Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

cannot find subject
by Jacobs, H (NP) 29 Apr '18

29 Apr '18

External Email - Use Caution Dear FreeSurfer, I just installed FreeSurfer6 on my computer and tried to run a subject (license file is set). I sourced freesurfer and have set the subjects_dir. However, when running the recon-all, I get the following error : ERROR: cannot find /Applications/freesurferv6/subjects/S006 And running echo $SUBJECT_DIR gives me this output: /Users/heidi/Desktop/tryout Any suggestions what may be the problem? Thank you Heidi

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POST-DOCTORAL FELLOWSHIP IN NEUROIMAGING
by Xiaosong He 28 Apr '18

28 Apr '18

POST-DOCTORAL FELLOWSHIP IN NEUROIMAGING THOMAS JEFFERSON UNIVERSITY/ SIDNEY KIMMEL MEDICAL COLLEGE, PHILA., PA. The Department of Neurology at Thomas Jefferson University/Jefferson Medical College has an opening for a Two-Year Postdoctoral Research Fellowship in Neuroimaging focusing on both clinical brain mapping and primary cognitive neuroscience investigations. The emphasis in our neuroimaging program is on cognitive and behavioral network organization and plasticity in neurologic disorders such as epilepsy. The lab focuses on the use of advanced network neuroscience measures to understand seizure networks and cognitive reorganization in epilepsy, and has had recent publications in Brian, Neurology, and Epilepsia, with some also prompting complimentary peer reviews. The lab is part of the Jefferson Comprehensive Epilepsy Center, an internationally-known epilepsy surgery program. Presurgical brain mapping studies are undertaken (MRI volumetrics, task-fMRI, resting state functional connectivity, diffusion imaging, neuropsychological assessment, electrophysiology/electrocortical stimulation) as well as post-surgical neuroimaging studies investigating clinical, cognitive, and behavioral outcomes. The pre-surgical brain mapping studies are conducted on a regular basis, utilized in image-guided surgery, and then made available for research. Studies in brain recovery and the cognitive reorganization of language and memory functions are emphasized, utilizing rich multi-modal datasets for the investigation of both cognitive and pathologic (e.g., seizure) networks. Thomas Jefferson University provides a high-level interdisciplinary research environment with grand rounds, seminars, case conferences, and opportunities to collaborate with faculty across departments such as neurosurgery and radiology. Successful applicants must have a strong background in image processing and analysis using programs such as MATLAB, SPM, Freesurfer, and FSL with a strong interest in clinical neuroimaging and cognitive neuroscience. Applicants must have a Ph.D. or MD in neuroscience, biomedical engineering, statistics, neurology, neuropsychology, radiology, or related field. Interested applicants should send a CV and cover letter stating experience and interests, 2-3 peer-reviewed publications. Anticipated start date is 7/1/18, but is flexible. Contact: Joseph I. Tracy, Ph.D., ABPP(CN). Director, Cognitive Neuroscience and Brain Mapping Laboratory, Thomas Jefferson Univ./Sidney Kimmel Medical Coll., Jefferson Hospital for Neuroscience, 901 Walnut Street, Suite #447, Phila., PA 19107, phone:#215-955-4661, e-mail: joseph.tracy(a)jefferson.edu. Thomas Jefferson University and Hospitals is an Equal Opportunity Employer. Jefferson values diversity and encourages applications from women, members of minority groups, LGBTQ individuals, disabled individuals, and veterans.

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mri_ca_register
by Aaron Tanenbaum 27 Apr '18

27 Apr '18

External Email - Use Caution Hello FreeSurfers, I am trying to find what the -l flag does for the program mri_ca_register program. Does not seem to be documented anywhere but i could be mistaken. Aaron Tanenbaum

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mri_watershed error/global region of the brain empty
by miracle ozzoude 27 Apr '18

27 Apr '18

External Email - Use Caution Hello FreeSurfer, While running recon-all on a subject, i got encountered an error during the watershed step (mri_watershed). How do i fix this problem? I have attached the recon-all.log and recon-all-status.log files. Thank you Best, Paul

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?h.area
by Joost Janssen 27 Apr '18

27 Apr '18

External Email - Use Caution Hi, Short: Is it possible to generate v6.-style ?h.area based on v5.1-recon output? If so, how? Long: I have 5.1 processed data and would like to re-generate ?h.area v6-style (Winkler et al. 2018). I would like to avoid complete rerunning through v6. Thanks, -joost

