Freesurfer April 2012

freesurfer@nmr.mgh.harvard.edu

123 participants
192 discussions

How to flatten time course on the cortex
by Kaveh Kohan 05 Apr '12

05 Apr '12

Hi FreeSurfer Users, I am new to the Freesurfer, I have a question regarding mapping of the resting state fMRI time courses on the cortex area. I apologise in case my question is naive. please bear with me: Is it possible to have time-courses sampled from cortex? I mean how can I get corresponding time-course for each vertex on the cortex ? I know that FreeSurfer can produce mask for cortex are but I would like to have time-courses on the flattened (2D) map; ie assuming that cortex is flattened, each pixel of the 2D flattened image which resides in the cortex (I guess it corresponds to a vertex on the cortex manifold?) is time-series. I have ran recon-all on the T1. All of those operation were done using a third party packages that uses freesurfer namely CMTK (http://cmtk.org) I do not exactly know how to use "bbregister" to register the parcellation on the resting-state fMRI image? I would be thankful if you can help. Thanks

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white matter hyper intensities
by Gregory Kirk 05 Apr '12

05 Apr '12

a collaborator just got a grant review that claimed There's a possibility that changes in cortical thickness in the insula might be a consequence of lesions (MR-hyperintensities) in the white matter. i would think that white matter hyper intensities would tend to enhance freesurfers ability to detect the white matter/grey matter boundary rather than cause an error. any comments as to the correctness of my thinking would be appreciated. thank you greg

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Stylus Input for Cortical Edits
by Jeff Stout 05 Apr '12

05 Apr '12

Hi All, We have a large number of subjects that need minor edits (orbital frontal cortex/eye issues subcortical parcellation etc.). To speed up the process I was wondering if a stylus input would help with the editing. Do the graphics tablets (stylus input) work with freesurfer editing? Do they end up being useful or is it not worth investing in? And if so, could someone recommend a brand (wacom?) that would work with Ubuntu 10.04 (or just linux in general). Thank you, Jeff Stout

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Problem with visualising hippocampal subfield segmentation
by Ed Gronenschild 05 Apr '12

05 Apr '12

Hi, I followed the instructions to visualize the hippocampal subfield segmentation by entering the command (in the subject's mri directory) freeview nu.mgz \ > -p-labels posterior_left_* posterior_Left-Hippocampus.mgz \ > -p-labels posterior_right_* posterior_Right-Hippocampus.mgz \ > -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt and got the following messages: 2012-03-27 11:54:37.043 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.083 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.154 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.156 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.168 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.170 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.182 freeview.bin[34414:907] invalid drawable 2012-03-27 11:54:37.184 freeview.bin[34414:907] invalid drawable QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT slot (QGroupBox::setShown(bool)) CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name left_CA2-3 CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB CTABrgbAtIndexi: index -1 was OOB Can not find index for color name right_CA2-3 CTABrgbAtIndexi: index -1 was OOB Nothing was shown on top of nu.mgz. All the left and righ posterior files are present. (Mac OS X 10.6.8, FreeSurfer version 5.1.0) Cheers, Ed

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mri_label2vol enquiry
by Johnson 04 Apr '12

04 Apr '12

Hi Can anyone tell me please how mri_label2vol works, I know what it does, but I need to know how it works to take the FS space to the original anatomy space: does it do registration or does it use a transformation matrix. If the latest which one, where can I find it? regards -- Johnson J. GadElkarim Research Assistant, Department Of Psychiatry, PhD Candidate, Department Of Electrical& Computer Eng., University Of Illinois at Chicago Mob: 312 - 376 - 7322 Email: jgadel2(a)uic.edu

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Mapping pf fsaverage surface to native volume
by René Besseling 04 Apr '12

04 Apr '12

Dear Freesurfer users, I've been trying to map a Qdec contrast sig.mgh to the native volume of a subject using mri_surf2surf (to get from Qdec fsaverage surface to native surface) and mri_surf2vol (to map from native surface to native volume cortical ribbon). However, the last step goes wrong: I get a nii with the same range of values as were in the surface, but the nonzero voxels are scattered all over, so I guess there is something wrong with the surface-to-voxel coordinate mapping. Below is my code, any ideas on what goes wrong? Best regards, Rene mri_surf2surf --hemi rh --srcsubject fsaverage --noreshape --sval sig.mgh --trgsubject subj01 --tval sig_2subj01.mgh mri_surf2vol --surfval sig_2subj01.mgh --hemi rh --fillribbon --identity sub01 --template subj01/mri/orig.mgz --o sig_2subj01_volumetric.nii

