Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30098 discussions

Using N3 MNI and N3 FS corrections
by Adam Martersteck 29 Feb '16

29 Feb '16

Hi Freesurfer users, I have a question about using the N3 algorithm twice for processing ADNI data: Is it okay for data to have undergone the ADNI N3 correction (Boyes et al. 2008 http://www.ncbi.nlm.nih.gov/pubmed/18063391) AND then pushed through the Freesurfer pipeline and undergo FS N3 correction (Zheng, Chee, and Zagorodnov 2009 http://www.ncbi.nlm.nih.gov/pubmed/19559796)? The problem stems from the fact that recent ADNI data has either undergone gradient warping correction (http://www.ncbi.nlm.nih.gov/pubmed/16300968) AND N3 correction or no corrections at all. The optimal solution would to have just been able to download the grad warp’d data and push that through. Thanks for any thoughts! Adam

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Neurohackweek: a summer school for neuroimaging and data science, September 5th-9th 2016
by Ariel Rokem 29 Feb '16

29 Feb '16

We are happy to announce a call for applications to participate in the first installment of the Neurohackweek summer school for neuroimaging and data science. This 5 day hands-on workshop, held at the University of Washington eScience Institute in Seattle, will focus on technologies used to analyze human neuroimaging data, on methods used to extract information from large datasets of publicly available data (such as the Human Connectome Project, Open fMRI, etc.), and on tools for making neuroimaging research open and reproducible. Morning sessions will be devoted to lectures and tutorials, and afternoon sessions will be devoted to participant-directed activities: guided work on team projects, hackathon sessions, and breakout sessions on topics of interest. For more details, see: http://neurohackweek.github.io/ We are now accepting applications from researchers in different stages of their career (graduate students, postdocs, faculty, and research scientists) to participate at: http://escience.washington.edu/neurohackweek2016-application Accepted applicants will be asked to pay a fee of $200 upon final registration. This fee will include participation in the course, accommodation in the UW dorms, and two meals a day (breakfast and lunch), for the duration of the course. A limited number of fee waivers and travel grants will be available. We encourage students with financial need and students from groups that are underrepresented in neuroimaging and data science to apply for these grants (email applications to: arokem(a)uw.edu) Important dates: April 18th: Deadline for applications to participate May 6th: Notification of acceptance June 1st: Final registration deadline On behalf of the instructors, Ariel Rokem, UW eScience Tal Yarkoni, UT Austin

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number of vertices
by Yang, Daniel 29 Feb '16

29 Feb '16

Dear FreeSurfer experts, Can you please indicate the number of vertices FreeSurfer use in each hemisphere to reconstruct the brain (e.g., cortical thickness)? Is there a fixed number or an approx. number? Many thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mail: daniel.yj.yang(a)yale.edu

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Re: [Freesurfer] How to invoke skullstrip adjustments and wm control points
by Ed Gronenschild 29 Feb '16

29 Feb '16

Hi Bruce, I'm confused about this. The manual-intervention workflow directives listed in recon-all (6 beta) tell that the series of commands should be: -autorecon2 -autorecon2-cp -autorecon3 -autorecon2 processes stages 6-23 and -autorecon2-cp process stages 12-23 So it seems to be a waste of time to process stages 12-23 twice. My question is: how to run stages 6-23 with control points? Cheers, Ed On 26 Feb 2016, at 14:13, <freesurfer-request(a)nmr.mgh.harvard.edu> <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Hi Ed > > if you run the skull stripping the autorecon2 and autorecon3 it should > detect and preserve your manual interventions > > cheers > Bruce > > > On Thu, 25 Feb 2016, Gronenschild Ed (NP) wrote: > >> Hi, >> >> I have made some manual skullstrip adjustments and added a >> number of control points in the white matter. >> How should I proceed with recon-all to incorporate both adjustments? >> >> Cheers, >> Ed >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>

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QDEC_ information extraction
by nellie 28 Feb '16

28 Feb '16

Dear Freesurfer Experts, Sorry to bother the mailing list again, but I really confused with the information extraction of significant clusters from QDEC. Basically, there were two main questions: (1)I have knew that the stimulation output summary was named “mc-z.abs.th20.sig.cluster.summary” and could be shown in the running terminal, but its detail was not consist with the display of inflated map. Just like the regions of postcentral and temporalpole did not show significantly on this map. How to explain this situation? Is it proper to use this summary as my research result? # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 4.165 90787 2844.40 -38.8 -50.9 -14.4 0.00010 0.00000 0.00020 4259 fusiform 2 -4.112 133001 925.06 -53.9 -15.8 44.4 0.02870 0.02660 0.03080 2169 postcentral 3 3.481 115941 1058.24 -26.0 5.6 -31.7 0.01410 0.01260 0.01560 2505 temporalpole 4 2.745 26991 1295.59 -6.0 37.6 -2.6 0.00350 0.00280 0.00430 2395 rostralanteriorcingulate (The command scrip was shown as:mri_surfcluster --in /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm28/abs/th20/mc-z.csd --mask /usr/local/freesurfer/subjects/qdec/Untitled/mask.mgh --cwsig /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/mc-z.abs.th20.sig.cluster.mgh --vwsig /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/mc-z.abs.th20.sig.vertex.mgh --sum /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/mc-z.abs.th20.sig.cluster.summary --ocn /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/mc-z.abs.th20.sig.ocn.mgh --oannot /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/mc-z.abs.th20.sig.ocn.annot --csdpdf /usr/local/freesurfer/subjects/qdec/Untitled/lh-Diff-PD-HC-Cor-thickness-similarity/mc-z.abs.th20.pdf.dat --annot aparc --cwpvalthresh 0.05 --surf white) (2)In the inflated map, tow significant clusters involved the regions of superiorfrontal (belong to Cluster 1),medialorbitofrontal(Cluster 1), caudalanteriorcingualte(Cluster 1), rostralanteriorcingualte(Cluster 1), and lingual(belong to Cluster 2), lateraloccipital(Cluster 2), fusiform(Cluster 2),inferiortemporal(Cluster 2).Is there any auto way to extract information (including the Talairach coordinates, cluster size and CWP) of these cortical areas, not just that of the two clusters? Looking for your reply. Many thanks! Cheers, Nellie

