Freesurfer March 2022

freesurfer@nmr.mgh.harvard.edu

86 participants
124 discussions

Re: [Freesurfer] mri_vol2vol anatomical to functional
by Manenti, Giorgio 31 Mar '22

31 Mar '22

External Email - Use Caution Hi Douglas, thank you for your time; I am trying to get the ribbon at functional space resolution (I need it to extract the white matter from my ROIs) Here I am copying the 2 commands (one using .reg file, the second using .lta) I am using, and the terminal terminal outputs. Attached you will also find 3 screenshots from freeview with 1) original ribbon https://secure-web.cisco.com/1jGfE_s0T0UpZC_37qNgkpXRnP-y87LEZivCMZpnxa5A-P… 2) ribbon transformed in functional space using the .reg file https://secure-web.cisco.com/1W46SeJXfyvYiIdzN0-Mgw8u9m_sVqChPLDxI9ZFbN355R… and 3) ribbon transformed using the .lta file https://secure-web.cisco.com/1D0QDP9T6GVwkO7J6BbTviZB6BzyWoBMt6z9cMQuKWuK6-… . (Please Note: I am using Matlab to integrate this analysis in the general pipeline, so the command are started by the s=system() function ) %%%%%%REG s=system(['mri_vol2vol --reg ' regpath ' --mov ' inputvol ' --targ ' funcTemp ' --o ' outputvol ]); regio_read_register: loading lta Matrix from regfile: 0.99982 -0.01069 -0.01533 -0.11505; 0.01423 -0.09676 0.99521 -0.84297; 0.01212 0.99525 0.09659 -5.72961; 0.00000 0.00000 0.00000 1.00000; movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz targvol FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1649422337 Final tkRAS-to-tkRAS Matrix is: 0.99982 -0.01069 -0.01533 -0.11505; 0.01423 -0.09676 0.99521 -0.84297; 0.01212 0.99525 0.09659 -5.72961; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 2.01888 -0.03096 0.02351 23.93213; 0.02447 0.19504 -2.18955 197.85437; -0.02873 -2.00955 -0.21287 240.49161; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done %%%%%%LTA s=system(['mri_vol2vol --lta ' ltapath ' --mov ' inputvol ' --targ ' funcTemp ' --o ' outputvol ]); Matrix from LTA: 0.99983 -0.01069 -0.01533 -0.11505; 0.01423 -0.09676 0.99521 -0.84293; 0.01212 0.99525 0.09659 -5.72960; 0.00000 0.00000 0.00000 1.00000; Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii INFO: src volume info differs from the one stored in lta. gets modified now. volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, -0.0000, -0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : (-0.0000, 1.0000, 0.0000) c_(ras) : ( 0.2540, 9.2232, 8.1562) file : Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz volume geometry: extent : (104, 104, 69) voxel : ( 2.0192, 2.0192, 2.2000) x_(ras) : (-0.9995, -0.0137, 0.0296) y_(ras) : ( 0.0126, -0.9991, -0.0397) z_(ras) : ( 0.0301, -0.0393, 0.9988) c_(ras) : ( 1.5530, 16.4346, 14.9788) file : bold/template.nii.gz INFO: dst volume info differs from the one stored in lta. gets modified now. volume geometry: extent : (104, 104, 69) voxel : ( 2.0192, 2.0192, 2.2000) x_(ras) : (-0.9995, -0.0137, 0.0296) y_(ras) : ( 0.0126, -0.9991, -0.0397) z_(ras) : ( 0.0301, -0.0393, 0.9988) c_(ras) : ( 1.5530, 16.4345, 