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Re: [Freesurfer] problem with pial surface reconstruction using T1 (MPRAGE) and T2 (SPACE) weighted images
by Emil H.J. Nijhuis 13 May '14

13 May '14

Dear Bruce & Matt, thank you for your help. @Bruce: I would be happy to send you the data, just let me know by e-mail which files you would need. @Matt: Could you please specify the commands for the flags -nsigma_above and -nsigma_below and how you would rerun the pipeline? Also what values would be recommended? I did not find any manual/help files regarding the flags, so it would be helpful to document it. NB. I found another thread in the maillist which probably relates to the issue: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/03355… . However I could not verify this, due to expired dropbox files. Yours, Emil Probably Emil¹s current example would be best because it is failing in your recon-all setup. Matt. On 5/9/14, 9:31 AM, "Bruce Fischl" <fis...(a)nmr.mgh.harvard.edu> wrote: >Hi Matt > >if you can send me an example I'll try to find time to take a look >Bruce >On Fri, 9 >May 2014, Matt Glasser wrote: > >> Hi Bruce, >> >> For whatever reason, sometimes the T2w surface adjustment will be way >>off. >> Adjusting the -nsigma_above <#> -nsigma_below <#> even a little bit up >>and >> down can get it out of the minimum and make it work, so there might be a >> bug. >> >> Peace, >> >> Matt. >> >> From: "Emil H.J. Nijhuis" <emil.nijh...(a)gmail.com> >> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> Date: Friday, May 9, 2014 at 4:53 AM >> To: <freesurfer(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] problem with pial surface reconstruction >>using T1 >> (MPRAGE) and T2 (SPACE) weighted images >> >> Dear Bruce, >> >> thank you for your help. >> >> attached I have put an fslview, tkmedit screen-shot of the T2 image and >>a tk >> surfer image of lh.woT2.pial. >> >> It appears that without consideration of the T2 this effect does not >>happen. >> >> What would be your recommendation if I would like to keep using the T2 >>weigh >> ted image? >> >> Yours, >> Emil >> >> Hi Emil >> >> how do the surfaces look before you apply the T2 deformation? And how do >> they look visualized over the T2 instead of the T1? >> >> cheers >> Bruce >> >> On Thu, 8 May 2014, Emil H.J. Nijhuis wrote: >> >> Hi, >> >> I have been using Freesurfer v5.3 to perform surface reconstruct for 1mm >> isotropic T1 (MPRAGE) and T2 (SPACE) weighted images from a Siemens 3T >>Trio >> scanner with a 32-channel head coil. Unfortunately for half of my >>subjects I >> receive an rather odd pial surface artefact, while the 'white' surfaces >>do >> not suffer from the same issue. >> >> The command line I have used was: >> >> recon-all -all -subjid <subjectid> -T2 <subjectdir>/mri/orig/T2.mgz >>-T2pial >> -3T >> >> Are you familiar with this issue and do you have some advice for me? >> >> Thank you very much for your help. >> >> Yours sincerely, >> >> Emil >> >> -- >> ---------------------------------------------- >> Emil H.J. Nijhuis, PhD >> Researcher - Division of Diagnostic and Interventional Neuroradiology >> University Hospital Basel >> Petersgraben 4 >> CH 4031 Basel Switzerland >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> >>freesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/li >>sti >> nfo/freesurfer >> _______________________________________________ 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. >>_______________________________________________ >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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lme and survival (time-to-event) analysis tools on github
by jorge luis 13 May '14

13 May '14

Hi everyone Just wanted to point out that all the technology required to implement the statistical methods used in our last paper: "Event time analysis of longitudinal neuroimage data. Neuroimage. doi: 10.1016/j.neuroimage.2014.04.015". is available on github: https://github.com/NeuroStats I will try to add more features when I have some time. There is already a new useful script included in lme to compute subject-specific random effects for mass-univariate analyses. The survival (time-to-event) statistical analysis toolbox works pretty similar to lme. You can load your neuroimage data from Freesurfer using the scripts in lme: fs_read_label.m, fs_read_surf.m, fs_read_Y.m and then perform a survival analysis alone or a lme-survival joint analysis. Hope those tools help you make new exciting findings! Cheers -Jorge

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LME Matlab toolbox
by Victor Montal Blancafort 13 May '14

13 May '14

Greetings, The aim of this mail is about some problems that I am facing using the standalone copy (that is becouse I am using v5.1) of the LNE Matlab Tool provided on the FreeSurfer Wiki ( http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) Currently, I am carrying out a longitudinal mass-univariate study. However, I get blocked when I try to open the smoothed thickness '.mgh' file obtained using the 'mris_preproc' and 'mri_surf2surf' command or also when I try to open the fsaverage sphere. Analyzing the code, I have realized that problems are caused due to that some '.m' files such as 'load_mgh.m' or 'read_surf.m' can't be opened because they are not provided on the package. Should I download them from another source or maybe there is another problem I am not realizing? Thank you in advance for you attention and your help! Bests, Victor

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EM registration: brain centroid
by Mark Plantz 13 May '14

13 May '14

Hi Freesurfers, Does anyone know if it is possible to manually set the brain centroid during the EM Registration step of the recon-all pipeline. I am using a non-default atlas, and have discovered that many of my difficulties have resulted from the brain centroid being incorrectly assigned to a region of black space. Thank you for the help! Best, MP

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Fwd: Overinclusion of brain volume during segmentation - Question
by Christina Chen 12 May '14

