Freesurfer

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30083 discussions

Gender and age based reconstruction
by Carissa Liana Grijalva 14 Aug '19

14 Aug '19

External Email - Use Caution Hello, I reached out the other day about if there was a way to specify the data is from a specific gender or age during the recon all code, such as a tag at the end. I was told that there is not way to tell recon-all about demographics/subject meta data, and not to worry about this during recon-all, but instead add age and gender as covariates in the model later. Does this mean FreeSurfer automatically finds the right regions regardless of age or gender? Does this work based on gray/white matter thresholds or something similar, so regardless of the demographics of the brain, it find the right regions? Thank you for your time. Best, Carissa Grijalva -- *Carissa Grijalva* *University of Arizona * *Biomedical Engineering PhD Program* *Undergraduate Research Opportunities Consortium Scholar* *NSF WAESO Research Fellow* *Society of Hispanic Professional Engineers*

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nu_correct error
by Z Hessam 14 Aug '19

14 Aug '19

External Email - Use Caution Hello Dear FreeSurfer Developers, I'm attempting to run some of data with recon-all code, and after some success run on several data, now I get the following error message even when I run those data that ran well before: nu_evaluate: crashed while running evaluate_field (termination status=134) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct Linux ubuntu 4.15.0-46-generic #49~16.04.1-Ubuntu SMP Tue Feb 12 17:45:24 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux I couldn't find any solution in previous emails, and the output of these 2 commands: 1) echo $FREESURFER_HOME 2) ls -l $FREESURFER_HOME/mni/bin/nu_correct were: 1)/media/hessam91/driver2/freesurfer 2)-rwxrwxrwx 1 8481 1590 20569 Jun 19 2015 /media/hessam91/driver2/freesurfer/mni/bin/nu_correct what can I do to solve this problem? thank you so much

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asegstats2table error - measure 63 expected 66
by Fernanda Hansen P. de Moraes 13 Aug '19

13 Aug '19

External Email - Use Caution Dear Freesurfer experts, We had just reprocessed our subjects with the -long flag fr the longitudinal processing, and when extracting volumes with asegstats2table I have the following error: WARN: SUBJ229_ses-1.long.SUBJ229_tmpl nmeasures = 63, expecting 66 for all our subjects on the list. I just found this older message about the same error ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-March/036502.ht… ), and I am now looking for the subject with 66 ROIs. However, for now, all of then present 45 ROIs. Is there any suggestion on how can we trespass this error? Regards, -- Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com Física Médica | Rede D'Or São Luiz Doutoranda em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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Research Assistant Job Opening
by Prakash Lab 13 Aug '19

13 Aug '19

External Email - Use Caution Hello, The Ohio State Clinical Neuroscience Laboratory directed by Dr. Ruchika Prakash is seeking to hire a Research Assistant (RA). Please see attached document for full description. Best Regards, The Clinical Neuroscience Laboratory [image: The Ohio State University] Lab Manager The Clinical Neuroscience Laboratory Department of Psychology 74 Psychology Building, 1835 Neil Avenue, Columbus, OH 43210 614-292-9568 Office ra(a)clinicalneurosciencelab.com www.clinicalneurolab.org Confidentiality Notice: This email transmission (including any documents, files or attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, you are hereby notified that any disclosure, copying or distribution, or any use of the enclosed or attached information is strictly prohibited. If you have received this transmission in error, please notify me immediately by return email and delete all materials without reading, copying, saving or printing them.

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Smooth surface overlay
by Jacobs, H (NP) 13 Aug '19

13 Aug '19

External Email - Use Caution Hi all, I created an overlay surface map of my analyses (with pvalues in log10) using R. Now I would like to smooth this map to extract clusters and I tried to use: mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 3 --sval lh_analyses.mgh --tval lh_analyses_smoothed.mgh --cortex This seems to work, but is there a way to also map the original values in the output surface overlay? I now have clusters that are colored yellow with no statistical information anymore. I also tried to use: mri_surfcluster --in lh_analyses.mgh --thmin 1.3 --thmax 6 --no-adjust --subject fsaverage --fwhm 3 --sum lh_analyses_smoothed_summary --hemi lh --sign pos But whether or not I add in the smoothing, the output is the same. Any help would be greatly appreciated. Thanks! Heidi

