Freesurfer May 2006

freesurfer@nmr.mgh.harvard.edu

50 participants
74 discussions

mri_vol2surf projfac-avg
by Don Hagler 15 May '06

15 May '06

In the stable3 version of mri_vol2surf, there is an option listed "projfac-avg". I can't tell if it is working or not. In the output messages, it says that ProjFrac = 0.5 (or whatever value is given with -projfrac) but there is no mention of the projfrac-avg min and max. Is the program doing what it is supposed to and not giving any relevant messages, or is the lack of messages an indicator that it is just doing the basic projfrac without averaging along the normal?

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two short questions, (flat maps, paint-sess)
by Sebastian Moeller 12 May '06

12 May '06

Dear fellow FreeSurfers, I got two small questions, I would be delighted to recieve some guidance on. The first one is for the monkey experts, I want to flatten the full hemispheres of my processed monkey brains, and I got around to cut away the medial wall to exclude those non-cortex areas from the map; where I am stuck now is making "tension relieve" cuts. Mainly my question is, what are the "canonical" cuts people make on monkey brains to flatten them fully (ideally I would like to see them on an inflated monkey hemisphre, but good landmarks would be also very welcome). Second question is about paint-sess/surf-sess. While trying to display my paint-sess created overlays on the inflated surfaces using surf-sess one out of three monkeys (total so far) gives real bad surface maps (they do not match the expected areas of activation from a tkmedit comparison run) and "spams" the surf-sess log with "MRISreadValues: vertex index out of range". If I set -projfrac from 0.5 to 1 I get acceptable maps for this monkey as well and no more errors. So to get to the point, what is the story behind -projfrac and what is it for? I would be really happy to learn more about this variable. Ahoi & Thanks in Advance Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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FS-FAST seq.info with multiple ntrs
by raij＠nmr.mgh.harvard.edu 12 May '06

12 May '06

Hi Doug, I have 3 functional runs that have a different number of TRs (from all subjects). The design is rapid event-related and the different runs are matched for statistical power despite that the number of trs is different for each run. I would like to contrast the runs with different ntrs as a first level analysis (within subjects to begin with). However there is only one seq.info file (that contains the ntrs value). Hence selxavg-sess fails if I try to analyze the runs at the same time. The Freesurfer wiki says that runs should have the same ntrs, but this is not possible in this case. Is there a way around this problem? For example, if selxavg-sess is the only step that reads the ntrs value, can I just change the contents of the seq.info file and do the selxavg-sess step for the runs separately? Or do other analysis steps also need a correct ntrs value? Also can I tell selxavg-sess to look for a custom filename instead of seq.info? This might make things more flexible. Thanks! -Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A. raij(a)nmr.mgh.harvard.edu

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recon-all error
by Joao Pereira 11 May '06

11 May '06

I have put my subjects through the recon-all procedure and most ended with no errors. But some ended with an error message, after the command line: mri_diff aseg.auto.mgz aseg.mgz saying: zcat: ~/.../mri/aseg.auto.mgz: unexpected end of file mghRead(~/.../mri/aseg.auto.mgz, -1): read error What is happening? Thanks! Joao Pereira

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(no subject)
by Sebastian Moeller 11 May '06

