Freesurfer

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17 participants
30099 discussions

tumor mask & extreme hydrocephalus- white matter is not recognized
by Andrea Horváth 12 Jun '14

12 Jun '14

Dear Freesurfer Experts, I have two questions: 1. How can I add a previously created a tumor mask along with the mprage to improve segmentation? 2. I ran recon-all on a subject with extreme hydrocephalus. Registration to Talairach space and skull stripping were OK. However, a part of occipital white matter was not recognized as white matter even after adding control points and running recon-all -autorecon2-cp -autorecon3 due to the large ventricle as you can see in the attachment. What can you recommend to fix this problem? Thank you for your help! Cheers, Andrea

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Segfault errors in tkmedit and tksurfer
by Joonkoo Park, Ph.D. 12 Jun '14

12 Jun '14

Hello, I've used FreeSurfer previously on a linux machine (from a previous lab). Now, I have just installed it on a Mac OSX, using the "freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg" version. I followed all the instructions on the installation page. However, there were segfault errors when running both tkmedit and tksurfer as follows: dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tkmedit > tkmedit started: Wed Jun 11 23:28:05 2014 > > /Applications/freesurfer/tktools/tkmedit.bin bert orig.mgz > > $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ > Set user home dir to /Applications/freesurfer > Set subject home dir to /Applications/freesurfer/subjects/bert > Using interface file /Applications/freesurfer/tktools/tkmedit.tcl > > Segfault > Setting global interpreter > xDebug stack (length: 2) > 01: main() > 01: Setting global interpreter > 00: > 00: > dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tksurfer > > Segfault > Initializing glut > xDebug stack (length: 1) > 00: > 00: Initializing glut > > Segfault > Initializing glut > dyn-152-3-184-222:freesurfer joonkoopark$ > Any idea what went wrong and how to fix it? Thank you! Joon

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freeurfer manual edits
by Jidan Zhong 12 Jun '14

12 Jun '14

Dear FreeSurfer Experts, I have two questions about freesurfer troubleshoot. My subjects are people with multiple sclerosis, so for most of them I need to add control points as well as edit white matter due to lesions. As far as I know, I should add control points and do recon-all -autorecon2-cp -autorecon3 to my subject and then edit white matter, do recon-all -autorecon2-wm -autorecon3. My question is, it seems there are some repeated steps for those two recon steps, and it takes so long to run them. Is there anyway that I can save some process steps and leave it to the last recon? To be specific, can I do recon-all -autorecon2-cp only after I added control points, then do recon-all -autorecon2-wm -autorecon3 after wm edits? I think it is reasonable as after -autorecon2-cp the new white matter surface is already generated and can help to detect wm failure. But I am not sure whether this makes sense to you guys. Another question is, some of my subjects they have degenerated white matter and grey matter, so some parts get so dark that freesurfer would not include it even in the pial surface. I attached one figure for your referece. If there is no white matter detected in that unlabled part (at the top of the figure), what should I do? should I leave it or just add some white matter and control points myself to get a better segmentation and surface? [The case I show in the attachment is much better than some other cases, whose brain has some parts so dark that even I can not tell which is grey matter or white matter from my experience..] Thanks! -- Regards, Jidan

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Corpus Callosum segmentation reliability
by Alessia Giuliano 12 Jun '14

12 Jun '14

Dear FreeSurefer team, in order to verify the reliability of the volumes of Corpus Callosum (CC) subregions estimated by FreeSurfer I have applied the recon-all on the same subject but in three different situations: 1. when the image was not preliminarly rotated;2. when an initial soft rotation was manually performed with SPM;3. when an initial rigid coregistration in MNI space was performed with SPM. Although the differences in image orientation between 1, 2 and 3 before the implementation of FreeSurfer were really small, the differences in the volumes of the CC subregions between 1, 2 and 3 are notable. How can I base on this evident variability my volumetric analysis of CC subregions? Do you have any suggestions to improve my approach to the CC segmentation? In order to make my results clear, I attach you a recapitulatory page and I send you a link to the FreeSurfer output in 1, 2 and 3 (https://www.dropbox.com/sh/k1z5o0e6sq90qq0/AABx38QxKvxDhUe2lV9imaa9a) Thank you, Alessia Giuliano

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Freesurfer installation problem
by Venkateswaran Rajagopalan 12 Jun '14

12 Jun '14

Dear All, I looked into the archives extensively but could not find a solution to my problem. I am having Ubuntu " Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux". I tried installing freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get the following error message mri_convert /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. tkmedit /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file not executable. I followed the instruction steps as given in freesurfer wiki. What am I doing wrong here?. Is there a installation wiki page for giving guidelines for ubuntu freesurfer installation. Thanks, any help will be greatly appreciated as I am trying to install freesurfer for the past 3 days without success. Thanks Venkat

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Dura correction using MEMPRAGE vs bandwidth-matched FLAIR
by Emad Ahmadi 11 Jun '14

11 Jun '14

Hi, We are at the start of a study on TBI, in which we’re obtaining MEMPRAGE and T2-SPACE-FLAIR images (the images are obtained in Lunder 6 scanner, and I wonder if I can find T1 & FLAIR matched sequences for morphormetry on that scanner). The pixel size of the MEMPRAGE sequence is 1mm isotropic, while the one for T2-SPACE-FLAIR is 0.5 x 0.5 x 1mm; they’re not bandwidth matched either (I’ve attached the details of the sequences we’re using). I just wanted to know if we should make changes to our T2-SPACE-FLAIR sequence and match it with the MEMPRAGE sequence to feed the FLAIR images into recon-all for dura correction, or if we should leave the T2-SPACE-FLAIR sequence as it is and use the four echoes of MEMPRAGE for dura correction (I mean, is dura correction using different echoes of MEMPRAGE as good as feeding FLAIR images into recon-all?) Thank you very much, Emad Emad Ahmadi, MD ----------------------------------------------- Postdoc Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

