Freesurfer

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30132 discussions

WM edits
by Alexopoulos, Dimitrios 26 Sep '18

26 Sep '18

External Email - Use Caution I'd like to make edits to correct the superior regions where then pial surface truncates WM (images below). Would it be more useful to use controls points in the WM or add WM to the wm.mgz. Jim [cid:image001.png@01D455A8.BDD9A0D0][cid:image002.png@01D455A9.1DD52950] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Cortical ribbon and the hippocampus
by Alon Baram 26 Sep '18

26 Sep '18

External Email - Use Caution Hello, I'm trying to understand what do the files ?h.ribbon.mgz include as part of the ribbon mask. It's obvious they include all the GM between the white and pial surfaces, but they also include some voxels which are not GM (according to aparc+aseg.mgz). For example, ?h.ribbon seems to include some of the hippocampus, but not all of it (seems to me like it's the ventral/inferior part that is included). How is it decided what is included in ?h.ribbon and what isn't? Thanks!

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Re: [Freesurfer] Reporting Cohen's D for a significant cluster
by Maksimovskiy, Arkadiy 26 Sep '18

26 Sep '18

Hi Bruce, I wanted to follow up on this as I was unsuccessful in doing what you suggested using Freeview (2.0)- entering numbers into the window does not change anything. Might there be another way to find out the Cohen’s D? Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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amygdala segmentation atlas influence
by Emily K Clarke 26 Sep '18

26 Sep '18

External Email - Use Caution Hello all, I have run the amygdala segmentation in my datasets to obtain volumes of nuclei. I am aware from the fswiki that the volumes should be interpreted with caution because of the reliance on the atlas. When running FS, is there a way to get some metric about how much the segmentation relied on the atlas relative information from the T1 being segmented. If this metric is not available to the user, is some version of it calculated by the software and therefore available internally. Thanks in advance for your help! raj

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Error when execute preproc-sess
by raul perez moraga 26 Sep '18

26 Sep '18

External Email - Use Caution Hello Freesurfer community I am trying to do a fMRI analysis and I am following the tutorial of FSFAST, but when I try to execute preproc-sess command I get a error if: Expression Syntax I used this command: preproc-sess -s resting -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Also I attach the output log. My Freesurfer version is 6.0.0 My OS CentOS Linux release 7.4.1708 (Core) Thank you. Raul

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Vertex position
by Karin Westin 26 Sep '18

26 Sep '18

External Email - Use Caution Hi! Is it possible to retrieve a map or table indicating exactly where on the cortex a vertex with a specific id number is located? Best and thanks, Karin

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Hippocampal-Amygdala subfields error
by Miguel Ángel Rivas Fernández 25 Sep '18

25 Sep '18

External Email - Use Caution Hello Freesurfer devs, I ran the hippocampal and amygdala subfields command in my sample and I get the following error in several subjects: *Constructing image-to-world transform from header information (asmr1.mgz)Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)Wrote image to file asmr2.mgzThis file does not contain MRI parametersThis file does not contain MRI parametersIn an assignment A(:) = B, the number of elements in A and B must be the same.Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)Constructing image-to-world transform from header information (asmr1.mgz)Constructing image-to-world transform from header information (/Applications/freesurfer/subjects/5232/tmp/hippoSF_T2_v21_HIPO-AMI_left/imageDump.mgz)Wrote image to file asmr2.mgzThis file does not contain MRI parametersThis file does not contain MRI parametersIn an assignment A(:) = B, the number of elements in A and B must be the same.Error in segmentSubjectT2_autoEstimateAlveusML (line 2147)* *MATLAB:subsassignnumelmismatchDarwin rmnlab1.inv.usc.es <http://rmnlab1.inv.usc.es> 17.4.0 Darwin Kernel Version 17.4.0: Sun Dec 17 09:19:54 PST 2017; root:xnu-4570.41.2~1/RELEASE_X86_64 x86_64T2 hippocampal subfields exited with ERRORS at jueves, 13 de septiembre de 2018, 21:37:33 CEST* What would be the reason? Thanks in advance, Best wishes, -- *Miguel Ángel Rivas Fernández*

