20892-1366 Phone: (301) 402-4419 E-Mail : rapuanokm(a)mail.nih.gov

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