Freesurfer

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30090 discussions

Running segmentation on spatially normalized data
by Lauren Stephanie Hopkins 12 Jul '17

12 Jul '17

Hi all: We ran FreeSurfer's recon sequence of anatomy files that had already been aligned to the MNI template - so spatially normalized. We're doing all of our processing in AFNI and the resulting segmentation output files open in AFNI's orig space, not in tlrc space. So basically we can't overlay the segmentation files on our anat+tlrc files where they should already be aligned to each other. When we converted the file to a .tlrc file with the AFNI command 3dcopy we could then overlay the mask on the normalized anatomy but it was no longer aligned. So I suppose my question is - is there any way to have the segmentation files maintain their positioning or output in .tlrc space so they are still aligned to our anatomy files? Thanks for any insight. Lauren

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mri_glmfit-sim ERROR cannot find mc-z.csd file
by Aly Negreira 12 Jul '17

12 Jul '17

Hi Freesurfer Community, I'm using FsFast on my dissertation data and trying to run a monte carlo correction on my functional data in the volume. I keep running into the below error. In attempting to troubleshoot, it looks like Yuko ran into a similiar issue (see archived email from Fri Dec 9 @ 12:26:46 EST in 2011) just not sure how to fix it! Please advice....I just want my PhD already! Thank you! Aly ERROR: cannot find /Applications/freesurfer/average/mult-comp-cor///cortex/fwhm10/abs/th13/mc-z.csd COMMAND: mri_glmfit-sim \ --glmdir GROUP_SESSID_HC_DISS_setwdelay/emotreg_mni305_4cond_fir_TR2_pf2_tpexclude_HC_DISS_setwdelay/bu_negVbu_neut/my-glm.wls/ \ --cache 1.3 abs \ --cwp 0.05\ --3spaces MAC INFO: OS X El Capitan Version 10.11.6 FREESURFER VERSION: -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 --------

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Re: [Freesurfer] UPDATE: Matlab Problem LME
by Diers, Kersten /DZNE 12 Jul '17

12 Jul '17

Hi Clara, thanks for the additional information, this is helpful! If you are calling the scripts with [lhRgs,lhRgMeans] = lme_mass_RgGrow(lhsphere, lhRe, lhTh0, lhcortex, 2, 95); then 'lhcortex' will contain the analysis mask, i.e. indices for those vertices for which the analysis will be performed. 'lhcortex' should already be a subset of the vertices specified by 'lhsphere', i.e. excluding some portions of the medial wall. If you have zero-valued columns in your data matrix, one thing worth trying is to remove the corresponding indices from 'lhcortex', i.e. further restrict the analysis mask. This should be done before the initial covariance estimation, i.e. prior to calling lme_mass_fit_init or lme_mass_fit_EMinit. In addition, it is of course worthwhile to investigate the cause of the zero-columns. Best, Kersten

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changing resolution and FOV
by Linda Eva Heidinger 12 Jul '17