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Re: [Freesurfer] mri_compute_volume_fractions
by Antonin Skoch 27 Apr '18

27 Apr '18

External Email - Use Caution Dhivya, this syntax works for me with version 6. With version 5.3.0 I am getting the same error mesage. I do not know how the correct syntax is with version 5.3.0. Antonin Skoch Yep , I am using "o" .I am running it on Ubuntu 16.04 and my freesurfer version is , freesurfer/5.3.0/bin/freesurfer mri_compute_volume_fractions --o test --regheader 002_S 002_S/mri/norm.mgz still I am getting , unknown option --o Trying to give as per documentation, which is --o outstem --regheader subject I am really sorry to bother you with so many questions. Is it something to do with version of freesurfer? ________________________________________ From: freesurfer-boun...(a)nmr.mgh.harvard.edu [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...(a)nmr.mgh.harvard.edu] Sent: Thursday, April 26, 2018 11:13 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions hmmm, are you sure you are using an "o" and not a "0"? And the --regheader syntax different than I thought, it requires two argments, a subject name and a template volume (if you are using the anatomical space, any of the conformed volumes such as the norm.mgz should be fine). For example, I run: mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz $Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname Linux hostname sulc.nmr.mgh.harvard.edu machine x86_64 user fischl setenv SUBJECTS_DIR /homes/4/fischl/links/subjects cd /autofs/space/tiamat_003/users/subjects mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz outstem test regfile (null) regtype 0 segfile aseg.mgz . . . On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: > External Email - Use Caution > > mri_compute_volume_fractions --o test --regheader > unknown option --o > > If I am not giving any input before arguments, it is not taking them. > > Thanks, > Dhivya > ________________________________________ > From: freesurfer-boun...(a)nmr.mgh.harvard.edu > [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...(a)nmr.mgh.harvard.edu] > Sent: Thursday, April 26, 2018 10:52 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_compute_volume_fractions > > just run the command as I sent it: > > mri_compute_volume_fractions --o test --regheader > > the aseg is the default name. You are putting it in the wrong place and it > thinks the aseg is a registration file > > On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: > >> External Email - Use Caution >> >> I am getting same Error with many permutations of arguments, >> >> mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader >> identity.nofile >> >> arg = 6 >> reading registration file 002_S/mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from 002_S/mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from 002_S/mri/aseg.mgz >> mri_compute_volume_fractions: could not load registration file from >> 002_S/mri/aseg.mgz >> >> >> Thanks, >> Dhivya >> >> >> >> ________________________________________ >> From: freesurfer-boun...(a)nmr.mgh.harvard.edu >> [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fis...(a)nmr.mgh.harvard.edu] >> Sent: Wednesday, April 25, 2018 6:21 PM >> To: Freesurfer support list >> Subject: Re: [Freesurfer] mri_compute_volume_fractions >> >> try >> >> mri_compute_volume_fractions --o test --regheader >> >> On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >> >>> External Email - Use Caution >>> >>> Thanks Bruce! >>> >>> I even tried with --regheader >>> >>> mri_compute_volume_fractions mri/aseg.mgz --o test --regheader >>> identity.nofile >>> >>> It gives me below error, >>> >>> arg = 6 >>> reading registration file mri/aseg.mgz >>> regio_read_register(): Success >>> Error reading inplaneres from mri/aseg.mgz >>> regio_read_register(): Success >>> Error reading inplaneres from mri/aseg.mgz >>> mri_compute_volume_fractions: could not load registration file from >>> mri/aseg.mgz >>> >>> Thanks, >>> Dhivya >>> ________________________________________ >>> From: freesurfer-boun...(a)nmr.mgh.harvard.edu >>> [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>> [fis...(a)nmr.mgh.harvard.edu] >>> Sent: Wednesday, April 25, 2018 6:01 PM >>> To: Freesurfer support list >>> Subject: Re: [Freesurfer] mri_compute_volume_fractions >>> >>> oh, this must be Doug's code, not mine. Try using --regheader instead >>> >>> And also please send us the full command and all screen output from it in >>> the future. >>> cheers >>> Bruce >>> On >>> Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >>> >>>> External Email - Use Caution >>>> >>>> Sorry for bothering with more questions! >>>> >>>> I am getting an error saying , >>>> >>>> mri_compute_volume_fractions: could not load registration file from >>>> identity.nofile >>>> >>>> And my command is, >>>> >>>> mri_compute_volume_fractions identity.nofile mri/aseg.mgz test >>>> >>>> and if I try to give in this format which the documentation says, >>>> >>>> mri_compute_volume_fractions [options] --o <outstem> --reg <regfile> >>>> >>>> Am I going wrong somewhere? >>>> >>>> Thanks, >>>> Dhivya >>>> ________________________________________ >>>> From: freesurfer-boun...(a)nmr.mgh.harvard.edu >>>> [freesurfer-boun...(a)nmr.mgh.harvard.edu] on behalf of Bruce Fischl >>>> [fis...(a)nmr.mgh.harvard.edu] >>>> Sent: Wednesday, April 25, 2018 4:22 PM >>>> To: Freesurfer support list >>>> Subject: Re: [Freesurfer] mri_compute_volume_fractions >>>> >>>> Hi Dhivya >>>> >>>> if you are doing it in the space of the anatomicals, then use >>>> identity.nofile as the reg file (which is a special file name that will >>>> internally create an identity matrix). The output stem is whatever you >>>> pick - it will be prepended to the files that are written with the volume >>>> fractions. >>>> >>>> cheers >>>> Bruce >>>> On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: >>>> >>>>> External Email - Use Caution >>>>> >>>>> Hi, >>>>> >>>>> I would like to get CSF/GM/WM segmentations from aseg.mgz or in other >>>>> words from labeled brain. Can I do that with mri_compute_volume_fractions >>>>> ? Also, I am not sure about the parameters to supply, >>>>> <reg file> and <output stem>? >>>>> >>>>> Could Someone point me to some documentation on how should use this >>>>> function to get the segmentations ? >>>>> >>>>> Thanks, >>>>> Dhivya

