Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

Re: [Freesurfer] Display data for Cortical thickness
by Bruce Fischl 04 Jul '11

04 Jul '11

Hi Antonella, those regions should be compiled in the stats/aparc.annot.ctab file that should be easy to import into excel or other packages for analsys and plotting. cheers Bruce On Mon, 4 Jul 2011, Antonella Kis wrote: > > > Good morning Bruce, > > I posted my message also to the list and I will appreciate any help I can > get ASAP. > > I used freesurfer (v.5.1.0) on one subject using the MRI data and I finished > the recon-all step and qcache -all. I was able to display the thickness map > but I would like to get a quatitative measure of cortical thickenss for my > subject for the 34 neuroanatomical regions per hemisphere(4 medial temporal, > 5 lateral temporal, 11 frontal, etc) and display this data in a table where > I want to include the number of vertices and the cortical tickness for > different regions: > > > > caudalanteriorcingulate, > caudalmiddlefrontal, > cuneus > entorhinal > fusiform > inferiorparietal > inferiortemporal > isthmuscingulate > lateraloccipital > lateralorbitofrontal > lingual > medialorbitofrontal > middletemporal > parahippocampal > paracentral > parsopercularis > parsorbitalis > parstriangularis > pericalcarine > postcentral > posteriorcingulate > precentral > precuneus > rostralanteriorcingulate > rostralmiddlefrontal > superiorfrontal > superiorparietal > superiortemporal > supramarginal > frontalpole > temporalpole > transversetemporal > insula > > MiddleFrontal > InferiorFrontal > OrbitoFrontal > FrontalLobe > CingulateCortex > MedialTemporal > LateralTemporal > Parietal > Occipital > Region R > unknown > bankssts > caudalanteriorcingulate > caudalmiddlefrontal > cuneus > entorhinal > fusiform > inferiorparietal > inferiortemporal > isthmuscingulate > lateraloccipital > lateralorbitofrontal > lingual > medialorbitofrontal > middletemporal > parahippocampal > paracentral > parsopercularis > parsorbitalis > parstriangularis > pericalcarine > postcentral > posteriorcingulate > precentral > precuneus > rostralanteriorcingulate > rostralmiddlefrontal > superiorfrontal > superiorparietal > superiortemporal > supramarginal > frontalpole > temporalpole > transversetemporal > insula > > MiddleFrontal > InferiorFrontal > OrbitoFrontal > FrontalLobe > CingulateCortex > MedialTemporal > LateralTemporal > Parietal > Occipital > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 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> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > I believe the thickness data is stored in lh. thickness and I should be able > to read it in matlab but I am not very shure how. > Also I want to estimate the cortical thickness for gyral based regions of in > terest ROIs. > The gyral-based ROIs should be derived from an automated labeling system tha > t subdivides the cerebral cortex on volumetric MRI > into 34 neuroanatomical regions per hemisphere. > I don't know how to do this so would you advise/teach me please? > Many thanks for your valuable help! > Antonella > ------------------------------ > > ____________________________________________________________________________ > > This e-mail may contain confidential, personal and/or health > information(information which may be subject to legal restrictions on use, > retention and/or disclosure) for the sole use of the intended recipient. Any > review or distribution by anyone other than the person for whom it was > originally intended is strictly prohibited. If you have received this e-mail > in error, please contact the sender and delete all copies. > >

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PET analyses in cortical regions
by Joao Pereira 04 Jul '11

04 Jul '11

Dear Freesurfers, My goal is to evaluate the cortical thinning patterns in some (cortical aparc) regions, and to relate that to loss of PET activation in the same regions. I would like to clarify the steps of the pipeline in Freesurfer (v5.0.0) for this purpose. >From my reading of previous discussions in the mailing list, I can see two possible ways of doing this - but I am not sure and I would like to ask for your feedback on them: First method: 1) Register all PET scans (already in ICBM152 space, enforced with SPM8) to the brain.mgz image of each subject to ensure the PET files are in MNI305 space, to be able to use Freesurfer's atlas, using bbregister or spmregister. 2) Use mri_vol2surf to project the PET data onto the surface of each subject. 3) Use mri_segstats to extract the statistics for each region. Second method: 1) (Same as above). 2) Use mri_annot2label on the relevant aparc regions. 3) Use results from the previous step in mri_label2vol to create the volume masks extracted from the cortical regions. 4) Apply mri_segstats on these (as above). Could you please clarify if I am on the right track, notably which method should be more robust (or correct...)? Also, does mri_segstats also give overall group statistics (mean, std) for each region, or must I use another function/average all subjects together for that? Thank you very much! Best, Joao Pereira Wolfson Brain Imaging Centre University of Cambridge

1 0

Creating a ROI mask
by leonardo kay 04 Jul '11

04 Jul '11

Hi freesurfer 's Can anyone help me how to create a ROI mask. I have read the Cortical Thickness of a Volume-defined ROI tutorial but it doesn't specify how to generate that ROI.nii file. How many points are needed? What brain image must be used as a reference? Any help will be greatly appreciated Best regards. -- Leo Kay.