11 May '06

Hi Eric, > Message: 1 > Date: Wed, 10 May 2006 09:37:43 -0400 > From: "Faden, Eric (NIH/NIMH) [F]" <fadeneric(a)mail.nih.gov> > Subject: [Freesurfer] Skull Stripping a Macaque > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <323E7EA8AF5B4F42BBEE78D8B88816FB5595EF(a)NIHCESMLBX3.nih.gov> > Content-Type: text/plain; charset="iso-8859-1" > > Hey all, > > Is anyone using freesurfers mri_watershed to strip macaque skulls? Yes, some people are, there was even a short tutorial/howto posted on this very list (maybe you can find it in the archives). > If so what options are you using? Inlined after your mail you can find the script I use for skull stripping. The take home message from the howto, at least for me, was to try different sets of parameters with "-surf_debug" to nicely visualize the results. Unfortunately I got the best results so far only with an additional step of manual editing of the brainmask, as my scans suffer from inhomogenities (surface coil used for transmit and receive). For the manual edit steps I recommend the fine skull stripping howto found somewhere at the freesurfer wiki. One thing that caused slight hickups for me, was r´the fact that the erase funtion of the volume brush does not write zeros but ones, which messed up the segmentation later on, as the voxels with a value of one got much brighter by the normalisation step, but I digress... > I am currently trying to use it but am getting really bad results. Care to compare brainmasks to see what you consider bad? > I am also open to suggestions of other programs to try. > > -Eric Ahoi Sebastian ------Cut and paste from here----- #! /bin/csh -f # use tkmedit to mark critical whitematter points #setenv FIX_VERTEX_AREA # set the source directory... set src_dir = ../mri # set the target directory and file_name set targ_dir = ../mri #set reg = rotate_conf_2_atlas.dat #set targ_vol = rawavg.mgz #set controlpoints = ../tmp/control.dat set in_vol = ${src_dir}/nu.mgz #orig.mgz set t1 = ${targ_dir}/T1.mgz # do the skull stripping # repeat with -surf_debug until the parameters are okay, the run without... #mri_watershed -surf_debug -atlas ${targ_dir}/${t1} ${targ_dir}/brainmask.auto.mgz #mri_watershed -surf_debug -atlas -wat+temp ${targ_dir}/${t1} ${targ_dir}/brainmask.auto.mgz #mri_watershed -surf_debug -h 25 -wat+temp ${targ_dir}/${t1} ${targ_dir}/brainmask.auto.mgz #mri_watershed -h 10 -wat -n ${targ_dir}/${t1} ${targ_dir}/brainmask.auto.mgz mri_watershed -atlas ${targ_dir}/${t1} ${targ_dir}/brainmask.auto.mgz # create the brainmask ##cp ${targ_dir}/brainmask.auto.mgz ${targ_dir}/brainmask.mgz # check results... tkmedit -f ${targ_dir}/brainmask.mgz -aux ${targ_dir}/T1.mgz #cp ${t1} ${targ_dir}/brain.mgz # does a register file already exist? #if !(-e ${targ_dir}/${reg}) then # cp ./${reg} ${targ_dir}/${reg} #endif # convert to cor? or turn this sucker so that it works with mgz? #TODO: normalize with control points... ----Cut and paste until here--------------- -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 moeller(a)brain.uni-bremen.de AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen

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problem with tksurfer display
by adam walczak 11 May '06

11 May '06

Hello, I tried to display my data in tksurfer but only half of the brain is rendered. This is strange (obviously), because this has never happened before...all previous times I have used tksurfer have worked fine. Is there any reason this might have happened? It appears as if the wm volume has only the front half done...could this be the reason? Thanks, Adam adam --------------------------------- Yahoo! Messenger with Voice. PC-to-Phone calls for ridiculously low rates.

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Volume measurements.
by Goradia, Dhruman D 11 May '06

11 May '06

Hi all, In the aseg.stats file there is a measurement called Brain segmentation volume. Can someone tell me what it is? Is this same as whole brain GM volume? If not is there a way to compute that? -Dhruman

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Ventricular Volume in FreeSurfer?
by anthony gallo 10 May '06

10 May '06

Hello All, I am wondering......... Does FreeSurfer log ventricular volume? -Anthony

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Problems with FSGD file
by Martin.Ystad＠student.uib.no 10 May '06

10 May '06

Hi, I'd like to try out some simple regression analysis on some of my data. I've completed the tutorial until the mri_glmfit step where I get the error message: ERROR: gdfRead: gruppefil.txt is not formated properly I really can't see what's wrong with my file, I've even copy-pasted one of the example files from the tutorial just to check if anything is working at all, but it didn't work either. GroupDescriptorFile 1 Title KognitivAldringTEST21 Class Class1 CLASS Class2 Variables Age Input fs568 Class1 54 Input fs569 Class2 59 Input fs572 Class2 67 Input fs573 Class1 46 Input fs574 Class1 52 Input fs577 Class1 46 Input fs578 Class2 68 Input fs579 Class1 47 Input fs580 Class2 74 Input fs583 Class2 61 Input fs585 Class2 62 Input fs587 Class2 56 Input fs588 Class2 59 Input fs592 Class1 49 Input fs593 Class2 56 Input fs594 Class2 58 Input fs597 Class2 61 Input fs599 Class1 46 Input fs601 Class2 65 Input fs603 Class2 68 Input fs608 Class2 70 DefaultVariable Age I've tried with classes, without classes, with more variables and so on, but nothing seems to work. Any ideas on why I get this error message? I used emacs, vim and open-office to create my FSGD file, gruppefil.txt. It's probably just a trivial mistake somewhere, but I just can't seem to find it... Thanks, MartinYstad University of Bergen, Norway

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Skull Stripping a Macaque
by Faden, Eric (NIH/NIMH) [F] 10 May '06

10 May '06

Hey all, Is anyone using freesurfers mri_watershed to strip macaque skulls? If so what options are you using? I am currently trying to use it but am getting really bad results. I am also open to suggestions of other programs to try. -Eric

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Freesurfer May 2006