Freesurfer February 2008

freesurfer@nmr.mgh.harvard.edu

71 participants
87 discussions

Extracting brain region with a mask
by Anil Roy 19 Feb '08

19 Feb '08

Hello All, I used mri_binarize to create stg masks (inclusive of gray and white matter). I'm trying to take this a step forward to see if I can extract the actual brain region encompassed by the mask - in other words, is there a way to cut out the portion of the brain that the mask encloses. So instead of this being a binary mask with stg =1 and everything else 0, could we get everything else to be 0 and stg to remain as it is. The main reason I want to do this is that I have some other software that can create intensity histograms for such extracted regions and also perform some other analysis. Thanks, Anil.

2 1

creating a custom overlay
by Catherine Hartley 19 Feb '08

19 Feb '08

Hi, I'm wondering whether it is possible to create an overlay consisting of a subset of clusters from a sig.mgh file, filtered according to custom criteria and preserving the significance value of each vertex in the remaining clusters so that the overlay can be thresholded as I choose. For example, if I wanted to remove a selected set of ten clusters from a sig.mgh file to yield a new one, is there an easy way to do this? Thanks, Cate

3 5

How to see the effect of external regressors?
by Zhen Zonglei 19 Feb '08

19 Feb '08

Dear FS and fsfast expert: We want to know the effect of some external regressors such as the reaction time of every trial. We found that external regressor can be integrated into the GLM model with mkanalysis-sess's 'extreg' option, but we did not find the way to do comparison of these external regressors and see the effects of them.Do you know how to do it with fsfast? Thanks in advance for any help! Zonglei Zhen

2 1

mri_label2vol
by bell0368＠umn.edu 19 Feb '08

19 Feb '08

Freesurfers, I wish to use a concatenated .mat file created using FSL tools within the mri_label2vol tool. Is this possible? Is it possible to convert a .mat file to a register.dat file, which seems to be the format that mri_label2vol expects? Also, what interpolation method does mri_label2vol use, out of curiousity. Chris Bell

2 1

Problem make_average_subject
by Juergen Haenggi 19 Feb '08

19 Feb '08

Dear FS experts I tried to run make_average_subject in the past with 92 subjects and got the following error: Cannot allocate memory. This is now on the to-do list of the FS website. Then I bought some additional RAM and changed from OS X tiger to leopard. Now I tried it again and get this error: [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit descriptors 4096 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% limit cputime unlimited filesize unlimited datasize 6144 kbytes stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 4096 memorylocked unlimited maxproc 266 [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% make_average_subject --subjects SNPs_Vp* limit: descriptors: Can't remove limit (Invalid argument) [Macintosh-3:/Applications/freesurfer/subjects] juergenhaenggi% I set the descriptor limit to 4096, but the make_average_subject command will not start anymore. Any idea what is wrong here? Thanks in advance Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

5 12

'.license' file
by Henrique Fernandes 19 Feb '08

19 Feb '08

The installation was successful! I have created the file in 'pico', as Nick Schmansky told me to do, and fortunately the file '.license' was successfully created. Thank you all for your kind attention, Regards, Henrique Fernandes

1 0

".license" file
by Henrique Fernandes 19 Feb '08

19 Feb '08

Thanks for the suggestions, I'm now having another problem. I created a .license file with the information about my license. Although, to keep the file stored I must have a name for it other else the system won't allow me to create that file. So, after giving a random name to the file, during the test for installation I received an error message like the one above: -------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- How should I create the file .license? Any suggestions? Thanks in advance fot he help, Regards Henrique Fernandes

3 2

Problem: 'source'
by Henrique Fernandes 19 Feb '08

19 Feb '08

Dear collegues, I had a problem during the installation of Freesurfer on my computer. I have a Mac Intel, and since the shell I'm using is the bash, I've entered those two lines written in the installation instructions: export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh The problem is that when I wrote the second line I received an error message like the one above: bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh bash: /Applications/freesurfer/SetUpFreeSurfer.sh: No such file or directory What would you recommend me to do? I would prefer to continue the installation only after solving this problem, since it is recommended by you to "perform the setup described at this point in the time". Hope you can solve my problem, and I'll be able to use your program very soon, Best regards, Henrique Fernandes _________________________ Researcher in Medical Imaging

2 1

FS download
by Gallo, Antonio (NIH/NINDS) [F] 18 Feb '08

18 Feb '08

Hi All, Just a couple of questions: 1) are there any differences between Linux-CentOS4 and Linux-CentOS5 as platforms for FS4.0.2.? 2) which version of FS should be downloaded for a 64bit machine with Linux-CentOS5 ? Thanks a lot for your help, Antonio

2 1

mri_ca_register error
by Alan Anticevic 16 Feb '08

16 Feb '08

Hi, I was hoping someone can help me with this issue. We are running the recon-all command on a bunch of subjects and most of them (16/21) process just fine (no errors and nice surfaces), however some (5/21) subjects encounter an error like this: Segmentation fault ERROR: mri_ca_register with non-zero status Darwin ccpmac1.wustl.edu 9.1.0 Darwin Kernel Version 9.1.0: Wed Oct 31 17:46:22 PDT 2007; root:xnu-1228.0.2~1/RELEASE_I386 i386 recon-all exited with ERRORS at Wed Jan 16 19:56:59 CST 2008 All the subjects were collected using the same pulse sequence (MPRAGE) and are of good quality. I attached an example log file. Any suggestions how fix this error? Any advice would be much appreciated. Thank you. Best, alan Alan Anticevic -------------------------------------------------------------------- Deptartment of Psychology - CCP Lab Washington University in St. Louis One Brookings Dr. Campus Box 1125 Tel: 314-935-8547 St. Louis, MO 63110 Email: aanticev(a)wustl.edu --------------------------------------------------------------------

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Freesurfer February 2008