Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

Different Sequences Longitudinal Stream {Disarmed}
by Backhausen, Lea 05 Nov '20

05 Nov '20

External Email - Use Caution Dear FreeSurfer experts, I am currently working on a longitudinal data set with 4 time points, acquired at one site with the same Siemens Trio 3T scanner. Unfourtunately, the T1 sequence differs slightly for one of these time points. These sequences have been measured: 1) repetition time (TR) = 2300 ms, echo time (TE) = 2.93 ms, inversion time (TI) = 900 ms, voxel size = 1.1 x 1.1 x 1.1mm, flip angle = 9°; matrix size = 256 x 256 x 160 mm 2) repetition time (TR) = 1900 ms, echo time (TE) = 2.26 ms, inversion time (TI) = 900 ms, voxel size = 1.0 x 1.0 x 1.0mm, flip angle = 9°; matrix size = 256 x 256 x 176 mm Is it possible to process these different sequences in the longitudinal stream (if e.g. one participant would have 3 data sets of sequence 1 and one data set of sequence 2)? Or would this cause too much bias? Thank you very much, kind regards! Lea Backhausen ------------------------------ Lea Backhausen Ph.D. Student (M.Sc. Psychology/Neuroscience) Department of Child and Adolescent Psychiatry, Faculty of Medicine of the TU Dresden, Germany http://secure-web.cisco.com/1uRUN3qw4_2ZQdVovG97ElQWo_5ofjkray9cxFwmREkCPYf…<http://secure-web.cisco.com/16jDYbTgO8Bi4O3L_8oBX-UxhLbIwNnO8u3tQFvD5bc-Ksr…>

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trac-preproc error
by Hasimoglu, Yasemin 05 Nov '20

05 Nov '20

Hi, I'm running Tracula on a longitudinal dataset and it's failing at the preproc stage for one subject with the following message: INFO: Distances between consecutive points in test subject's space are 16 13 12 14 WARN: Could not find satisfactory control point fit - try 4967 Finding center streamline INFO: Step is 3 voxels WARN: Turning off deviation check for center streamline INFO: Step is 3 voxels WARN: Turning off FA check for center streamline INFO: Step is 3 voxels WARN: Turning off overlap check for center streamline INFO: Step is 3 voxels WARN: All checks already off. Exiting. Selecting 5 points on center streamline ERROR: Selected streamline has fewer than 5 points Linux zorii.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Wed Oct 28 04:11:51 EDT 2020 It looks like the problem is with one specific pathway. I checked the brainmask and the inter and intra-subject registrations and they all look fine to me, so I'm not sure what else to check. The trac-all.log file is quite large, I attempted to attach it in this email several times, but it always gets rejected, so I'm not attaching it for now. I would greatly appreciate any advice! Best, Yasemin

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LGI quality control {Disarmed}
by Nelson, Eric 05 Nov '20

05 Nov '20

External Email - Use Caution Hello, I am using FreeSurfer 7.1.1 to run LGI and have done so successfully. I am now trying to quality check my data using tksurfer as described on the wiki tksurfer my_subject_id lh inflated -overlay lh.pial_lgi However the LGI overlay is not covering the entirety of the inflated brain. Specifically the medial frontal surface and some subcortical are not measured for LGI. Here is a link of the overlay images for a few subjects: https://secure-web.cisco.com/1FvGKanOWU0exqsmfZZWyCdCgTFgqf8kB2BXdsF-5A035k…. I<https://secure-web.cisco.com/1yytrZan4Ml7C4NJTkc91uplhrETEPm4MAwDFEYaEAXtVl…>. I haven't been able to find any images of what this overlay should look like so I don't know if this is expected or if something has gone wrong with the processing. Any feedback would be greatly appreciated Best, Eric

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(no subject)
by saman fouladi 05 Nov '20

