Freesurfer

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30088 discussions

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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Re: [Freesurfer] Contrasts for GLM DODS with both discrete as continues covariates
by Douglas N Greve 15 Feb '11

15 Feb '11

Yes, that all looks correct. The only other thing you may want to do is to demean (ie, remove the mean from) your continuous variables. When you test for a difference in thickness (as opposed to slope), you are implicitly testing at your variables=0. Eg, if age is one of your variables, then you are testing at age=0 (birth). If there is not an interaction between age and group, then this is not a problem. If there is an interaction, then the difference will depend on what age you compute the difference. So, it's a good idea to test for an interaction between group and your continuous variables. The contrasts would basically look the same (ie, four 0.25s, four -0.25s, and 24 zeros), they will just be rearranged differently. doug Habets P (SP) wrote: > Hi Doug, > > Just a final check that my fsgd and contrasts are properly defined. > This is now my fsgd file > > GroupDescriptorFile 1 > Title fsgd_pat_con.txt > MeasurementName CorticalThickness > > Class controls_male_mdeft > Class controls_female_mdeft > Class controls_male_adni > Class controls_female_adni > Class patients_male_mdeft > Class patients_female_mdeft > Class patients_male_adni > Class patients_female_adni > > Variables Age Education Handedness > > Input C001 controls_female_mdeft 25 6 100 > Input C002 controls_female_mdeft 27 6 100 > Input C003 controls_male_mdeft 46 5 -89.47368622 > Input C004 controls_female_mdeft 43 4 100 > Input C005 controls_male_mdeft 25 8 100 > Input C006 controls_male_mdeft 19 7 100 > Input P001 patients_male_mdeft 32 7 -100 > Input P002 patients_female_mdeft 46 3 -23.07691956 > Input P003 patients_male_mdeft 26 6 100 > Input P004 patients_female_mdeft 19 6 60 > Input P005 patients_male_mdeft 23 5 100 > Input P006 patients_male_mdeft 21 3 100 > > My hypothesis is than patients differ from controls with regard to cortical thickness, regressing out the effects for gender scantype age educational level and handedness. > So my contrast is: > 0.25 0.25 0.25 0.25 -0.25 -0.25 -0.25 -0.25 and 24 zero's (together 32 regressors) > > Is this properly defined? > Thx! > Bw Petra > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Friday, February 11, 2011 5:10 PM > To: Habets P (SP) > Cc: freesurfer(a)nmr.mgh.harvard.edu; Gronenschild Ed (NP) > Subject: Re: [Freesurfer] Contrasts for GLM DODS with both discrete as continues covariates > > Hi Petra, you have mixed up a class with the level of a factor (an easy > thing to do). From your FSGD, it looks like you would need 8 classes, > each class would be a combination of a level from each factor. So one > class would be control-male-adni, etc. Once you have a proper FSGD file, > FreeSurfer will create the proper design matrix. After you looked at the > FSGD examples on the wiki? Do a search for FSGD, and they will pop up. > > doug > > Habets P (SP) wrote: > >> I want to run a GLM DODS in Freesurfer to test whether patients differ >> from controls with regard to cortical thickness, meanwhile I want to >> control for several variables, both discrete as continues. >> >> This is my manually made fsgd file >> >> GroupDescriptorFile 1 >> >> Title fsgd pat con.txt >> >> MeasurementName Cortical Thickness >> >> Class controls >> >> Class patients >> >> Class female >> >> Class male >> >> Class mdeft >> >> Class adni >> >> Variables Age Education Handedness >> >> input C002 controls female mdeft 27 6 100 >> >> input C003 controls male mdeft 46 5 -89.47368622 >> >> input C004 controls female mdeft 43 4 100 >> >> input P001 patients male mdeft 32 7 -100 >> >> input P003 patients male mdeft 26 6 100 >> >> input P004 patients female mdeft 19 6 60 >> >> The problem I have is how to specify contrasts, on the Freesurfer >> website I found that : >> >> For DODS, the number of regressors is Nc*(Nv+1) >> >> In my case that would be 6* (3+1) = 24 >> >> Would the contrast than be: >> >> 1 -1 and 22 zero's >> >> Does Freesurfer automatically create the correct design matrix using >> the fsgd file? Because it is not clear to me how I should create the >> design matrix with some discrete variables as confounders. >> >> Bw Petra Habets >> >> * * >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Fw: Question about FreeSurfer Tutorial
by Tali Shrem 15 Feb '11

15 Feb '11

Hi, I was trying to use the FreeSurfer tutorials for the first time, and had a problem whenever I tried to use the command tksurfer. After I defined FREESURFER_HOME, TUTORIAL_DATA and SUBJECTS_DIR I tried to visualise a surface. The result was that a window opened where the surface should have appeared but nothing appeared in it (however, the menu underneath did open properly). Here is the terminal output: assafs $ tksurfer 004 lh inflated -annot aparc.annot subject is 004 hemi is lh surface is inflated surfer: current subjects dir: /usr/local/freesurfer/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /mnt/newdataarch2/Leon_Lab/Experiments/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial Reading image info (/usr/local/freesurfer/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial/004) Reading /usr/local/freesurfer/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial/004/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/AudSpaceAdaptation/PitchSpace/buckner_data/tutorial_subjs/group_analysis_tutorial/004/mri/orig.mgz surfer: vertices=152763, faces=305522 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Found embedded color table in annotation. 9938 vertices did not have an annotation! surfer: single buffered window surfer: tkoInitWindow(004) Window type not found! surfer: failed, trying double buffered window surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % I am using Linux version Fedora, Release 12 (Constantine). The FreeSurfer version I am using is stable v.5.0.0. Thanks, Tali Shrem

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Re: [Freesurfer] Probabilistic V1 labels to volume
by Douglas N Greve 14 Feb '11

14 Feb '11

When you say the original T1, do you mean the data directly from the dicom files? FS analysis is generally done in our "conformed" space (1mm isotropic, 256^3). One of those volumes is called "T1" and one is called "orig" -- this understandably confuses a lot of newbies (and oldbies). doug Jennifer Evans wrote: > > The original T1 to start with would be good. I did try: > > bbregister --s $SUBJ --mov T1.mgz --reg register.dat --t1 --init-header > > but I can't figure out whether I've got a problem viewing it or with > the commands. > > Thanks, > Jen > > On 02/14/2011 05:49 PM, Douglas N Greve wrote: >> What volume do you want to project them to? >> doug >> >> Jennifer Evans wrote: >>> Hi there, >>> >>> I'm not really familar with freesurfer and am missing the step on what >>> to register to create the register.dat file required to use >>> mri_label2vol to convert the probabilistic V1 label file outputs from a >>> single subject to a volume. I thought the labels are already on the >>> surface/volume and registered... but using an identity matrix isn't >>> right. Which volumes/command create/s the right register.dat file? I >>> rooted around in the wiki but couldn't figure out the right >>> relationships. >>> >>> Thanks, >>> Jen >>> >>> _______________________________________________ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Probabilistic V1 labels to volume
by Jennifer Evans 14 Feb '11

14 Feb '11

Hi there, I'm not really familar with freesurfer and am missing the step on what to register to create the register.dat file required to use mri_label2vol to convert the probabilistic V1 label file outputs from a single subject to a volume. I thought the labels are already on the surface/volume and registered... but using an identity matrix isn't right. Which volumes/command create/s the right register.dat file? I rooted around in the wiki but couldn't figure out the right relationships. Thanks, Jen

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