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FreeSurfer 6.0.0 CentOS 7 compatibility
by Vanzo, Davide 25 Sep '18

25 Sep '18

Hello, According from few messages in this mailing list, FreeSurfer 6.0.0 should be compatible with CentOS 7. However in the official documentation I cannot find any related statement. Moveover, the download web page still shows only CentOS 6 as supported platform. Could you please clarify if the current stable release works correctly on CentOS 7 or not? Thank you. Best regards -- Davide Vanzo, PhD Application Developer Adjunct Assistant Professor of Chemical and Biomolecular Engineering Advanced Computing Center for Research and Education (ACCRE) Vanderbilt University - Hill Center 201 www.accre.vanderbilt.edu

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longitudinal hippocampal aseg editing
by Rebecca Ray 25 Sep '18

25 Sep '18

External Email - Use Caution Martin, That is the point. I have edited the hippocampus in the -long 2 times and the recon does not maintain my edits. I would love any help to changes I should be making to my recon statement to maintain my edits. Rebecca Hi Rebecca, aseg edits to subcortical structures need to be done in the -long stage. (see here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits ) Best, Martin On Thu, 2018-09-06 at 14:37 -0700, Rebecca Ray wrote: >* External Email - Use Caution *>* HELP *>* ---------- Forwarded message ---------- *>* From: Rebecca Ray <rayr5 at gene.com <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> *>* Date: Thu, Sep 6, 2018 at 12:05 PM *>* Subject: longitudinal hippocampal aseg editing *>* To: freesurfer at nmr.mgh.harvard.edu <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *> > >* I have 2 time points on 60 subjects with most being in some form of *>* AD. There are considerable differences in hippocampal volume between *>* time points. I edited the raw images before making the template. I *>* then had to edit the aseg template image and there were still *>* problems on the -long images. I tried to edit and rerun autorecon2- *>* noaseg and autorecon3 and it does not appear to be keeping my edits. *> >* What am I doing wrong? *> >* Rebecca *> >* _______________*

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Research Assistant Job, Chicago, IL
by Jaiashre Sridhar 25 Sep '18

25 Sep '18

External Email - Use Caution Research Assistant job available at Northwestern University’s Mesulam Cognitive Neurology and Alzheimer’s Disease Center in Chicago, IL. Job Summary: This position is within Dr. Emily Rogalski’s laboratory, which focuses on aging and dementia research including Alzheimer’s, primary progressive aphasia, frontotemporal dementia and SuperAging. The research assistant will be responsible for analysis of neuroimaging datasets, in order to contribute to neuroscientific studies of normal aging and pathological aging. Duties include coordinating PET and MRI scans, and analyzing the resultant structural and functional imaging data. The candidate will also be administering and scoring neuropsychological tests. Additional duties include working on graphics for manuscripts and grants or other general lab responsibilities. Minimum qualifications: - The candidate must hold a Bachelor’s degree - Familiarity with scripting in Python/Bash/MATLAB/R - A two-year commitment is requested Preferred qualifications: - Relevant backgrounds would be in Neuroscience, Biology, Psychology, and Biomedical Engineering - Experience using Freesurfer or other neuroimaging platforms - Experience administering and scoring neuropsychological tests Interested candidates, please email your CV to jaiashre.sridhar(a)northwestern.edu<mailto:jaiashre.sridhar@northwestern.edu>. A job posting will be available soon at careers.northwestern.edu<http://careers.northwestern.edu/>. --- Jaiashre Sridhar, MS Research Project Coordinator Northwestern University | Mesulam Cognitive Neurology and Alzheimer’s Disease Center 320 E. Superior St. | Searle 11-579 | Chicago IL 60611 Phone: (312) 503-1749 | Email: jaiashre.sridhar(a)northwestern.edu<mailto:jaiashre.sridhar@northwestern.edu> Web: www.brain.northwestern.edu<http://www.brain.northwestern.edu>

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