14.9788) file : FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii volume geometry: extent : (256, 256, 256) voxel : ( 1.0000, 1.0000, 1.0000) x_(ras) : (-1.0000, -0.0000, -0.0000) y_(ras) : ( 0.0000, 0.0000, -1.0000) z_(ras) : (-0.0000, 1.0000, 0.0000) c_(ras) : ( 0.2540, 9.2232, 8.1562) file : Anatomy_Processed/hum_15496.long.long002/mri/orig.mgz movvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon.mgz targvol FSfast_struc/all_sub/f02_Sess03/bold/ecc_lh/conjunction_pe/v1_trai_vol.nii outvol Anatomy_Processed/hum_15477.long.long002/mri/lh.ribbon_func.mgz regfile FSfast_struc/all_sub/f02_Sess03/bold/register.dof6.lta invert 0 tal 0 talres 2 regheader 0 noresample 0 interp trilinear (1) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1649445621 Final tkRAS-to-tkRAS Matrix is: 0.99828 0.04446 -0.03809 2.43217; 0.03729 0.01869 0.99913 9.13850; -0.04513 0.99884 -0.01700 12.13850; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 2.01577 -0.07692 -0.09781 28.12225; -0.09113 -0.03433 -2.19744 198.19705; -0.07530 -2.01747 0.04112 244.54424; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done Many thanks again, Best Giorgio Message: 10 Date: Sun, 27 Mar 2022 17:16:25 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] mri_vol2vol anatomical to functional To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <50029d97-24be-17a3-2358-3c93982dea41(a)mgh.harvard.edu> Content-Type: text/plain; charset=UTF-8; format=flowed I'm not sure I understand what you are saying or what the problem is. Can you provide the actual command line you are using, all the terminal output, and a picture that shows what the problem is? On 3/23/2022 2:46 PM, Manenti, Giorgio wrote: > External Email - Use Caution > > Dear Freesurfer experts, > > I am getting problems to transform my xh.ribbon.mgh from anatomical 256x256x256 to functional 104x104x69 space. > > When converting the ribbon via ? mri_vol2vol ?reg REGfile ?mov INPUT ?targ funcTEMPLATE ?o OUTPUT ? and checking via freeview, i am getting the right functional space dimensions but the INPUT and OUTPUT .mgz are never overlapping. Why am i getting this misplacement ? Is this problem due to the register file i provide or maybe it is just a visualisation error (perhaps freeview is not the best way to check the conversion). > > I tried to change REGfile by providing the 1) init.register.dof6.dat and 2) register.dof6.lta (changing ??reg with ?lta?). I am getting an almost perfect merge when using the .lta file but still the two volumes are misaligned. > I tried mri_label2vol as well, but as expected i got worse results. > > To provide a minimum more detail, after recon-all i process the anatomy with the longitudinal recon. At that point i use the longitudinal anatomy to register the functional data, which i process by 1) mk-template 2) topup & applytopup. > > Many thanks in advance > Warm regards > > Giorgio > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://secure-web.cisco.com/1hfmecYxKY1NpcMzDGJ7lJmVMNisZgCocWDE73UzXQE8q4…