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Using mprage flag.
by Aaron Tanenbaum 26 Apr '18

26 Apr '18

External Email - Use Caution Hello FreeSurfers When should I use the MPRAGE flag for recon-all? Aaron Tanenbaum

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mri_compute_volume_fractions
by Srinivasan, Dhivya 26 Apr '18

26 Apr '18

External Email - Use Caution Hi, I would like to get CSF/GM/WM segmentations from aseg.mgz or in other words from labeled brain. Can I do that with mri_compute_volume_fractions ? Also, I am not sure about the parameters to supply, <reg file> and <output stem>? Could Someone point me to some documentation on how should use this function to get the segmentations ? Thanks, Dhivya

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aparcstats2table for white surface total area
by Sian Emma Davies 26 Apr '18

26 Apr '18

External Email - Use Caution Hello, Forgive me, I'm new to FreeSurfer. I wish to collate values of white surface total area from all my subjects into a single table, so that I can control for this in my analyses. I understand this value is in the aparc.stats files for each participant and hemisphere, so I have tried: aparcstats2table -subjectfile sublist -hemi lh -meas WhiteSurfArea -tablefile aparc_stats_lh.wsa.table but WhiteSurfArea isn't an option for -meas. Please let me know if you can help, Many thanks, Emma Davies PhD Student Department of Psychiatry University of Cambridge Douglas House 18b Trumpington Road Cambridge CB2 8AH

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recon-all with T1 and T2 images
by Heidi Lindroth 26 Apr '18

26 Apr '18

External Email - Use Caution Hello, I have processed the majority of my T1 images using the general recon-all command. After reviewing segmentation, a number of images have the pial surface included in the gray matter. I re-ran an image with the recon-all command combining the T1 and T2 images and it greatly reduced the segmentation errors. Going forward, are there quality differences between those images processed with only recon-all versus those processed with recon-all T1 & T2? Can I still combine images processed with T1 only and those with T1 & T2 in the same analysis? Or, do I need to rerun all scans with the recon-all T1 & T2 command? Thank you, Heidi Lindroth BSN RN PhD Candidate | School of Nursing Program Assistant | School of Medicine and Public Health, Department of Anesthesiology Predoctoral Fellow | Veterans Administration (Madison WI) University of Wisconsin-Madison 701 Highland Avenue, Madison WI 53705 608-219-4294 | hlindroth(a)wisc.edu<mailto:hlindroth@wisc.edu>

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Freesurfer