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Re: [Freesurfer] Freesurfer base file question
by Douglas N Greve 04 Apr '12

04 Apr '12

Hi Tina, sorry no one got to your first email. Sometimes emails do fall through the cracks, so always feel free to repost. It is not clear to me what command you are running or what you are trying to do. Can you supply more detail? doug On 04/02/2012 11:55 AM, Tina Jeon wrote: > > Hi Doug could you please answer these questions that I posted on the > listserv. Your help would be much appreciated to an upcoming project > on cortical development. Thank you. > > I noticed that the newest version of freesurfer does not output a > > ?h.base.mgh file, which contains vertices, but no triangular meshes > and corresponding gyral labels from the color look up table. > > Question: > > 1). Why does my cortical labels created using tksurfer correspond to > the vertices in the base.mgh file and not the pial surface that I drew > the surface on? > > 2). Is there a file in place of the ?h.base.mgh file in the newer > version of freesurfer? i.e. called a different name? > > My goal is to figure out which surface aligns with my manually created > cortical labels for visualization. > > I am running version FSv5.0.0 on Centos4_x86_64 bit. > > Many thanks, > > Tina Jeon > > > ------------------------------------------------------------------------ > > UT Southwestern Medical Center > The future of medicine, today. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Questions about recon-all process flow in build 5.0.0
by Winter, Warren 04 Apr '12

04 Apr '12

Hi, I have a few questions about the process flow for the last stable build (5.0.0). After looking over http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all , https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable , and http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags , it looks like there's some inconsistency in the info on these pages that's left me a bit confused about what processing steps are and aren't invoked by autorecon2-wm, and autorecon-pial. On the 'Other Useful Flags' page, it looks as though autorecon2-wm doesn't invoke maskbfs / mri_mask, but on the recon-all page as well as in the mailing list archives it's said that autorecon2-wm runs processes both prior to autorecon2-pial and including the processes called on by autorecon2-pial. (By the way, is autorecon-pial a separate command from autorecon2-pial? Is the only difference that the former runs all the autorecon3 steps whereas the latter ends at the last step of autorecon2?) If autorecon2-wm doesn't run maskbfs / mri_mask, then wouldn't a subject who has both had pial edits done to their brainmask.mgz and wm edits done to their wm.mgz end up generating parcellation stats that don't reflect the pial edits? If that's the case, then would adding a -maskbfs flag before autorecon2-wm and -autorecon3 solve the problem? And autorecon2-cp starts with -normalization2, right? On the http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction page it says that it starts running at -normalization, which would be far earlier in the pipeline. Finally, should one always wait to make pial edits or WM edits after adding control points and reprocessing from autorecon2-cp? It looks to me as though throwing control points and WM edits and/or pial edits simultaneously at a reprocessing stream wouldn't pose any problems for the file dependencies, but that you might be able to do better pial and/or WM edits after seeing the newly generated surfaces and the newly segmented wm.mgz after recon-all has incorporated the control points. Thanks so much for your help! Warren -- Warren Winter Research Coordinator Children's Hospital Boston Sheridan Laboratory of Cognitive Neuroscience Division of Developmental Medicine 1 Autumn Street, AU 650 Boston, MA 02215 857-218-5224

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hippocampal segmentation
by Rashmi Singh 04 Apr '12

04 Apr '12

Hello, I converted the aseg. mgz files to nii format and created a hippcampal mask with 3dcalc. Using AFNI I opened the hippocampal mask as overlay on the brainmask .nii image as underlay. For some subjects the hippocampus is not at the correct position. Please advise. Thanks, Rashmi. ________________________________ This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health Insurance Portability and Accountability Act (PL 104-191) and its various implementing regulations and must be protected in accordance with those provisions. Healthcare information is personal and sensitive and must be treated accordingly. If this correspondence contains healthcare information it is being provided to you after appropriate authorization from the patient or under circumstances that don't require patient authorization. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Redisclosure without additional patient consent or as permitted by law is prohibited. Unauthorized redisclosure or failure to maintain confidentiality subjects you to application of appropriate sanction. If you have received this correspondence in error, please notify the sender at once and destroy any copies you have made.

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temporal pole
by Righart, Ruthger Dr. 04 Apr '12

04 Apr '12

Dear Freesurfer experts, I have a problem of cortical segmentation of the temporal pole (see attached image), while the rest of the cortex segmentation is fine. This problem can probably not be solved by using control points as the intensity values of the white-matter (T1.mgz value) seem very low in this area (i.e., <100). Is there another way to solve this problem? Suggestions are very much appreciated! Ruthger Righart

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Freesurfer April 2012