Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

Postdoctoral Fellowship in Aging Research
by Anqi Qiu 04 Apr '14

04 Apr '14

Job description: National University of Singapore (NUS) is a leading global university centre in Asia. It offers a global approach to education and research, with a focus on Asian perspectives and expertise. Computation functional anatomy laboratory at NUS (http://www.bioeng.nus.edu.sg/cfa) focuses on brain and cognition studies using neuroimaging techniques. Our group is leading a large-scale aging neuroimaging project from birth in Singapore. The project examines neurocognition, high angular resolution diffusion imaging (HARDI), resting-state fMRI, and structural MRI. We are looking for a research fellow who is interested in multi-modal MRI studies in aging, especially, who is interested in understanding aging processes of anatomical and functional connectivity and their relations with cognition as well as genetic regulation on aging brain processes. We offer high salary with medical and other benefits. Requirements: Ph. D or MD Research background on infant brain is preferable but necessary Knowledge in statistical analysis is necessary Good communication and writing skills in English language If you are interested in the jobs listed above, please send your CV to Associate Prof. Anqi QIU Department of Biomedical Engineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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question about how to calculate COV for MNE
by Joseph Dien 04 Apr '14

04 Apr '14

Hi, I have a question about how to calculate the COV for the MNE software. As I understand it from Section 4.17 of the 2.7.3 MNE manual, if one is averaging together COV matrices, one weights them by the number of observations going into each one. I also see from Section 4.17.2 that these are technically not covariance matrices so much as sum-of-squares matrices where the epochs going into each variable has been baseline corrected. Assuming my understanding so far is correct, my question is about how to proceed when making linear combinations of COV matrices, as in a difference wave, as discussed in Section 6.3. Would the following be the correct procedure? Compute the COV separately for the two conditions (say standard and rare oddballs). Subtract the two COV matrices to obtain C0. Then calculate C by dividing by Leff, which in turn is calculated as Leff= (L1*L2)/(L1+L2) where L1 is the number of observations in the first COV matrix and L2 is for the second. But if done in this way, the two COV matrices would not be weighted by their relative sample sizes. So would I also weight them by L1 and L2 during the subtraction, as done for averaging per 4.17? But then what is the purpose of the Leff calculation? Or is the idea that one would calculate a single COV based on both conditions and then one would modify COV by Leff to reflect that the signal-to-noise ratio has been reduced by combining two averages with differing sample sizes? But in the case where both samples equal, say, 10, Leff would end up equalling 100/20=5. Dividing C by 5 seems like too much. Anyway, very confused. Any guidance would be appreciated. Respectfully, Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist Maryland Neuroimaging Center University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com

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Re: [Freesurfer] Standard surface tessellation
by Chris McNorgan 04 Apr '14

04 Apr '14

Hi Justin, This is quite similar to a question I had asked previously: https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33421.html I believe the solution is to generate a 14000 vertex template, and then appy mri_surf2surf to all 10 subjects, which will map the vertices of all 10 subjects to your template. The 10 transformed surfaces should then correspond with one another. Chris Subject: [Freesurfer] Standard surface tessellation From: jeongwon(a)pet.wayne.edu Date: 14-04-03 03:47 PM To: freesurfer(a)nmr.mgh.harvard.edu Dear FreeSurfer, I am a beginner in FreeSurfer and wonder if it is possible in FreeSurfer to apply the same triangulation across multiple subjects, i.e. the same number of vertices and triangles at the anatomically identical locations. For instance, I have 10 subjects and want to have pial (or white matter) surfaces of individual subjects consisting of 14000 vertices which are anatomically matched. Any suggestion will be greatly appreciated. Justin.

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Subcortical segmentation for PAG
by Jeni Chen 03 Apr '14

03 Apr '14

Hi, Just wondering if the periaqueductal gray is part of the automatic segmentation process and if we can obtain the volume. I checked the aseg table but didn't see it, however, I somehow remember seeing it before... Was it ever included? Thanks. Jeni

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Standard surface tessellation
by jeongwon＠pet.wayne.edu 03 Apr '14

03 Apr '14

Dear FreeSurfer, I am a beginner in FreeSurfer and wonder if it is possible in FreeSurfer to apply the same triangulation across multiple subjects, i.e. the same number of vertices and triangles at the anatomically identical locations. For instance, I have 10 subjects and want to have pial (or white matter) surfaces of individual subjects consisting of 14000 vertices which are anatomically matched. Any suggestion will be greatly appreciated. Justin.

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missing Freesurfer wiki pages
by Gabor Perlaki 03 Apr '14

03 Apr '14

Dear all, Most of the links on https://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction page do not work. If I clik for example on FsTutorial/SkullStripFix the following message will popup: "This page does not exist yet. You can create a new empty page, or use one of the page templates." Is there a new page for the recommended workflow which works fine? Thanks, Gabor

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preprocessing question
by Eiran Harel 03 Apr '14

