Freesurfer

freesurfer@nmr.mgh.harvard.edu

24 participants
30076 discussions

problem with flattening
by Doris Tsao 04 Feb '07

04 Feb '07

Hi, I'm trying to make flatmaps of some monkey brains, and am having the following problem: the map never unfolds properly, there is always a section where it folds over itself. Any idea what that's due to? thanks! doris

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Problem with T1 intensities
by Dan Dillon 03 Feb '07

03 Feb '07

Dear FreeSurfers, I have a subject whose T1.mgz white matter values are consistently around 160, instead of 110. I figure I will have to tweak mri_normalize and re-run autorecon1 to fix this--am I right? If so, any tips regarding what flags and arguments will help address this problem? Thanks! Dan Dillon

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some questions about volumes of aseg, .aparc, .aparc.2005s
by Woo Suk, Tae 03 Feb '07

03 Feb '07

.Bold { font-weight: bold; } .Title { font-weight: bold; font-size: 18px; color: #cc3300; } .Code { border: #8b4513 1px solid; padding-right: 5px; padding-left: 5px;color: #000066; font-family: 'Courier New' , Monospace;background-color: #ff9933; } Dear Freesurfer experts. I have some questions about calculated volumes by freesurfer. 1. Are the volumes in aseg, .aparc, .aparc.2005s absolute volumes measured in naive space or volumes measured after spatial normalization. 2. How much accurate the volumes (hippocampus, amygdala, thalamus, insula, precentral, etc) in aseg, .aparc, .aparc.2005s. And they are verified? 3. Are the volumes in lh(or rh).aparc gray matter volumes? 4. What is meaning G_*, and S_* in lh(or rh).aparc.a2005s? 5. How can I separately see the strucures of .aparc, .aparc.2005s in pial surface rendering? Woo Suk, Tae Ph.D Seoul, Korea

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timecourse overlay
by T. Song 02 Feb '07

02 Feb '07

Hi Bruce: Is there a way that I can load the MEG timecourse data on the freesurfer surface? Is it possible that we could get the timecourse waveform for a specific point on the surface? Thanks! Tao

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transforms
by Chacko Cherian 02 Feb '07

02 Feb '07

Hello all, Is there some information on the wiki about the srctoDst voxel-to-voxel transform and the rastoRAas transform? THAnks Chacko. ____________________________________________________________________________________ Sucker-punch spam with award-winning protection. Try the free Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/features_spam.html

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converting from siemens IMA to mgz
by Binyam Nardos 02 Feb '07

02 Feb '07

Hi all, I just loaded raw structural scans into one of my subject directories. They are of siemens IMA format and I used the following command: mri_convert -it siemens -ot mgz 001/ 001.mgz I then got the following error: reading from 001/... ERROR: could not parse 001/ ERROR: siemensRead(): 001/ I tried finding similar problems in the threads but nothing yet. Appreciate any help, Binyam Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601 The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.

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Variability and randomness in algorithms
by Bo Shi 02 Feb '07

02 Feb '07

Hi, Sorry to dredge up an old thread, I was curious about the details on where randomness is introduced in the following programs (beyond the normal floating points issues): > mris_smooth -seed 1234 > mris_sphere -seed 1234 > mris_fix_topology -seed 1234 > mris_ca_label -seed 1234 I assume that the Segonne, Grimson, and Fischl paper on the genetic algorithm for cortical surface correction applies to mris_fix_topology? Is it also the case that the randomness is injected in other min/maximization-type algorithms in the other functions? > RE: [Freesurfer] variability > Nick Schmansky > Thu, 21 Dec 2006 10:14:12 -0800 > > Valentina, > > The randomization in the algorithms accounts for about a 0.02% change > in thickness results. You can disable randomness (or rather, force > seeding the rng with same number) by including the flag -norandomness > with recon-all. This flag is available in v3.0.4. > > In older versions, do this to disable randomness: create a file called > xopts containing this text: > > mris_smooth -seed 1234 > mris_sphere -seed 1234 > mris_fix_topology -seed 1234 > mris_ca_label -seed 1234

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mri_convert orientation
by Fornito, Alexander 01 Feb '07

01 Feb '07

Hi, I'm trying to convert a series of siemens dicom mosaic format files to analyze format, while reorienting at the same time. Running the command below converts and reorients only the filename specified in the command line (which is the first file in the series), whereas leaving out the --out_orientation flag converts all the files in the series. Is it only possible to convert AND reorient one file at a time? Or is there something I'm missing that would allow me to convert and reorient all the files in the series with a single command? Thanks, Alex mri_convert -it siemens_dicom 93663320 -ot analyze test_ --out_orientation LPS Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 email: alexander.fornito(a)wh.org.au