05 Nov '20

External Email - Use Caution hi I run in linux command:""""""""""""""""""""""""""""""""""""""""""" aparcstats2table --hemi lh --subjects /home/team33/MRI4/subj10/stats --parc aparc.a2009s --meas meancurv --tablefile /home/team33/ aparcstats.txt""""""""""""""""""""""""""""""""""""""""""" but show below error an i can not solve it nix: """"""""""""""""""""""""""""""""""""""""""" File "/usr/local/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' """"""""""""""""""""""""""""""""""""""""""" I changed the code several times, but in all cases there is this error. This error also happens to asegstats2table. please help me

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Re: [Freesurfer] Troubleshooting -parallel flag for Freesurfer, error in the cortical ribbon mask stage during recon-all {Disarmed}
by Andy Worth 05 Nov '20

05 Nov '20

External Email - Use Caution Hello, We've experienced random crashes when using the -parallel flag with the official FS docker container at https://secure-web.cisco.com/1Db9ik7eIvMj7kgkeTafe0s_PlT0VyO4BIvoM6Chj4jvye…. It looks like this issue: https://secure-web.cisco.com/1RTUH2ziWrAzuafGfyVCoxnmVd6xWSC1pjYKx0ENFxB4V7…. Is there a fixed recon-all that I can use with that image (or maybe a new image coming soon)? Thanks, Andy Worth Scientific Solutions Engineer he, him, his <http://secure-web.cisco.com/1vnPdwWhDIRo0dgACPHUy8Cs0L0bRI0jZF0TyQMe6r95oCZ…>

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Question about smoothing for extracting anatomical stats {Disarmed}
by Hye Min Shin 05 Nov '20

05 Nov '20

External Email - Use Caution Hello experts, So I understand that when doing mri_glmfit you want to use smoothed surface maps to comply with random field theory while controlling for multiple comparisons (as discussed here: https://secure-web.cisco.com/1pNAU-NVIkRxQvX9B5btXENpnudT80URPA00UsXPU064w3…) But I was also wondering whether we have to smooth surface maps when using mri_anatomical_stats to extract anatomical measurements? I see that mri_anatomical_stats has the option to smooth by # of iterations but is there a way to know how many # of iterations would equal let's say 15 FWHM? Best, Julia Shin

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mri_convert error
by Georgina Angelopoulou 05 Nov '20

05 Nov '20

External Email - Use Caution Dear Freesurfer Developers, I am sorry I did not include the error message. I am attempting to convert some dicom files to mgz via mri_convert command. However, for only 5 participants from my cohort I get the following error. Could you please help me to resolve the problem? (base) Georgias-MBP:HC21 georgina$ mri_convert 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm 001.mgz mri_convert.bin 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm 001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm... Starting DICOMRead2() dcmfile = /Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm dcmdir = /Users/georgina/Downloads/HD/HC21 ERROR: GetDICOMInfo(): dcmGetDWIParams() 9 DICOM File: /Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491068177.dcm break DICOMRead.c:5228 Ref Series No = 201 Found 172 files, checking for dicoms ERROR: GetDICOMInfo(): dcmGetDWIParams() 9 ERROR: GetDICOMInfo(): dcmGetDWIParams() 9 DICOM File: /Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316491025102.dcm break DICOMRead.c:5228 First Sorting Computing Slice Direction Vs: -0.99478 0.102 0.0033 Vs: -0.994779 0.102 0.0033 Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 82 ndcmfiles = 82 PE Dir = (dicom read) CTABreadASCII(/Applications/freesurfer/FreeSurferColorLUT.txt): could not open file Too many open files ERROR: reading /Applications/freesurfer/FreeSurferColorLUT.txt Loading pixel data ERROR: /Users/georgina/Downloads/HD/HC21/1.3.46.670589.11.38127.5.0.4944.2019102316490992042.dcm is not a dicom file 70092 Requested element (18 9089) not found in DCM_GetElementVM Thank you in advance, Georgina

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mri_glmfit_sim error
by Basavaraju, Rakshathi 05 Nov '20