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Recon-all problem
by Mohamed Ali Bahri 28 Feb '16

28 Feb '16

Dear Experts, I have the following error with recon-all (freesurfer v 5.3). Anybody have an idea about this problem? Many thanks in advance, Mohamed --------------------------------------------------------orig_nu.log file-------------------------------------- Iteration 1 Fri Feb 26 14:13:20 CET 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.20504/nu0.mnc ./tmp.mri_nu_correct.mni.20504/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20504/0/ -iterations 1000 -distance 50 Can't locate MNI/Startup.pm in @INC (you may need to install the MNI::Startup module) (@INC contains: /usr/local/freesurfer/mni/share/perl5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /usr/local/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct line 37. ERROR: nu_correct -- Dr. Mohamed Ali Bahri, 1er Logisticien de Recherche, Cyclotron Research Centre, University of Liège, Belgium m.bahri(a)ulg.ac.be

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cortex mask
by Ali Radaideh 27 Feb '16

27 Feb '16

Dear FreeSurfer Experts, We have two high resolution datasets (T1 and T2* images). T2* is co-registered to the T1 volume. The T1 volume was processed in freesurfer using the recon-all and we want to use the segmented cortex (by freesurfer) as a mask to extract the cortex from the T2* volume. Would it be possible, please, to let us know which command to use to transfer the segmented cortex to the native space of T1 and T2*?. Many thanks in advance, Ali -- *Ali M. Al-Radaideh. PhDHead of Department of Medical ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite University, Zarqa, JordanW.phone +962 5 3903333 ext.5422, 5355, 5364Email: ali.radaideh(a)hu.edu.jo <ali.radaideh(a)hu.edu.jo>* *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= <http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=>*

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Announcing the Copenhagen FreeSurfer Course 2016
by Melanie Ganz 27 Feb '16

27 Feb '16

We are pleased to announce a European FreeSurfer Course that will be held from August 10th to 12th, 2016 in Copenhagen, Denmark. The course will be organized by the Neurobiology Research Unit, Copenhagen University Hospital in cooperation with the Laboratory for Computational Neuroimaging of the Athinoula A. Martinos Center for Biomedical Imaging. Registration will open on March 15th, however, you can put your name on our list of students now by emailing the course organizers at fs-cph(a)nru.dk! You will still have to do a formal registration later when they are ready to accept payments on March 15th, however, you can reserve your spot in the course before then by emailing them. For upcoming news and further information, please visit: http://fscph2016.nru.dk/ or contact us under fs-cph(a)nru.dk. -------------------------------------------------- Organizing Team FreeSurfer Course Copenhagen 2016 http://fscph2016.nru.dk/ fs-cph(a)nru.dk

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Freesurfer course in Tours, France, 26-27 May 2016
by Christophe Destrieux 27 Feb '16

27 Feb '16

Dear colleagues, It is our pleasure to host a FreeSurfer course in Tours, Loire Valley, France, 26-27 may. This event is coorganized by the brain and imaging laboratory, INSERM U930-Université François Rabelais of Tours (France) and by the Martinos Center. It will be limited to 64 participants and will focus on surface-based analysis of individual and group morphological data and on tractographic analysis using FreeSurfer tools. See you in Tours next May! Registration and information : http://freesurfer2016.sciencesconf.org/?lang=en — Christophe Destrieux, Unité « Imagerie et Cerveau » UMRS INSERM U930, Université François Rabelais de Tours Service de Neurochirurgie Laboratoire d’Anatomie, Faculté de Médecine, 10 Bd Tonnellé - 37032 Tours - France Bureau: +33 2 47 36 61 36 | Fax +33 2 47 36 62 07 | Mel Bureau: christophe.destrieux(a)univ-tours.fr Web : http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/>

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FS on Macaque
by Narkhede, Atul 26 Feb '16

