Freesurfer

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30088 discussions

How to Divide the Brain Surface Parcells to more regions
by Mahshid Fouladivanda 01 Aug '19

01 Aug '19

External Email - Use Caution Dear Freesurfer Experts, I would like to divide the surface parcellations of the neonatal brain. The parcells were extracted using Draw_EM (Developing brain Region Annotation With Expectation-Maximization), an atlas based segmentation, from cortical and sub-cortical. As I understand from help comments, mris_divide_parcellation would help, but it needs annotation file to be imported as input. I do not have the annotation file. I would appreciate it if you could help me how to divide my parcells in more regions? Regards, Mahshid

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How to Create Cortex Parcellation Using "mri_aparc2aseg"?
by Mahshid Fouladivanda 01 Aug '19

01 Aug '19

External Email - Use Caution Dear experts, I have a segmentation file of all the tissues in the brain and the ribbon file which were extracted by another toolbox rather than freesurfer. Also, I have created the annotation file using "write_annotation.m". Now, I wanna create a parcellation file based on the segmentation and annotation files using "mri_aparc2aseg" in freesurfer. Bellow is the command I entered in the terminal and extract the parcels: mri_aparc2aseg --s subject name --annot annotation name --o output name and I used the segmentation file as the "aseg.mgz" for the above command. Now, I am wondered that do I select the right aseg file or not?? Any help would be appreciated. Regards, Mahshid

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Re: [Freesurfer] Running FSL randomise on FS cortical thickness data
by Antonin Skoch 01 Aug '19

01 Aug '19

External Email - Use Caution Dear Mark, I would suggest to use PALM instead: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide PALM supports surface-based data. Each vertex has different area, which has to be accounted when the cluster size is computed. Antonin Skoch Dear Freesurfer experts,Hi. We are analyzing cortical thickness data in Freesurfer, longitudinal data in 55 subjects using the linear mixed effects package. We are finding a number of siginificant clusters, and would like to correct for multiple comparisons with permutation testing. We have already run about 2000 permutations, and would like to use TFCE available in randomise rather than empirical methods to set parameters such as the cluster forming threshold. So, the simple question is, how do we convert our FS format data (these are F statistics at each vertex) into a format which can be read into randomise? Thanks for any advice you can provide. Best, Mark

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UC San Diego - Postdoctoral Research Fellow Position
by Roberson, Mary 31 Jul '19

31 Jul '19

External Email - Use Caution Hello Freesurfer Community, University of California, San Diego Research Fellow Position Postdoctoral research fellow position in genomic studies of neuropsychiatric disorders at University of California, San Diego Dr. Chi-Hua Chen's laboratory is looking for highly motivated individuals to join our team for imaging genomics research in neuropsychiatric disorders and Alzheimer's disease at the Center for Multimodal Imaging and Genetics at UC San Diego. Our research projects include 1) genotype-phenotype mapping to identify genetic variants associated with brain structure in human population samples, all with MRI and genotype data; 2) translational research for genomic-guided drug target identification for brain disorders. For qualified candidates, there are excellent opportunities to pursue research interests in neuroimaging genomics, statistical modeling, bioinformatics, and brain disorders in a multi-disciplinary research setting. Salary and benefits are commensurate with research experience and accomplishments, and determined by NIH guidelines. The position is available to start immediately. The successful applicant should have: * PhD in biostatistics, bioinformatics, statistical genetics, computer science, neuroimaging or a related field. An MS or BS is acceptable if there is an exceptional record of past experience. * Knowledge of programing in Linux shell scripts, R, python or Matlab * Knowledge in biostatistics, bioinformatics or machine learning * Experience to manipulate genomic or neuroimaging datasets * Excellent analytical and problem-solving skills * Good skills in written and spoken English If interested, please email a cover letter, a current CV, and contact information for three references to Mary Roberson at: mmroberson(a)ucsd.edu. Position will be open until filled. Thank you, Mary Roberson Mary M Roberson | Executive Assistant Center for Multimodal Imaging and Genetics (CMIG), Department of Radiology UC San Diego | 9452 Medical Center Drive | MC-0841| La Jolla, CA 92037 Office: 858.534.8259 | Email: mmroberson(a)ucsd.edu<mailto:mmroberson@ucsd.edu> Drs. Ahrens | Bae | Brewer | Chang | Chen | Dale | Du | McEvoy | White [cid:image001.png@01D547AC.D4B7CCE0] The information transmitted in this e-mail is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination, or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this e-mail in error, please contact the sender and delete the material from any computer.

