Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Beginner question
by David Grayson 26 May '11

26 May '11

Hey folks, I am totally new to freesurfer, so please forgive me… I am trying to open up an atlas in freesurfer that is in 4dfp.ifh format (or nii, if you like). Can anyone tell me how? Otherwise, I could try to reconstruct it straight from the T1 anatomical run, but when I try the following command, taken from the tutorial recon-all -i Scan_0002_Img_0160_MR.1.3.12.2.1107.5.2.32.35139.2011042716283971836201295 -subject 106382 –all I get errors at the nu_correct step, and it terminates. And I am running these commands in NX, if that makes any difference Thank you in advance for your help! David

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FreesurferEnv and matlab directory creation
by Peter J. Molfese 26 May '11

26 May '11

In the Mac version of Freesurfer, the FreeSurferEnv.sh script creates a matlab folder at ~/matlab. Can I change this location for running freesurfer on a grid (either Sun Grid Engine or Apple XGrid) where I won't always have access to a user folder? For instance, Xgrid runs jobs as an unprivileged user in a private directory (e.g. /private/var/xgrid/agent/tasks/TGSBflaF/working). Currently when I submit a job which sets up the freesurfer environment by calling the setup file and then a which to verify the environment is correct. The output shows that it executed the script and can now locate recon-all in /usr/local/freesurfer. But then I get a series of errors or warnings about matlab directory creation. Can I ignore these or silence them? Script: #!/bin/bash #setup Freesurfer export FREESURFER_HOME=/usr/local/freesurfer . $FREESURFER_HOME/SetUpFreeSurfer.sh which recon-all Output: INFO: /var/empty/matlab/startup.m does not exist ... creating /usr/local/freesurfer/bin/recon-all mkdir: /var/empty/matlab: Permission denied touch: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 213: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 214: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 215: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 216: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 217: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 218: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 219: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 220: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 221: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 222: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 223: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 224: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 225: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 226: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 227: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 228: /var/empty/matlab/startup.m: No such file or directory /usr/local/freesurfer/FreeSurferEnv.sh: line 229: /var/empty/matlab/startup.m: No such file or directory grep: /var/empty/matlab/startup.m: No such file or directory grep: /var/empty/matlab/startup.m: No such file or directory grep: /var/empty/matlab/startup.m: No such file or directory Peter J. Molfese, Ph.D. Postdoctoral Associate Haskins Laboratories 300 George Street, Suite 900 New Haven, CT 06511 peter.molfese(a)yale.edu

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Announcement: FreeSurfer gets social
by Martin Reuter 26 May '11

26 May '11

Hi everyone, FreeSurfer finally becomes more social! You can now 'like' us on Facebook: http://www.facebook.com/FreeSurferMRI (there is no option to hate us or express any more complex feelings, sorry ...) or follow us on Twitter: http://twitter.com/FreeSurferMRI to always be up to date. Additionally you can also reach our pages at http://freesurfer.net and the wiki at http://freesurfer.net/fswiki now isn't that easy to remember? You know how it is, you are on the road, for some reason google is not working (or you just don't want to let them know how often you look at our awesome but slightly old fashioned pages) and you just need to find out how to run your analysis .... freesurfer.net :-) The 'surfer.nmr.mgh.harvard.edu' links (in case they are hardwired in you brain by now) will of course continue to work. Cheers, your FreeSurfer Team

1 0

Repeated measures ANOVA with covariate
by Mayuresh K 26 May '11

26 May '11

Hi freesurfer experts, Is there a way to perform a repeated measures ANOVA with a between subjects factor (two groups)? I am interested in comparing cortical thickness differences between the matched scans between the two groups i.e. measures*group interaction. How would I setup this design in freesurfer? Thanks, Mayuresh

3 2

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

2 2

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.

4 5

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

2 1

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

2 2

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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