Freesurfer May 2014

freesurfer@nmr.mgh.harvard.edu

139 participants
206 discussions

Choi2012 convert to FSL MNI152 2mm
by Kathy L. Pearson 10 Jul '14

10 Jul '14

To convert an example Choi2012 file to FSL 2mm space in FreeSurfer 5.2, I have tried both of the mri_vol2vol commands below. The results as shown in freeview are offset by several voxels from the original. Is there a transform or an intermediate step that can make this work -- or a different command? Also, is there a recommended way to extract each individual value (here 1 ... 7) to create separate masks in FSL 2mm space? Thanks for any advice, Kathy Pearson #!/bin/bash input=$FREESURFER_HOME/average/Choi_JNeurophysiol12_MNI152/Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz mri_vol2vol --mov $input --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --o output1.nii.gz --no-save-reg --interp nearest --precision uchar mri_vol2vol --targ $input --mov $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --inv --reg $FREESURFER_HOME/average/mni152.register.dat --o output2.nii.gz --no-save-reg --interp nearest --precision uchar # Compare results freeview $input output1.nii.gz output2.nii.gz&

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GLM: what does "mris_preproc" do?
by ye tian 18 Jun '14

18 Jun '14

Hello Freesurfers, I understand that the output of "mris_preproc" can be the input of "mris_glmfit". In mris_glmfit, a GLM is performed. Does "mris_preproc" give you a smoothed average of all the subjects? If that's the case, how can you perform a GLM with just the average? Don't you need the data (smoothed or not) of all subjects? Thank you very much! Sincerely, Ye

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Re: [Freesurfer] Compatibility Tracula v.5.3 and recon v.5.2 longitudinal
by Anastasia Yendiki 13 Jun '14

13 Jun '14

Hi Yoon - If you are getting an error from longitudinal tracula, do check the tracula updates at the link that I gave you in my previous email. As for 5.2 recon-all, others can chime in here, but like I said it is not recommended to use it. Sorry about that. a.y On Thu, 22 May 2014, Yoonho Chung wrote: > Thanks for the quick response! > > If I already have all the T1 data processed using recon-all with FS v5.2, do you think it is okay to switch the stream to FS v.5.3 and run Tracula? - without having to do the recon-all again for the T1 data? It is because I am also experiencing DTI longitudinal error due to the OS issue (according to other threads). And if possible, I would like to avoid having to redo all the recons if we have to switch it to v5.3. > > Thanks again! > Yoon

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Longitudinal design
by Tudor Popescu 07 Jun '14

07 Jun '14

Dear FS list, I have structural data from a learning study (pre&post-training scans, with 3 groups). Although the training was only one week, I'm guessing from an analysis point of view, this still qualifies as longitudinal. I want to check for - the main within-subjects effect of time point (pre&post) - the main between-subjects effect of group (treatment A, treatment B, control), - the time x group interaction I intend to look at thickness, surface area, volume, and lGI. I read on the wiki<http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing>that FS is currently not optimal for longitudinal analyses. I intend my FreeSurfer analysis to supplement a VBM analysis done in FSL. In case it is in fact a good idea to do this, my questions (not covered in the 'longitudinal' wiki page) are: 1) Can QDEC be used for such an analysis, and if so, what would be different as compared to a cross-sectional (no temporal/within factor) study? 2) Also, is the pre-processing stage any different? 3) In FSL, for longitudinal designs you do stats on images obtained as the difference between consecutive time points. Does this have to be done in FreeSurfer as well, and if so, is it done at the recon-all level or only at the stats (QDEC) level? Thanks! Tudor

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Freesurfer gifti-Surface in Matlab
by Bastian Cheng 06 Jun '14

