Freesurfer February 2011

freesurfer@nmr.mgh.harvard.edu

103 participants
152 discussions

FS 5.1
by Derin Cobia 16 Feb '11

16 Feb '11

All, Just curious about the current estimated timeline for version 5.1, trying to schedule some projects around it. Thanks! -Derin

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Re: [Freesurfer] (no subject)
by Marco Loggia, PhD 16 Feb '11

16 Feb '11

Cara Angela, La maggioranza degli utenti di questa mailing list (incluso il team di freesurfer, che mi ha chiesto di risponderti) non parla italiano. Per comunicazioni future ti suggerirei di scrivere in inglese, in modo da assicurarti assistenza diretta dal team. Per preprocessare i tuoi dati devi seguire questi step: 1) Utilizzando il comando 'setenv' devi specificare il path completo della directory contenente i tuoi soggetti. Per esempio, se la tua directory si trova in /DATI/SOGGETTI, devi usare il comando: setenv SUBJECTS_DIR /DATI/SOGGETTI 2) cd $SUBJECTS_DIR 3) mkdir -p NOMESOGGETTO/mri/orig 4) mri_convert FILE_NAME.nii NOMESOGGETTO/mri/orig/001.mgz 5) recon-all -s NOMESOGGETTO -autorecon-all Questo dovrebbe funzionare. In bocca al lupo! Marco _____________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

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Re: [Freesurfer] Hemisphere separation error
by Bruce Fischl 15 Feb '11

15 Feb '11

but who decided 0.7mm iso was the right setting for the scanner? Can you change that? what kind of scanner and coil is it? On Tue, 15 Feb 2011, Evan Luther wrote: > Sorry about that! Hear they are. The reason why we want .7 mm resolution is > because that is the resolution of the volume anatomies we obtain from the > scanner. > > Thanks again! > > On Tue, Feb 15, 2011 at 4:39 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> can you load them with the -segmentation flag in tkmedit so I can see them >> as a color overlay? And is there a reason you need 0.7mm data? That's why it >> is *so* noisy >> >> On Tue, 15 Feb 2011, Evan Luther wrote: >> >> Hey Bruce, >>> >>> Here are the aseg and aseg.auto_noCCseg files. Our data is at a .7 mm >>> resolution. >>> >>> Thanks! >>> >>> On Tue, Feb 15, 2011 at 4:15 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >>>> wrote: >>> >>> what does the aseg look like n that case? And what resolution is your >>>> data? >>>> >>>> On Tue, 15 Feb 2011, Evan Luther wrote: >>>> >>>> Hey Bruce, >>>> >>>>> >>>>> I also do not understand why I could not use the aseg but if I do not >>>>> set >>>>> the noaseg flag I get a result like the picture I have attached where no >>>>> cut >>>>> is made. I have also attached a picture of the slanted cut. I am not >>>>> sure >>>>> why this occurred and also why it only occurred on one subject's >>>>> anatomy. >>>>> >>>>> Thanks for the help! >>>>> >>>>> -Evan >>>>> >>>>> On Tue, Feb 15, 2011 at 2:21 PM, Bruce Fischl < >>>>> fischl(a)nmr.mgh.harvard.edu >>>>> >>>>>> wrote: >>>>>> >>>>> >>>>> Hi Evan >>>>> >>>>>> >>>>>> can you send some coronal images showing where it is slanted? I also >>>>>> don't >>>>>> understand why you can't use the aseg. What resolution are you >>>>>> acquiring >>>>>> the >>>>>> data at? >>>>>> cheers >>>>>> Bruce >>>>>> >>>>>> On Tue, 15 Feb 2011, Evan Luther wrote: >>>>>> >>>>>> Hello All! >>>>>> >>>>>> >>>>>>> I am currently trying to create a high resolution anatomy by manually >>>>>>> changing some parameters throughout the recon-all process. I have >>>>>>> currently >>>>>>> hit a road block at the fill portion of the recon-all process. So far >>>>>>> I >>>>>>> have >>>>>>> tried this high resolution reconstruction on two subject's anatomies. >>>>>>> In >>>>>>> both subjects I used the flag -noaseg as well as seed points for the >>>>>>> CC, >>>>>>> pons, left hemisphere, and right hemisphere at the fill step because >>>>>>> otherwise the fill command would use the aseg file for seed points and >>>>>>> subsequently the hemispheres would not get separated at all. >>>>>>> >>>>>>> Now here is the kicker, in one subject's anatomy this worked fine. It >>>>>>> split >>>>>>> the hemispheres down the middle without a problem. However on the >>>>>>> other >>>>>>> subject the cut between the hemispheres is slanted, assigning portions >>>>>>> of >>>>>>> the right hemisphere to the left. I do not know how to correct this >>>>>>> problem. >>>>>>> I have tried using different seed points and not inputting seed points >>>>>>> and >>>>>>> this has yielded the same results. Any suggestion? >>>>>>> >>>>>>> thank you, >>>>>>> >>>>>>> Evan Luther >>>>>>> >>>>>>> >>>>>>> >>>>>>> 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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Re: [Freesurfer] Hemisphere separation error
by Bruce Fischl 15 Feb '11

