Freesurfer February 2016

freesurfer@nmr.mgh.harvard.edu

123 participants
179 discussions

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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(no subject)
by Maheen Siddiqui 26 Feb '16

26 Feb '16

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missing orientation tag
by Ahearn, T 26 Feb '16

26 Feb '16

Hello, I've a few images that will not process due to a missing orientation tag. I've looked at the header and 0020,0037 is missing. For a similar sagittal image I found the following .. 0020,0037 Image Orientation (Patient): -0.0753529518842\0.99712705612182\0.00771582638844\0.06153532490134\0.01237302832305\-0.9980282187461 ... approximately 0\1\0\0\0\-1 I used dcmodify to insert this tag but it still would'nt process. Is there another tag that I need to look at? Will assuming perfect sagittal alignment make a difference to the freesurfer output? Any thoughts/help appreciated Thanks Trev The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.

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Recon-all error
by m.bahri＠ulg.ac.be 26 Feb '16

26 Feb '16

Dear Experts, I have the following error with recon-all (freesurfer v 5.3) in the orig_nu.log file. Could anyone help to solve the problem? Many thanks, Mohamed -------------------------------------------------------- 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

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Changing coordinate system of surfaces generated by recon-all FS
by Maheen Siddiqui 26 Feb '16

26 Feb '16

Dear FreeSurfer Users, I have a head surface mesh and a pial surface mesh obtained after segmentation of a T1 MRI scan. I am going to importing these into Homer2 Atlas Viewer as subject anatomy. However before I can do this import successfully, I need to bring the two meshes into the same coordinate system. At the moment they are in different coordinate systems (as pictured) and I need to bring the pial surface mesh into the head surface mesh. I am a little unsure how to do this. Does anybody have any experience with this? Or any advice on what I could do possibly? Thanks, Maheen _______________________________________________ Freesurfer mailing list Freesurfer(a)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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Annotation file's LUT
by Faeze Vedaei 25 Feb '16

25 Feb '16

Hi Freesurfer experts, I want to have all the label files extracted from the annotation file base on Destrieux atlas. I used the command mri_annotaion2label to do this. The result is just 75 labels. Are these all the regions included in annotation file? Can you let me know how I can access to all the regions (structure name) contained in annotation file? Thanks, Faezeh Vedaei

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Minor adjustment to RB_all_2008-03-26.gca
by Kok, JG (neuro) 25 Feb '16

25 Feb '16

Hi, I wish to split the putamen in an anterior part and a posterior part in >60 subjects which have been analyzed by the recon-all stream (FS version 5.3.0). Ideally, I would split the putamen in the atlas (e.g., at the coronal plane through the anterior commissure) and apply this "new" atlas to all subjects, one of the advantages being the bias that would be introduced by splitting the putamena manually in all subjects would be avoided. After some time trying to make this happen, I now think this could be achieved by adjusting RB_all_2008-03-26.gca and applying something like "mri_ca_label -align subject_norm.mgz subject_talairach.m3z RB_all_2008-03-26.gca subject_aseg.auto_noCCseg.PUTAMENA_SEPARATED.mgz". The problem is that till now I wasn't able to figure out how to correctly read the binary file RB_all_2008-03-26.gca. I tried to use the MATLAB function load_gca.m, but that seems to only work up to version 4 of the .gca file format (as GCA_VERSION is set to 4 in the function), and RB_all_2008-03-26.gca seems to be version 5. Also, when trying to read the file anyway in MATLAB using the code written for version 4 and below (by setting GCA_VERSION to 5.0), the code fails (the first gibbs_nlabels is already way too large, although I suspect the error occurs earlier). My questions: 1. Do you think I am following the right track to achieve a sensible splitting of the putamena this way? Or should I try something else? 2. Is there a newer load_gca.m file around which is able to read a version 5 .gca file? Or could you point me to the difference in the design of the version 5 .gca file compared to that of the version 4 file so that I can rewrite load_gca.m? Cheers, Jelmer ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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How to invoke skullstrip adjustments and wm control points
by Gronenschild Ed (NP) 25 Feb '16

25 Feb '16

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

3 2

Problem with brainstem substructures segmentation
by Riccardo Gubellini 25 Feb '16

25 Feb '16

Dear Freesurfer users, We have downloaded the Freesurfer 6.0 version since we are really interested in the brainstem segmentation. We are working with a pc equipped with a 3.6 GHz CPU and 16 GB RAM. We installed freesurfer6.0 on a virtual machine Linux (CentOs 6.7) enabling 4vcpu 11Gb of RAM. Disk space was 50 GB and after installation we have 15 GB free for data. We have launched recon-all –all for some cases and everything went right. Then we have tried to launch recon-all –all –s nameofsunbject –brainstem-structures and the process, after about 6 hours, stacks, during the SegmentSubject process and after having computing hyperparameters for estimation of Gaussian parameters. Do you have any ideas of what is happening? Thank you for your help! Riccardo Gubellini

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Freesurfer February 2016