[Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

External Email - Use Caution Dear all, depends the Segmentation of hippocampal subfields and nuclei of the amygdala pipeline on the fs-recon all pipeline? I made some changes mainly by defining control points to fix intensity normalization in my dataset and rerun recon all. I´m

[Freesurfer] running recon -all and trac -all from different FreeSurfer home

External Email - Use Caution Hello, FreeSurfer Developers, I'm trying to run trac -all (I prepared the configuration file following the instructions from v. 5.3) on a set of subjects already processed with recon -all in another computer with a different FREESURFER HOME, and I'm ge

[Freesurfer] How to transfer previous FS edits to the new runs?

External Email - Use Caution Dear Freesurfer experts, I have run subcortical segmentation with FS development version 6.0. I did manual edits to these runs. Now I’m running the same data with FS stable version 6.0. I tried to run the data with stable version from the same locat

Re: [Freesurfer] running recon -all and trac -all from different FreeSurfer home

Hi Costanza - can you please attach your configuration file? Best, a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Costanza Gianni' Sent: Wednesday, June 5, 2019 6:49:02 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] running recon -al

Re: [Freesurfer] running recon -all and trac -all from different FreeSurfer home

External Email - Use Caution Hi Anastasia, I've attached the configuration file. Best, Costanza Il giorno mer 5 giu 2019 alle ore 15:07 Yendiki, Anastasia < ayend...@mgh.harvard.edu> ha scritto: > Hi Costanza - can you please attach your configuration file? > > Best, > a.y > --

Re: [Freesurfer] Fwd: freesurfer picture

Hi Abby have you tried using freeview? It is a lot more flexible than qdec and supports a bunch of different color maps cheers Bruce On Wed, 5 Jun 2019, Abby tang wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to get some pictures about my

[Freesurfer] CSF mask

External Email - Use Caution Dear Freesurfer experts, Is there any way to obtain a CSF mask in Freesurfer similar to that obtained with the SPM segmentation (see attached)? Thank you in advance. Best regards, Marina. ___ Freesurfer mai

Re: [Freesurfer] Fwd: freesurfer picture

External Email - Use Caution *Hi Bruce* *I have tried freeview, but I don't know what file should be loaded in freeview. After qdec processing, what file format should be selected to load freeview?* *best wish* *Abby* Bruce Fischl 于2019年6月5日周三 下午9:53写道： > Hi Abby > > have you t

Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

External Email - Use Caution Yes! The changes will probably be tiny, though. Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Boris Rauchmann Reply-To: Freesurfer support list

[Freesurfer] How to get a circle mask on surface

External Email - Use Caution Dear Freesurfer experts, Now I would like to find the peak vertex showed significant group effect in a given ROI (e.g. left insula), then draw a 5-mm-radius circle mask centred this peak point. May I know whether it is applicable and how should I do it

Re: [Freesurfer] How to get a circle mask on surface

Hi Lizhi the easiest way to approximate this is to generate a label that is just the peak vertex, then use the label editing tools in the current dev version of freeview to dilate it 4-5 times. cheers Bruce On Wed, 5 Jun 2019, Zhi Li wrote: External Email - Use Caution

Re: [Freesurfer] How to get a circle mask on surface

External Email - Use Caution Hi Bruce, Thank you very much for your kind reply. We have dozens of ROIs and hundreds of individuals, we need to draw the mask for each individual. May I know If I could do it in command lines? If it is applicable, which commands/functions should I re

Re: [Freesurfer] How to get a circle mask on surface

Hi Lizhi you could do it once on fsaverage then map the resulting label to all your subjects. They won't be circular in the individuals though (or really in fsaverage, but at least closer to circular). Or if you can find the peak vertex in each subject and create a label from it you can use m

Re: [Freesurfer] running recon -all and trac -all from different FreeSurfer home

Hi Costanza - When you use "\" in a shell script to continue a command onto the next line, make sure that the "\" is the very last character of the line (see second to last entry in your bvec list. On a separate note, you'll have to specify the bval file(s). Best, a.y __

Re: [Freesurfer] How to get a circle mask on surface

External Email - Use Caution Hi Bruce, Thanks. I found a command from a previous post which seems capable of generating a surface data file in which all the vertices = 0 except the peak vertex: mri_volsynth --temp $SUBJECTS_DIR/yoursubject/surf/lh.curv --pdf delta --delta-crsf ve

[Freesurfer] label a ROI

External Email - Use Caution Dear Freesurfer experts, I am trying to create a mask and run the analysis into it considering just the following anatomical regions: (1) inferior frontal gyrus pars opercularis (IFGOp) (2) inferior frontal gyrus pars orbitalis (IFGOr) (3) infe

[Freesurfer] error matlab segmentHA

External Email - Use Caution I have installed matlab 2018b and removed 2014b. When I run segmentHA_T1.sh the error reported below occurs: MATLAB is exiting because of fatal error /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 37:3955 Killed: 9

Re: [Freesurfer] label a ROI

Hi Francesca what analysis do you want to run? cheers Bruce On Wed, 5 Jun 2019, Francesca Pentimalli wrote: External Email - Use Caution Dear Freesurfer experts, I am trying to create a mask and run the analysis into it considering just the following anatomical regions:

Re: [Freesurfer] label a ROI

External Email - Use Caution Dear Bruce, Thank you very much for answering! We are doing a study on correlating dyslexia, at an early stage, with various factors in children. Specifically, our goal is to look at how the 12 regions of the brain, that I mentioned in the previous em