15 Feb '11

can you load them with the -segmentation flag in tkmedit so I can see them as a color overlay? And is there a reason you need 0.7mm data? That's why it is *so* noisy On Tue, 15 Feb 2011, Evan Luther wrote: > Hey Bruce, > > Here are the aseg and aseg.auto_noCCseg files. Our data is at a .7 mm > resolution. > > Thanks! > > On Tue, Feb 15, 2011 at 4:15 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> what does the aseg look like n that case? And what resolution is your data? >> >> On Tue, 15 Feb 2011, Evan Luther wrote: >> >> Hey Bruce, >>> >>> I also do not understand why I could not use the aseg but if I do not set >>> the noaseg flag I get a result like the picture I have attached where no >>> cut >>> is made. I have also attached a picture of the slanted cut. I am not sure >>> why this occurred and also why it only occurred on one subject's anatomy. >>> >>> Thanks for the help! >>> >>> -Evan >>> >>> On Tue, Feb 15, 2011 at 2:21 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu >>>> wrote: >>> >>> Hi Evan >>>> >>>> can you send some coronal images showing where it is slanted? I also >>>> don't >>>> understand why you can't use the aseg. What resolution are you acquiring >>>> the >>>> data at? >>>> cheers >>>> Bruce >>>> >>>> On Tue, 15 Feb 2011, Evan Luther wrote: >>>> >>>> Hello All! >>>> >>>>> >>>>> I am currently trying to create a high resolution anatomy by manually >>>>> changing some parameters throughout the recon-all process. I have >>>>> currently >>>>> hit a road block at the fill portion of the recon-all process. So far I >>>>> have >>>>> tried this high resolution reconstruction on two subject's anatomies. In >>>>> both subjects I used the flag -noaseg as well as seed points for the CC, >>>>> pons, left hemisphere, and right hemisphere at the fill step because >>>>> otherwise the fill command would use the aseg file for seed points and >>>>> subsequently the hemispheres would not get separated at all. >>>>> >>>>> Now here is the kicker, in one subject's anatomy this worked fine. It >>>>> split >>>>> the hemispheres down the middle without a problem. However on the other >>>>> subject the cut between the hemispheres is slanted, assigning portions >>>>> of >>>>> the right hemisphere to the left. I do not know how to correct this >>>>> problem. >>>>> I have tried using different seed points and not inputting seed points >>>>> and >>>>> this has yielded the same results. Any suggestion? >>>>> >>>>> thank you, >>>>> >>>>> Evan Luther >>>>> >>>>> >>>>> >>>> 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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Re: [Freesurfer] Hemisphere separation error
by Bruce Fischl 15 Feb '11

