Freesurfer

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30067 discussions

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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'Best practice' for dealing with lesioned brains
by King, Daniel (Research Student) 11 Jul '17

11 Jul '17

Dear Freesurfer Team, I am attempting to complete a surface reconstruction on a dataset with traumatic lesions both to the grey and white matter. I am hoping to get some opinions on what would be considered as the 'Best practice' pipeline for dealing with such a dataset. We have access to T1 and T2-FLAIR images for a moderately large dataset and thus require a pipeline as fully-automated as is possible whilst still relatively accurate. I have seaerched the mailing list archives but many just relate to white matter lesions in MS for example. My current thoughts were to use the T1 and Fair images with the -FLAIRpial flag in recon-all to improve pial segmentation, but also using an automated lesion segmentation tool to conduct lesion filling. However, I know this is more effective for white than Gray matter lesions due to the greater intensity variability in the Gray matter compared to the white matter. Any reccomendations would be greatly appreciated. Cheers Dan

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Extract smoothed cortical thickness whole-brain vertex-wise
by Nicolette Schwarz 10 Jul '17

10 Jul '17

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.fsaverage.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

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questions mri_glmfit-sim
by Van Der Deijl, Rosanne 10 Jul '17

10 Jul '17

Dear Freesurfer team, I have two more questions about mri_glmfit-sim. 1. In the summary file I get a list of all the inputs/outputs, but I don't understand what all of them mean. Could you explain the ones I highlighted in bold? 2. Is it possible to a priori set the area threshold, so that I only get clusters larger than a certain size? # Input rh.CALMlong.thickness-spc.fwhm15/CALMlong_contrast2/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi rh # surface white # group_avg_surface_area 82167.6 # group_avg_vtxarea_loaded 1 # annot aparc # SUBJECTS_DIR /local_mount/space/avadhuti/1/users/gdesbord/CALM_data// # SearchSpace_mm2 75762.5 # SearchSpace_vtx 148554 # Bonferroni 0 # Minimum Threshold 1.3 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # Area Threshold 0 mm^2 # CSD thresh 1.300000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 1.70172 at vertex 163606 # Overall min -2.48953 at vertex 90839 # NClusters 32 # FixMNI = 0 Thank you very much in advance. Kind regards, Rose

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