26 Feb '16

Hi FS Experts, I am relatively new to FS and have been trying to analyze macaque brains recently. I used the following tutorial: Freesurfer on Macaque There are hardly any good tutorials or references on how one could generate a freesurfer surface using freesurfer. There are many problems to following the standard human analysis that simply does not work well for the macaque brain. Below is a work-in-progress tutorial on how to generate freesurfer surfaces. This tutorial requires FSL and it's associated tools, as well as a working installation of freesurfer. The easiest way of getting all this is to download the VirtualBox image of FreeSurfer from the MGH website and voila! Anyways, here goes the rough draft: 1. You should have a high-contrast, low noise MPRAGE of your monkey's brain. We typically use 0.35 mm isotropic voxel resolution, and scan between 9 to 12 times (each scan runs for 15 minutes) to generate a good mean image. 2. You should also aquire a T2 image while you acquire your MPRAGEs, as this will make skull extraction (a BIG deal with monkeys) much easier. 3. You must get your images in the orientation that FSL likes (nifti files, with very particular dimension ordering). You can use fslswapdim function for this. If you are converting dicoms from the scanner to nifti's using the mri_convert command (from the FreeSurfer distribution), make sure to pass the "--sphinx" argument to it. After this, run fslswapdim inputvol.nii LR PA IS outputvol.nii to correct the dimension directions as FSL likes it. Check with fsl_view. 4. If the images are properly aligned, you can now use the FSL Brain Extraction Tool (BET) to rip out the brain. Here, you can pass the T2 image for a much better skull stripping. Alternatively (haven't tried it, but in theory should work), you can generate a brain mask using the T2 by thresholding it, then filling the volume and cutting the brain out of the hi-res anatomical with this. 5. Once you have a nice clean skull-stripped brain, you'll have to correct for the non-uniform intensity across the image. This can be achieved easily by FreeSurfer's implementation of the MNI's N3 correction tool. Apply this using "mri_nu_correct", as follows: mri_nu_correct --i skulStrippedBrain.nii --o skull_stripped_nu.nii --distance 24 The distance factor may need to be adjusted, depending on what type of coil you used, and how big your monkey is, etc. Increasing the distance factor makes the program look for lower-frequency modulations of the intensity, whereas smaller numbers (better for phased-array coils) look for higher spatial frequency modulations. 6. You can then use the FSL FAST tool to segment your volume into white, gray, and csf. Output the white matter image for FreeSurfer, and leave the rest alone. 7. Make a new subject directory in keeping with the FreeSurfer system by using mksubjdirs. 8. Now comes the fun part: FreeSurfer wants 1mm isotropic voxels, but your images are 0.35 mm iso, so if you ask FreeSurfer to work with them, it will have to downsample them to 1mm. That's no fun, so we play a trick. 8a. Start Matlab. Make sure to download the NIFTI toolbox from the NIFTI website. Using load_nii, load the image you want to prep, like this: nii = load_nii('mynifti.nii'); Make sure the nifti file is not compress (not "niil.gz"). Then modify nii.hdr.pixeldim to reflect 1 mm voxel ( = [1 1 1 1 0 0 0], or just replace the 0.35 in the size vector by 1's). nii.hdr.pixeldim = [1 1 1 1 0 0 0]; Now save the volume, keeping track of what you did: save_nii(nii, 'newNiftiName.nii'); 8b. Finally, convert to MGZ format, and make sure to tell it to CONFORM: mri_convert -c invol_fake1mm.nii outvol_fake1mm.mgz Now, do this for all your volumes. Then they'll be ready for FreeSurfer. 9. Fill in your white matter surface: 9a. load in tkmedit, like this: tkmedit -f /directory/brain.mgz 9b. In tkmedit, make note of the VOXEL coordinates (bottom left of window, top row) for the corpus calosum and the pons. 9c. Go back to the command prompt and exceute the following on the white matter image: mri_fill -CV 192 172 214 -PV 192 249 194 /subj/mri/wm/wm.mgz ../filled/filled.mgz where CV and PV reflect the corpus callosum VOXEL coordinates, and PV that of the pons. 9d. Check the results in tkmedit. Should be cute. 10. Now, we follow the recon-all dev table, which uses mri_pretess as follows: mri_pretess ../filled/filled.mgz 255 ../brain/nu.mgz ../filled-pretess255.mgz Then, mri_tessellate ../filled-pretess255.mgz 255 ../lh.orig.nofix Then, mris_extract_main_component ../lh.orig.nofix ../lh.orig.nofix mris_smooth -nw ../lh.orig.nofix ../lh.smoothwm.nofix mris_inflate -no-save-sulc ../lh.smoothwm.nofix ../lh.inflated.nofix mris_sphere -q ../lh.inflated.nofix ../lh.qsphere.nofix And now, repeat this for the righ hemisphere (rh.orig) posted by brainmeister I have the following questions: 1) What steps would follow after the mentioned steps in the tutorial, so as to get the statistical results. 2) Is there any other macaque atlas, other than F99 atlas that I should be using for cortical and subcortical volumetrics. 3) Ones I have the atlas, where should I store it, so that FS can access it? 4) Are there any other tutorials that can help me do this. Thanks a lot for your help and comments. Best, Atul

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