Freesurfer August 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
75 discussions

problem with diff-flirt
by Marcus Belke 14 Aug '07

14 Aug '07

Hi we are currently working on the DTI data and we are trying to get the mc-step running using diff-flirt. it does not work, although the unpacking and the dtrecon seem to work fine. I have attached the log-file and copied the error message at the bottom. Can anyone help? Thanks a lot! Best regards, Marcus -------- ERROR MESSAGE-------- ... ... Registering volume 1 flirt -in ./tmp/diff-flirt-8311/f-001.img -ref ./tmp/diff-flirt-8311/f-000.img -out ./tmp/diff-flirt-8311/f-001.img -omat ./tmp/diff2diff-001.mat -verbose 3 -dof 12 -searchrx -15 15 -searchry -15 15 -searchrz -15 15 -cost mutualinfo -searchcost mutualinfo -bins 256 WARNING!!!! Multiple image files detected: ./tmp/diff-flirt-8311/f-000.nii.gz ./tmp/diff-flirt-8311/f-000.img ./tmp/diff-flirt-8311/f-000.hdr STOPPING PROGRAM ERROR: flirt failed with status 1 ___________________________________________________________ Want ideas for reducing your carbon footprint? Visit Yahoo! For Good http://uk.promotions.yahoo.com/forgood/environment.html

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(no subject)
by Troy Mcan 13 Aug '07

13 Aug '07

Hi,I am wondering if part of this process can be turned into a script:I am forming ROIs in freesurfer using tksurfer and a long list of talairach coordinates. Here is my process:1) I use the "select_talairach_point x y z" function, then I click the point that is highlighted on the brain from the command, and note the vertex point.2) Once all of the talairach coordinates have been entered in with this method, the brain surface is filled with a bunch of "dots." I manually scan the brain and note which points form the boundary of the region.3) Using the command "mark_vertex # 1", I mark the boundary vertices of this "spotted region". Once these are marked, I use the command "path_new_path_from_marked_vertices".4) This forms a path around the boundary vertices. I use the "make closed path" button to close this boundary, then fill it in and save it as a label.I am looking for a way to keep the list of talairach points saved in a file. I have upwards of 200 points that I need to type in continually for each subject, and I would like to bring them into tksurfer in one step (scripted, perhaps?) and have them marked on the brain surface, so I can manually proceed to find the boundary vertices, etc.etc. I am not too concerned with scripting anything past step 1.I would greatly appreciate any help! Thanks! _________________________________________________________________ Messenger Café — open for fun 24/7. Hot games, cool activities served daily. Visit now. http://cafemessenger.com?ocid=TXT_TAGLM_AugWLtagline

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tkmedit dev version
by Chuan.Chih.Yang＠rwth-aachen.de 13 Aug '07

13 Aug '07

Dear list, I have a problem to open tkmedit under dev version, here is the message I got. [MPIB7193-R-52c:~] jackie% tkmedit X Error of failed request: BadRequest (invalid request code or no such operation) Major opcode of failed request: 129 (Apple-DRI) Minor opcode of failed request: 1 () Serial number of failed request: 15 Current serial number in output stream: 15 [MPIB7193-R-52c:~] jackie% Thank you for the help jackie

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Fixing defects on inflated brain
by Nandita Shetty 13 Aug '07

13 Aug '07

Hi, I ran the first two steps of recon-all and it completed with no errors. I took a look at the inflated brain and it (the shape) does not seem right. There are some dimples, bumps etc which I know how to fix but I cant seem to figure out what is causing the deformed shape. If you could give me a pointer or two regarding this, it would be very helpful. Thanks in advance ! :) Env : nmrstdenv Machine name : Marvin SUBJECTS_DIR : /autofs/space/marvin_001/users/MRI/WMA/ SUBJECT : 002201

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show the results
by Ning Liu 10 Aug '07

10 Aug '07

I copied some subjects' data to my computer, but i cannot run the surfer here is the command line: tksurfer MGH_Ruphert lh inflated screen output surfer: current subjects dir: /Users/lning/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /Users/lning/subjects/MGH_Ruphert surfer: ### Could not find anatomical header information -- When was the last time you had a conversation with the moon or made a wish on a falling star? The time is now.

