Freesurfer March 2017

freesurfer@nmr.mgh.harvard.edu

148 participants
263 discussions

Image size and resolution and their effects on Registration.
by Jeffrey Crawford 30 Mar '17

30 Mar '17

Hello everyone! Normally, I use Freesurfer on studies where the MRI scans are all taken with the same voxel parameters and , thus, all have the same image dimensions. However, now I am using a data set where I am presented with two different types of image dimensions and I unsure of the size limitations that Freesurfer can process while still being analytically viable. My understanding is that Freesurfer warps the image to fit the registration, but if the dimensions are too small to begin with, wouldn't that cause a lot of generalized pixels that could be inaccurate or cause fuzzy detail? The more I thought about this dilemma, the more I thought that giving Freesurfer the largest image possible would allow it to shrink it to whatever is most necessary for the registration and would, thus, maintain as much detail as possible for segmentation. However, I just couldn't find a defined limit as to the smallest image that Freesurfer could accurately segment. So, from this train of thought, here is my question: Would it be problematic to have Freesurfer process both of the example scans attached to this e-mail and then use the processed brains in the same analysis? The images attached are titled for their x , y, and z dimensions respectably. Any help or advice people could provide would be greatly appreciated. Hope all is well, Jeff

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Open position at Boston/Children's Hospital for bilingual research assistant (Spanish-English)
by Gaab, Nadine 30 Mar '17

30 Mar '17

The Gaab Lab<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.thegaablab.com_&d=C…> at Boston Children's Hospital is looking for a Research Assistants for a number of new projects examining language and reading development from infancy to adolescence. This includes subject recruitment for pediatric research studies (for English and Spanish speaking families) which will include close interaction with pediatricians in the Boston area, scheduling of pediatric research subjects, database maintenance, implementation and maintenance of analysis software; pediatric testing (including MRI/fMRI scanning of young children and infants<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.babymri.org_&d=BQMF…>) and data analyses (psychometrics, psychophysics and structural/functional magnetic imaging), stimuli design and administrative work (e.g., preparation of internal review board proposals). We are in particular looking for someone who is bilingual (English-Spanish) and who has experience with the administration of standardized tests (in English and Spanish). The position is ideal for anyone considering future graduate study in cognitive (developmental) neuroscience, developmental psychology, education, computer science, cognitive science or neuroscience. Bachelor's Degree in computer science, psychology, cognitive science, neuroscience, math, or related field required. Comfort with a heterogeneous computing environment (Linux/Unix, Mac, and Windows) as well as some programming experience preferred; knowledge of psychological experiment software (E Prime, Presentation, etc.) and/or fMRI analyses software helpful. Prior experience with infants and children would be very helpful. Spanish language knowledge is required. Demonstrable pre-existing interest in developmental psychology/ cognitive neuroscience desired; knowledge of neuroanatomy, statistics or machine learning helpful. Must be self-motivated and able to work in a fast-paced, changing environment and must like working with infants, children and families. Start date September or October 2016. Please first apply to Nadine.gaab(a)childrens.harvard.edu<mailto:Nadine.gaab@childrens.harvard.edu> with a cover letter and CV. "If we knew what it was we were doing, it would not be called research, would it?" A. Einstein (1879-1955) Nadine Gaab, PhD Associate Professor of Pediatrics Boston Children's Hospital/Harvard Medical School Department of Medicine/Division of Developmental Medicine Laboratories of Cognitive Neuroscience Mail stop code: BCH3178 1 Autumn Street (Office 643); Boston, MA 02115 nadine.gaab(a)childrens.harvard.edu<mailto:nadine.gaab@childrens.harvard.edu> phone: 857-218-3021 www.gaablab.com<http://www.gaablab.com/> Twitter: Nadine Gaab (@GaabLab)

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smoothing kernel
by Trisanna Sprung-Much 30 Mar '17

30 Mar '17

Hi there I am wondering whether there is an acceptable FWHM to use to smooth surface data (for instance, a probability map)? Many thanks Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Qcache
by Manuel Delgado 30 Mar '17

30 Mar '17

Dear list, When processing the data for longitudinal analysis (or even for cross sectional) the -qcache has to be run before editing or after all the edits have been done? Thank you -- *Manuel Delgado Alvarado, MD* Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN

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FREEVIEW: Registration visualization
by Marco Martinolli 30 Mar '17