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Display data for Cortical thickness
by Antonella Kis 04 Jul '11

04 Jul '11

Good morning, I used freesurfer (v.5.1.0) on one subject using the MRI data and I finished the recon-all step and qcache -all. I was able to display the thickness map but I would like to get a quatitative measure of cortical thickenss for my subject for the 34 neuroanatomical regions per hemisphere(4 medial temporal, 5 lateral temporal, 11 frontal, etc) and display this data in a table where I want to include the number of vertices and the cortical tickness for different regions: caudalanteriorcingulate, caudalmiddlefrontal, cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula MiddleFrontal InferiorFrontal OrbitoFrontal FrontalLobe CingulateCortex MedialTemporal LateralTemporal Parietal Occipital Region R unknown bankssts caudalanteriorcingulate caudalmiddlefrontal cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula MiddleFrontal InferiorFrontal OrbitoFrontal FrontalLobe CingulateCortex MedialTemporal LateralTemporal Parietal Occipital I believe the thickness data is stored in lh. thickness and I should be able to read it in matlab but I am not very shure how. Also I want to estimate the cortical thickness for gyral based regions of interest ROIs. The gyral-based ROIs should be derived from an automated labeling system that subdivides the cerebral cortex on volumetric MRI into 34 neuroanatomical regions per hemisphere. I don't know how to do this so would you advise/teach me please? Many thanks for your valuable help! Antonella ------------------------------ ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

1 0

Re: [Freesurfer] Thickness measurements stats
by Ignacio Letelier 03 Jul '11

03 Jul '11

Sorry I didn't realize since you have the same domain. Ok, Let's say I do know the mean cortical thickness value of a subject. Then is it possible know what brain areas differ more from that mean value by using a color map visualization (I.e. for example: red = higher deviations, deep blue = lower deviations)? So this way I can determine where there may exist some kind of dysplasia. Best regards. 2011/7/1 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > can you post this kind of thing so others can answer? I still don't > understand though. stdv of what? > > > On Fri, 1 Jul 2011, Ignacio Letelier wrote: > > Let's say I want to know if there is a way to know where is the highest >> stdv in the same subject, using a color map visualization in qdec or >> something? >> >> Best regards. >> >> 2011/7/1 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Ignacio >> >> you mean different from the median in that subject? Easy enough to do >> in matlab, but we don't have anything out of the box to do it >> >> cheers >> Bruce >> >> On Fri, 1 Jul 2011, Ignacio Letelier wrote: >> >> Hi forum >> >> Is it possible to get statistical maps of cortical thickness >> differences in the same subject? I.e. to know what areas differ most from >> the median >> >> >> -- >> Ignacio >> >> >> >> >> 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<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. >> >> >> >>

2 1

Error in preproc-sess in ver. 5
by Anders Hougaard 02 Jul '11

02 Jul '11

Hi all, While attempting to pre-process data for a retinotopy analysis with the following command: preproc-sess -surface song lhrh -fwhm 5 -sf sessid I get the following error when motion correction is started: Logfile is /Users/andershougaard/Programmer/freesurfer/retinotopy/log/mc-sess01-bold.log ------------------------------------------- /Users/andershougaard/Programmer/freesurfer/retinotopy/sess01 RunList: 001 002 ------- ************************** ----------- ------- Motion Correcting Run 001 ----------- ------- ************************** ----------- sess = sess01 Lør 2 Jul 2011 11:59:31 CEST mc-afni2 --i 001/f.nii --t 001/template.nii --o 001/fmcpr.nii --mcdat 001/fmcpr.mcdat ERROR: cannot find AFNI command 3dvolreg Any suggestions? Regards, Anders

1 0

Trac-all: using bvecs/bvals from FSL folder
by Jared Saletin 01 Jul '11

01 Jul '11

Hi Freesurfer experts, I was wondering if you all had some advice for getting trac-all up and running. I'm trying to work up a trac-all configuration file for a group of subjects, previously processed in FSL. We extracted the Siemens bvec and bval files for the FSL pipeline when importing the dicoms through dicom2nii. I know FSL bval and bvec files are organized in a different matrix shape from what Trac-all wants. Has anyone had sucess with transforming these files? Should/do I need to worry about whether to flip the orientation on bvec files as the images seem to get flipped in the early steps of Trac-all? Also is it possible to feed the configuration file a list of bvec files (for each subject) similar to how we feed it the dicom directory for each subject, or should I create a configuration script for each subject pointing to their bvec file specifically. Thanks in advance for help! Cheers, Jared

3 5

questions about drawing functional rois
by Katie Bettencourt 01 Jul '11

01 Jul '11

I'm trying to draw an ROI by selecting the center of activation for a particular contrast and then selecting nearby voxels within a certain range (for example. say 20 voxels). Ideally I'd like to select only the voxels within this range that are activated by my contrast. However, I can't see how to do this, any help would be appreciated. Thanks, Katie

2 8

Thickness measurements stats
by Ignacio Letelier 01 Jul '11

01 Jul '11

Hi forum Is it possible to get statistical maps of cortical thickness differences in the same subject? I.e. to know what areas differ most from the median -- Ignacio

2 1

freesurfer_home undefined variable
by Kat Mott 01 Jul '11

01 Jul '11

Hi there, I just installed freesurfer onto a mac os x. My computer seems to default to bash, so I created a .bashrc file in my home directory and added the lines: export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh but just in case I also created a .cshrc and added the c shell version of that code. I also created the .license file as per the installation instructions. Then I opened up the terminal, in bash, and did the export and source thing again. I also updated the SetUpFreeSurfer file so that it has the correct path: /Applications/freesurfer. However, when I try to test the installation and type in recon-all -s bert -autorecon1 (i have to use sudo as well bc it keeps telling me i don't have write permission) I always get back FREESURFER_HOME: Undefined variable. I've seen several other people post this same problem to this forum in the past but no one has ever posted a response that I can see. I tried reinstalling, and typing in the command from different directories, and sourcing again, but I always get back the same response. The really frustrating thing is, when I type echo $FREESURFER_HOME I get back /Applications/freesurfer which is correct! Any thoughts on what I'm doing wrong here? Thanks in advance.

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Freesurfer July 2011