Freesurfer June 2012

freesurfer@nmr.mgh.harvard.edu

124 participants
195 discussions

freesurfer labels to binary masks for use as targets in fsl probtrackx
by Ludersdorfer, Philipp 25 Jun '12

25 Jun '12

Dear Freesurfers, I want to run FSL probtrackx and use Freesurfer labels (aparc + asec) as seed and targets. I followed the instructions from here http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html to define the seed and the transformation. However, I have problems defining Freesurfer labels as targets. These targets should be binary volume masks and they should be in the same space as the seed (hence, in the freesurfer conformed structural space). Now, I am not sure how to transform the labels into such binary masks. As I see it, one option would be to take the aparc+aseg.mgz image and use mri_binarize to create such binary masks (one by one), e.g., mri_binarize --i aparc+aseg.mgz --o left_fusiform.nii.gz --match 1007 I am not confident that this is the correct way. In the Freesurfer mailing list, I read something that using mri_annotation2label and afterwards mri_label2vol is a better way. However, in that specific case from the mailing list the person also wanted the masks to be in native structural space something I dont need to have. So basically, my question is whether the mri_binarize option is correct. Thanks a lot in advance (I know that there are several related threads in the mailing list archive but nothing really answered my question). Philipp --- Philipp Ludersdorfer Department of Psychology and Center for Neurocognitive Research University of Salzburg Hellbrunner Strasse 34 5020 Salzburg

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Question Regarding Contents of FreeSurfer
by Alexander Thomas 23 Jun '12

23 Jun '12

Dear FreeSurfer, I am looking for a database of brain areas and their associated functions. Is it the content of the FreeSurfer software? For example, if I point to a certain brain area (e.g. Broca's area), will FreeSurfer tell me its associated function (e.g. speech production)? Thank you

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how to save edited lh.white using matlab
by Leon 22 Jun '12

22 Jun '12

Hi, FreeSurfer Experts I checked the archive but did not find what I want: I removed part of the lh.white and lh.pial and want to save the edited lh.white and lh.pial in matlab. However, I could not find the corresponding matlab function for read_surf to write the edited surface? Could someone tell how I can save edited ?h.white and pial surfaces using matlab functions? Many thanks Leon

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FW: Segmentation stats unevenly allocating volumes to Unkown, Insula, and the Corpus Callosum in our data set
by ntandon＠bidmc.harvard.edu 22 Jun '12

22 Jun '12

We're having a problem where some of our subjects show insula volumes in the aparc.stats file, but others do not show insula but show unknown and corpus callosum volumes in the file. All subjects were run in Freesurfer 5.1. We did some testing on our dataset and found that in cases where the insula was missing and unknown was present, the unknown is much larger. We also understand that the unknown volume is more than just the insula, so a simple substitution is not possible. We want to know a few things: 1) In cases where Freesurfer cannot allocate to the insula, is that volume automatically added to the 'unknown' volume? 1) If there's a way to somehow force volumes to go to these labels consistently throughout our data set (i.e. to each of insula, CC and unknown rather than only to some of them.) 2) If that' s not possible (i.e. if there's no way to maintain consistency in output) then will measures from the other regions (everything besides insula, CC or unknown) will be affected by the difference? Thanks, Neeraj

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ERROR: cannot find -cw256
by Liat Levita 22 Jun '12

22 Jun '12

Hello All, I am geting the following error: see below: Did I miss something in the installation? Sorry if I have. Thank you for your help in advance. Liat --------------------------------------------------------------------- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Kernel info: Darwin 10.8.0 i386 --------------------------------------------------------------------- Please include the following additional information in your report: 1) subject name -2037 2) the entire command-line executed recon-all -i -cw256 MR000001 -all -s 2037 3) the error message generated [psmacll1:P1192_freesurfer/2037/7_YNICT1A] liat% recon-all -i -cw256 MR000001 -all -s 2037 ERROR: cannot find -cw256 Darwin psmacll1.york.ac.uk 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 recon-all -s exited with ERRORS

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Gray to white matter signal intensity ratio (GWR)
by Charlotte Bernard 22 Jun '12

22 Jun '12

Dear Freesurfer users, I have just read the paper of Salat et al 2011 "Hippocampal degeneration is associated with temporal and limbic gray matter/white matter tissue contrast in Alzheimer's disease". I wonder how we can calculate the Gray to white matter signal intensity ratio (GWR)? Is there a script implemented in Freesurfer for that? Thanks for all Charlotte