30 Mar '17

Hello everyone, I am quite new to FreeSurfer and I have a doubt for the visualization of the data on a registered surface.Is it enough to load in freeview the surface.reg with overlayed the data like in: freeview -f lh.sphere.reg:overlay=lh.sulc or freeview -f lh.sphere.reg:annot=aparc.annot Doing like this the results do not change at all between subject and aligned subject and so I do not know wheter it was a problem in the registration itself or in the visualization.Actually, my surface is not really lh.sphere.reg, but itis the output from the first step of CVS registration (the surface step); but anyway it is always in the format lh.xxx.sphere.reg. Second question (less important): I am trying to visualize in the same freeview window multiple spheres (subject, template and aligned subject) and I use the offset position flag to fix them at the right distance in the space.Anyway, the spheres are not translated in the space with respect to the origin but roto-translated; so the spheres do not show the same face to the viewer but a slightly different one on each sphere.Is there a way in Freeview to load the spheres at the same time and make them show the same face at the same moment? CheersMark

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different filtering of brainmask.mgz in v5.3 and v6.0 - is it an issue to keep brainmask.mgz from v5.3?
by Antonin Skoch 29 Mar '17

29 Mar '17

Dear experts, I am reprocessing a group of subjects originally processed and edited in v5.3, by version v6.0. Due to the fact that some subjects had brainmask.mgz edited, I kept the brainmask.mgz from v5.3 to save time in editing (i.e. did not use -clean-bm in recon-all -all). I noticed that the brainmask.auto.mgz (from v6.0) is more aggresively filtered than brainmask.mgz (from v5.3) in basal ganglia (they have intensity 110 in v6.0 in contrast to v5.3) and also generally in white matter (much more voxels are 110 in v6.0 than in v5.3). Is it an issue? As I looked to the recon-all stream, the brainmask.mgz is in fact probably used only as mask for mri_em_register, mri_ca_normalize, mri_ca_register and mri_normalize, so the voxel intensities does not matter. Could you confirm that? Does it pose a problem to mix the subjects with brainmask.mgz created in v5.3 (and edited) with new subjects processed from scratch by v6.0? I considered to create v6.0 brainmask.mgz while keeping edits by remasking v6.0 T1.mgz by v5.3 brainmask.mgz using mri_mask T1.mgz brainmask_v5.3.mgz brainmask.mgz -keep_mask_deletion_edits but I do not know whether this is in fact necessary. Could you please comment on? Regards, Antonin Skoch

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Problem with fsgd file
by Yann Quidé 29 Mar '17

29 Mar '17

Dear all, I am sure it is something obvious, but I am stuck with that error. I am trying to analyse data and prepared my fsgd file, but when trying to use mri_glmfit, Terminal returns me the error gdfReadHeader: reading group_age_sex.fsgd ERROR: gdfRead: group_age_sex.fsgd is not formatted properly. The first string is 'GroupDescriptorFile', should be 'GroupDescriptorFile' As you can read, I did not misspelled the GroupDescriptorFile and even added a 1 after! (as GroupDescriptorFile 1), as mentioned in the wiki. It does not seem to be any “useless" tab in the fsgd file. I have attached an exemple (I just left 1 subject) Thanks for your time. Yann

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fslmaths like utility for surface overlays?
by Michael Kranz 29 Mar '17

29 Mar '17

Hi, Is there a way to create a subject specific overlay with an intensity value of 1 (or another constant value across the entire cortical mantle)? (I'm thinking a command like fslmaths in FSL but on the surface for each vertex). Best, Mike -- Michael Kranz Graduate Research Assistant |Beckman Institute University of Illinois 314-323-1329

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PVC on DTI
by Eduard Vilaplana Martinez 29 Mar '17

29 Mar '17

Dear Freesurfer experts, Does anyone have any experience on surface PVC in DTI? Concretely, I'm analysing cortical mean diffusivity (all on surface) and I am wondering whether the PVC pipeline for PET (petsurfer) would work on that case. Thanks for your help, Edu V.