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How to change intensity bounds parameters in recon-all
by Caroline Chwiesko 31 Jul '19

31 Jul '19

External Email - Use Caution Dear Freesurfer experts, I have a similar problem as what was mentioned previously on this support list. I ran recon-all on all of my subjects and I am currently in the manual editing process. I noticed that for a lot of my subjects there are spots in the images where the white matter extends into the gray matter. So its looks like a systematic error with my data. I attached images of two different subjects as an example. I found the advice to change the intensity bounds parameters for mri_segment and mris_make_surfaces, but I don t know exactly how to do this. I am very new to freesurfer and I could not find the proper information on the freesurfer_wiki websites for recon-all, mri_segment and mris_make_surfaces. 1) What is exactly the parameter that I would need to change in mri_segment and mris_make_surfaces? 2) What is the recon-all command that I would need to run to change those default parameters after I made already manual changes to the brain mask (removing voxels) and added control points? Thank you very much in advance Our Freesurfer version is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c we run it on Linux, kernel version 4.15.0-46-generic, Ubuntu 18.04.1 LTS [image: Screen Shot 2019-07-30 at 12.09.01 PM.png] [image: Screen Shot 2019-07-30 at 12.18.32 PM.png]

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Re: [Freesurfer] Failure of mri_robust_template in fmriprep
by Frederick, Blaise B. 31 Jul '19

31 Jul '19

Ø Hi Blaise Ø * I can't even find an exit(-9) in the code. If you can track down and send us the inputs to mri_robust_template I can try to replicate it locally. Or wait for Martin to comment :) Ø Ø Bruce * Well that’s a bit disturbing… Could this be a signed vs. unsigned integer weirdness? Is there a return code of 247? If I did the math right, -9 is the two’s complement of an unsigned 247. Is there a place I could put the files so you can replicate it? I can get all the inputs. Blaise ------------------------------------------------------- Blaise Frederick Associate Professor of Psychiatry/Biophysicist Harvard Medical School/McLean Hospital bbfrederick(a)mclean.harvard.edu http://www.nirs-fmri.net

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FSL questions
by Yang, Weiqi 31 Jul '19

31 Jul '19

Dear FreeSurfers, I would like to use fsleyes for imaging. Does anybody know how to source it? And what fsl command I should use if I want to extract all ROIs in aparc+aseg file and get their uptake value from PET image? I know how to do it for a single ROI. I am just wondering if there is an easy way to extract data for all ROIs. Thanks, Weiqi

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make_average_subject error
by Niels Janssen . 31 Jul '19

31 Jul '19

External Email - Use Caution Dear all, I have seen this error mentioned several times on the list but I have never seen a solution posted. It is claimed that there is a patch and a README that explains the patch at: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ In this folder there are a bunch of files but there is no README so I am not sure what exactly I need to do. I tried replacing the files in my /usr/local/freesurfer/bin with those in this patch folder but the error remains. This error appears with all my data sets that I have tried. So it doesnt seem to be something specific to my data. Loading aseg from /media/fMRI_21/studyname/freesurfer/avgsub3/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter Segmentation fault (core dumped) Linux nielsj-XXXYYY 4.18.0-25-generic #26~18.04.1-Ubuntu SMP Thu Jun 27 07:28:31 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s avgsub3 exited with ERRORS at mié jul 31 12:05:20 WEST 2019 -- Niels Janssen Brain Imaging Laboratory Institute of Biomedical Technologies Institute of Neurosciences University of La Laguna Tenerife, Spain https://sites.google.com/view/nielsjanssen/

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Re: [Freesurfer] ppmi
by Tosun, Duygu 30 Jul '19

30 Jul '19

External Email - Use Caution Is this for PPMI project? We can provide total hippo volumes if needed. > On Jul 31, 2019, at 1:48 AM, eric f <ejf(a)icsi.berkeley.edu> wrote: > > I don't think it will take 20h, probably more like 10-12h, so that's > only 1.5 years:). Most people who are running it that many data sets > have access to a computational cluster (on ours it would only take a few > weeks). Alternatively, you can try buying cloud-based computational > power (eg, amazon web services). > >> On 7/30/19 4:56 PM, Jiajun Luo wrote: >> >> External Email - Use Caution >> >> Hi, >> >> Now I have T1 and T2 images (dcm files) and want to calculate the >> hippocampal volume. I find it takes ~20h to run recon-all -all and >> then ~40min to run -hippocampal-subfields-T1. However, I need to >> calculate the hippocampal volume for more than 1,000 individuals >> (which means it may take ~3 years to complete). Do you know how I can >> improve my efficiency? >> >> Thank you! >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e…

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Help for Hippocampal Calculation
by Jiajun Luo 30 Jul '19

30 Jul '19

External Email - Use Caution Hi, Now I have T1 and T2 images (dcm files) and want to calculate the hippocampal volume. I find it takes ~20h to run recon-all -all and then ~40min to run -hippocampal-subfields-T1. However, I need to calculate the hippocampal volume for more than 1,000 individuals (which means it may take ~3 years to complete). Do you know how I can improve my efficiency? Thank you!

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