Freesurfer May 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
219 discussions

ADNI longitudinal brain volume in normal subjects
by shi yao wang 30 May '17

30 May '17

We are working on a longitudinal study for brain volume compartment in the specific population. I am wondering if there are any longitudinal brain volume data for normal patients? I saw some studies using ADNI normal data as reference, but cannot find them. thanks! Lawrence Emory University

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Segmentation fault (core dumped) error
by Devin Sodums 29 May '17

29 May '17

Hello FreeSurfer developers, I'm attempting to run recon-all on a T1 image and keep getting the same error message: Segmentation fault (core dumped) The recon-all seems to crash when running mris_volmask. I'm not sure what the problem is, as I have ran recon-all successfully on over 50 similar T1 files. I have searched for this error on the list serv and see that it can happen due to low memory. I have tried running the recon-all alone, without any other ones, and still have had the same issue. Is there any other possible fix I could look into? I have attached the recon-all.log file, and here is my operating system info from the VirtualBox Ubuntu system I am using: Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Thank you, Devin Sodums

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Freeview error
by Schumman Resonance 28 May '17

28 May '17

Hi, Newbie question. When I try to upload a surface to Freview I get the following error: [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Thanks, Kev

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Three Groups, Two Covariate (Age, Gender)
by stdp82＠virgilio.it 27 May '17

27 May '17

Hi list,I have difficulty to build a fsgd for Three Groups - 1 Factor, Two Covariate (Age, Gender).Please could you provide an example?ThanksStefano

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Haskins Pediatric Atlas use in FS
by John Hettema 26 May '17

26 May '17

To FreeSurfer team, I have child MRI data for which it would be best to use a pediatric atlas/template for warping, alignment, and labeling. I am aware of the Haskins Pediatric Atlas that AFNI includes as an optional dataset for this purpose in the FreeSurfer anatomical rendering it performs before running functional analyses. However, the AFNI team were unable to tell me how to connect to this atlas outside of AFNI. I.e., when I just run FreeSurfer for volume and surface reconstruction. How may I include this atlas in the usual running of FreeSurfer? Is there a specific command line flag I can use to specify it instead of the default adult one? Do I need to download some specific .gcs file? Thanks. Jack

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Re: [Freesurfer] [EXTERNAL] Re: Haskins Pediatric Atlas use in FS
by John Hettema 26 May '17

26 May '17

Hi Peter, Thank you so much for picking up on this. Yes, I guess I mean template - I am still new to FS and get some of the terms/procedures mixed up. Jenni Pacheco at NIH (copied) is helping to bring our group up to speed. Hopefully she can clarify further. I would appreciate being able to use those data in our research with FS. It would be good for hear what the FS staff have to say also. Jack -----Original Message----- From: Molfese, Peter [mailto:peter.molfese@yale.edu] Sent: Friday, May 26, 2017 9:57 AM To: john.hettema(a)vcuhealth.org Cc: jenni.pacheco(a)nih.gov; freesurfer(a)nmr.mgh.harvard.edu Subject: [EXTERNAL] Re: [Freesurfer] Haskins Pediatric Atlas use in FS Hi Jack- I created the Haskins Pediatric Atlas and saw your message on the Freesurfer list. I’m not sure I fully understand your question, would you like to use the Haskins Template (Atlas is technically the label/segmentation) as your template in Freesurfer? If it’s “as simple as” running through the steps on this page (https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) I suspect I can generate that in a couple of weeks. The GCS file seems to be more useful for actual atlas labeling. It may be possible for us to do some of this with the tools that exist (https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceLabelAtlas) Freesurfer experts, would you be willing to weigh in on options? All of these pediatric data (N=75) were run through Freesurfer 5.3 with manual edits. Best, Peter > To FreeSurfer team, > > I have child MRI data for which it would be best to use a pediatric > atlas/template for warping, alignment, and labeling. I am aware of the > Haskins Pediatric Atlas that AFNI includes as an optional dataset for > this purpose in the FreeSurfer anatomical rendering it performs before > running functional analyses. > > However, the AFNI team were unable to tell me how to connect to this > atlas outside of AFNI. I.e., when I just run FreeSurfer for volume and > surface reconstruction. > > How may I include this atlas in the usual running of FreeSurfer? > > Is there a specific command line flag I can use to specify it instead > of the default adult one? > > Do I need to download some specific .gcs file? > > > > Thanks. > > Jack

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white mater parcellation
by Cleudiana Lima 26 May '17

26 May '17

Dear Freesurfer expert; I'm new to Freesurfer. I have used wmpar to analyze white matter. So, Is there another tool to parcellation just deep white matter ? Thanks. -- Cleudiana Lima

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create symmetric mask on surface
by Meiling Li 26 May '17

26 May '17

Dear freesurfer experts I created a binary mask on fsaverage4(eg: lh.mask.fs4.mgh) with 30 vertices included in the mask on the left hemisphere, how can i obtain a symmetric mask on the right hemisphere that covered the same regions like the mask on the left hemisphere? Thanks! Meiling

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How to visualize the result with mri_glmfit and --table aparc flag
by Duy Nguyen 26 May '17

26 May '17

Dear FreeSurfer experts I have come across with this issue as I don't know how visualize the result after mri_glmfit done using --table aparc flag instead of --y. Do I use Matlab to do it? Please give me the instructions briefly as I've just started doing this? Any help is appreciated! Warmest regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme(a)gmail.com <duy.nguyenbme(a)gmail.com>*

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mri_glmfit-sim output error
by Duy Nguyen 26 May '17

26 May '17

Dear FreeSurfer experts, When I try to run mri_glmfit-sim, the output came out like this: cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd lh.gender-age.fsgd --C lh-Avg-thickness-FemaleMale.age.mtx --C lh-Avg-thickness-FemaleMale.intercept.mtx --C lh-Avg-thickness-Gender.diff.mtx --C lh-Avg-thickness-Gender*Age-Inter.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir SURFACE: fsaverage lh set: No match. [toibigi2007@localhost glm1]$ mri_glmfit-sim --help After I ran the command line like the following: mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 2 neg --cwp 0.05 --2spaces Please point me out what goes wrong with this command. Any help would be appreciated! Thank you and warmest regards, *--v-- Peace --v--* *Duy Nguyễn * *Biomedical Engineering Department- IU HCMC* *Cell: (+84)909999056* *Email: duy.nguyenbme(a)gmail.com <duy.nguyenbme(a)gmail.com>*

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Freesurfer May 2017