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pars triangular and BA44 segmentation bug?
by Enikő Plózer 22 Jun '12

22 Jun '12

Dear all, I've 80 subjects fully processed by freesurfer. I had a look at the segmented volumes and something is very strange. For pars opercularis we get greater volumes in the left side in most of our subjects, which seems to be fine (assuming left lateralized language in most of our subjects). However the pars triangularis and BA44 were greater on the right-side in most of our subjects (BA44 was greater on the right side in all of our subjects), which is interesting. We checked the left/right labels in tkmedit with a subject, who have highly asymmetric lateral ventricles. Tkmedit labeled the ventricles correctly, and the lateral ventricle volumes in the aseg.stats seemed to be also correct. Is it a known issue in freesurfer? I use freesurfer 5.1.0 under Ubuntu 10.10. I'd appreciate any help on this issue. Thanks a lot, Eniko

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bbregister
by Kushal Kapse 21 Jun '12

21 Jun '12

hi fellow FS users, i am running bbregister (bbregister --s 083010_004498 --mov 083010_004498/bbl1_frac2back1_231.nii.gz --bold --reg register.dat --init-fsl). it shows me following error: FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = -27, ref det = -1 FSLDIR: Undefined variable. i did run bbregister few weeks ago and it did run fine....but i am not able to understand this problem .... please let me know if possible.... thanks kk

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Re: [Freesurfer] correcting for normal inter-cranial variability
by carl＠nmr.mgh.harvard.edu 21 Jun '12

21 Jun '12

Will you may get a quick telegraphic reply on this, these are each really separate and quite complex questions and you will likely get many answers For subcortical volumes, while dividing by TICV has become a common solution and we have done it, it is not the optimal method. Introduces fixed error for all structures in a subject. See footnote in Buckner paper on this. If you are doing between group analysis, analysis of covariance is preferable. Proc glm or mixed in SAS, easy in other packages This can handle as covariates ICV, and depending on your population, you can add handedness, gender, IQ or the kitchen sink. Another plus for covariance is that you get an interpretable group mean, a real number that can be compared to the literature instead of some weird fraction. For surface, we have used the (third root of TICV), squared, based on suggestions by Bruce Fishl, I don't see why covariance with this as the term would not be slightly preferable to diving for the same reasons as above. For thickness, two schools of thought. Some do no correction. Others use mean thickness over the whole brain of the individual or a subregion. It has been convincingly argued that what you use and whether you use it it depends again on the question you are actually asking. There are some very good and smart threads on this if you search. Mike Harms I seem to recall Carl Schwartz >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> hi miro, as per me, i would suggest to divide ICV with TotalGrayVol and other aseg.stats files' global measures to remove the invariability across these measures. divide ICV to totalgrayvol,corticalwhitemattervolume,supratenorialvol,subcorticalgrayvol...this will remove any in-variability within those measures across ICV...... hope that helps kk ----- Original Message ----- From: "Miro Drahos" <miroslav.drahos(a)ucsf.edu> To: freesurfer(a)nmr.mgh.harvard.edu Sent: Thursday, June 21, 2012 2:21:13 PM Subject: [Freesurfer] correcting for normal inter-cranial variability Hi all, When analyzing output measures from FreeSurfer, what is the proper way to correct for normal anatomical variability before comparing between subjects? Which variable should be used to calculate normalized measures? volumetric measures -- total intra-cranial volume? total brain volume? surface measures -- total surface area? thickness measures -- mean thickness? Thank you! Miro Drahos Hi all, When analyzing output measures from FreeSurfer, what is the proper way to correct for normal anatomical variability before comparing between subjects? Which variable should be used to calculate normalized measures? volumetric measures -- total intra-cranial volume? total brain volume? surface measures -- total surface area? thickness measures -- mean thickness? Thank you! Miro Drahos

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correcting for normal inter-cranial variability
by Miro Drahos 21 Jun '12

21 Jun '12

Hi all, When analyzing output measures from FreeSurfer, what is the proper way to correct for normal anatomical variability before comparing between subjects? Which variable should be used to calculate normalized measures? volumetric measures -- total intra-cranial volume? total brain volume? surface measures -- total surface area? thickness measures -- mean thickness? Thank you! Miro Drahos

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Freesurfer June 2012