[Freesurfer] Unsubscribe Mailing List

Hi Freesurfer Team Please unsubscribe my email from the list Email: duynguyen@gmail.com Thanks -- Sent from Iphone ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Yes! I got better results now! Thanks!! On Thu, Feb 22, 2018 at 12:57 AM Kirstie Whitaker wrote: > Hi Foucalt, > > I think you need to set the threshold to slightly larger than 0 otherwise > you're taking the center of mass of the whole image (including the 0s) when > really

Re: [Freesurfer] Search angle limitation in the flirt registration

you should post your question to the FSL list (they developed and support flirt) On 02/21/2018 05:34 PM, Yixin Ma wrote: > Hi freesurfer developers and users, > > I'm writing to ask about the search angle limitation (--searchrx, -- > searchry and --searchrz) in the flirt function. I use the

[Freesurfer] Search angle limitation in the flirt registration

Hi freesurfer developers and users, I'm writing to ask about the search angle limitation (--searchrx, -- searchry and --searchrz) in the flirt function. I use the search angle option a lot for limited angle search, which usually generate a better registration result compared with the broad angle

[Freesurfer] Extraction of cortical thickness in native space

Hello, We are attempting to extract cortical thickness values from a pre-defined ROI in MNI space. Originally, we had followed the instructions detailed here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness for extraction in MNI space, but now wanted to extract

Re: [Freesurfer] Surface Errors

yes, filedrop should be find thanks On 02/21/2018 04:44 PM, Emily Schwartz wrote: > Hi Doug, > > I definitely can. I cannot use FTP from this computer for some reason. Can I > upload it via filedrop and should I send it to your email? > > Thanks, > > Emily > > >

Re: [Freesurfer] Surface Errors

Hi Doug, I definitely can. I cannot use FTP from this computer for some reason. Can I upload it via filedrop and should I send it to your email? Thanks, Emily From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on

Re: [Freesurfer] Surface Errors

I'm a little surprised you are getting them so frequently. Can you upload a couple of subjects so I can take a look? On 02/21/2018 02:52 PM, Emily Schwartz wrote: > Hi Doug, > > I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so > often? > > Best, > > Emily >

Re: [Freesurfer] Lookup Table

Hi Jason, You can use mri_binarize to extract a wm-hypointensities.mgz volume and view that over the orig.mgz. The following will make a binary volume called wm-hypointensities.mgz from all voxels in the aseg.mgz with an intensity of 77 - all voxels labeled wm-hypointensities: mri_binarize

Re: [Freesurfer] Surface Errors

Got it, thank you so much! Best, Emily From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, February 21, 2018 10:23 AM To: Freesurfer support list

Re: [Freesurfer] Surface Errors

Hi Doug, I am using V6.0.0 (x86_64) on Ubuntu. Should I not be getting these errors so often? Best, Emily From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu]

Re: [Freesurfer] Surface Errors

btw, what verions of FS are you using? On 02/21/2018 01:25 PM, Emily Schwartz wrote: > Got it, thank you so much! > > Best, > > Emily > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl >

[Freesurfer] Lookup Table

Hi, When viewing MRI mgz images in Freeview, is it possible to only look at certain structures specified in the look up table? That is, to only view colorization of one structure to view it more concisely? Specifically, we want to look at wm-hypointensities to see lesion approximations.

Re: [Freesurfer] Problem with cortical parcellation of rh but not lh

Hi Amal we need the entire directory tree for that subject cheers Bruce On Wed, 21 Feb 2018, Amal Achaibou wrote: Hi, Yes I've seen it for multiple subjects. I'm using version 6. Here are the results for one participants, let me know if you need any other file. Thanks Amal

Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Hi Foucalt, I think you need to set the threshold to slightly larger than 0 otherwise you're taking the center of mass of the whole image (including the 0s) when really you want to exclude the 0s and only look at the individual regions. I changed --thmin 0 to --thmin 0.1 and the results looked

[Freesurfer] local gyrification index - contrast and doss vs. dods

Dear Freesurfer Developers, I'm following the very well-documented steps proposed by Marie Schaer for measuring local gyrification index in the paper "How to Measure Cortical Folding from MR Images: a Step-by-Step Tutorial to Compute Local Gyrification Index"

Re: [Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

Andrew, Thank you for the confirmation. Best regards -- Davide Vanzo, PhD Application Developer Adjunct Assistant Professor of Chemical and Biomolecular Engineering Advanced Computing Center for Research and Education (ACCRE) Vanderbilt University - Hill Center 201 www.accre.vanderbilt.edu On

Re: [Freesurfer] FreeSurfer 6.0.0 CentOS 7 compatibility

Hi Davide, Yes, the centos6 freesurfer6.0 download is compatible with centos7 best Andrew On February 20, 2018 at 5:59:04 PM, Vanzo, Davide (davide.va...@vanderbilt.edu) wrote: Hello, According from few messages in this mailing list, FreeSurfer 6.0.0

[Freesurfer] Ask for unsubscribe from the mailinglist

Hi, Can I unsubscribe from the FreeSurfer mailing list? My email address is: neuy...@gmail.com Thanks! Ying ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in

Re: [Freesurfer] Surface Errors

Hi Emily it is a segmentation error, but it's a pretty small one. It will mess up the thickness in a region a few mm^2. You could fix it by editing the wm.mgz if you really care about that spot cheers Bruce On Wed, 21 Feb 2018, Emily Schwartz wrote: > Hi Doug, > > Thank you for getting back

Re: [Freesurfer] How would one run N4 bias corrected T1 and T2 images through FreeSurfer v6.0 REPOST

Hi Eric, I think the easiest way to avoid N3 is to simply add the -nonuintensitycor flag to recon-all and create a symbolic link from nu.mgz to orig.mgz it as otherwise recon-all will end with an error. I'm not sure about the nomenclature of the T2 file, but you should do the same. Best, Falk

Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Attach name file and result file. Thank you for your time! Best, Foucault On Wed, Feb 21, 2018 at 5:24 PM, zuxfoucault Wong wrote: > Hi Kirstie, > > Thank you very much for the suggestions! > I modified my snippet to prevent it from looping the same value and still >

Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Hi Kirstie, Thank you very much for the suggestions! I modified my snippet to prevent it from looping the same value and still got the same results? ## input=($(cat ./names_68parc.txt)) labels=() hemis=() j=0 for i in "${input[@]}"; do if [[ $i == lh_* ]]; then hemis[j]="lh" i=$(echo $i |