12 Jul '17

Hello freesurfer experts: I am doing the following steps in the script below: (1) Use recon -all to calculate the freesurfer T1 anatomical which requires a single DICOM file to be calculated from each subject. (2) Use the functional Bold time series data originally derived from DICOM files for that subject and preprocess them: correct for slice timing and do regular AFNI registration of the images using the first volume as reference but do not spatially smooth. (3) We then use this Bold series after preprocessing by converting AFNI to NifTi by using 3dAFNItoNIFTI and inputing it into bbregister which computes a spatial registration matrix between the bold image and the T1 anatomical. (4) We now compute a coregistration using mri_cvs_register from the individual brain to a template brain for the volumetric non-linear morphing. It requires an anatomical scan of the subject that has been processed in freesurfer as in step (1). In our case we will use the standard brain cvs_avg35_inMNI152 as the target/template. (5) Next, we move the bold image from the individual space into the standard or template space. We use the command mri_vol2vol where we input the AFNI Bold image converted to NifTi and the bbregister matrix and template in (4) above to obtain the Bold in this template space. The script that does this is given below: # FreeSurfer commands nmr-std-env setenv SUBJECTS_DIR <path to the directory where all MRI data for this study reside> setenv SUBJECT <my subject code> cd $SUBJECTS_DIR # First, run FS recon-all on the T1 (MEMPRAGE) anatomical as usual. recon-all -subjid $SUBJECT -i temp_${SUBJECT}/001.mgz -all -openmp 4 # Second, do co-registration at the individual level between the hires anatomical and the bold (functional) image. # In the below example the already motion corrected (and otherwise preprocessed) bold data for run 005 are in # $SUBJECTS_DIR/$SUBJECT/bold/005/005.mc.nii # Use boundary-based registration (bbregister) - this by far the most accurate tool. # Note: This is rigid 6 DOF. It is almost always best to use rigid DOF 6 for within-subject registration. bbregister --mov $SUBJECT/bold/005/005.mc.nii --frame 0 --bold --s $SUBJECT --init-fsl --reg boldregister.dat --fslmat ${SUBJECT}_anat2bold.mat # Just in case, let us make FSL type coregistration matrices as well. convert_xfm -omat ${SUBJECT}_bold2anat.mat -inverse ${SUBJECT}_anat2bold.mat # Now, we will compute a group-level coregistration from the individual brain to a template brain for both volumetric non-linear morphing. # We will use the standard brain cvs_avg35_inMNI152 as the target/template. mri_cvs_register --mov $SUBJECT --mni --outdir $SUBJECT/cvs_CVS35MNI152 --openmp 8 # Finally, we can move the bold image from the individual spac into the standard space: mri_vol2vol \ --mov $SUBJECT/bold/005/005.mc.nii \ --targ $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/norm.mgz \ --o Grand_Average/${SUBJECT}_CVS35MNI152_005.mc.nii \ --m3z $SUBJECT/cvs_CVS35MNI152/final_CVSmorph_tocvs_avg35_inMNI152.m3z \ --noDefM3zPath \ --interp nearest \ --reg $SUBJECT/bold/boldregister.dat \ --no-save-reg \ We have successfully run the script but the result: /${SUBJECT}_CVS35MNI152_005.mc.nii is too large (47 gigs) to run on our computers using four runs for the next step which is AFNI 3dDeconvolve. We would like to down sample this Bold aligned to the template image file to the resolution and FOV of the original Bold image file in step (2) above. I believe freesurfer converts everything to freesurfer space (1mm^3 256^3) but instead we want the matrix to be 128X130X32 or downsized. How would you do this? Thanks!

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FreeSurfer on Windows 10 64-bit
by Peter Stanwell 12 Jul '17

12 Jul '17

Dear all, I'm looking to set up FreeSurfer on a Windows 10, 64-bit OS. Has anyone tried this using the Linux BASH shell on the latest (anniversary) version of Windows 10? If so, any tricks to to watch out for? Best, Peter

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viewing mri_glmfit FDR corrected results
by marco mcsweeney 11 Jul '17

11 Jul '17

Dear FreeSurfer experts, I ran my group analysis using mri_glmfit and found a number of significant clusters showing cortical thickness differences between 2 groups. I used tksurfer to visualize the results and used FDR to correct for multiple comparisons. My question is about how do I correctly get the FDR corrected results showing cluster number, size, MNI coordinates etc. as I would if I used QDEC? I have searched through the archives and have found what looks like the answer, but I'm not convinced that the method I used is correct. I used 1) mri_glmfit-sim --glmdir lh.group_diff.glmdir --cache 1.3 abs --cwpvalthresh .99 and 2) less lh.group_diff.glmdir/contrast.txt/cache.th13.abs.sig.cluster.summary However when I visualize the FDR corrected results with tksurfer or freeview I can see a couple of clusters not listed in the summary. Am I missing something? Thank you so much in advance. Any help or advice would be greatly appreciated. Best wishes Marco

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Stanford University Job Opportunities: Postdoctoral Fellowships in Computational Modeling of Brain Networks
by Sheena Chand 11 Jul '17

