Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Error in preproc-sess in ver. 5
by Anders Hougaard 02 Jul '11

02 Jul '11

Hi all, While attempting to pre-process data for a retinotopy analysis with the following command: preproc-sess -surface song lhrh -fwhm 5 -sf sessid I get the following error when motion correction is started: Logfile is /Users/andershougaard/Programmer/freesurfer/retinotopy/log/mc-sess01-bold.log ------------------------------------------- /Users/andershougaard/Programmer/freesurfer/retinotopy/sess01 RunList: 001 002 ------- ************************** ----------- ------- Motion Correcting Run 001 ----------- ------- ************************** ----------- sess = sess01 Lør 2 Jul 2011 11:59:31 CEST mc-afni2 --i 001/f.nii --t 001/template.nii --o 001/fmcpr.nii --mcdat 001/fmcpr.mcdat ERROR: cannot find AFNI command 3dvolreg Any suggestions? Regards, Anders

1 0

Trac-all: using bvecs/bvals from FSL folder
by Jared Saletin 01 Jul '11

01 Jul '11

Hi Freesurfer experts, I was wondering if you all had some advice for getting trac-all up and running. I'm trying to work up a trac-all configuration file for a group of subjects, previously processed in FSL. We extracted the Siemens bvec and bval files for the FSL pipeline when importing the dicoms through dicom2nii. I know FSL bval and bvec files are organized in a different matrix shape from what Trac-all wants. Has anyone had sucess with transforming these files? Should/do I need to worry about whether to flip the orientation on bvec files as the images seem to get flipped in the early steps of Trac-all? Also is it possible to feed the configuration file a list of bvec files (for each subject) similar to how we feed it the dicom directory for each subject, or should I create a configuration script for each subject pointing to their bvec file specifically. Thanks in advance for help! Cheers, Jared

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questions about drawing functional rois
by Katie Bettencourt 01 Jul '11

01 Jul '11

I'm trying to draw an ROI by selecting the center of activation for a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks, Katie

2 8

Thickness measurements stats
by Ignacio Letelier 01 Jul '11

01 Jul '11

Hi forum Is it possible to get statistical maps of cortical thickness differences in the same subject? I.e. to know what areas differ most from the median -- Ignacio

2 1

freesurfer_home undefined variable
by Kat Mott 01 Jul '11

01 Jul '11

Hi there, I just installed freesurfer onto a mac os x. My computer seems to default to bash, so I created a .bashrc file in my home directory and added the lines: export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh but just in case I also created a .cshrc and added the c shell version of that code. I also created the .license file as per the installation instructions. Then I opened up the terminal, in bash, and did the export and source thing again. I also updated the SetUpFreeSurfer file so that it has the correct path: /Applications/freesurfer. However, when I try to test the installation and type in recon-all -s bert -autorecon1 (i have to use sudo as well bc it keeps telling me i don't have write permission) I always get back FREESURFER_HOME: Undefined variable. I've seen several other people post this same problem to this forum in the past but no one has ever posted a response that I can see. I tried reinstalling, and typing in the command from different directories, and sourcing again, but I always get back the same response. The really frustrating thing is, when I type echo $FREESURFER_HOME I get back /Applications/freesurfer which is correct! Any thoughts on what I'm doing wrong here? Thanks in advance.

1 0

bad skull strip - but doesn't affect surfaces
by Tetiana Dadakova 01 Jul '11

01 Jul '11

Dear list, For one of my subjects the skull strip is bad, but it doesn't (visually) affect neither surfaces nor segmentation (see the image in the attachment). In this case, do I have to edit the skull strip? Can it affect some calculation? Thank you, Tanja.

3 2

Rejoindre mon réseau sur LinkedIn
by Paula Diniz via LinkedIn 01 Jul '11

01 Jul '11

LinkedIn ------------ Paula Diniz souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Paula Diniz http://www.linkedin.com/e/-wptfe6-gpl23w9p-41/vLfSn8bYH8_5DFBPLmfTK84Tj6M6D… Voir l'invitation de Paula Diniz http://www.linkedin.com/e/-wptfe6-gpl23w9p-41/vLfSn8bYH8_5DFBPLmfTK84Tj6M6D… ------------------------------------------ SAVEZ-VOUS que vous pouvez être le premier informé quand un membre de votre réseau change de poste ? Les "Nouvelles du réseau" sur votre page d'accueil LinkedIn vous informe des évolutions de carrière dans votre réseau. Soyez informé(e) en premier ! http://www.linkedin.com/ -- (c) 2011, LinkedIn Corporation

1 0

error in qdec design analyze
by Sophy Zhu 01 Jul '11

01 Jul '11

Hi Freesurfers, There existed an error "Error in Analyze: Couldn't open file /usr/local/freesurfer/subjects/PD1/surf/lh.thickness.fwhm10.fsaverage.mgh", when I clicked on the button "Analyze" in qdec design. I have only done "recon-all" with my data (PD-MPR group and Controled-MPR group). Did I miss one step before qdec analysis? Thanks

2 1

queue software and routine to remove dura from brain
by Knut J Bjuland 30 Jun '11

30 Jun '11

Hi What kind of queue software is used for Freesurfer to enable multiple instance across several CPU in mulit-core system? Is thesse software available in either Fedora or Ubuntu? I am working with 14 years old image which has enlarged ventricles. What is the recommend setting to remove non-brain tissue like dura from the MRI pictures? Cheers Knut J Bjuland

3 2

Trouble downloading freesurfer v4.4
by Rachel Steinhorn 30 Jun '11

30 Jun '11

My lab uses freesurfer v4.4, and I'd like to install it on my PC, but the download doesn't seem to be available from the Archives. When I click on any version of the archived file or try to save it to disk, I get a page saying "The connection was reset, The connection to the server was rest while the page was loading." Trying to download other releases, such as v5.0 and v4.0.5, produces the same message. The mirror offered for some releases gives me a blank page. Are the files available elsewhere, or will they be put back up at some point? The version I'm looking for is for Mac OS 10.6 (freesurfer-Darwin-leopard-i686-stable-pub-v4.4.0-full.dmg) Thank You, Rachel Steinhorn

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