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FREESURFER Maintaining vertex Id during transformations
by Alison McDonnell 30 Mar '22

30 Mar '22

External Email - Use Caution Hi all, I have been able to create my flat map in freesurfer and then do calculations using it to find a point. I then want to map that point back into the 3D space maintaining the coordinates. I was wondering if anyone had done something similar before and had any ideas. I am using MATLAB for the calculations and transformations. Ali

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Re: [Freesurfer] password request for file FS_7_2_0_Ubuntu_18_04_06.ova.7z
by fsbuild 30 Mar '22

30 Mar '22

External Email - Use Caution Hello Roya, Sending the info to your email shortly. - R On Mar 30, 2022, at 09:37, Roya Afshari <roya.afshari(a)unibas.ch> wrote:        External Email - Use Caution        Hello,I hope this email finds you well.I would like to request for the password to FS_7_2_0_Ubuntu_18_04_06.ova.7z file to be able to expand it.Thank you for your time.Roya AfshariPhD studentDivision of Radiological Physics, Department of Radiology,University Hospital Basel, Basel, Switzerland_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Job opportunity (ResearchAssistant) at Boys Town National Research Hospital
by Sahil Bajaj 30 Mar '22

30 Mar '22

External Email - Use Caution Please apply at https://secure-web.cisco.com/1yo0ekSWIR0Yp45MZ3-6sWQmS9wHjqoQSAfI0CL1kuo7zD… Job ID18893 GENERAL SUMMARY Under the general supervision of appropriate Research Program Director or of a Research Associate, works on various phases of research studies being performed, including data entry and analysis, subject recruitment and testing. MAJOR RESPONSIBILITIES & DUTIES - Assists in data collection and managing databases. Will be responsible for entering data from testing, managing subject files and keeping track of subject compensation. - Assists in the recruitment, scheduling, and testing in research studies using human subjects. Will assist in advertising for new studies, phone screens of potential participants, scheduling testing and administering behavioral testing. - Uses computers to analyze results of experiments. Will assist in processing imaging data and collecting behavioral data for different research projects. - Utilizes Boys Town vehicle to complete requirements of the position. - Knowledge, Skills and Abilities Required - Ability to apply knowledge gained through coursework in psychology, biology, chemistry, physics, neuroscience and/or computer science. - Ability to operate a personal computer. - Ability to apply math aptitude in order to perform data analyses and generate results. - Ability to communicate well, both orally and in writing. REQUIREMENTS OF THE JOB: Bachelor's degree in psychology or neuroscience or related area or equivalent Previous research experience working with human subjects, preferred Good interpersonal skills, close attention to details, math aptitude, and flexibility in duties performed Must possess a valid driver's license with a good driving record and pass an annual Motor Vehicle Registration (MVR) check. About Boys Town: Boys Town has been changing the way America cares for children and families since 1917. With over a century of service, our employees have helped us grow from a small boarding house in downtown Omaha, Nebraska, into one of the largest national child and family care organizations in the country. With the addition of Boys Town National Research Hospital in 1977, our services branched out into the health care and research fields, offering even more career opportunities to those looking to make a real difference. Our employees are our #1 supporters when it comes to achieving Boys Town's mission, which is why we are proud of their commitment to making the world a better place for children, families, patients, and communities. Unique perks to Boys Town employees and their families include free visits to Boys Town physicians and free prescriptions under the Boys Town Medical Plan, tuition assistance, parenting resources from our experts and professional development opportunities within the organization, just to name a few. Working at Boys Town is more than just a job, it is a way of life. Date Posted: March 15, 20222 *Boys Town National Research Hospital is a tobacco free campus.* This advertisement describes the general nature of work to be performed and does not include an exhaustive list of all duties, skills, or abilities required. Boys Town is an equal employment opportunity employer and participates in the E-Verify program. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity and/or expression, national origin, age, disability or veteran status. To request disability-related accommodation in the application process, contact us at 1-877-639-6003.

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Re: [Freesurfer] SAMSEG (Lesion Mask Pattern) ... ah, [0 0]
by Cerri, Stefano 30 Mar '22

30 Mar '22

Hi Randy, The default option is 0 for each input scan as no assumption on the MRI contrast and order of the input scans is made. We strongly recommend users to use the value of 1 for both T2w and FLAIR scans and 0 for T1w scans. The mask is reducing false-positive lesions by applying intensity constraints, but it also indirectly leads to better lesion segmentation overall as the model parameters are better estimated. So in general it's hard to disentangle its effect. Hope it helps, Stefano From: Subject: Re: [Freesurfer] SAMSEG (Lesion Mask Pattern) ... ah, [0 0] To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <1991518757.1033.1648594478958(a)mail.yahoo.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear experts,? I think have answered my own question, but it does raise one more. >From the early lines in the reporting thread, I see that without "--lesion-mask-pattern" flag, the default appears to be [0 0].?? New question:? From an accuracy/precision standpoint, what do you think the impact would be on lesion detection? Thanks again (and in advance) -Randy -----Original Message----- From: daedalus39(a)aol.com To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Sent: Tue, Mar 29, 2022 4:24 pm Subject: SAMSEG (Lesion Mask Pattern) Dear experts, I inadvertently omitted the lesion mask pattern [0 1] when running SAMSEG, and while it ran to completion, there were fewer voxels present in the lesion mask (both at thresh 0.3) when I re-ran SAMSEG using the LMP.? ?The SAMSEG run included a T1 and a co-registered T2-FLAIR image. I am curious as to what the software defaults to in the absence of the --lesion-mask-pattern information.

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password request for file FS_7_2_0_Ubuntu_18_04_06.ova.7z
by Roya Afshari 30 Mar '22

30 Mar '22

External Email - Use Caution Hello, I hope this email finds you well. I would like to request for the password to FS_7_2_0_Ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1uT35qjETx2PBJuQg2agRxnXoPV7XDxnsMIStfOfoxzdC5…> file to be able to expand it. Thank you for your time. Roya Afshari PhD student Division of Radiological Physics, Department of Radiology, University Hospital Basel, Basel, Switzerland

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Postdoc available at the Central Institute of Mental Health
by Loeffler, Martin 30 Mar '22