12 May '14

Hi! I've attached 2 pictures of some brain scans on Freesurfer -- is there any way we can fix the huge underinclusion of the gray matter, hopefully without changing the surfaces of the white matter? What should be done with these scans to fix them? Thanks! Christina On Thu, Mar 20, 2014 at 2:32 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > cortical stats reported by asegstats2table use the surfaces, not the > cortical segmentation in aseg.mgz > doug > > On 03/20/2014 05:29 PM, Christina Chen wrote: > > Thanks a lot!! I have a follow up question: > > > > We use the command > > > > asegstats2table > > > > to output the subcortical volumes (and other whole brain volumes) to > > table. If the aseg is incorrect, can we still believe those values? > > > > Thanks, > > Christina > > > > > > On Thu, Mar 20, 2014 at 1:27 PM, Bruce Fischl > > <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > > > > Hi Christina > > > > if the aseg is incorrect but the surfaces are right, then you > > don't need to worry about it. This is the reason we typically use > > the surfaces instead of the aseg for things like brain > > volume/cortex modeling. > > > > cheers > > Bruce > > > > On Thu, 20 Mar 2014, Christina Chen wrote: > > > > Hi! > > If the cortical surface outlines are fine, but there is an > > overinclusion of > > brain volume during segmentation, how should I fix this? Can > > we calculate > > brain volume based on the cortical surface outlines -- if so, > how? > > > > Thanks! > > Christina > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto: > 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. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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Paradigm files
by Emily Boeke 12 May '14

12 May '14

Hi Freesurfers, I am doing some analyses for an experiment where paradigm files were automatically generated by Matlab during stimulus presentation. The script was designed to make paradigm files for an older version of freesurfer, so the files only have 2 columns. I am going to adjust these files so that they can be read by FS 5.3 (add in the extra columns needed). I noticed that there is a line for each TR as opposed to for the onset of each stimulus, for example, it looks something like this: 0 2 2 2 4 2 6 2 8 1 10 1 12 1 14 3 16 3 instead of 0 2 8 1 14 3 Is this a problem? Can I leave it as is and then just add a column of 2s and a column of 1s? Thanks! Emily

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2x3 DODS analysis question?
by Khadka, Sabin 12 May '14

12 May '14

Hi all, I am trying to run 2x3 factorial model correcting for age, sex and intracranial volume. Just to give you insight in my data I have my fsgd file as GroupDescriptorFile 1 Title DODS analysis 2x3 factorial Class MaleGroup1Low Class MaleGroup1Medium Class MaleGroup1High Class MaleGroup2Low Class MaleGroup2Medium Class MaleGroup2High Class FemaleGroup1Low Class FemaleGroup1Medium Class FemaleGroup1High Class FemaleGroup2Low Class FemaleGroup2Medium Class FemaleGroup2High Variables Age normVol Input SUB001 MaleGroup1Low 18 0.4 . . . And also my contrast files as Group1Group2.mtx [1 1 1 -1 -1 -1 1 1 1 -1 -1 -1]/3 MainEffectState.mtx 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 HighvLow.mtx -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 -0.5 0 0.5 HighvMed.mtx 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 0 -0.5 0.5 GroupxState-interaction.mtx 0.5 -0.5 0 -0.5 0 0.5 0.5 -0.5 0 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5 0.5 0 -0.5 -0.5 0 0.5 I'd appreciate if anyone could please let me know that my design is correct. Thanks for help. -Sabin

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Error running recon-all on hpc computers
by Natalie Garcia 12 May '14

12 May '14

Hi all, I'm trying to run recon-all on some data using one of the hpc clusters at my institution using FreeSurfer v. 5.3.0. I've used 4.5.0 without a problem but I'm trying to rerun the data with the new version. I keep getting this error (FreeSurfer's log file is attached here) regarding the mni/bin folder. Could this be an error on their end? Not sure if maybe 5.3 wasn't installed correctly on the hpc machines. Any help is really appreciated! Thanks, Natalie -- Natalie V. Garcia Graduate Fellow, Cognitive Neuroscience Department of Psychology The Pennsylvania State University 423 Moore Building University Park, PA 16802 nvg109(a)psu.edu

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bbregister to register a .annot file to MNI space
by Nathan Hutcheson 12 May '14

12 May '14

Hello, I am trying to use bbrestier to take an .annot file of a particular structure and register it to MNI space. I want to be able to use one of the FreeSurfer parcellations of the ACC (lh.caudalanteriorcingulate.label) and do a fMRI BOLD extraction in FSL in MNI space. Below is the command I used and the error message I am getting. Please let me know if what I am doing makes any sense or if I am way off base. Input > bbregister --s fsaverage --mov > /u/home/n/nhutche/temp/labels/lh.caudalanteriorcingulate.label --t1 > --init-fsl --reg register.dat > > Output > mkdir: cannot create directory `./tmp.bbregister.6489': Permission denied > > Log file is register.dat.log > > register.dat.log: Permission denied. > Take care, Dr. Nathan Hutcheson Postdoctoral Researcher University of California Los Angeles Semel Institute 760 Westwood Plaza C8-202 Los Angeles, CA 90024 T: 770.841.1694 nathanhutcheson.com <http://www.linkedin.com/pub/nathan-hutcheson/3a/7a8/a46>

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A question about installation
by 木村一皓 12 May '14

12 May '14

Hi, I would like to install "Freesurfer," but I have a problem. I now only have a PC running Windows OS. So I am wondering if I could use "Freesurfer" by windows.(say in "VMware Player") Or should I buy Macintosh or somtehing because of memory problems? Sorry for my really novice question, Ikko Kimura

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