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Re: bad surfaces?
by Glenn Lawyer 01 Feb '07

01 Feb '07

Hi, I'm wondering if I missed something between the 3.0.3 and 3.0.4 release. Does the latest version constrain medial pial surfaces across hemis? There was a question on this on 5 may 2006, (quoted below) and at that time there was no constraint. > no, they aren't constrained across hemis, although of course they should be. > --Bruce > On Fri, 5 May 2006, Josh Snyder wrote: >> I see this on a ton of datasets. Is it a known issue? Is there an easy >> correction? Thanks,Josh freesurfer-request(a)nmr.mgh.harvard.edu wrote: > > Message: 3 > Date: Wed, 31 Jan 2007 12:16:19 -0600 (CST) > From: Derin Cobia <derin(a)conte.wustl.edu> > Subject: [Freesurfer] Bad surfaces? > > I reran our subjects from "final_surfaces" on through autorecon3 using > 3.0.4 to correct for the pial surface crossover at the midline (as > recommended by Bruce). > -Derin > > > > ****************************************** > -- -------------------------------------- I'm only in it for the glory . + Glenn Lawyer + + +352 661 967 244 + + Instituttgruppe for psykiatri + + Postboks 1130 Blindern + + 0318 Oslo + + http://folk.uio.no/davidgl + +++++++++++++++++++++++++++++++++++:)

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tkmedit/tksurfer fail at startup with X BadValue errors
by Graham Wideman 31 Jan '07

31 Jan '07

Folks: On an installation that had been working, suddenly we're getting fatal errors on starting either tkmedit or tksurfer. These appear to be errors trying to perform X functions. Command lines and responses shown below. I am not aware of recent changes to the environment (new software installed etc) that would relate to this... but one never knows. 1. Anyone happen to know exactly what solves this? 2. Any clues as to how to troubleshoot would be helpful (eg: is there a log that these programs write into at this early of a stage in startup?) Thanks, Graham ================= Initialization ================= [graham@gwlinux ~]$ tcsh [graham@gwlinux ~]$ source /brain-bin/fs_20060528/centos4/freesurfer/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos4-stable-pub-v3.0.3 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /brain-bin/fs_20060528/centos4/freesurfer FSFAST_HOME /brain-bin/fs_20060528/centos4/freesurfer/fsfast SUBJECTS_DIR /data/Structural/FreeSurfer_2007/segmixtest/bxbaseline FUNCTIONALS_DIR /brain-bin/fs_20060528/centos4/freesurfer/sessions MINC_BIN_DIR /brain-bin/fs_20060528/centos4/freesurfer/mni/bin MINC_LIB_DIR /brain-bin/fs_20060528/centos4/freesurfer/mni/lib PERL5LIB /brain-bin/fs_20060528/centos4/freesurfer/mni/lib/perl5/5.8.0 GSL_DIR /brain-bin/fs_20060528/centos4/freesurfer/lib/gsl QTDIR /usr/lib/qt-3.3 TCLLIBPATH /brain-bin/fs_20060528/centos4/freesurfer/lib/tcltktixblt/lib FSL_DIR /brain-bin/fs_20060528/centos4/freesurfer/fsl ================= tkmedit: ================= [graham@gwlinux ~]$ which tkmedit /brain-bin/fs_20060528/centos4/freesurfer/bin//tkmedit [graham@gwlinux ~]$ tkmedit X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 78 (X_CreateColormap) Value in failed request: 0x0 Serial number of failed request: 15 Current serial number in output stream: 17 [graham@gwlinux ~]$ ================= tksurfer ================= [graham@gwlinux bxbaseline]$ tksurfer 85432 rh white surfer: current subjects dir: /data/Structural/FreeSurfer_2007/segmixtest/bxbaseline surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /data/Structural/FreeSurfer_2007/segmixtest/bxbaseline surfer: Reading header info from /data/Structural/FreeSurfer_2007/segmixtest/bxbaseline/85432/mri/T1.mgz surfer: vertices=184105, faces=368206 surfer: single buffered window Received X error! Error code : 2 Request code : 78 Minor code : 0 Error text : 'BadValue (integer parameter out of range for operation)' Received X error! Error code : 12 Request code : 1 Minor code : 0 Error text : 'BadColor (invalid Colormap parameter)'

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