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free surfer download issues
by Jeffrey Dutschke 09 Aug '07

09 Aug '07

Hi all, I have tried several times to download the free surfer software, and have thus far failed to do so because the download stalls at around 800mB into the file download. Are you able to advise as to how I might overcome this problem. Specifically I have tried to download both the Apple intel i686 and tiger file. I have been unsuccessful in attempts to download it using a web-browser, a ftp client, and through the terminal command line. I hope to be able to use the software to generate the surface of the brain of a sheep for which we have CT and MIR scan data for an FE model of impact and injury. Thankyou Jeffrey Dutschke

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Problem met on fsfast tutorial data
by lan lin 09 Aug '07

09 Aug '07

I followed the Fsfasttutorial to learn fsfast. But when I run tkregister-sess -s mgh-101.1 -regheader, I always get such error message tkregister-sess logfile is /san1/acat/free/fun/fsfast-tutorial/fb1-preproc-study/log/tkregister- sess.log -------------------------------------------------------------- Session: /san1/acat/free/fun/fsfast-tutorial/fb1-preproc-study/mgh-101.1---------------- Thu Aug 9 15:19:10 MST 2007 ERROR: fbph1-101 is not in SUBJECTS_DIR SUBJECTS_DIR is /san1/acat/free/fun/fsfast-tutorial/fb1-preproc-study thanks

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RE: [Freesurfer] determining sizes of clusters at given CWP cutoff
by Don Hagler 09 Aug '07

09 Aug '07

There is no reason why you shouldn't be able to get the cut-off size from monte carlo simulations. It just depends on the program you use to do it. For example, AFNI's AlphaSim gives cluster sizes as a function of corrected p-value. By the way, monte carlo simulations are a waste of time. Keith Worsley's "Random Field Theory" method (http://www.math.mcgill.ca/keith/fmristat/toolbox/stat_threshold.m) can be used to directly (in seconds) estimate the cluster size thresholds given: total surface area number of vertices fwhm smoothness I've found (Hagler et al., Smoothing and cluster thresholding for cortical surface-based group analysis of fMRI data, NeuroImage, 2006) that RFT and monte carlo simulations give practically identical results. See the attached matlab script for a wrapper around Worsley's code to calculate the cluster size thresholds using RFT. >From: Robert Levy <levy(a)nmr.mgh.harvard.edu> >To: Freesurfer(a)nmr.mgh.harvard.edu >Subject: [Freesurfer] determining sizes of clusters at given CWP cutoff >Date: Fri, 03 Aug 2007 11:44:33 -0400 > >Hi, > >I was trying to figure out if there is any way to determine the exact size >at which clusters becomes significant given a specified significance, and >it appeared from the mc-corrected overlay that in this overlay the clusters >do not continously change in size but appear discretely at a given >threshold and are the same size at higher thresholds in an all-or-nother >sort of way. I take this to mean that because the monte carlo simulation >was performed at a given threshold, the clusters at that threshold size are >corrected for mutiple comparisons based on the probability distribution of >the chance data (though I don't know the details). Because it is done in >this way, it seems I would either have to run several monte carlo >simulations, at successively higher minimum thresholds, in order to arrive >at the critical cutoff sizes for significance. This is impractical, so I >guess my question is, does the way in which the monte carlo simulations are >done preclude the possibility of getting the cluster sizes at which they >will have a certain CWP value, or is there some way of doing this? > >Thanks, >Rob > >-- > >Robert P. Levy, B.A. >Research Assistant, Manoach Lab >Massachusetts General Hospital >Charlestown Navy Yard >149 13th St., Room 2611 >Charlestown, MA 02129 >email: levy(a)nmr.mgh.harvard.edu >phone: 617-726-1908 >fax: 617-726-4078 > >http://nmr.mgh.harvard.edu/manoachlab > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _________________________________________________________________ Messenger Café open for fun 24/7. Hot games, cool activities served daily. Visit now. http://cafemessenger.com?ocid=TXT_TAGHM_AugHMtagline

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mri_watershed
by nima＠nmr.mgh.harvard.edu 08 Aug '07

08 Aug '07

hi, Under freesurfer, how can I force mri_watershed to create 5012 triangles (ico 4) instead of 20480? cheers nima

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Preproc-sess failed for tutorial data
by lan lin 08 Aug '07

08 Aug '07

I followed the Fsfasttutorial to learn fsfast. But when I run preprocessing (preproc-sess -s mgh-101.1 -fwhm 5), I always get following error message /san1/acat/free/fun/fsfast-tutorial/fb1-preproc-study/mgh-101.1 cat: seq.info: No such file or directory cat: seq.info: No such file or directory cat: seq.info: No such file or directory ERROR: seq.info file does not appear to be formated correctly Try running fixseqinfo-sess. ERROR: mc-sess failed thanks Lan

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Freesurfer August 2007