30 Mar '22

External Email - Use Caution The Central Institute of Mental Health (CIMH) stands for cutting-edge international research and groundbreaking treatment concepts in psychiatry, psychotherapy, child and adolescent psychiatry, psychosomatics and addiction medicine. The Department of Cognitive and Clinical Neuroscience (Scientific Director: Prof. Dr. Dr. h. c. Dr. h. c. Herta Flor) is looking for a talented, highly motivated postdoctoral fellow, to join a multimodal human neuroimaging research group with strong roots in experimental psychology. Our BMBF funded research examines neural circuits underlying chronic musculoskeletal pain. In the current project we focus on the improvement of the treatment of chronic musculoskeletal pain disorders through a personalized therapy approach with cross-disease multilevel diagnostics and mechanism-oriented interventions. We employ learning models and machine learning approaches to improve patient stratification. Our methods concentrate on experimental psychological designs, neuropsychological assessments, functional magnetic resonance imaging (fMRI), and peripheral physiology Our requirements * Ph.D. in psychology, neuroscience or related fields * Experience in at least one of the imaging modalities (fMRI, MEG, EEG, fNIRS) * Excellent teamwork, time management and organizational skills * Expertise in statistics (R, JASP, SPSS) and experimental designs (Presentation, Matlab) * Programming skills (Matlab, Python) and experience with neuroimaging analysis software (e. g. FSL, SPM, FreeSurfer) * Strong publication record in peer-reviewed scientific journals * German language skills are an advantage Responsibilities * Become part of a multidisciplinary team working on psychobiological and clinical research questions * Participation in grant writing and scientific publications * Participation to clinical interviews and questionnaires as well as patient recruitment * Presentation of study-related outcomes at key scientific meetings What you can expect * An interesting job in a clinical center and leading research institute * Pleasant colleagues and a friendly working atmosphere * Departmental introduction and familiarization * Internal and external further education and training opportunities * Job ticket * Good accessibility and central location in the heart of Mannheim * Good compatibility of work and family * Remuneration according to TV-L and the associated social benefits according to the collective bargaining regulations of the public service Severely disabled, who are equally qualified will be preferred. Salary is based on the German TV-L pay scale, including the social benefits of the German public service sector Contact If you have any questions, please contact Herta Flor, email: Herta.Flor(a)zi-mannheim.de<mailto:Herta.Flor@zi-mannheim.de>, phone number +49 621 1703-6302 or Martin Löffler, email: Martin.Loeffler(a)zi-mannheim.de<mailto:Martin.Loeffler@zi-mannheim.de> +49 621 1703-6349. We are pleased to receive your application via the online career portal until April, 15th, 2022 (https://secure-web.cisco.com/1VLfuJU_rnnl9fgjvpflyO_Ee8Uy_9ByRDPS1PRf-PsbHU…) .

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SAMSEG (Lesion Mask Pattern)
by daedalus39＠aol.com 29 Mar '22

29 Mar '22

External Email - Use Caution Dear experts, I inadvertently omitted the lesion mask pattern [0 1] when running SAMSEG, and while it ran to completion, there were fewer voxels present in the lesion mask (both at thresh 0.3) when I re-ran SAMSEG using the LMP. The SAMSEG run included a T1 and a co-registered T2-FLAIR image. I am curious as to what the software defaults to in the absence of the --lesion-mask-pattern information.

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FreeSurfer license key error
by Koustav Chatterjee 29 Mar '22

29 Mar '22

External Email - Use Caution Dear FreeSurfer experts, I have reinstalled FreeSurfer 6 in my new system following the FreeSurfer wiki. I have saved the 'licence.txt' in /usr/local/freesurfer. However, I am getting following error- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://secure-web.cisco.com/16tgEh0sPXTbDRDMUvw9zB7Em9ZdUbHl0MZ9k7-9-sJxU6u… to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. ------------------------------------------------ Please help me resolving the issue. Thank you. KC

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Tracula tracts do not display correctly and have large volume
by Goeckner, Bryna 29 Mar '22

29 Mar '22

External Email - Use Caution Hi Freesurfer Experts, I have run into a problem with several subjects ranging over several different tracts (usually just one tract per subject) where a tract will not display correctly in merged_avg16_syn_bbr.mgz or in the individual pathway (ex: lh.cbv_avg16_syn_bbr/path.pd.nii.gz) without first adjusting thresholds. I also discovered that the volume in pathstats.overall.txt in these cases is significantly higher than the average – on the order of 10 times bigger. I know there is mention of using “set reinit=1” to repair tracts that are too small or missing. Would this be recommended here as well or is there another better direction to take? I am including a link to the trac-all.log for a subject whose rh.ilf is problematic. Please let me know of there is any other information you need and thanks for your help! https://secure-web.cisco.com/1-H9YB7x0pcdABFBAqsjeogpPsh-50RChRNS5qTyoP0bcn… Bryna Goeckner (she/her) Graduate Student Medical College of Wisconsin Neuroscience Doctoral Program

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Freesurfer March 2022