Re: [Freesurfer] error in pre-processing in TRACULA

Thanks, Anastasia. I did as you told me, and I could run preprocessing without error! Thank you so much!! Anri ** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ** WATANABE ANR

Re: [Freesurfer] Cortical gray matter surface area

Sorry, my mistake. I did mean surface area rather than volume. I am unsure as to how to find the total surface area of the cortical gray matter as ?.aparc.stats file only report WhiteSurfArea. Thanks, Will Message: 17 Date: Wed, 27 Aug 2014 00:48:29 -0400 From: Douglas Greve Subject: Re: [Freesur

Re: [Freesurfer] recon-all normalization: bias field output

Hi Barbara, I'm not aware of any way that you can do it directly by passing arguments to recon-all (some might correct me on that), but it is possible: 1) As N3 models the bias as a multiplicative effect uncorrected = corrected * bias, the simplest way is to divide each voxel of the volume bef

[Freesurfer] recon-all normalization: bias field output

Dear all, Is there a way to output the N3's (non-parametric normalization step) output? I am interested in the bias field that was computed to correct the image intensities. Thank you for your help, Barbara ___ Freesurfer mailing list Freesurfer@nmr.m

[Freesurfer] seed-based functional connectivity: mkcontrast-sess

Dear FreeSurfer community, I was wondering what my contrast-matrix should look like when doing a first-level analyses since there is no task involved. I tried looking at the -help flag, but I can’t see any options for setting a matrix without entering the numb of conditions. This was the comma

Re: [Freesurfer] trac-all -prep error field map error

Anastasia, I'm not sure how I can give tracula the phase difference maps, can you provide an example? As a reminder, I've run a wrapper script around epidewarp which takes our dicom images and converts them into a phase difference map (it is based on the script that was authored by Doug Greve for

[Freesurfer] questions about mri_make_bem_surfaces

Hi I have questions about the use of the function: mri_make_bem_surfaces I need to create a surface from a set of MRIs in DICOM format. I would like if someone could help me. The only reference I have of the function is: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_make_bem_surfaces and does

[Freesurfer] Obtaining volume measures based on T2 image

Dear Freesurfer experts, I have a project where I would like to compute volumes of the olfactory bulb. I understand olfactory bulb is currently not in the freesurfer atlases, so I would need to manually trace it for me to get the volume measures. Given that olfactory bulb appears easier to be seen

[Freesurfer] FW: does Tracula correct for CSF contamination

Dear Tracula users, does anyone know whether or not Tracula uses any corrections for CSF contamination? Thanks for your time, Laura -- Laura Anderson, B.A. Graduate Student Clinical / Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112 _

Re: [Freesurfer] problem with format of CT dicoms

Awesome! Thanks a lot for your help! m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, August 22, 2014 2:28 PM To: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] problem with format of CT dicoms

Hi Doug, You can use ImageJ to read in the slices and reslice them any way you want with whatever thicknesses you want. Regards,   Don   > > I did this and it converts, but the slice thickness looks wrong. I don't know > how to fix it because we always trust the slice thickness in the dicom >

Re: [Freesurfer] asymmetry analyses

You can copy the rh gyrification index to xhemi/surf/lh gyrification index, ie, copy it to xhemi/surf, but change the name so that it appears to be lh instead of rh doug On 8/27/14 5:47 AM, angela.fav...@unipd.it wrote: > Hi Doug, > is there a way to perform asymmetry analyses for local gyrifi

[Freesurfer] White matter lesions

Dear Freesurfer Experts, I am hoping to do some WML analyses in some patient groups by using the measure of T1 hypointensities derived from the ASEG analyses. Is there a way to view and check the accuracy the WML mask for each subject? Also, how may I go about performing a voxelwise analyses of t

[Freesurfer] Qdec Help

Hello, I am running Qdec analysis on about 100 subjects and correcting with FDR. Once I do this I click the "find clusters and go to max" button and Qdec gives me a plot of all the data as well as taking me to the max vertex in the #1 cluster. I want to extract the data from the table so that I

Re: [Freesurfer] asymmetry analyses

Hi Doug, is there a way to perform asymmetry analyses for local gyrification index? In my xhemi folders there is no LGI surface. thank you Angela > > You can use --paired-diff-norm instead of --paired-diff, this will compute > > (L-R)/((L+R)/2) > > You can then divide the output by 2, eg, > > fs