15 Feb '11

what does the aseg look like n that case? And what resolution is your data? On Tue, 15 Feb 2011, Evan Luther wrote: > Hey Bruce, > > I also do not understand why I could not use the aseg but if I do not set > the noaseg flag I get a result like the picture I have attached where no cut > is made. I have also attached a picture of the slanted cut. I am not sure > why this occurred and also why it only occurred on one subject's anatomy. > > Thanks for the help! > > -Evan > > On Tue, Feb 15, 2011 at 2:21 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > >> Hi Evan >> >> can you send some coronal images showing where it is slanted? I also don't >> understand why you can't use the aseg. What resolution are you acquiring the >> data at? >> cheers >> Bruce >> >> On Tue, 15 Feb 2011, Evan Luther wrote: >> >> Hello All! >>> >>> I am currently trying to create a high resolution anatomy by manually >>> changing some parameters throughout the recon-all process. I have >>> currently >>> hit a road block at the fill portion of the recon-all process. So far I >>> have >>> tried this high resolution reconstruction on two subject's anatomies. In >>> both subjects I used the flag -noaseg as well as seed points for the CC, >>> pons, left hemisphere, and right hemisphere at the fill step because >>> otherwise the fill command would use the aseg file for seed points and >>> subsequently the hemispheres would not get separated at all. >>> >>> Now here is the kicker, in one subject's anatomy this worked fine. It >>> split >>> the hemispheres down the middle without a problem. However on the other >>> subject the cut between the hemispheres is slanted, assigning portions of >>> the right hemisphere to the left. I do not know how to correct this >>> problem. >>> I have tried using different seed points and not inputting seed points and >>> this has yielded the same results. Any suggestion? >>> >>> thank you, >>> >>> Evan Luther >>> >>> >> >> 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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details about surf2vol
by Aaron Alexander-Bloch 15 Feb '11

15 Feb '11

Dear all, I am hoping to use surf2vol to generate high resolution masks of the gray/white surface, so something like the following command: mri_surf2vol --sd /subj/dir/ --identity subid --hemi lh --surf white --mkmask --o volume.mgz --template ./template.mgz However I'm wondering about what exactly the algorithm does. I understand that the vertices are placed at the closest voxel in the template space. But does the algorithm take into account information about the faces/lines of the mesh in addition to the vertices? If so, how? If not, does that imply a limit to the resolution of the template space that should be used with the command? Thanks very much in advance for any help. Best, Aaron Alexander-Bloch PhD student, University of Cambridge

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question regarding correction for multiple comparisons...
by Joe Andreano 15 Feb '11

15 Feb '11

Hi All, I've been doing whole-brain functional analyses using glmfit and mri_volcluster. As I understand it, correction for multiple comparisons is done on a cluster level with this command, by specifying a minimum cluster size and then applying a threshold within each cluster. This is working ok, but I'd like to compare it with another method of multiple comparison correction. Is there a command that will allow me to do multiple comparison correction on a voxel level, such as family-wise error, by adjusting the threshold for each voxel? Thanks, Joe Andreano _________________________________ Joseph M. Andreano, PhD Research Fellow Interdisciplinary Affective Science Lab Massachusetts General Hospital _________________________________

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Hemisphere separation error
by Evan Luther 15 Feb '11

15 Feb '11

Hello All! I am currently trying to create a high resolution anatomy by manually changing some parameters throughout the recon-all process. I have currently hit a road block at the fill portion of the recon-all process. So far I have tried this high resolution reconstruction on two subject's anatomies. In both subjects I used the flag -noaseg as well as seed points for the CC, pons, left hemisphere, and right hemisphere at the fill step because otherwise the fill command would use the aseg file for seed points and subsequently the hemispheres would not get separated at all. Now here is the kicker, in one subject's anatomy this worked fine. It split the hemispheres down the middle without a problem. However on the other subject the cut between the hemispheres is slanted, assigning portions of the right hemisphere to the left. I do not know how to correct this problem. I have tried using different seed points and not inputting seed points and this has yielded the same results. Any suggestion? thank you, Evan Luther

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subcortical roi
by fabrizio piras 15 Feb '11

15 Feb '11

Dear FS experts, I run recon all on several patients, manual edited all the outputs and rerun recon all. I'm interested in subcortical segmentation and I extracted all the data with the aseg stats command. Is it now possible to select a structure (let's say the accumbens) and save it as a .nii (or wathever format) ROI in ordero to export it and open it with other softwares (e.g. mricron, fsl etc)? thank you in advance Fabrizio Piras --------------------------- Fabrizio Piras Ph.D. --------------------------- Fondazione I.R.C.C.S. Santa Lucia Laboratorio di Neuropsichiatria via Ardeatina 306 tel +390651501547 fax +390651501213

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fMRI-EEG Post-Doc Open Position
by Jose Soares 15 Feb '11

15 Feb '11

Hi all, there is an open position to fMRI-EEG, http://www.eracareers.pt/ opportunities/index.aspx?task= global&jobId=22187 Best, Jose

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Freesurfer February 2011