Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30093 discussions

Writing FSL compatible ascii files
by Melanie Ganz 13 Feb '17

13 Feb '17

Dear all knowing list, we are just playing around with the MSM code within FSL and noticed that if we try to convert surface data to ascii like e.g. this mri_convert --ascii funcdata.nii funcdata.asc it produces an ascii file that looks good when opened in a text editor, but doesn't seemt o be able to be read in by FSL. But if we just read and write the nii file to text in matlab this works. We think the issue is created by the type of end of line character used by FS. Does anyone else have experience with this? Could this be an idea to update to make the compatibility with FSL easier? Cheers from Copenhagen, Mel -- Melanie Ganz-Benjaminsen, 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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Re: [Freesurfer] tractstats2table error
by Adarsh Nellore 12 Feb '17

12 Feb '17

Hi Anastasia, Thanks a lot for willing to help me out, but I'd really appreciate if you may please let me know what the next steps might be since I'm getting the same error for tractsstats2table. Regards, Adarsh

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Postdoctoral Fellow in Multivariate Analysis and Machine Learning
by Anqi Qiu 10 Feb '17

10 Feb '17

Job description: Computation functional anatomy laboratory at National University of Singapore focuses on the development of medical image analysis methods, including image segmentation, registration approaches, multivariate statistical analysis, machine learning, and classification algorithms. Our group is particularly working on multi-modal magnetic resonance imaging of the brain and derives mathematical/statistical models for characterizing variations of the brain anatomy and function and their associations with clinical phenotypes and/or genetics. We are seeking for research fellows who are interested in developing and employing data mining approaches for understanding high dimensional brain image and/or genetic data. The candidate with experience on high dimensional data or 3D image analysis will be seriously considered. Requirements: Ph. D on computer vision, statistics, electrical engineering, or biomedical engineering Good communication and writing skills in English language Experience using neuroimaging packages such as SPM, FSL, NiPy etc. If you are interested in the jobs listed above, please send your CV to Associate Prof. Anqi QIU Deans Chair Department of Biomedical Engineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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Postdoctoral Fellow in Multivariate Analysis and Machine Learning
by Anqi Qiu 10 Feb '17

10 Feb '17

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Re: [Freesurfer] tractstats2table error
by Adarsh Nellore 10 Feb '17

10 Feb '17

Hi Anastasia, I had tried "inputs" when running the command but had a typo when pasting it in this forum. I tried again just to make sure and it didn't work.

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Re: [Freesurfer] tractstats2table error
by Adarsh Nellore 10 Feb '17

10 Feb '17

Hi Anastasia, Thanks a lot for your response. I tried tractstats2table with and without the space between "--" and "input" and it still didn't work. Regards, Adarsh

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tractstats2table error
by Adarsh Nellore 10 Feb '17

10 Feb '17

Hi there, I generated tractographies using the TRACULA pipeline and I'm not trying to generate the necessary statistics for them using tractstats2table. This is the command I'm using: tractstats2table -- input /usr/local/freesurfer/subjects/control_data/diffusion_tracs/Control200/dpath/lh.slft_PP_avg33_mni_flt/pathstats.overall.txt --overall --tablefile /usr/local/freesurfer/subjects/control_data/diffusion_tracs/Control200/dpath/lh.slft_PP_avg33_mni_flt.All.table However, no matter what I change in this command, whether it be parameters or syntax, I get the following error: File "/usr/local/freesurfer/bin/tractstats2table", line 138 print 'ERROR: inputs are not specified' ^ SyntaxError: Missing parentheses in call to 'print' I'd really appreciate any advice on how I may be able to get past this error as soon as possible. Thanks a lot!

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-trac-all -prep FS 5.3 Memory Allocation Issue
by Abigail Waters 10 Feb '17

10 Feb '17

Hello - I'm attempting to run the -trac-all -prep command with FS 5.3. I am running into the same memory allocation issues on my Mac that were present in earlier versions of Freesurfer/Tracula. See below: MRIallocSequence (218, 182, 1):could not allocate 158784 bytes for the 44th slice Cannot allocate memory I have attempted the pre-processing with multiple and single subjects. I have successfully processed a single subject on this machine before, and have not updated to the latest Freesurfer since that subject (as all MPRAGE scans were reconstructed is FS 5.3). There is sufficient memory available and the MPRAGE scans were reconstructed correctly. Any thoughts on how to solve the issue would be appreciated. Please let me know if you need any additional information. Thanks! Abby

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Intensity Re-scaling Relative to Full Brain Atlas
by Anderson Napolitano 10 Feb '17

10 Feb '17

Hi Experts! Per step 3 of the following tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer I wanted to re-scale the the intensities relative to the full brain atlas. The command: --no-rescale removes scaling relative to the Pons and the command: --rescale <Ids> rescales the intensities relative to the region determined by Ids. Would listing all the regions on the --rescale command be the right approach to rescale the intensities relative to the atlas? If so, how do I determine which Ids is which? Thank you in advance! -Anderson

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Fwd: FreeSurfer group analysis visualize data
by Xiuyi Wang 10 Feb '17

10 Feb '17

Hi, I am learning GroupAnalysis using FreeSurfer 5.3 on Linux system. I followed the detailed instruction on the tutorial website. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis But I got an error message when running this command to visualize uncorrected significance map with freeview. This is the command I typed: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:a nnot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness -age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d I received this error message: Unrecognized sub-option flag ‘annot_outline’ I browsed the internet and found that “That option is only available in the development version of freeview. You can try removing :annot_ouline=1 from the command-line and turn it on manually from the GUI.” So I deleted “:annot_outline=1” and the command line is : freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:o verlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d But I received another error message: Did not find any volume geometry information in the surface. I found some researchers also have encountered this problem, but it has not been solved. Could you please tell me the solution of the problem? Thank you for your suggestion. Best. Xiuyi Wang

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