Freesurfer

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30089 discussions

orig.mgz versus T1.mgz
by C.P.E. Rollins 02 May '18

02 May '18

External Email - Use Caution Thanks Bruce. Will the orig.mgz file be different from the raw data in any significant way? Thanks again, Colleen -------- Original Message -------- Subject: orig.mgz versus T1.mgz Date: 2018-04-30 11:54 From: "C.P.E. Rollins" <cper2(a)cam.ac.uk> To: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> 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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Mapping left to right for fsaverage 5 (ico5)
by Davide Tabarelli 02 May '18

02 May '18

External Email - Use Caution Dear all, I have a question about left-right sphere based co-registration. I have a scalar quantity defined on the fsaverage5 ico5 surfaces and I would like to map left to right hemisphere. I’ve computed left_right registered spheres by running following commands in the fsaverage5 folder: mris_curvature -w lh.white mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right mris_curvature -w rh.white mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated mris_left_right_register lh.sphere rh.sphere lh.sphere.left_right rh.sphere.left_right As far as I understood, the lh.sphere.left_right contains the lh mesh warped to be consistent with the anatomical landmarks on rh. Thus in mapping or interpolating, I have to use vertices in lh.sphere.left_right and map/interpolate them to rh.sphere. Is that correct? There is a better way to do that? Moreover I cannot find information about the “thresh” and “distances” arguments in mris_left_right_register help. Maybe those options are not fine for the fsaverage ico5 ? Thank you all in advance. D. — Davide Tabarelli, Ph.D. Center for Mind Brain Sciences (CIMeC) University of Trento, Via delle Regole, 101 38123 Mattarello (TN) Italy

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Freeview surface volume misalignment
by Kambiz Tavabi 01 May '18

01 May '18

External Email - Use Caution Hi all, I am not sure why I occasionally hit this issue, but for reasons, I don't know the surfaces and the corresponding volume in Freeview are misaligned. This is not the case in tkmedit. In this particular case the surface(s) were created using: (1) mri_convert input.nii output.mgz (2) fsl_rigid_register -r rawavg.mgz -i output.mgz -o output_reg.mgz (3) mri_make_bem_surfaces [image: alignment.png] Thanks in advance. Kambiz

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question about hippocampal vols
by Anik Dar 01 May '18

01 May '18

External Email - Use Caution Hi All, I have run quantifyHAsubregions.sh hippoSf <T1>-<analysisID> <output_file> <OPTIONAL_SUBJECTS_DIR> and have the volumes for the hippocampal subfields. From which of the following segmentation files are these volumes computed from ? lh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.CA.mgz lh.hippoAmygLabels-T1.v21.FS60.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.FS60.mgz lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.HBT.FSvoxelSpace.mgz lh.hippoAmygLabels-T1.v21.HBT.mgz lh.hippoAmygLabels-T1.v21.mgz Please let me know. Thanks Ani

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Call for PRIME-MICCAI 2018 papers **1st International Workshop on PRedictive Intelligence in MEdicine **
by Islem Rekik 01 May '18

01 May '18

External Email - Use Caution Dear all, We present the 1st edition of the *PR*edictive *I*ntelligence in *ME*dicine (*PRIME*) workshop in conjunction with *MICCAI 2018* in Granada, Spain. The main aim of PRIME is to propel the advent of predictive models in a broad sense, with application to medical data. We hope that PRIME workshop becomes a nest for high-precision predictive medicine, one that is set to transform multiple fields of healthcare technologies in unprecedented ways. We welcome contributions fitting the following research topics (*but not limited to*): Modeling and predicting disease development or evolution from a limited number of observations; Computer-aided prognostic methods (e.g., for brain diseases, prostate cancer, dementia, acute diseases, neurodevelopmental disorders); Forecasting disease/cancer progression over time; Predicting low-dimensional data (e.g., behavioral scores, clinical outcome, age, gender); Predicting the evolution or development of high-dimensional data (e.g., shapes, graphs, images, patches, abstract features, learned features); Predicting high-resolution data from low-resolution data; Predicting image modality from a different modality (e.g., data synthesis); Predicting missing data (e.g., data imputation or data completion problems). --------- *** Paper Submission *** Paper submission deadline, June 11 via https://cmt3.research. microsoft.com/PRIME2018 <https://cmt3.research.microsoft.com/PRIME2018> <https://cmt3.research.microsoft.com/PRIME2018> For more information visit http://tiny.cc/prime2018 <http://tiny.cc/prime2018> <http://tiny.cc/prime2018> *Flyer (if not attached, **check)*: http://basira-lab.com/wp- content/uploads/2018/01/PRIME-MICCAI_2018_flyer_final.pdf <http://basira-lab.com/wp-content/uploads/2018/01/PRIME-MICCAI_2018_flyer_fi…> <http://basira-lab.com/wp-content/uploads/2018/01/PRIME-MICCAI_2018_flyer_fi…> --------- *** Important dates *** - Paper submission deadline: June 11, 2018 - Author notification: July 15, 2018 - Camera-ready: July 20, 2018 - Workshop date: September 16, 2018 --------- *** Keynote Speakers *** Prof Dinggang Shen (University of North Carolina) Dr Ender Konukoglu (ETH Zurich) Dr Ipek Oguz (University of Pennsylvania) Dr Kilian M. Pohl (Program Director in the Center of Health Sciences at SRI International) --------- *** Highlights *** - Proceedings will be published in *Springer Lecture Notes in Computer Science (LNCS)* (EI, ISTP indexed). - The PRIME 2018 *Best Paper Award* will be granted to the best overall scientific paper. If you have any questions, please contact me, Islem Rekik at irekik(a)dundee.ac.uk Please feel free to forward this email to those who might be interested. We are looking forward to your PRIME submissions! Sincerely, The PRIME 2018 Chairs ---------- Islem Rekik (University of Dundee, UK), Point of Contact: irekik(a)dundee.ac.uk Gozde Unal (Istanbul Technical University, Turkey) Ehsan Adeli (Stanford University, US) Sang-Hyun Park (Daegu Gyeongbuk Institute of Science and Technology, South Korea)

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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.microsof t.com/CNI2018 *Download flyer using*: http://basira-lab.com/wp-content/uploads/2018/04/CNI-MICCAI-2018.tiff <http://basira-lab.com/wp-content/uploads/2018/04/CNI-MICCAI-2018.tiff> 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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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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