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Re: [Freesurfer] Registration of Functional Data to the Inflated Brain
by Sherryse Corrow 11 Jun '14

11 Jun '14

ATT: Doug G Hi Doug, I ran it again with —debug as the first argument as you suggested and have attached the terminal output. Thanks for your help. We are quickly approaching a deadline to get this figured out so we greatly appreciate your help! Thank you so much! It’s been a while since I posted so I included previous messages below. I am never able to keep the thread together for some reason. Best, Sherryse ________________________________ Douglas N Greve<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Tue, 27 May 2014 15:46:24 -0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> recon-all will not produce the registration file you are looking for. It should be produced by reg-feat2anat. Try running it with --debug as the first argument and post the terminal output to the list doug ________________________________ Bruce Fischl<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:…> Fri, 30 May 2014 12:53:23 -0700<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:…> Hi Sherryse mostly I'll leave this for Doug. Have you tried using bbregister directly? It might be embedded within reg-feat2anat, I'm not sure Bruce ________________________________ Thanks Bruce. The problem is that the registration itself is not working properly. Recap: The goal is to view the functional data on the inflated brain. We ran recon-all, checked that registration, then attempted to register the functional data to the free surfer anatomical. My understanding is that running reg-feat2anat should create a folder (featdir/reg/freesurfer) with register.dat and anat2exf.register.dat files in (among others). The folder is created and some of the files are created, but those two are not. Although, I should note that there is a file created within this folder called anat2exf.register.dat.init. But I am not sure what the ³init² is for or what it means. The terminal output from running reg-feat2anat is attached. I can see now that there are errors in the output (I am slowly figuring how how to use FreeSurfer!). Any suggestions you have are greatly appreciated! Thanks! Sherryse -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre 360A-2550 Willow Street Vancouver, BC, V5Z 3N9 Tel: 604-875-4111 ext 67672 Cell: 604-315-6717 sherryse.corrow(a)eyecarecentre.org<mailto:sherryse.corrow@eyecarecentre.org>

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From NIfTI T1 to its volume cortical thickness map in MNI152 space.
by Fred Sampedro 11 Jun '14

11 Jun '14

Dear FreeSurfer experts, I am interested in analyzing group differences in cortical thickness with an application-specific GLM model that is build to work on MNI152 volume data. For that, my plan is to obtain a "cortical thickness volume in MNI152 space" for each of my MRI scans. My input data are nifti T1 scans. Here is my pipeline proposal for each T1 scan: INPUT: FOO_SUBJECT.nii FREESURFER CALLS (in $SUBJECTS_DIR): 1) recon-all -i FOO_SUBJECT.nii -subjid foosub 2) recon-all -all -subjid foosub 3) mri_surf2vol --surfvalpath /foosub/surf/lh.thickness --o foosub_cth_vol_lh #(?) 4) mri_surf2vol --surfvalpath /foosub/surf/rh.thickness --o foosub_cth_vol_rh #(?) 5) #should I merge lh and rh (?) how (?) let it be foosub_cth_vol 6) fslregister --s foosub_cth_vol --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat #should I convert it to MNI152 space (?) and how (?) 6) mri_fwhm --i foosub_cth_vol --o smoothed_foosub_cth_vol # should I smooth it (?) and how (?) OUTPUT to statistical analysis: smoothed_foosub_cth_vol (?) As you can see, I am pretty new to freesurfer and I have a lot of technical and conceptual gaps in this pipeline. Any advice on how to robustly accomplish this task would be much appreciated, as well as any advice regarding whether it would be a bad idea to try to carry out this kind of procedure in the first place. The context of the application is to apply the same ad-hoc statistical groupal analysis to PET, VBM GM, and cortical thickness data for all subjects. Thanks a lot in advance, Fred Sampedro

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aparc manual correction
by elisa veronese 11 Jun '14

11 Jun '14

Dear FreeSurfer users, can anybody tell me if and how it is possible to manually correct an uncorrect parcellation of the CC, i.e. if the rostrum is uncorrectly assigned to the CC_Mid_Anterior label instead of the CC_Anterior label? Thank you. Best Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php <http://icbn.uniud.it/tiki-index.php>*

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Clusterwise Correction for Multiple Comparisons
by wangzhiwei3233 11 Jun '14

11 Jun '14

Hi, Doug and all, I have two quesiotns about clusterwise correction for multiple comparsion. I run 2 corrections,and commands are as follows: a. mri_glmfit-sim --glmdir g2v0.weight --cache 1.3 abs --cwpvalthresh .05 --2spaces b. mri_glmfit-sim --glmdir g2v0.weight --cache 1.3 pos --cwpvalthresh .05 --2spaces Question 1 : Should the postive clusters from result of command a be same as the result from command b? If yes, why cluster size from reslut of command b is lager than postive cluster from command a in my case?(see results) Resluts form a: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 7 5.208 45661 482.74 -6.7 42.3 -22.2 0.01030 0.00900 0.01160 888 medialorbitofrontal 8 5.103 84832 433.13 -32.0 30.7 -2.3 0.02270 0.02080 0.02460 1156 lateralorbitofrontal Resluts form b: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 6.483 140982 864.69 -14.8 58.9 -6.1 0.00360 0.00260 0.00479 1416 rostralmiddlefrontal 2 5.103 84832 808.07 -32.0 30.7 -2.3 0.00599 0.00459 0.00739 2186 lateralorbitofrontal Question 2 : Is the simulation from pre-cached independent from my results waiting for being corrected? Thanks a lot! Wilder 2014/06/11

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