Freesurfer

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30099 discussions

Trying to make GCA atlas, problem with talairach file
by N/A N/A 15 Oct '14

15 Oct '14

Hi Freesurfers, I am trying to make an atlas using the GCA algorithm and the error message I just got is asking for the talairach.xfm file. The scans I am using were originally run through freesurfer 3.1 and talairach processing was not done. What do you suggest I do to use these scans in my atlas I am trying to create? Kind regards, Alexarae

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mri_anatomical_stats for volume
by Vy Dinh 15 Oct '14

15 Oct '14

Dear experts, Can one use mri_anatomical_stats to extract volume information? I have a set of labels that has been mapped to each subject's native space (using mri_label2label; the original labels were extracted from group comparisons using mri_glmfit). I have successfully extracted the thickness measures using mri_anatomical_stats and am curious if this can be done with the labels from my volume group comparisons as well. This is the command I used for the extracting the thickness measures: mris_anatomical_stats -l $label -t $hemi.thickness -b -f $sublabel $sub $hemi Thanks in advance, -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health

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Issues launching tksurfer
by Claire Morley 15 Oct '14

15 Oct '14

Good Morning, I have a quick question regarding the launch of tksurfer. I have recently downloaded Freesurfer onto a Mac OSX after having some experience with it on a previous Mac. However, it had been preinstalled on that Mac, and I am afraid that I have perhaps installed it wrong on this one as when I test the launching of qdec and tksurfer, nothing happens. The terminal doesn`t spit out a command error, but it never launches the program. This was also a problem on the previous Mac for qdec but not for tksurfer. Therefore, I have tried to install everything again from square one and am not sure why now neither program is launching. I am simply trying to test the command "tksurfer bert lh pial". My environment is setup with Freesurfer and I am trying to launch from the surfs directory, as that worked on the previous Mac, but it is still giving me nothing. Any tips you could provide me with? All the best, Claire -- *We shall not cease from exploration. And the end of all our exploring will be to arrive where we started and know the place for the first time- T.S. Eliot*

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T2/FLAIR for pial surface refinement
by Eva Hilland 15 Oct '14

15 Oct '14

Dear FreeSurfer experts I have been trying to do a test with T2/FLAIR for pial surface refinement, with T1 and FLAIR NiFti images for one subject, FS v5.3. As described in Release Notes i updated the recon-all script in /freesurfer/bin. I have also tried to do the -bbr-init-header . I used the forllowing commands: 1) recon-all -s [subject_name] -i T1.nii -all (wich ran succesfully.) 2) recon-all -autorecon3 -s [subject_name] -FLAIR FLAIR/flair.nii -FLAIRpial I have tried this many times the past week, on my MacBookPro and also on my lab computer running on Linux RedHat 6. But I get the "recon-all exited with ERRORS" every time, with the error message "Cannot allocate memory". I attached the recon-all.log. I also pasted the system information for my computer at the end of this e-mail. Is there anything I do wrong in the command? Does this process require a more powerful computer than you would need for regular recon-all? Thank you very much in advance! Best regards, Eva lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 6 On-line CPU(s) list: 0-5 Thread(s) per core: 1 Core(s) per socket: 6 Socket(s): 1 NUMA node(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 44 Stepping: 2 CPU MHz: 2659.928 BogoMIPS: 5319.85 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 12288K NUMA node0 CPU(s): 0-5

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QAtools - tkmedit snapshots all black (X server issue?)
by Melanie Ganz 15 Oct '14

15 Oct '14

Hi, I am trying to use the QA tools and take some tkmedit snapshots. I can get everything to work fine in Boston, but when I run on our local Linux server what tkmedit shows looks correct, but the output gifs of tkmedit are all black with no content. The tksurfer images show and save fine. I am suspecting that it is an x server issue with how I log into our Linux cluster here, but has anyone had the same problem before? Cheers, Mel -- Melanie Ganz, MSc, Ph.D. Neurobiology Research Unit University of Copenhagen Rigshospitalet Rockefeller Center Juliane Maries Vej 28/30, 3. DK-2100 Copenhagen Denmark phone: +45 3545 6718 e-mail: Melanie.Ganz(a)nru.dk web: http://melanie.clausundmelanie.de/

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Post-docs positions on MR-PET method development and application in Lyon (France)
by Marjorie Villien 15 Oct '14

15 Oct '14

Dear all, We are offering two post-doc positions on a newly installed MR-PET scanner in Lyon (France), at the CERMEP, for the LILI project (“Lyon Integrated Life Imaging: hybrid MRI-PET”). The application deadline is quite soon, before October the 28th, since the positions begin in January 2015. For details please see the attached PDFs. Best, Marjorie Villien -- -- Marjorie Villien, PhD Research Engineer CERMEP - imagerie du vivant 59 boulevard Pinel 69677 BRON Cedex - FRANCE Phone: (33) 04 72 68 86 34

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FIR analysis on regions of interest...
by Joseph Andreano 14 Oct '14

14 Oct '14

Hi All, I'm trying to extract signal from an ROI in an analysis that I specified as FIR. Using funcroi-config and funcroi-table-sess, I'm able to produce an output file that gives me a single value for each participant. What I'm trying to do is to get a value for each TR in the time window I specified so that I can generate a time course for that ROI. I know that this was possible with the older analysis tools in the older version of freesurfer (ie func2roi-sess and roisummary-sess, but the newer tools are just giving me a single (presumably averaged) value. Does anyone know how I can get a timecourse for my ROI? Thanks, Joe _________________________________ Joseph M. Andreano, PhD Postdoctoral Researcher Interdisciplinary Affective Science Laboratory Massachusetts General Hospital _________________________________

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cortical surface area measurement and vertex-wise analysis
by Emma Thompson 14 Oct '14

14 Oct '14

Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks!

4 7

CentOs 7
by will brown 14 Oct '14

14 Oct '14

Hi, Is Freesurfer compatible with CentOs 7? Thanks, Will Brown

2 1

Re: [Freesurfer] excluding labels
by Adam, Ruth 14 Oct '14

14 Oct '14

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