Freesurfer

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30132 discussions

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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masking ?h.curv with a label
by Ritobrato Datta 21 Jun '12

21 Jun '12

Hi, I have created a ?.cortex.label on canine brain. How do I apply this label to the ?h.curv and ?.sulc so that I get rid of the medial wall FOREVER ? Thanks a lot Ri

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color table for custom labels
by Ritobrato Datta 21 Jun '12

21 Jun '12

Hello All, I have created some labels and want to assign distinct colors to each and save it so that I can assign the same colors when I load them again. How do I do it ? Thanks Ri

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how much talairach registration affects segmentation?
by Gabor Perlaki 21 Jun '12

21 Jun '12

Dear all, I've subjects processed by freesurfer 5.1.0. We checked the talairach transformation. It seems to be not so bad, but sometimes the zoom or the roation are not the best, which may affect the TIV, however we're actually not interested in TIV. Does this "talairach transformation issue" affect the cortical and subcortical segmentation somehow? I read that this transformation is used by later algorithms as seeding point. We checked the skull stripped image, white matter segmentation, surface between white and gray (yellow line) and between gray and pia (red line). Everything seems to be fine. The subcortical segmentation also seems to be good. Does the initial talairach transformation have any influence on the volumes calculated during the subcortical/cortical segmentations? I'd appreciate any help, thnaks, Gabor

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qdec_glmfit problem
by Nicolai Grüner-Hegge 20 Jun '12

20 Jun '12

Dear FreeSurfer, I am emailing you to ask for your help with the qdec_glmfit command (I got the command from the following link: http://www.freesurfer.net/fswiki/qdec_glmfit) My issue is that I do not know how to turn my raw data into the .dat file required by the command (you used qdec.table.dat as an example). Could you please tell me how I can turn my raw data into the .dat file that is required for the qdec_glmfit command to work? Thank you for your time! Best Regards, Nicolai

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