11 Jul '17

Stanford University's Department of Psychiatry & Behavioral Sciences is seeking to hire full time post-doctoral fellows in Computational Modeling of Brain Networks for their Cognitive & Systems Neuroscience Laboratory. This lab is headed by Dr. Vinod Menon who has broad multidisciplinary expertise that spans several scientific disciplines and has published extensively on various aspects of human cognition and brain function. Explore our lab website for more information: http://med.stanford.edu/scsnl.html. Please, distribute job posting (below) appropriately in your department. We thank you for your support. POSTDOCTORAL FELLOWSHIP IN COMPUTATIONAL MODELING OF BRAIN NETWORKS The Stanford Cognitive and Systems Neuroscience Laboratory invites applications for a postdoctoral fellowship in human brain network analysis and modeling. We seek candidates with strong research backgrounds in one or more of the following areas: resting-state and task-evoked fMRI connectivity, structural HARDI-based connectivity, neurophysiological modeling of brain networks, Bayesian modeling, machine learning, and deep neural networks. Candidates must have strong computational skills and a PhD in computational neuroscience, computer science, physics, biomedical engineering or related fields. This is an exciting opportunity to work on multiple NIH- and Stanford-funded projects using multimodal (fMRI, optogenetic, DTI, EEG) brain imaging techniques in multiple clinical populations and normative groups. The successful candidate will develop a vigorous research program that contributes to, and complements, ongoing research studies. The candidate will have access to state-of-the-art brain imaging and HPC/GPU facilities.Please email a CV, statement of research interests and relevant background, and names of three referees to Drs. Vinod Menon and Aarthi Padmanabhan at scsnl.stanford+postdoc(a)gmail.com<mailto:scsnl.stanford@gmail.com> Best, Sheena _________________ Sheena Chand Research Administrative Assistant Department of Psychiatry & Behavioral Sciences Stanford University|School of Medicine Email: schand05(a)stanford.edu<mailto:schand05@stanford.edu> Desk: (650) 498-9821

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Please post to list: Subject: Stanford University Job Opportunities: Postdoctoral Fellowships in Computational Modeling of Brain Networks
by Sheena Chand 11 Jul '17

11 Jul '17

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freeview command error
by Yagmur Ozdemir 19 11 Jul '17

11 Jul '17

Hello, I am installing Freesurfer with my limited coding knowledge and this problem with freeview came up when I was trying to view the volumes of recon-ed subject. lab@lab-ThinkStation-E31:~/Desktop/freesurfer/subjects$ freeview -v practice/mri/T1/mgz No command 'freeview' found, did you mean: Command 'treeview' from package 'treeview' (multiverse) freeview: command not found I checked and freeview is in the bin, and I even tried to install it according to its file by sourcing tcl_setup and others, but then this error comes up: lab@lab-ThinkStation-E31:~/Desktop/freesurfer/bin$ source tcl_setup bash: tcl_setup: line 47: syntax error near unexpected token `setenv' bash: tcl_setup: line 47: ` if ( -e $TCLLIBPATH/tcl8.3 ) setenv TCL_LIBRARY $TCLLIBPATH/tcl8.3' Can someone please give me any direction for how to solve this issue. I would appreciate the help very much. (Freesurfer version 6 & Ubuntu 16.04) Thank you all, Idil

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Re: [Freesurfer] Simple math with freesurfer surface
by Van Der Deijl, Rosanne 11 Jul '17