05 Nov '20

External Email - Use Caution Hi all, I ran a multiple comparison correction for a surface based analysis with this command: mri_glmfit-sim --glmdir rh.project.glmdir --cache 2 abs --cwpvalthresh .05 --2spaces But I am getting the following error: cannot find /usr/local/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm38/abs/th13/mc-z.csd What might this error mean? I searched in the mail archives but could not get any proper answer. Kindly help me. Thanks

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Re: [Freesurfer] .mgh file unknown, GLM paired analysis {Disarmed}
by Agurne Sampedro Calvete 05 Nov '20

05 Nov '20

External Email - Use Caution Dear FS experts, I have removed the backslashes "\" and now it works, so problem solved. Thank you very much. Regards, Agurne Neuropsychology of Severe Medical Conditions Research Team Dpt of Methods and Experimental Psychology Faculty of Psychology and Education University of Deusto neurolab.deusto.es Avda. de las Universidades 24, 48007, Bilbao (Spain) Phone: +34 944139000 (ext. 3015) El lun., 2 nov. 2020 a las 18:27, Agurne Sampedro Calvete (< a.sampedro(a)deusto.es>) escribió: > Dear Freesurfer Experts, > > I am trying to perform a paired analysis in FreeSurfer following this > tutorial https://secure-web.cisco.com/1GGOE7lAk9DEhVom372ksbhQpoUEm3yIVLX4YqDE8HfMpe… and I > have some problems when running the spatially smooth. > > I ran the following command: mri_surf2surf --s fsaverage --hemi lh --fwhm > 5\ --sval lh.paired-diff.thickness.mgh \ --tval > lh.paired-diff.thickness.sm05.mgh > > And I found this error: > ERROR: lh.paired-diff.thickness.mgh unknown freesurfer > > This file is in my subject directory, but when I see the file properties, > in the "file type" box it says: unknown. I have read that other users have > experienced the same error. > > What can I do to solve this problem? > > Thanks in advance. > > Kind regards, > > Agurne Sampedro > > > > Neuropsychology of Severe Medical Conditions Research Team > > Dpt of Methods and Experimental Psychology > Faculty of Psychology and Education > > University of Deusto > > neurolab.deusto.es > > > > Avda. de las Universidades 24, > > 48007, Bilbao (Spain) > > Phone: +34 944139000 (ext. 3015) >

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Join the Brainhack donostia
by Vicente Ferrer 05 Nov '20

05 Nov '20

External Email - Use Caution The Basque Center on Cognition, Brain and Language (BCBL) is holding a free online next week. We hope that it can be of interest to this community, and that you could forward others this information. At the BCBL, we are organizing the third edition of Brainhack Donostia (https://secure-web.cisco.com/1GC1hh4vsRCGfthBadagfSojiEis8P2rIcxlvHWMBmSe1m…) an event focused on neuroscience and the promotion of open-source resources in an accessible way across disciplines and experience levels. This year's edition is taking place from November 9 through November 13: it will be held online and will be completely free. The focus of BHD2020 will be OpenScience, covered from a variety of pertinent perspectives (e.g., MEG, fMRI and fNIRS). We are going to have the cream of the crop as invited speakers, check the schedule here: https://secure-web.cisco.com/1nN_lXzurOj1ntsI3lbjeAWTurwndamZGsnyiXQE9Xqhw7…. Even though we will be physically distant, there will be the possibility to come together and socialize on the Brainhack Donostia GatherTown platform. We will be using the platform to host exciting social activities throughout the event. Stay tuned for the social activities program! We invite all neuroscience aficionados, students of neuroscience-related subjects, professors and professionals to participate. Registrations are now open at https://secure-web.cisco.com/1d3VTvJ1ukmPmrYp15NgAyjM96L0VJDHuND2s9vyXzTZc5…. Best regards, Vicente Ferrer Predoctoral Researcher BCBL http://secure-web.cisco.com/12Abv6l6_PtwWS0hk38LzFrcDpN7GEtPA16QooQuy_XnRh0… Legal disclaimer/Aviso legal/Lege-oharra: http://secure-web.cisco.com/15zTX7kAQnbTPpg6u_ChbnA89bSxwOzqP4KMe91gP9IM05T…

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