03 Apr '14

Dear freesurfers, I have installed freesurfer and fsl on my Mac: -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl I am trying to run Preproc-sess command: preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm 5 -fsd bold -stc odd -per-run -force and get this error: mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 -nerode 0 ERROR: cannot find either fslmaths for avwmaths Any suggestions? Thanks! Eiran [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_01.jpg]<http://www.tasmc.org.il/be-well/Pages/default.aspx> [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_02.jpg] <https://www.facebook.com/ichilov.medical> [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_03.jpg] <http://twitter.com/tasmc1> [http://www.tasmc.org.il/DocLib/SIGN/sign_smallHE_04.jpg] <http://www.youtube.com/tasmc1> [http://www.tasmc.org.il/DocLib/SIGN/sign_smallEN_05.jpg] <http://www.tasmc.org.il/sites/en/Pages/default.aspx>

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normalization problem
by Gregory Kirk 03 Apr '14

03 Apr '14

Hi, i ran about 260 subjects and got good results for all but 30. the 30 that failed all seemed to have the same problem with normalization. the original were done with v5.1 i reran one with 5.3 and the problem was reduced. I attached a slice of the T1 from each. the 5.3 rerun produced a good quality brainmask.mgz, the originalrun with 5.1 failed to produce the brainmask.mgz the original orig.mgz volumes look fairly decent, they were aquired on a good 1.5T scanner. since it ran much better on 5.3 im thinking some defaults were changed and perhaps i can add some flags with new default values to get 5.1 to produce usable results, i.e. the 230 other subjects have been inspected and im thinking they really really don't want to reinspect all of them after running on 5.3 can you suggest options/flags that i can try to rerun with 5.1 thanks greg

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Re: [Freesurfer] LGI - Statistical Analysis
by Marie Schaer 03 Apr '14

03 Apr '14

Hi Kenza, (I added the freesurfer mailing list in copy, please post there) You have to set the min threshold at 1 when you overlay the lGI, then you should not see any gray regions anymore. Not sure I understood your problem with the statistical analyses, maybe there is simply no significant difference? If you could complete the lGI without problem (which is the case if you have the ?h.pial_lgi files), and if you are certain of your statistical design, then it simply means that there is nothing which is more significant than the given significance threshold (you can play with the significance threshold to explore that as well, and visualize the data in plots at some vertices in qdec). Best, Marie On Apr 3, 2014, at 4:57 AM, Kenza Drissi-kaÃ¯touni <kenza.drissi-kaitouni(a)polymtl.ca> wrote: > > > Dear Marie, > > I have been trying to use the lgi implemented in Freesurfer. I was able to > obtain results, but unfortunately, when I overlay visualize them as an overlay > of ?h.pial_lgi on the ?h.pial surface in tksurfer, I still see gray regions > which shouldnt be... What can I do to fix this problem? > > Also, when I perform a statistical analysis on the data I obtained, only 2 small > spots appear for lh and none for rh. I strongly suspect this is because of the > gray regions where no lgi was apparently calculated/retained. Is it so? > > Thank you very much for you time, > Kenza Drissi-Kaitouni > B.Sc. Biomedical Engineering > Ecole Polyetchnique de Montreal > > D.E.S.S Biomedical Engineering >

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Inconsistent results of the same subjects from different Freesurfer processing
by Zixuan Yang 02 Apr '14

02 Apr '14

Dear FreeSurfers, I have been processing a group of subjects, firstly using Freesurfer V5.1.0 or V5.3.0, then V5.3.0 after making some editing on WM and pial surface, using the <recon-all> command, without the <-no-isrunning> option. I have below message at the beginning of the recon-all after editing: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/zixuan/Work/FS/RE_EDIT Actual FREESURFER_HOME /usr/share/freesurfer -rw-r--r--. 1 zixuan users 957929 Dec 20 16:52 /home/zixuan/Work/FS/RE_EDIT/D3358/scripts/recon-all.log Linux NIL.Melbourne 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/share/freesurfer Previous: /share/apps/freesurfer/5.3.0 #-------------------------------------------- #@# Mask BFS Wed Apr 2 17:11:43 EST 2014 /home/zixuan/Work/FS/RE_EDIT/D3358/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz However all subjects have been finished without error, which is not the case as what you have discussed in the mail archive. recon-all -s <subjID> finished without error at Mon Mar 24 03:38:36 EST 2014 The problem is, I found the cortical thickness in regions that I didn't edit not consistent before and after re-processing, with about 2-10% differences. For some subjects, I have only edited minor pial surface (e.g. entorhinal cortex only), yet it seems that all values have been affected. My question is 1), shall I consider my results valid, despite of the "dismatch" thing? Is there any other factors other than editing will affect the final value? 2), I have about 30 subjects processed with V5.1.0, (atrophic brain +++ with heavy editing - extreme time consuming), yet I still found some pial to edit this time, and processed them with V5.3.0. Shall I consider the values valid provided the message "without error", despite the different FreeSurfer versions? Apologies for cross posting, I didn't found any cases similar to mine in the mail archive. Many thanks and kind regards, Zixuan -- Zixuan YANG Ph.D candidate Centre for Healthy Brain Ageing (CHeBA) School of Psychiatry, UNSW Medicine NPI, Euroa Centre, Barker Street, Randwick NSW 2031 AUSTRALIA T: +61 (2) 9385 0427 W: www.cheba.unsw.edu.au<http://www.cheba.unsw.edu.au/> E: z.yang(a)student.unsw.edu.au<mailto:s.reppermund@unsw.edu.au> ______________ Mailing address: University of New South Wales Randwick Campus, Building R1f 22-32 King Street, Randwick NSW 2031 Australia

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