Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

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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how to pass openmp option to mri_cvs_register through Tracula-prep?
by Salil Soman 07 Jun '14

07 Jun '14

Hi, I noticed that openmp is set to 1 in mri_cvs_register. However, I do not see a way to pass on this parameter to to mri_cvs_register through dmrirc for tracula - prep. Can anyone point me to how this can be done? Thanks! Sal

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Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans
by Martin Reuter 07 Jun '14

07 Jun '14

The one that comes with Freesurfer. It's always the same. Best Martin Sent via my smartphone, please excuse brevity. -------- Original message -------- From: Elijah Mak <fkm24(a)medschl.cam.ac.uk> Date:06/04/2014 10:54 AM (GMT-05:00) To: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed scans Hi Martin, Many thanks for your help! How is fsaverage created? I ran all my recon-alls (cross, base, and longs) in a single $Subject_DIR folder. Then , I moved the longs and bases to another folder for organizational purposes, which explains why the fsaverage is missing. Is the fsverage study-specific? Or can I point the path of the fsverage to the same fsaverage that came with the original installation of Freesurfer? Many thanks again. Best Regards, Elijah On Wed, Jun 4, 2014 at 3:17 PM, Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> wrote: > Hi Elijah, > > Just create a link > ln -s pathtofsaverage ./ > > Usually this is done during recon-all > > > Sent via my smartphone, please excuse brevity. > > > -------- Original message -------- > From: Elijah Mak > Date:06/04/2014 7:17 AM (GMT-05:00) > To: Martin Reuter ,freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] v.5.3 Longitudinal Analysis on v.5.0 processed > scans > > Hi Martin, > > We corresponded about the longitudinal pipeline earlier. Your help has > been much appreciated. I am now at the stage where I am ready to > perform QDEC analyses using the 2-stage method. > > In my Subject DIR, I have all the longs (Tp1 and 2) and their > corresponding bases. However, when i run the following command > > long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness > --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label > --time years --qcache fsaverage --sd $SUBJECTS_DIR > > > It says that fsaverage is missing. > > Can I simply copy the fsverage folder from the default Freesurfer > "subjects" folder? > > Many thanks! > Best Regards, > Elijah > > On Wed, Jan 15, 2014 at 10:15 PM, Martin Reuter > <mreuter(a)nmr.mgh.harvard.edu> wrote: >> Hi Elijah, >> >> >> On 01/15/2014 04:10 PM, Elijah Mak wrote: >> >> Hi Martin, >> >> Thank you for your help. >> >> By re-processing, do you mean running recon-alls all over again? >> >> >> Yes. 5.0 is old and it is better to run everything with 5.3 from beginning >> to end. If you have a lot of data or a lot of edits, you can try running >> -base and -long in 5.3 and keep the independent (cross sectional) stuff in >> 5.0, but I don't recommend mixing versions. >> >> >> >> Could you elaborate on the advantage of creating a new subjectsdir and >> copying over the orig dirs for each subject? >> >> This way you keep a backup copy of your old 5.0 processed data (to lookup >> edits etc). If you have a script that calls recon-all with the -i flag for >> inputs, you don't need to copy the mri/orig dirs (it will grab the data >> from >> the dicoms again). Copying the orig dirs and dropping -i will skip that >> step. >> >> >> On a related note, would it be better to run the full recon-all pipeline >> for >> each subject? I have been running batches of subjects at each stage (i.e. >> autorecon1, autorecon2, and finally autorecon3). >> >> Yes, full pipeline (-all) on all subjects is what I usually do. You can >> run >> individual steps and check intermediate results if you like, but I usually >> run everything and check everything at the end. >> >> Best, Martin >> >> >> >> Thank you again. >> >> Best Wishes, >> Elijah >> >> >> >> >> On Wed, Jan 15, 2014 at 9:02 PM, Martin Reuter >> <mreuter(a)nmr.mgh.harvard.edu> >> wrote: >>> >>> Hi Elijah, >>> >>> if you have minimal edits, I'd recommend to reprocess the data from >>> scratch with 5.3 (that is supposed to be the same as using the -clean >>> flag >>> when rerunning 5.3 on top of the old 5.0 data). But I'd recommend to >>> create >>> a new subjectsdir, copy over the subjedid/mri/orig dirs for each subject >>> and >>> rerun from scratch with 5.3 the independent, base and long runs. >>> >>> Best, Martin >>> >>> >>> >>> On 01/13/2014 06:18 PM, Elijah Mak wrote: >>> >>> 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 >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> -- >>> Martin Reuter, Ph.D. >>> Assistant in Neuroscience - Massachusetts General Hospital >>> Instructor in Neurology - Harvard Medical School >>> MGH / HMS / MIT >>> >>> 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 >>> reuter(a)mit.edu >>> Web : http://reuter.mit.edu >>> >>> 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. >> >> >> >> >> -- >> >> Elijah Mak, B.A. >> >> Doctoral Candidate | Psychiatry >> >> University of Cambridge | Department of Psychiatry >> >> Trinity College, Cambridge, CB2 1TQ >> >> >> >> -- >> Martin Reuter, Ph.D. >> Assistant in Neuroscience - Massachusetts General Hospital >> Instructor in Neurology - Harvard Medical School >> MGH / HMS / MIT >> >> 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 >> reuter(a)mit.edu >> Web : http://reuter.mit.edu > > > > -- > Elijah Mak, Gates Scholar > > PhD Candidate | Psychiatry > > University of Cambridge | Department of Psychiatry > > Trinity College, Cambridge, CB2 1TQ > > -- Elijah Mak, Gates Scholar PhD Candidate | Psychiatry University of Cambridge | Department of Psychiatry Trinity College, Cambridge, CB2 1TQ

