Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

freesurfer 4.5 download
by Yuko Yotsumoto 17 Feb '11

17 Feb '11

Hi, I'm trying to download freesurfer 4.5 for leopard-ppc, but connection keeps failing. Could someone check the link? http://www.freesurfer.net/pub/dist/freesurfer/4.5.0/ Thank you, Yuko Yotsumoto

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mc-z precached and FWHM
by Chris Hyatt 17 Feb '11

17 Feb '11

When the GLM for a group of subjects is computed using mri_glmfit, a residual FWHM value is computed and stored in the file 'FWHM.dat'. When running a subsequent mri_glmfit-sim, using a pre-cached Monte-Carlo Z (mc-z) simulation for clusterwise correction for multiple comparisons, there appear to be separate simulations for a range of FWHM values stored (for each hemisphere, lh and rh) in /freesurfer/average/mult-comp-cor/fsaverage/?h/cortex/ from 01 to 30 (1 to 30 mm? - fwhm01, fwhm02, etc). My question is, if the value in FWHM.dat for the original mri_glmfit for a hemisphere is say, 15.294 mm, does mri_glmfit-sim (mc-z) use interpolated data from fwhm15/ and fwhm16/ in its calculations, or does it choose the nearest value (in this case, fwhm15)? Thanks, Chris Hyatt Olin Neuropsychiatry Research Center Institute of Living

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converting a vertex (or a set of vertices) from one space to another
by Joonkoo Park 17 Feb '11

17 Feb '11

Dear FreeSurfers, I have a set of vertices in the fsaverage surface space that I want to convert (or remap) to each subject's native surface space. What's the easiest way to do this? I thought of mri_label2label, and this will involve making label files. Are there any easier methods, either using FS directly or using matlab? Joon

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output of mris_anatomical_stats
by Marco Loggia, PhD 16 Feb '11

16 Feb '11

Dear all, In mris_anatomical_stats, the "average cortical thickness" value comes with a measure of dispersion around the mean. Is this Standard Deviation? If so, is there a way to plot the 95% confidence intervals instead? Thanks, 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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Between Task Analysis
by Mandy Nagy 16 Feb '11

16 Feb '11

Hi all, We are attempting to do an analysis for subjects that came in on two different days to perform two similar but different tasks (one learning condition, one control). Each of the tasks is structured such that there are 30sec rest epochs alternating with 30sec active (typing) epochs for a total of 12.5 minutes (the task begins and ends with rest). We are trying to compare the typing period for the control task to the typing period for the learning task. We currently have first-level analyses of each of the tasks (active condition vs. null rest condition). Can we do within-subject comparisons and then do a group analysis on those? Or did we need to concatenate the learning and control conditions in the first-level analysis? If that is the case, how would you suggest that we do this? Paradigm file: 0 0 30 1 Rest 30 1 30 1 Typing 60 0 30 1 Rest 90 1 30 1 Typing 120 0 30 1 Rest 150 1 30 1 Typing 180 0 30 1 Rest 210 1 30 1 Typing 240 0 30 1 Rest 270 1 30 1 Typing 300 0 30 1 Rest 330 1 30 1 Typing 360 0 30 1 Rest 390 1 30 1 Typing 420 0 30 1 Rest 450 1 30 1 Typing 480 0 30 1 Rest 510 1 30 1 Typing 540 0 30 1 Rest 570 1 30 1 Typing 600 0 30 1 Rest 630 1 30 1 Typing 660 0 30 1 Rest 690 1 30 1 Typing 720 0 30 1 Rest Thanks in advance! --Mandy Nagy

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question regarding T1-data quality
by Eveline Geiser 16 Feb '11

16 Feb '11

Dear List, we recorded this anatomical data on a clinical scanner (Philips Achieva 3T) with the following parameters: eight-channel sense head coil, TE 2.3 ms TR = 20ms, angle = 20degree. do you think it is usable? thanks for your reply -- --------------------- Eveline Geiser PhD Massachusetts Institute of Technology Department of Brain and Cognitive Sciences phone: +617 324 63 71 e-mail: egeiser(a)mit.edu http://web.mit.edu/gabrieli-lab/

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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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