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Re: [Freesurfer] Petsurfer mri_gtmpvc error
by Agrawal, Shubhi (NIH/NINDS) [E] 29 Mar '17

29 Mar '17

Thanks for the response. I ran the command again with FWHM 6, but am getting a 'MatrixAlloc(23680000,100): allocation failed' error. mri_gtmpvc --i OutBrick_run_008.nii --reg template.reg.lta --psf 6 --seg gtmseg.mgz --default-seg-merge --o gtmpvc.output This is the output log file- $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /home/agrawals8/freesurfer/subjects cd /home/agrawals8/freesurfer/subjects/NIH047 mri_gtmpvc --i mri/OutBrick_run_008.nii --reg mri/template.reg.lta --psf 6 --seg mri/gtmseg.mgz --default-seg-merge --o gtmpvc.output sysname Linux hostname ndsw-eeg-dreifuss.ninds.nih.gov machine x86_64 user agrawals8 vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 Loading seg for gtm mri/gtmseg.mgz Loading ctab mri/gtmseg.ctab Reading mri/gtmseg.lta Data load time 24.9 sec nmask = 23680000, nsegs = 100, excluding segid=0 FWHM: 6 6 6 Std: 2.54797 2.54797 2.54797 nPad 13, PadThresh 0.0001 Segmentations used for rescaling 174 Pons MEM: Size 479268 Peak: 956464 RSS: 339992 Data: 338176 Stk: 92 MEM: Size 10095992 Peak: 10095992 RSS: 969132 Data: 9954900 Stk: 92 MEM: Size 10189788 Peak: 10190808 RSS: 1062848 Data: 10048696 Stk: 92 System specs for this computer- CentOS 6.7, 7 Processors- Intel Xeon CPU @2.2GHZ, Memory 11GB, Available disk space 419 GB. Regards Shubhi ________________________________________ From: freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: Thursday, March 23, 2017 10:08 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 157, Issue 61 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Petsurfer mri_gtmpvc error (Douglas Greve) 2. Re: contrast between two independent CTh maps? (Uquillas, Federico D'Oleire) 3. Re: A Bug in Monte-Carlo Simulation. (Douglas Greve) 4. Re: Qdec 1.5 (Douglas Greve) 5. Re: Fw: PETsurfer surface based analysis (miracooloz(a)gmail.com) 6. Re: LME mass univariate model (Bronwyn Overs) 7. Re: Qdec 1.5 (Duy Nguyen) 8. Correcting Skull-Strip Errors - Watershed Algorithm Question (Abhinav Kurada) 9. Petsc Error in Freesurfer v6.0 (Michael ONeill) 10. Re: Thickness asymmetry and LH/RH corresponding vertices in fsaverage (Dorian P.) ---------------------------------------------------------------------- Message: 1 Date: Wed, 22 Mar 2017 17:11:49 -0400 From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Petsurfer mri_gtmpvc error To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <7422f5df-b0e5-587b-d71c-7dd2cc14aba3(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" FWHM should be the impulse response FWHM for your scanner. This is a number (eg, the HR+ is about 6), not the string 'FWHM' On 3/22/17 4:16 PM, Agrawal, Shubhi (NIH/NINDS) [E] wrote: > Hi, > I am trying to run SGTM partial volume correction in Petsurfer by > following the tutorial on the wiki. Every step preceding mri_gtmpvc > has been successful and the coregistration looks good. > the last step, mri_gtmpvc command gives an error- > Segmentation fault (core dumped) > > This is the information from the log file- > > $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ > setenv SUBJECTS_DIR /home/agrawals8/freesurfer/subjects > cd /home/agrawals8/freesurfer/subjects/NIH047 > mri_gtmpvc --i mri/OutBrick_run_008.nii --reg mri/template.reg.lta > --psf 6 --seg mri/gtmseg.mgz --default-seg-merge --auto-mask FWHM .01 > --o gtmpvc.output > sysname Linux > hostname ndsw-eeg-dreifuss.ninds.nih.gov > machine x86_64 > user agrawals8 > vgthresh 0.001000 > nReplace 18 > 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 > Loading seg for gtm mri/gtmseg.mgz > Loading ctab mri/gtmseg.ctab > Reading mri/gtmseg.lta > MEM: Size 479268 Peak: 955936 RSS: 339984 Data: 338176 Stk: 92 > MEM: Size 570956 Peak: 955936 RSS: 431688 Data: 429864 Stk: 92 > Data load time 25.9 sec > nmask = 2680458, nsegs = 100, excluding segid=0 > FWHM: 6 6 6 > Std: 2.54797 2.54797 2.54797 > nPad 13, PadThresh 0.0001 > Segmentations used for rescaling > 174 Pons > MEM: Size 422356 Peak: 955936 RSS: 283024 Data: 281264 Stk: 92 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer March 2017