06 Jun '14

Dear Freesurfer-Experts, I would like to create gifti-surfaces to use in matlab. That's what I am doing so far (latest FS-Version): mris_convert lh.white lh.white.gii I then try to open it using the "gifti" command (g=gifti('file.gii')) (http://www.artefact.tk/software/matlab/gifti/) however, I get an error message from matlab: >>>>>>>>>>> ??? Attempt to reference field of non-structure array. Error in ==> gifti.subsref at 28 varargout{1} = this.data{j}.space.MatrixData; Error in ==> gifti.struct at 17 [values{i,:}] = subsref(this(:), substruct('.',names{i})); Error in ==> gifti.display at 17 eval([display_name ' = struct(this);']); >>>>>>>>>>>>>>> Am I missing something? Is there anything special with the .gii file form FS? here is the surface file I created with mris_convert: http://we.tl/B2n4Ex6ifJ I am able to open the gifti file with freeview. I also updated the gifti-toolbox in matlab to the latest version. Any help is appreciated!

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Seg fault
by Cooke, Gillian 06 Jun '14

06 Jun '14

Hi, I've been working with Freesurfer for years and have suddenly been getting this fault: tkmedit started: Fri May 30 10:08:23 2014 /Applications/freesurfer/tktools/tkmedit.bin ACCE633_1 brainmask.mgz -aux T1.mgz -surfs $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Users/gilliancooke Set subject home dir to /Volumes/HealthAging/ACCE/Freesurfer/ACCE633_1 Using interface file /Applications/freesurfer/tktools/tkmedit.tcl Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: Any suggestions? Many thanks, Gill _____________________ Gillian Cooke, Ph.D. Postdoctoral Research Associate Lifelong Brain & Cognition Lab Beckman Institute University of Illinois, Urbana

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Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing
by Douglas Merkitch 05 Jun '14

05 Jun '14

Dear Martin and FreeSurfer experts, Thanks for your response. I have just finished re-running some subjects from scratch in 5.3 and it appears that the edits from brain.finalsurfs.manedit.mgz are not being applied to the longitudinal subject directories. Just to clarify, I have been doing ALL of the pial surface edits in the brain.finalsurfs.manedit.mgz, not just the pial surface edits that have extended into the cerebellum. The rationale for doing this is mainly continuity, as the previous research assistant made all pial surface edits in this way because of a response she had received from the FS forum saying that there shouldn't be any problem with performing all the pial surface edits in the brain.finalsurfs.manedit.mgz file. Is there something in the FreeSurfer longitudinal processing code that would treat edits near the cerebellum of the brain.finalsurfs.manedit.mgz file differently from those made in other parts of the brain (e.g. lateralorbitofrontal, dura, etc.,)? Can you think of anything else that would be causing this or anything that I could try to get the longitudinal processing stream to incorporate the edits from the brain.finalsurfs.manedit.mgz file? Thanks for your help! Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu> Begin forwarded message: From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits & longitudinal processing Date: May 2, 2014 4:20:17 PM CDT To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Hi Doug, so you 1. edited the cross sectionals and surfaces look fine (make sure you edit the brain.finalsurfs.manedit.mgz file, which you create as a copy of the brain.finalsurfs.mgz) 2. checked/edited the base and surfaces look fine too 3. ran the longitudinal from scratch (w/o any edits) and then in the long, the surface looks not good? Edits should automatically be copied from cross->long (if the manedit file exist). Surfaces are taken from the base to initialize longitudinal processing. That is why both step1 and step2 above are important. Step3 is a good idea to make sure that the longs are not polluted by some earlier edits. For example edits from cross are only copied over if the long has no manedit file, else only the edits in the long will be used. (I think this also answers some of the questions in the archive mail 1 you cite below, the archive mail 2 is a question about cross sectional processing, but I think there the problem is that brainmask.finalsurfs.mgz was edited directly, not the manedit file, so edits probably get overwritten). I also have the feeling that we fixed something about the editing in longitudinal processing after 5.1, but cannot find it documented on the wiki (so not sure). You may want to try to run this with 5.3 if it does not work with 5.1 Best, Martin On 05/02/2014 10:45 AM, Douglas Merkitch wrote: Dear Freesurfer experts, I have a question regarding longitudinal edits. Specifically the brain.finalsurfs.manedit.mgz file and the longitudinal processing stream in Freesufer 5.1 on a Mac (freesurfer-i686-apple-darwin9.8.0-stable5-20110525). The problem that I am having is that the edits saved in the brain.finalsurfs.manedit.mgz file do not carry over when processing longitudinally. Previous posts have addressed this topic, but have not (to my knowledge) solved the issue. Please see the threads from the Freesurfer archive below for a brief context: 1. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg27695.html 2. http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33471.html Please let me know if more information is needed to understand the issue. Any insight/ideas regarding this issue would be greatly appreciated! Thanks, Doug Doug Merkitch Neurological Sciences Rush University Medical Center Phone: (312) 563-3853<tel:%28312%29%20563-3853> Fax: (312) 563-4660<tel:%28312%29%20563-4660> Email: Douglas_Merkitch(a)rush.edu<mailto:Douglas_Merkitch@rush.edu> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu> reuter(a)mit.edu<mailto:reuter@mit.edu> Web : http://reuter.mit.edu<http://reuter.mit.edu/> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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v.5.3 Longitudinal Analysis on v.5.0 processed scans
by Elijah Mak 04 Jun '14