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Method development for coupled EEG-fMRI (2x full EPSRC PhD studentships)
by Etienne B. Roesch 07 Jun '14

07 Jun '14

Method development for coupled EEG-fMRI (2x full EPSRC PhD studentships) The goal of the project is to develop novel methods for the joint analysis of signals from electroencephalography (EEG) and functional magnetic resonance imaging (fMRI), when they are obtained concurrently. Technological advances of the last 10 years make it possible for scientists to record both modalities concurrently, in what is now known as coupled EEG-fMRI. By simultaneously recording these two modalities, scientists can potentially say where and when neural activity is occurring, whereas previously researchers had to settle for one or the other. This engineering feat, however, has not yet been met with the ability to make use of the combination of these signals to infer more knowledge than would otherwise be gathered in separate experiments. Filling this gap is the ambition of the present project. This is a method project, which requires skills and knowledge in neuroscience, applied mathematics/statistics/physics and programming. Candidates who have a strong background in at least two of these three fields are encouraged to apply, if they are enthusiastic about the third. Two full studentships are available, and we expect to appoint one candidate who is stronger in empirical work and a second who is stronger in analytics. Candidates are expected to have had some prior exposure to at least one of the two modalities, but will receive training in both. The two students will be supervised by Dr. Etienne Roesch and receive support from Dr. Michael Lindner and Prof. Tom Johnstone, with R&D support from Brain Products, one of the world’s leading manufacturers of MRI-compatible EEG systems. The group led by Dr. Roesch fosters interdisciplinary thinking, and students will have the opportunity to engage in ongoing empirical and modelling work related to perception and action. The Centre for Integrative Neuroscience and Neurodynamics (CINN) is host to a research-dedicated 3T Siemens TRIO, with a full license for sequence development, and a full suite of MR-compatible systems. Additionally, the students will be granted access to the cluster of NVIDIA Tesla GPUs and other facilities at CINN, as well as at the Brain Embodiments Laboratory, in the School of Systems Engineering. The University of Reading is ranked as one of the UK’s 20 most research-intensive universities and as one of the top 200 universities in the world (Times Higher Education 2013). Our campus was voted first in the Times Higher Education Student Experience survey and has a Green Flag Award. It is situated 25 minutes West of London. Reading University Students’ Union was voted the 6th best in the UK (National Student Survey 2012). Essentials: Commitment to academic research and personal development; Ability to work collaboratively; Effective interpersonal and communication skills, including writing to a high standard, document preparation for technical notes and journal papers; Experience of work in interdisciplinary settings; Attention to details. Desirables: Self-guided work in developing statistical designs and approaches in research; Creative approach to problem solving; Ability to work independently; Experience in giving presentations and conveying complex ideas clearly. Eligibility: Applicants should hold a minimum of a UK Honours Degree at 2:1 level or equivalent in a relevant subject. Please note that due to restrictions on the funding this studentship is for UK/EU applicants only. Funding Details: Studentship will cover Home/EU Fees, pay the Research Council minimum stipend (£13,863 in 2014/15) for up to 3 years and include funding for international conferences. How to apply: To apply for this studentship please submit an application for a PhD in Cybernetics (full time) to the University – see http://www.reading.ac.uk/Study/apply/pg-applicationform.aspx . In the section ‘Research proposal’, please upload or copy-paste your covering letter. When prompted as part of your online application, you should provide details of the funding you are applying for, quoting the reference GS14-68. Once you have submitted your application, you should receive an email to confirm receipt of your online application. Please forward this email, along with your covering letter and CV (as pdf), to Dr. Etienne B. Roesch, e.b.roesch(a)reading.ac.uk, by the application deadline. Application Deadline: Monday 14th July 2014 (interviews in August) Further Enquiries: Please contact Dr. Etienne B. Roesch, e.b.roesch(a)reading.ac.uk. ––– Dr. Etienne B. Roesch Lecturer (Assistant Professor) in Cognitive Science University of Reading, UK http://doodle.com/MeetWithEtienne Too brief of an email? Here's why! http://emailcharter.org

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tracula cvs_reg taking greater than 24 hours
by Salil Soman 06 Jun '14

