Freesurfer April 2018

freesurfer@nmr.mgh.harvard.edu

118 participants
177 discussions

problem using mri_vol2label for subcortical regions
by Lucia Billeci 30 Apr '18

30 Apr '18

External Email - Use Caution Dear Freesurfer Experts, I want to use mri_vol2label to obtain labels for subcortical regions. I tried the following command: mri_vol2label --c $SUBJECTS_DIR/fsaverage/mri/aseg.mgz --id 8 --l ./tests_label/8.label However I get the same vertex index for all the row, equal to -1: -1 -14.000 -92.000 -31.000 0.0000000000 -1 -17.000 -92.000 -31.000 0.0000000000 -1 -18.000 -92.000 -31.000 0.0000000000 This happens for all the regions I selected. I have also tried adding the option —surf, as you suggested in previous posts: mri_vol2label --c $SUBJECTS_DIR/fsaverage/mri/aseg.mgz --id 8 --l ./tests_label/8.label --surf fsaverage lh white But I have the following error message: ERROR: dim mismatch between surface (163842) and input (16777216) Could you please help me? Thanks a lot in advance Best regards Lucia Billeci _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ Dr. Lucia Billeci, PhD Institute of Clinical Physiology (IFC) National Research Council (CNR) via Moruzzi 1, 56124, Pisa, Italy e-mail: lucia.billeci(a)ifc.cnr.it _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

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Call for Papers: Connectomics in NeuroImaging Workshop at MICCAI 2018, Granada (Spain)
by Islem Rekik 30 Apr '18

30 Apr '18

External Email - Use Caution Hello Colleagues, The attached call for full-length papers flyer provides information about the 2nd International Workshop on Connectomics in NeuroImaging (*CNI 2018*), which will be held in parallel with the 21st International Conference on Medical Image Computing and Computer-assisted Intervention (MICCAI 2018) in Granada Spain. CNI 2018 is a full day workshop that will take place September 20th, 2018. Our topics of interest cover (but are not limited to): (1) New developments in connectome construction from different imaging modalities, (2) Development of data driven techniques to identify biomarkers in connectome data, (3) Brain network modeling and formal conceptual models of connectome data, (4) Machine learning algorithms and connectome data analysis, and (5) Evaluation and validation of connectome models. If you have research that fits into the scope of our workshop detailed on our website ( http://munsellb.people.cofc.edu/cni.html) we encourage you to submit a paper or an abstract! *** Why submit to the CNI workshop? *** - Three great keynote speakers, presentations and poster sessions with accompanying power pitches will provide you with ample opportunity for exchanges and discussions; - There will be an INCF sponsored Best Paper Award; - Accepted papers will be published in an LNCS proceedings and will be invited to submit to a special issue journal; - Discuss your science and collaborate with international computational neuroscientists and clinicians in an intimate setting. *** Full length paper submission *** Paper submission deadline, June 11 via https://cmt3.research. microsoft.com/CNI2018 For more information visit http://munsellb.people.cofc.edu/cni.html *** Full length important dates *** Submission deadline: 11:59 PM PST, June 11th, 2018 Notification of acceptance: July 2nd, 2018 Camera-ready deadline: 11:59 PST, July 16th, 2018 Workshop date: Sept. 20th, 2018 *Also, if you know other colleagues that may be interested in submitting a full length paper, please feel free to pass along our workshop information to them. * We look forward to your participation! If you have any additional questions, please contact Brent Munsell ( munsellb(a)cofc.edu) or Ai Wern Chung (aiwern.chung(a)childrens.harvard.edu) ========================= CNI 2018 Chairs Islem Rekik, University of Dundee Ai Wern Chung, Boston Children's Hospital, Harvard Medical School Markus Schirmer, Harvard Medical School Guorong Wu, University of North Carolina, Chapel Hill Brent Munsell, College of Charleston

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Combining -3T and -mprage flags
by King, Daniel (Research Student) 30 Apr '18

30 Apr '18

External Email - Use Caution Hi Freesurfer community, I am currently running Freesurfer 6.0 and have run a number of 3T MPRAGEs through recon-all. I have also run these with the -mprage and -3T flags to compare outputs. I have therefore ended up with four runs of the same test patients: 1) Without flags 2) With the -3T flag only 3) With the -mprage flag only 4) With both the -3T and -mprage flag (in terms of order of operations I had the mprage flag then the 3T flag) However, when checking the outputted volume and CT measurements the values for the run 2 (just 3T flag) and the run 4 (with both flags) produce identical measurements. Does this mean that the mprage flag does not operate in the presence of the 3T flag? It was my assumption that the two flags call very different changes to the recon-all pipeline (-3T affects Taliarch atlas used and the nuintensity correction whilst -mprage affects mri_segment and mri_normalize parametres). In this case is there still any benefit in running both of the flags or is the 3T flag making the mprage flag redundant? Best wishes Dan Daniel King PhD Candidate in Neurosciences, School of Life and Health Sciences & Aston Brain Centre (SW505), Aston University, Aston Triangle, B4 7ET West Midlands, UK Email: kingdj(a)aston.ac.uk<mailto:kingdj@aston.ac.uk> Twitter: @danieljking8

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orig.mgz versus T1.mgz
by C.P.E. Rollins 30 Apr '18

30 Apr '18

External Email - Use Caution Dear Freesurfer developers, A collaborator shared with me Freesurfer outputs, but I would like to some analyses requiring the scans in NIFTI format. I understand mri_convert should do the trick for this, though I was wondering whether I should use "orig.mgz" or "T1.mgz" to convert back to the original T1 NIFTI files. Many thanks, Colleen

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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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Freesurfer April 2018