Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30071 discussions

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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Re: [Freesurfer] orientation in freeview
by Antonin Skoch 10 Feb '17

10 Feb '17

Dear Zhewei, I think that the problem you report is caused by the fact, that .mat file from FLIRT codes vox2vox transformation, so that cannot be applied to another dataset (in your case fMRI) unless it has the same geometry as the original image the .mat file was generated on. Antonin Can you send your freeview command line and pictures of the mismatch? On 2/9/17 5:58 PM, Zhewei Wang wrote: Hi all, I have a problem maybe relevant to the orientation of images in freeview. I have two images, one is fMRI and one is MRI. They are produced from the same machine at the same time. I loaded both of them in freeview and it showed they are matched very well, even they have different resolutions, different orientation (fMRI is LAS and MRI is PSR), different sform and qform. I registrated MRI to MNI152, and a transformation matrix is generated. I apply this matrix on fMRI, then I got the wrong result: I loaded the fMRI after transformation and MNI152 in freeview, they are not matched. I use /flirt/ for registration. Can anyone explain to me why it happened? At beginning they are shown matched in freeview, even they have different orientation. After apply same transformation, they are shown not matched in freeview even they have same orientation now (both are LAS). Thank you so much. Zhewei

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orientation in freeview
by Zhewei Wang 10 Feb '17

10 Feb '17

Hi all, I have a problem maybe relevant to the orientation of images in freeview. I have two images, one is fMRI and one is MRI. They are produced from the same machine at the same time. I loaded both of them in freeview and it showed they are matched very well, even they have different resolutions, different orientation (fMRI is LAS and MRI is PSR), different sform and qform. I registrated MRI to MNI152, and a transformation matrix is generated. I apply this matrix on fMRI, then I got the wrong result: I loaded the fMRI after transformation and MNI152 in freeview, they are not matched. I use *flirt* for registration. Can anyone explain to me why it happened? At beginning they are shown matched in freeview, even they have different orientation. After apply same transformation, they are shown not matched in freeview even they have same orientation now (both are LAS). Thank you so much. Zhewei

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Freesurfer