Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

Edits to aseg
by Tamara Tavares 20 Jan '17

20 Jan '17

Hello, After I make edits to my aseg output in the longitudinal stream, do I just run the following command to recreate the final volumes: recon-long -autorecon2-noaseg -subjid <Subj_ID> I assume the -subjid is the name of the edited time point and <Subj_ID> is the name of the recreated volumes? Thank you, Tamara

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'nuisance factors adjusted' values
by hiroki.sato＠med.tohoku.ac.jp 19 Jan '17

19 Jan '17

Dear experts, I have some questions. I did Qdec group analysis with three nuisance factors. And one region remained after FDR correction. Then I did 'mri_surfcluster' specifying the FDR-determined voxel-wise threshold as the --thmin. After that I ran 'mri_segstats' and got the values. 1)Are these values 'nuisance factors adjusted' values? 2)If not, is there a way to get 'nuisance factors adjusted' values using FreeSurfer? Best Regards, Hiroki

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Feature requests/bug reports in FS 6
by Chris Adamson 19 Jan '17

19 Jan '17

Freesurfer devs, I have a few issues to report for FS6. Bugs: defect-seg needs to use white.preaparc rather than white. My fixes were to change the mris_seg2annot call on line 114 to include -surf white.preaparc and comment out the mri_segstats call on line 122 Feature requests: Freeview It really needs a 3D brush. What would be nice for segmentation images is the ability to double click on a label on the list on the left and have the viewer automatically centre on voxels having that label in the image. Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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aparc stats file output
by Marianna Riello 19 Jan '17

19 Jan '17

Dear Freesurfer users, I have a question on the 'aparc.stats' file output: Which of your label corresponds to: Ventro and Dorso Lateral Prefrontal Cortex? Supplementary motor areas? Putamen? Angular Gyrus? Thank you for your help Sincerely, Marianna

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Multiple --meas files in mri_glmfit
by Garikoitz Lerma-Usabiaga 19 Jan '17

19 Jan '17

Hi list, is it possible to have multiple --meas files in mri_glmfit? For example, for a group of 40 subjects, to check in every vertex if there is a relation between CT and the t of a fMRI contrast. Thanks! Gari

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Error running mri_info on OS X (but not Linux)
by Valerie Beck 19 Jan '17

19 Jan '17

Hi, When I run mri_info on my mac (OS 10.11.6) using Freesurfer 5.3, I keep getting this error: WARNING: file /Volumes/skol/VT_MR_2_UD/TVUD1_010/study/cmrr_retinotopy_389_13/IM-0010-0001.dcm does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header But when I run mri_info on my linux machine (Ubuntu 16.04) using Freesurfer 5.3, it runs without error and can read the header info just fine. I looked on the freesurfer wiki and didn’t see any known issues related to this. Thoughts? ~Valerie Valerie M. Beck, Ph.D. Postdoctoral Researcher Department of Psychological and Brain Sciences University of Delaware 108 Wolf Hall Newark, DE (302) 455-8465 vbeck(a)psych.udel.edu<mailto:vbeck@psych.udel.edu>

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mri_mcsim OSX last version
by Garikoitz Lerma-Usabiaga 19 Jan '17

19 Jan '17

Hi list, mri_mcsim on FS5.3 is giving a strange error in osx 10.11, in the wiki a newer Linux version is available and indicates to ask for other versions. Is it possible to have the last osx version? thanks! Gari

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Registration Checking Problems
by Anderson Napolitano 19 Jan '17

19 Jan '17

Good Morning Experts, I am having trouble checking the registration per step 2 of the pet surfer tutorial: http://freesurfer.net/fswiki/PetSurfer. The line: mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta worked just fine but when checking the registration using the line: tkregisterfv --mov template.nii.gz --reg template.reg.lta --surfs I get the following output: set: Variable name must begin with a letter Any advice as to how to resolve this issue will be greatly appreciated. Thanks, Anderson Napolitano?

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mris_make_surfaces error with bbr-init-header
by Sneha Pandya 19 Jan '17

19 Jan '17

Hi all, I have successfully ran recon-all on my subjects with multiple T1s. We want to use flair to refine pial surfaces as for all the subjects pial surfaces are messy and will demand lots of control point edits. After successfully running entire recon-all stream I am running following command to incorporate flair: recon-all -autorecon3 \ -s SUBJ \ -bbr-init-header \ -FLAIRpial \ -bigventricles \ -openmp 12 \ -qcache When I run above command recon-all exits while implementing mris_make_surfaces with an error "Cannot allocate memory" Can someone guide what is happening? Is it that there are large topological error or bbr-init-header flag will only run if I run recon-all from autorecon1 to autorecon3 stage? Thanks, Sneha

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Re: [Freesurfer] pial surface regeneration NOT WORKING
by Bruce Fischl 19 Jan '17

19 Jan '17

Hmmm, not sure what's going on. Can you try this: cd /mnt/Local_Data/Reliability/Matt/5514syxa_110502_3Tnu_HFBd_wmseg/scripts setenv DIAG 0x04048 mris_sphere -w 0 -seed 1234 ../surf/lh.inflated ../surf/lh.sphere and send us the output? On Thu, 19 Jan 2017, Sanjana Shellikeri wrote: > > Hi Freesurfer Developers, > > > We are attempting to regenerate the pial surfaces from an edited > brainmask.mgz. We deleted dura voxels (precentral and postcentral gyri both > hemispheres) on the original brainmask.mgz on Freeview. The command we ran > is: > > > recon-all -autorecon-pial -subjid [subjectID] > > > There was no error output, however, the process hangs indefinitely (>36 > hours) after 'randomSeed 1234' and the pial surfaces have not been > regenerated. > > > Please see the attached text file which contains the terminal output of the > command. > > > We are using xUbuntu 12.04 and freesurfer-Linux-centos4-stable-pub-v5.3.0. > > > > Regards, > > Sanjana Shellikeri, PhD Student > > Department of Speech-Language Pathology > Faculty of Medicine, University of Toronto > 160-500 University Ave. > Toronto, ON M5G 1V7 > sanjana.shellikeri(a)mail.utoronto.ca > >

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Freesurfer January 2017