06 Jun '14

Hi, I am running tracula prep step using doregcvs=1, and the case has been processing for greater than 1.5 days now. To get it to run, I had to follow the instructions from here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36133.html Any suggestions if I am doing something wrong, or if I can expect this step to end? Thanks, S The latest output lines (over several hundred total) are below: ---------- unfolding failed - restoring original position -------------------- 0003: dt=4.250000, rms=0.867 (0.000%), neg=0, invalid=1530 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=0.250... 0000: dt=0.000, rms=0.867, neg=0, invalid=1530 orig dt = 0 in gcamFindOptimalTimeStep iter 0, gcam->neg = 21980 after 238 iterations, nbhd size=2, neg = 551 starting rms=0.830, neg=551, removing folds in lattice.... iter 1, dt=2.048000: new neg 27008, old_neg 551, delta -26457, rms=0.780 (6.086%) Numerical result out of range orig dt = 0 in gcamFindOptimalTimeStep iter 2, dt=0.002294: new neg 23842, old_neg 27008, delta 3166, rms=0.772 (1.003%) Numerical result out of range orig dt = 0 in gcamFindOptimalTimeStep iter 3, dt=0.000573: new neg 23004, old_neg 23842, delta 838, rms=0.766 (0.745%) Numerical result out of range -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System

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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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How to deal with a skewed T1 image
by Vy Dinh 06 Jun '14

06 Jun '14

Dear Freeesurfer community, I've attached a coronal view of a T1 image in tkmedit that is slightly oriented away from the center. The subject has been processed through the initial recon-all -all process without any error, but I am afraid that this orientation may cause a problem later on in my processing. Do I need to do any correction or should the normalization process correct the skewed orientation? Thank you, -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health

2 1

?need to edit pial surf in med temp lobe
by Kev 05 Jun '14

05 Jun '14

Dear freesurfers, Basic question that arose when reviewing the attached screenshots (salmon rectangles: axial and coronal view of same location). How much editing would require this subject in terms on pial surface? Is the highlighted area computed in lobar cortical thickness? Thanks and regards, Kev

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error when make_average_subject
by Qijing Yu 05 Jun '14

05 Jun '14

Hi Freesurfer, I ran into the following error when running make_average_subject. The following output is shown after make_average_surface is done. /Volumes/fMRI/Scanner_Data setenv SUBJECTS_DIR /Volumes/fMRI/Scanner_Data/ sdout /Volumes/fMRI/Scanner_Data/ mri_convert /Volumes/fMRI/Scanner_Data//P022/output/mri/orig.mgz /Volumes/fMRI/Scanner_Data//average/tmp/make_average_vol-tmp-87329/orig-P022/output.mgh --apply_transform /Volumes/fMRI/Scanner_Data//P022/output/mri/transforms/talairach.xfm -oc 0 0 0 mri_convert /Volumes/fMRI/Scanner_Data//P022/output/mri/orig.mgz /Volumes/fMRI/Scanner_Data//average/tmp/make_average_vol-tmp-87329/orig-P022/output.mgh --apply_transform /Volumes/fMRI/Scanner_Data//P022/output/mri/transforms/talairach.xfm -oc 0 0 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Volumes/fMRI/Scanner_Data//P022/output/mri/orig.mgz... TR=2200.00, TE=4.26, TI=1200.00, flip angle=9.00 i_ras = (-1, -1.16415e-10, 1.27329e-11) j_ras = (1.0732e-10, -7.26432e-08, -1) k_ras = (3.49246e-10, 1, -7.07805e-08) INFO: Reading transformation from file /Volumes/fMRI/Scanner_Data//P022/output/mri/transforms/talairach.xfm... Reading transform with LTAreadEx() INFO: Applying transformation from file /Volumes/fMRI/Scanner_Data//P022/output/mri/transforms/talairach.xfm... --------------------------------- INFO: Transform Matrix (linear_ras_to_ras) 1.182 0.047 -0.032 -0.505; -0.064 1.202 0.238 18.683; 0.093 -0.236 1.271 -31.892; 0.000 0.000 0.000 1.000; INFO: Transform dst volume info is not used (valid flag = 0). INFO: LTA dst geometry information missing! We assume that the dst volume passed is the same as the dst for the transform. INFO: LTA src geometry information missing! We assume that the src volume passed is the same as the src for the transform. mghWrite(/Volumes/fMRI/Scanner_Data//average/tmp/make_average_vol-tmp-87329/orig-P022/output.mgh, -1): could not open file --------------------------------- Applying LTAtransformInterp (resample_type 1) writing to /Volumes/fMRI/Scanner_Data//average/tmp/make_average_vol-tmp-87329/orig-P022/output.mgh... ERROR: failure writing /Volumes/fMRI/Scanner_Data//average/tmp/make_average_vol-tmp-87329/orig-P022/output.mgh /Volumes/fMRI/Scanner_Data ERROR: mri_convert failed. ERROR: make_average_volume Thank you very much in advance for helping out! Best, Qijing

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