[Freesurfer] anisotropic input data

Dear freesurfers, I wondered is it okay to analyze isotropic data which was converted to the anisotropic one. The original data has (0.390625, 0.390625, 1.5) mm size and (512, 512, 104) voxels. It obtained from 3T scanner. I know the Freesurfer recommend isotropic data (1,1,1)mm. Does it have an

Re: [Freesurfer] anisotropic input data

Hi EK it's an empirical question. That is *very* anisotropic, so I suspect that there will be unavoidable biases in things like thickness maps which will be more accurate in regions in which the folds happen to place the cortex in the high resolution plane. That said, if the CNR is good enough

Re: [Freesurfer] anisotropic input data

Thank you for the answer. But I still confuse to convert the data. Does this mean is it 'not okay' to convert the anisotropic data to the isotropic? Then should I analyze the original one? 2012년 5월 4일 금요일에 Bruce Fischl님이 작성: > Hi EK > > it's an empirical question. That is *very* anisotropic, so I

Re: [Freesurfer] anisotropic input data

if you give it to recon-all it will convert it internally, so you don't need to convert it yourself On Fri, 4 May 2012, EK Kim wrote: Thank you for the answer. But I still confuse to convert the data. Does this mean is it 'not okay' to convert the anisotropic data to the isotropic? Then should

[Freesurfer] TRACULA

Hello,Is it possible to track fibers with TRACULA from the cortical parcelation masks obtained from recon-all or do we have to use the white matter parcelation to do so?Another question: if I use QDEC to find the areas with significant difference in the cortical tickness between two groups, is it p

Re: [Freesurfer] anisotropic input data

Thank you, but again I think that there might be no internal convert in my data from the recon-all log files. The other data set I used had records about internal convert in their recon-all log file representing as (1 1 1)mm but this data was not. So I worry about whether correct internal convert

Re: [Freesurfer] anisotropic input data

You could run mri_info on the orig.mgz to verify the dimensions. On Fri, 4 May 2012, EK Kim wrote: Thank you, but again I think that there might be no internal convert in my data from the recon-all log files. The other data set I used had records about internal convert in their recon-all log f

Re: [Freesurfer] load multiple overlays with different colors

Dear Michael, I try to install Python and Pysurfer following the instructions (using *easy_install -U pysurfer *and additional packages using*EPD*). It didn't show error during the install process. Now I want to test it. In Terminal I typed: Pysurfer fsaverage lh infalted then it shows follo

Re: [Freesurfer] load multiple overlays with different colors

Hi Kathy, subprocess.check_output was introduced in python 2.7. You use 2.6 I recommend to upgrade if possible. Otherwise we need to fix this Alex On Fri, May 4, 2012 at 3:44 PM, keepmoon wrote: > Dear Michael, > > I try to install Python and Pysurfer following the instructions > (using easy

Re: [Freesurfer] anisotropic input data

run: mri_info $SUBJECTS_DIR/$subject/mri/orig.mgz and you should see that it is 1mm isotropic cheers Bruce On Fri, 4 May 2012, EK Kim wrote: Thank you, but again I think that there might be no internal convert in my data from the recon-all log files. The other data set I used had records a

[Freesurfer] Postdoc - Neuroimaging of language

A post-doctoral research position is available in the laboratory of Dr. Rutvik Desai at the University of South Carolina. The lab focuses on cognitive neuroscience of language and semantic memory using fMRI, TMS, patient studies, and computational modeling. Excellent facilities for fMRI, TMS, tDCS,

Re: [Freesurfer] surfaceRAS to Talairach

For going from MNI to Talairach (or vice-versa) there are also the transforms that Lancaster derived -- these are citable because they are published. See http://brainmap.org/icbm2tal/ which contains links to the relevant matlab scripts. cheers, -MH On Thu, 2012-05-03 at 12:54 -0400, Douglas N

Re: [Freesurfer] anisotropic input data

Yes I found it :) Thank you for your help! Sincerely, EK. 2012/5/4 Bruce Fischl > run: > > mri_info $SUBJECTS_DIR/$subject/mri/**orig.mgz > > and you should see that it is 1mm isotropic > > > cheers > Bruce > On Fri, 4 May 2012, EK Kim wrote: > > Thank you, but again I think that there might

Re: [Freesurfer] load multiple overlays with different colors

Hi Alex, Thanks for your suggestion! I download Python 2.7 and install it. In my computer: ~/Library/Python, here are 3 version Python (2.3, 2.5, 2.6 ). there is no 2.7 ~/Library/Python. It reminds me create a directory in /Users/Kathy/library/Python/2.7. When I use easy_install -U Pysurfer,

[Freesurfer] tracula

Hello,Is it possible to track fibers with TRACULA from the cortical parcelation masks obtained from recon-all or do we have to use the white matter parcelation to do so?Another question: if I use QDEC to find the areas with significant difference in the cortical tickness between two groups, is

[Freesurfer] question

Hi I have a problem with one of my recon. It failed with error. If I check the brain mask.mgz and T1.mgz images on Tkmedit, I can see that the brain mask is mislocated: it includes the cerebellum and the neck but not the real brain. I don't understand how I can fix it. If someone can help me, I

[Freesurfer] 164k to fsaverage

Hi all. (apologies to those on both free surfer & caret list serves) I've having issues trying to convert some regions that are in .label.gii format. I'm trying to take them from Caret 164k mesh space into fsaverage space to be viewed on Free Surfer. I've successfully brought similar data