04 Jun '14

Greetings Freesurfer Community, I am running a longitudinal study using Freesurfer v.5.3 to compare rate of cortical thinning between 2 groups of subjects. I hope I can seek some expert advice on the following situation: All data (both the baseline and follow-up) has been processed independently using recon-all. This has been done on Freesurfer 5.0. Since then, I have upgraded to Freesurfer v5.3 to utilize the linear mixed effect capability. For the construction of base and longs, I understand that it is important to add -clean flag to my recon-all strings to overwrite brainmask.mgz etc. When must this be done? I am still new to Freesurer, and I'd greatly appreciate any advice regarding workflow. Many Thanks, Elijah -- Elijah Mak, B.A. Doctoral Candidate *|* Psychiatry University of Cambridge *| *Department of Psychiatry Trinity College, Cambridge, CB2 1TQ

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meshes/surfaces for sub-cortical structures
by Tanya 01 Jun '14

01 Jun '14

Hi Freesurfers, I'm wondering whether the meshes (list of vertices+faces) corresponding to structures such as the hippocampus and amigdala are available as part of the Freesurfer output? In the /surf folder there are only the meshes of whole brain structures (cortex, pial, WM...). Is there any utility function to generate the meshes for the smaller structures? Thank you!

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problems with cortical surface area maps
by Lars M. Rimol 31 May '14

31 May '14

Hi, I have generated surface area maps for a sample of subjects (using [mris_preproc --fsgd *.* --target fsaverage --hemi *h --meas area --out *.mgh). When I created a mean image across all subjects (163842 x 1) and looked at it in tksurfer, I noticed a pattern on the surface that's a little troubling. Please see the attached image file (patterninmeanareaimg_ allsubjs_unsmoothed.jpg). I sampled the curv files to ico (with *mris_preproc*) for all subjects and looked at them individually (I have attached a few figures). I did find four resampled curv.mgh's that looked unusual, but removing them did not change the pattern seen in the attached figure. I also looked at some of the individual area files resampled to ico (using make_average_subject) and the outliers there were identical with the ones identified using the resampled curv-files (perhaps unsurprisingly). All these images are unsmoothed. So I'm at a loss here. Any suggestions on what to do next in terms of trouble shooting? (PS! I have attached the resampled curv and area files for a normal subject in lh_104_curvsjekk_lateral.jpg and lh_104_areasjekk_lateral.jpg, and for an unusual subject in lh_81_UNUSUAL_curvsjekk_lateral.jpg and lh_81_areasjekk_lateral.jpg. The three other subjects that seemed unusual looked like subject 81, and all the other subjects looked like 104.) Thank you! -- yours, Lars M. Rimol, PhD St. Olavs Hospital Trondheim, Norway

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Freesurfer May 2014