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reconstructing female vs male data
by Carissa Liana Grijalva 13 Aug '19

13 Aug '19

External Email - Use Caution Hello, I am a graduate student at the University of Arizona and we have been using the FreeSurfer Program to reconstruct MRI data from healthy patients and patients with a mild cognitive impairment. We are comparing the statistics for different brain regions, however, we would like to take age and gender into consideration. Does the main atlas used to map/segment regions in the brain have a default (male) brain or certain age? If so, is there a way to specify the data is from a female during the recon all code? Such as a tag at the end? Is it possible to include something like this for age as well? Thank you for your time. Best, Carissa Grijalva -- *Carissa Grijalva* *University of Arizona * *Biomedical Engineering PhD Program* *Undergraduate Research Opportunities Consortium Scholar* *NSF WAESO Research Fellow* *Society of Hispanic Professional Engineers*

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Which registration file to choose when to using tksurfer
by Hang Zeng 13 Aug '19

13 Aug '19

External Email - Use Caution Dear freesurfers, I ran the retinotopy pipline (like preproc-sess, mkanalysis-sess, Selxavg3-sess) and now I want to view the results with tksurfer. When I call tksurfer <subject> <hemisphere> inflated and try to overlay the reall.nii.gz and imag.nii.gz, I need to choose a registration file. I don't see any registration file in the eccen or polar folder, but in the '/Sess/bold' folder I see the ''init.register.dof6.dat', 'register.dof6.dat.mincost', 'register.dof6.dat.param', 'register.dof6.dat.sum', 'register.dof6.dat~' and some other files. I am not sure whether the ''init.register.dof6.dat' is the right one to choose. Or did I miss some steps? Also, I am wondering what do the angle.nii, angle.masked.nii and fieldsign.nii mean. Thank you so much! Zoe

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hippocampal subfields {Disarmed}
by 郑凤莲 13 Aug '19

13 Aug '19

External Email - Use Caution Dear experts, I have segmented hippocampus into 13 subfields using FS6.0. Then, I want to study the function connectivity between sibfields. How can I utilize this template to do this research? Is it possible? Thanks for your reply in advance. Sincerely, Zhemg | | 郑凤莲 | | 邮箱：zhengfenglian0105(a)163.com | 签名由网易邮箱大师定制

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Deconvolution with FSFAST
by Caspar M. Schwiedrzik 12 Aug '19

12 Aug '19

External Email - Use Caution Hi! I was wondering whether it is possible to do deconvolution of an fMRI time series with FSFAST? Specifically, I would like to get a deconvolved signal from a region of interest to prepare predictors for a PPI analysis. Additional considerations: data is from an event-related design, and was acquired with MION contrast agent. I found some older documentation on selxavg2, but I am not sure whether that still applies (I am using version 5.3). Also, I do not need an event-related average as output, but a continuous time series. Thanks for any advice! Caspar

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overlay on subcortical surfaces
by cr439＠cam.ac.uk 12 Aug '19

12 Aug '19

External Email - Use Caution Dear Freesurfer Experts, As it happens for cortical surface mapping I would like to obtain the same for subcortical structures. I have generated the subcortical surfaces using fsaverage brain’s aseg.mgz with the tool given in: https://github.com/thomas-vincent/nipic/wiki/%5BFreesurfer%5D-Get-surfaces-… <https://github.com/thomas-vincent/nipic/wiki/[Freesurfer]-Get-surfaces-of-s…> With this I would like overlay data on them. I have used mrf_vol2surf command mri_vol2surf --src sub_me_c.nii --out lh.sub_me_c_surf.mgz --hemi lh --mni152reg as my overlays are in MNI space. However, I am not able to overlay these on the surface. I think this is because the data file that is generated (lh.sub_me_c_surf.mgz) hasn’t got the same number of vertices as the subcortical generated surface (163842 vertices of the overlay file to 37722 vertices of the surface file). Could you advice me on the best way to approach this? Many thanks. Best wishes, Catarina -------------------------------------------- Dr Catarina Rua Post-Doctoral Researcher University of Cambridge Telephone: 01223 746 458 Email: cr439(a)cam.ac.uk

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