Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Unpacking DICOM directory
by Ed Gronenschild 26 May '11

26 May '11

Hi, I'm trying to use unpacksdcmdir and noticed that it only works with Siemens DICOM files. I don't understand this restriction, because the two tags on which is scanned (run/series number, tag 0x20,0x11 and protocol name, tag 0x18,0x1030) are present also in e.g. Philips DICOM files (I even assume that both these tags are present in all DICOM files, as it is a standard). So my question is: is it possible to remove the restriction and make the tool more generally applicable? Kind regards, Ed

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letters of support
by Bruce Fischl 26 May '11

26 May '11

Hi All, I am preparing the competing renewal for the main R01 that funds FreeSurfer engineering, documentation, development and support. It would be extremely helpful to have letters from our user community to indicate the importance of this type of support, which of course is not the usual hypothesis-based NIH R01. Specifically, if people could indicate: 1. How many datasets you have been able to run through FS. 2. How you think FS has improved since 2006 since the grant began (in terms of level of support, robustness of the tools, documentation, etc....) 3. A (brief) description of the type of research you are using FS for, with citations for papers that you have published using FS if any. 4. Some indication of whether the support you get from us was important in your ability to carry out this research. thanks, Bruce

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FS5.1 OSX: message during the first step : dyld: library not loaded
by Hyunwoo Lee 26 May '11

26 May '11

Dear FreeSurfer Hello, I am currently trying the following freesurfer version: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwi…> and I noticed the following. During the first step ( recon-all -i invol1 -i invol2 -subjid your_subject_name ), the console displays the following messages: ------------------------------------------------------------------------------- Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is ******* Actual FREESURFER_HOME /Applications/freesurfer Darwin mrs.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:17:16 PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386 dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib Referenced from: /Applications/freesurfer/bin/mri_robust_register Reason: image not found Trace/BPT trap dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib Referenced from: /Applications/freesurfer/bin/mri_robust_register Reason: image not found Trace/BPT trap ----------------------------------------------------------------------------- I confirmed that the above message does not appear on the linux version of FS5.1. So, I was wondering if the above situation will cause any problem down the pipeline? I just kept it running for ~18 hours and it seems to be going fine (i.e. at least no problem until the "mris_ca_label" step) Thank you very much, and I look forward to hearing from you.

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fsaverage of freesurfer v5
by Dai Dai 25 May '11

25 May '11

hi, all does freesurfer v5 have multiple fsaverage subjects with varying number of vertices? see the following mails; where does fsaverage6 locate? -------------------------------------------------------------------- Nick Schmansky nicks at nmr.mgh.harvard.edu Fri Sep 10 15:23:09 EDT 2010 * Previous message: [Freesurfer] two questions about freesurfer * Next message: [Freesurfer] memory error and WM edits * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] 1. in freesurfer v5, there are now multiple fsaverage subjects with varying number of vertices. fsaverage6 has about 40,000 vertices per hemi, so you can just include the flag: --target fsaverage6 after the -qcache flag, and it will use that as the target instead of fsaverage (producing files like 'rh.thickness.fsaverage6.mgh', which will have 40K thickness samples). -------------------------------------------------------------------- On Fri, 2010-09-10 at 15:19 +0800, Dai Dai wrote: > Hi, all > > I am a new user of freesurfer and now I have two questions. > > 1. For my work, the number of vertex in surface data is too much to > process. How can I downsample the surface mesh as well as the > curvation file (e.g. thickness)? The vertex number of fsaverage > template is ~160,000, normally more than that of every subject. Can I > construct an average surface of less vertexes or downsample the > fsaverage surface to that of ~20000 vertexes and then transform all > the subjects using these templates with less vertexes (using recon-all > -qcache)? 2011-05-26 Dai Dai

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qdec error message
by Olivier Piguet 25 May '11

25 May '11

Good afternoon, When running qdec, I receive the following error message: Writing to /Volumes/workingdata/FTD/T1/subjects/qdec/Untitled/contrasts.sig.mgh reading group avg surface area 822 cm^2 from file ERROR: could not find volume /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig. Does it exist? Reading in average area /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.white.avg.area.mgh reading group avg surface area 1041 cm^2 from file ERROR: could not find volume /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig. Does it exist? Reading in average area /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.pial.avg.area.mgh reading group avg surface area 822 cm^2 from file ERROR: could not find volume /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig. Does it exist? I have run all subjects with qcache and I am using fsaverage. I have checked the files in the fsaverage folder. Although the file orig. does not exist, there is a file called orig.mgz in the mri folder. I have tried to rename this file (i.e., removing the 'mgz' part) but this did not remove the error. Any suggestion would be appreciated. Thanks Olivier Piguet Neuroscience Research Australia Sydney NSW, Australia

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for low resolution monitors, tksurfer dialog fix
by Krish Subramaniam 25 May '11

25 May '11

Hi all, It's been pointed out that tksurfer's "Configure Overlay Display" dialog gets clipped for low resolution monitors where it's impossible to see and interact with the buttons. This is how it looks: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksu… ( Thanks to Gonzalo Rojas Costa ) To fix this ( only for FS v5.1.0 ), copy the file ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksu… to $FREESURFER_HOME/lib/tcl/ The new dialog should look like this: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksu… -Krish

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Export table of cluster stats from Qdec
by Jeni Chen 25 May '11

25 May '11

Hi, I have 2 questions regarding Qdec: 1. We would like to save the results of 'cluster stats' (the printout on the terminal after pressing the "Find clusters and go to max" button) to a text file. Is there a way to do that? Or is it automatically saved in somewhere and where would that location be? 2. Also, would it be possible to save the plot information at cluster's max in a particular region and later on read them in a text or excel file? Thank you for your help. Jeni

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analysis interpretion question
by Ilana Hairston 25 May '11

25 May '11

Hi there, I have two behavioural variables that are inversely related to each other. One was correlated with thinning of the posterior insula (using glm_mri), while the other is positively correlated with the putamen volume (extracting aseg tables and running in SPSS). The region of the insula is basically adjacent to the putamen. So i'm wondering whether these findings are related, and how would i go about teasing this apart. Thanks ilana

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Freesurfer GLM and measurement of an interaction
by Chris Hyatt 25 May '11

25 May '11

For a two factor GLM analysis with two levels, I'm uncertain as to why the Freesurfer GLM measurement of the interaction effect of say, group and gender, is a t-test and not an F-test. In my case, my factors are group (healthies vs patients) and gender (male vs female). For a 2x2 two-way ANOVA analysis, the measurement of an interaction is always an F-test. For example, on the following Freesurfer FSGD Wiki page (Four Groups (Two Factors/Two Levels), No Covariates) http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G0V under Contrast 7, it claims the gender-x-handedness is a t-test. Is this contrast a t-test or actually an F-test? Thanks, Chris

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new FreeSurfer release, v5.1
by Nick Schmansky 25 May '11

25 May '11

FreeSurfer Users, The long anticipated, much awaited, release v5.1 of FreeSurfer is finally here. It's everything 5.0 should have been, and now much more! The ReleaseNotes page describes the new features and changes: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes and the Download page will take you to the tarballs: https://surfer.nmr.mgh.harvard.edu/fswiki/Download As always, we recommended not mixing results in a group study processed with other versions or across OS platforms. This new version can still be used to view and post-process results, or to re-run recon-all (edits are retained). The FreeSurfer Team

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