Re: [Freesurfer] labels used by freesurfer

hey all! ok.. sorry guys i detected a calculation mistake… !! and the now calculated values seem to be close enough to be correct… anyway… the brainsegvol - brainsegvolnotvent number is different to adding all ventricle volumes number like —> 21782 and 20980 … any idea why ? which way of

Re: [Freesurfer] Left & Right flip on asymmetric MNI template

sorry, we don't know anything about this template or ch2better. If you just want to flip the image left right, you can mri_convert --left-right-reverse-pix input.nii output.nii On 09/18/2017 01:42 AM, yskim wrote: > Dear Freesurfer experts, > I recently received manually segmentated MR data

Re: [Freesurfer] hippocampus subfields in longitudinal dataset

Thank you! A quick followup question: I'm interested in running the new devel version (e.g., segmentHA_T1_long.sh from https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala) on my data which was originally processed using the longitudinal pipeline in version 5.3.

Re: [Freesurfer] R: Re: FS-FAST longitudinal analyis

I don't understand what you don't understand. Isn't the web page clear enough? Are those 5 steps on the web page? On 09/18/2017 02:20 AM, std...@virgilio.it wrote: > Thanks, but I not understand if the follow step that you suggested me > should be used also for FS-FAST analysis. > >

Re: [Freesurfer] Saving results in volume space

On 09/15/2017 02:13 PM, Martin Juneja wrote: > Hi experts, > > I have three questions. I would really appreciate any help. > > (1). I ran following commands to estimate relationships between LGI > and Behav data: > > mris_preproc --fsgd Behav.fsgd --target fsaverage --hemi lh --meas >

Re: [Freesurfer] R: Re: R: Re: FS-FAST longitudinal analyis

oh, I see now. In fsfast, you would 1. run isxconcat-sess on each time point separately (stacks all subjects into one file) 2. Compute the difference between the time points, eg, fscalc tp1.nii.gz sub tp2.nii.gz -o diff.nii.gz 3. Then continue from "Create Second FSGD File" on the wiki.

[Freesurfer] R: Re: R: Re: FS-FAST longitudinal analyis

My apologies for the trivial question. Anyway, the web page reports information for cortical thickness analysis. I understand it. No information I found on fs-fast longitudinal analysis. Thus, when I run fs-fast longitudinal analysis, the steps 1-5 should be performed? Or they are only for

Re: [Freesurfer] Saving results in volume space

Dear Douglas, Thanks a lot for your reply. Could you please clarify why I have to add 0.3 because I am using a positive sign? How did Do you mean if I want to use threshold of 3, then adding 0.3 to this so threshold of 3.3 should be used ? If I use --sim-sign abs, do you think then there is no

Re: [Freesurfer] labels used by freesurfer

On 09/18/2017 05:47 PM, Benjamin Luerweg wrote: > > *am i right that numbers out of the wmparc file of e.g. the insula > are just the volumes of the white matter part of e.g. the insula? > * *no, insula is a gray matter cortical structure. the insulaWM in the wmparc file is just WM

Re: [Freesurfer] labels used by freesurfer

am i right that numbers out of the wmparc file of e.g. the insula are just the volumes of the white matter part of e.g. the insula? would it be ok to add the volumes of the aparc file as the grey matter volume.. to get the complete volume of e.g. the insula? kind

Re: [Freesurfer] labels used by freesurfer

is that the same for the cingulate gyrus? or is cyng really a white and grey matter splitted structure? > Am 18.09.2017 um 23:50 schrieb Douglas N Greve : > > > > On 09/18/2017 05:47 PM, Benjamin Luerweg wrote: >> >> *am i right that numbers out of the wmparc

Re: [Freesurfer] labels used by freesurfer

Yes, same for cingulate. I don't really know what you are referring to in terms of mixed structures. Maybe some subcortical structures are thought of in this way On 09/18/2017 05:52 PM, Benjamin Luerweg wrote: > is that the same for the cingulate gyrus? or is cyng really a white and grey >

Re: [Freesurfer] hippocampus subfields in longitudinal dataset

Yes, no problem! As long as you explain it in any publication that might come out of these analyses. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On

Re: [Freesurfer] Saving results in volume space

On 09/18/2017 05:35 PM, Martin Juneja wrote: > Dear Douglas, > > Thanks a lot for your reply. > Could you please clarify why I have to add 0.3 because I am using a > positive sign? How did > Do you mean if I want to use threshold of 3, then adding 0.3 to this > so threshold of 3.3 should be

Re: [Freesurfer] Saving results in volume space

Thank you so much Douglas. That's really helpful. On Mon, Sep 18, 2017 at 2:41 PM, Douglas N Greve wrote: > > > On 09/18/2017 05:35 PM, Martin Juneja wrote: > > Dear Douglas, > > > > Thanks a lot for your reply. > > Could you please clarify why I have to add 0.3

Re: [Freesurfer] Hippocampal subfield segmentation error

Hi Mamun, There is a little bug in the script. I’ll fix the dev version ASAP, but rather than downloading a gigabyte, I’d suggest that you simply edit quantifyHAsubregions.sh (found in $FREESURFER_HOME/bin/) and replace these two lines:

[Freesurfer] R: Re: FS-FAST longitudinal analyis

Thanks, but I not understand if the follow step that you suggested me should be used also for FS-FAST analysis. Specifically, I'm refferring to: 1Sample each individual's surface onto the average surface. 2Compute the difference between each of the pairs in the average surface space.

[Freesurfer] FreeSurfer6 on Ubuntu

Dear FreeSurfer Developers Is FreeSurfer 6 available on Ubunto? If so, does it work properly? Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

Re: [Freesurfer] FreeSurfer6 on Ubuntu

Dear Fereshte, yes it is. Just download the .tar.gz file for the linux os from the FreeSurfer download and install page (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) and subsequently follow the well written installation guide. Wrt your second question: jop, it does. However,

Re: [Freesurfer] Hippocampal subfield segmentation error

Hi Eugenio It is working. Thank you very much. Kind regards Mamun On Tue, Sep 19, 2017 at 7:55 AM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > Hi Mamun, > > There is a little bug in the script. > > I’ll fix the dev version ASAP, but rather than downloading a gigabyte, I’d >