Freesurfer March 2017

freesurfer@nmr.mgh.harvard.edu

148 participants
263 discussions

Smooth overlay in command line
by Dorian P. 23 Mar '17

23 Mar '17

Is it possible to set the smooth overlay option (i.e. no of iterations) from command line instead of freeview? I am taking some screenshots that would look nicer with a smoothed overlay. Dorian

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Editing insula label
by Katherine Damme 23 Mar '17

23 Mar '17

Hello FreeSurfer Group, I am trying to edit my insula labels which are regularly over inclusive on the right hemisphere (see coronal image for medial extension). When I use the label editing tool many of the voxels erase. However there are a number of scattered voxels that won't go away, no matter which view I select them in (see sagittal image for sticky voxels). I am using the drawing tool set to 2 voxels as recommended by the wiki. Is there any reason that these tools may not edit a set of voxels? Thank you! Kate Damme

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Petsc Error in Freesurfer v6.0
by Michael ONeill 23 Mar '17

23 Mar '17

This problem has been resolved by installing Freesurfer v6.0 on a Ubuntu 16.04 64-bit guest OS with "fixed disk space" instead of "Dynamically allocated". Michael The opinions, conclusions and other information expressed in the above message, or contained within attachments to the above message, are not given or endorsed by Beaumont Hospital unless otherwise indicated by an authorised representative independent of this message. This e-mail message and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. This e-mail has been scanned for viruses. This e-mail and all attachments are confidential and may be privileged. If you have received this e-mail in error, notify the sender immediately. Do not use, disseminate, store or copy it in any way.

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Thickness asymmetry and LH/RH corresponding vertices in fsaverage
by Dorian P. 23 Mar '17

23 Mar '17

Hi all, I have a bunch of thickness files in fsaverage space (already smoothed at fwhm). I was wondering whether is possible to compute quickly an asymmetry overlay for each one, but it's turning more difficult than I thought. Vertex indices are different between lh and rh. So I started looking at fsaverage_sym, which has already registrations lh-rh. I thought this would be a nice shortcut to avoid registering every subject again. But there are a couple of confusing points: 1. Why isn't lh.inflated well aligned between fsaverage and fsaverage_sym (see figure below) ? [image: Inline image 1] 2. I found an old post in 2012 <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-December/026957.…>, in which Donald advises to not run analyses on a simple left-right registration because one hemisphere would be more processed than the other. Since I might want to run some analyses, can you please explain what is the best way to get asymmetry surfaces (possibly by avoiding new registrations)? Why wouldn't a simple L-R registration of fsaverage be ok? I run the analyses in R and don't necessarily need the glm tools within FS. Thank you in advance. Dorian

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Correcting Skull-Strip Errors - Watershed Algorithm Question
by Abhinav Kurada 23 Mar '17

23 Mar '17

The initial running of recon-all autorecon-1 autorecon-2 for a sample scan resulted in a bad skull strip. I am attempting to troubleshoot the issue through running just the skull strip portion of the recon-all pipeline again, followed by adjusting the watershed parameters. During re-running -skullstrip, I am given a mri_watershed Error: read failed (the em_register portion of the -skullstrip flag ran without interruption). I have attached the corresponding log. Is there a way to fix this watershed error (when I have tried to run the watershed command by itself, the command is not recognized)? https://share.polymail.io/v1/z/f/NThkMzUzYTU4ODA4/Vp21pl8rsUD4Tvw7tgnoOONDL… https://share.polymail.io/v1/z/f/NThkMzUzYTU4ODA4/Vp21pl8rsUD4Tvw7tgnoOONDL…

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LME mass univariate model
by Bronwyn Overs 22 Mar '17

22 Mar '17

Dear mailing list, I am trying to run a LME model using the matlab tools, but I’m unsure how to specify the model we wish to run. We have a qdec file that contains the following columns: fsid, fsid-abse, years between scans, age at baseline, gender, group We want to specify a model where we can examine four interaction terms (years*age, years*group, age*group, years*age*group), as well as random effects for the intercept, years and age. My questions are: 1. How do we specify a model that will include the random effects we want? 2. How do we compare our full model (3 random effects) with a model excluding the random effect for age? Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265 neura.edu.au <http://neura.edu.au/> <https://twitter.com/neuraustralia> <https://www.facebook.com/NeuroscienceResearchAustralia> <http://www.neura.edu.au/help-research/subscribe>

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PETsurfer surface based analysis
by miracle ozzoude 22 Mar '17

22 Mar '17

Hello, I am working through the PETsurfer surface based analysis and i have couple of question a) Since the procedure is the same as surface based analysis for cortical thickness except mri_vol2surf, Can I use the procedure for thickness? b) What is the difference between mris_preproc and mri_concat. If I use mris_preproc, do I also need to use mri_concat? Also, can I use mris_preproc instead of mri_concat? c) Can I use mri_surf2surf in place of mris_fwhm? If no, why? d) While researching PETsurfer surface based analysis in the forum, I came across multiple trends that used the "--projfrac" flag in both mri_vol2surf command and mris_preproc command. At what stage should I include this flag and why? e) If I want to perform a multimodal analysis using thickness&PET or Surface area&PET, Can anyone confirm if this is the correct steps. - Perform surface base analysis for cortical thickness from step 1 (mris_preproc) to correction for multiple comparison - Perform PET surface based analysis from step 1 (gtmseg) to step 5. While conducting mri_glmfit, include the smoothed thickness map (?h.thickness.10B.mgh) as pvr (per vertex regressor) - e.g. mri_glmfit --y lh.pet.10.mgh --fsgd your.fsgd dods --pvr lh.thickness.10B.mgh --C contrast.mtx --surf fsaverage lh --cortex --glmdir pvr.lh.pet.thickness.glmdir - Lastly, build a new monte carlo correction for multiple comparison. Thank you Best, Paul

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A Bug in Monte-Carlo Simulation.
by June Kang 22 Mar '17

22 Mar '17

Dear Freesurfer Developers, 6.0 Stable in OS X seems to have some bugs. Monte-Carlo simulation works fine in 10mm FWMH, but error shows up in 5mm or 0mm as below. ###Error Code### ERROR: CSDread(): could not open /Applications/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm4/abs/th13/mc-z.csd ERROR! Error in Monte Carlo simulation: Error running mri_surfcluster! ###Error Code### I found that the actual directory contains cud file is fwhm04, and not fwhm4, so after I copied fwhm04 to fwhm4 in cortex directory, the simulation works.I think it’s small bug, but can make many people (like me) confused. Bests,J.

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contrast between two independent CTh maps?
by Uquillas, Federico D'Oleire 22 Mar '17

22 Mar '17

Dear FreeSurfer experts, I’ve been trying to find a way to get a map of the difference between two independent CTh association maps but can’t seem to find a solution. I have two maps of independent groups (one is N=15, the other N=20) I would like to compare. Is there maybe a way to do a sig1.mgh – sig2.mgh and then visualize this? Not sure how to go about it. I’m basically trying to visualize what is left over after subtracting one map from the other (independent samples t-test of sorts). Thank you so much for any help you may be able to provide! Best regards, Fred

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Petsurfer mri_gtmpvc error
by Agrawal, Shubhi (NIH/NINDS) [E] 22 Mar '17

22 Mar '17

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

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Freesurfer March 2017