11 Jul '17

Dear Bruce, To be honest, I'm not sure, but I think I want the average of the scalar fields over the surface. I want to have some way of putting the thickness overlays on the surfaces of all my subjects together and visualizing this (I have pre-post data so I'd like to have a visualization of pre-average/added and one for post-average/added). Hope this makes sense, thank you! - Rose ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of freesurfer-request(a)nmr.mgh.harvard.edu [freesurfer-request(a)nmr.mgh.harvard.edu] Sent: Tuesday, July 11, 2017 12:00 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 21 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: Extract smoothed cortical thickness whole-brain vertex-wise (Nicolette Schwarz) 2. Re: help with code interpretation (Leanne Hunt) 3. Re: Fwd: surface inaccuracies around the optic chiasm (Bruce Fischl) 4. Re: Extract smoothed cortical thickness whole-brain vertex-wise (Bruce Fischl) 5. error with mri_glmfit --frame-mask (Sadie Marvel) 6. Re: Extract smoothed cortical thickness whole-brain vertex-wise (Nicolette Schwarz) 7. questions mri_glmfit-sim (Van Der Deijl, Rosanne) 8. Simple math with freesurfer surfaces (Van Der Deijl, Rosanne) 9. Re: Simple math with freesurfer surfaces (Bruce Fischl) 10. Re: Extract smoothed cortical thickness whole-brain vertex-wise (Bruce Fischl) 11. 'Best practice' for dealing with lesioned brains (King, Daniel (Research Student)) 12. BBRegister + partial FoV fail (Paul Glad Mihai) 13. Re: BBRegister + partial FoV fail (Bruce Fischl) 14. Re: BBRegister + partial FoV fail (Paul Glad Mihai) 15. Re: BBRegister + partial FoV fail (Bruce Fischl) 16. freeview command error (Yagmur Ozdemir 19) 17. Re: freeview command error (Bruce Fischl) 18. Re: freeview command error (Yagmur Ozdemir 19) 19. Re: freeview command error (Bruce Fischl) 20. Re: freeview command error (Yagmur Ozdemir 19) ---------------------------------------------------------------------- Message: 1 Date: Mon, 10 Jul 2017 12:12:57 -0400 From: Nicolette Schwarz <nic(a)u.northwestern.edu> Subject: Re: [Freesurfer] Extract smoothed cortical thickness whole-brain vertex-wise To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAKomUUrrwL7hSpRDgdh57BC920xVfkd-vqBqXNfCH=qG6GbfFQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Bruce, Thank you for your answer! I have tried: mris_convert -c lh.thickness.fwhm10.fsaverage.mgh lh.sphere.reg test.asc but get this: ERROR: number of vertices in lh.thickness.fwhm10.fsaverage.mgh does not match surface (163842,141823) Why might that be? Thank you in advance! Nic On Saturday, July 8, 2017, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Nic > > the problem isn't a surface/volume one, it's that the file > lh.thickness.fwhm10.fsaverage.mgh is on the fsaverage surface not on the > individual subject one. If you run that command using the sphere.reg from > fsaverage (or any other surface from the lh fsaverage) it should work > > cheers > Bruce > > > > On Fri, 7 Jul 2017, Nicolette Schwarz wrote: > > Hello everyone, >> >> >> I'm pretty new to FS and can't seem to find the solution for my problem. >> >> >> I am trying to write whole-brain vertex-wise cortical thickness (CT) data >> from each participant into ascii files. In my original analysis, each >> participant's average CT in clusters derived from a whole-brain GLM were >> extracted and used in a second analysis. I'd like to extract CT >> vertex-wise >> to perform a whole-brain version of this second analysis. I need the >> smoothed and "fsaveraged" (to get the same # of vertices across >> participants >> in a template space) CT values to match the cluster data and that seems to >> be tricky. >> >> >> This works: mris_convert -c lh.thickness lh.sphere.reg test1.thickness.asc >> >> This doesn't work: mris_convert -c lh.thickness.fwhm10.fsaverage.mgh >> lh.sphere.reg test2.lh.thickness.asc # ERROR: number of vertices in >> lh.thickness.fwhm10.fsaverage.mgh does not match surface (163842,124874) >> >> >> I presume the issue is that ?h.thickness.fwhm10.fsaverage.mgh is a volume >> file while ?h.sphere.reg is a surface file. So I've tried to convert >> volume to surface (created a folder test1/surf and copied both >> fsaverage/surf/lh.sphere.reg and sub/surf/lh.thickness.fwhm10.f >> saverage.mgh >> there) using different combinations of mri_vol2surf, e.g.: >> >> >> mri_vol2surf --srcsubject test1 --src lh.thickness.fwhm10.fsaverage.mgh >> --trgsubject test1 --surfreg lh.sphere.reg --regheader test1 --hemi lh --o >> test.surf >> >> >> This doesn't work as it wants me to specify a type but I have no clue what >> the type for the surface is (or better, it doesn't seem to be an option >> going by mris_convert). Other combinations asked for --reg files and I >> played with tkmedit2 but none of this is working out. >> >> >> Also, is ?h.sphere.reg an appropriate choice and would it have to be >> smoothed to FWHM=10 prior to mris_convert? >> >> >> Trying to solve this has me going in all kinds of circles and I'm unsure >> about this approach anyway. Hence, I would truly appreciate any help. >> >> >> Thank you very much in advance, >> >> >> Nic >> >> >> >> >> -- >> ?Nicolette Schwarz, Ph.D. >> Postdoctoral Research Fellow >> http://heartbrain.hms.harvard.edu >> >> >> -- ? Nicolette Schwarz, Ph.D. Postdoctoral Research Fellow http://heartbrain.hms.harvard.edu

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