Re: [Freesurfer] Help with group analysis

2022-09-25 Thread Douglas N. Greve
look at the fsgd examples to see if any fit your situation. Note that the input needs to be something like Input    310211    LR 1    15,5    2,678785    645292,6651 152275,2 ie, "LR" instead of "1", etc using commas (,) instead of points (.) may cause problems On 9/25/2022 1:10 PM, fernanda

Re: [Freesurfer] Help with group analysis

2022-09-25 Thread fernanda rohrsetzer
External Email - Use Caution I'm sorry! attached the FSGD file. Em dom., 25 de set. de 2022 às 14:10, Douglas N. Greve < dgr...@mgh.harvard.edu> escreveu: > no fsgd file was attached. Also, have you looked at >

Re: [Freesurfer] confirmation of processes/commands used in full processing pipeline

2022-09-25 Thread Douglas N. Greve
On 9/20/2022 5:01 PM, Harriott, Emily M wrote: External Email - Use Caution Dear FreeSurfer experts, I hope this email finds you all doing well. I'm a second-year doctoral student (and beginner FreeSurfer user) trying to use FreeSurfer to segment gray and white matter in 90 T1

Re: [Freesurfer] Help with group analysis

2022-09-25 Thread Douglas N. Greve
no fsgd file was attached. Also, have you looked at https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples ? On 9/23/2022 10:04 AM, fernanda rohrsetzer wrote: External Email - Use Caution Hi Freesufer's, I need to run a group analysis but I don't know how to do it, the error always

Re: [Freesurfer] White matter normalization of FLAIR images

2022-09-25 Thread Douglas N. Greve
it looks like you are using v6. In v6, the flair might not have been normalized On 9/23/2022 3:53 PM, Fischl, Bruce R.,PHD wrote: I think you need to add something like -FLAIRpial or -T2pial so it uses it (in which case it will first normalize it), but hopefully someone else can confirm

Re: [Freesurfer] SAMSEG - modification of the template files

2022-09-25 Thread Douglas N. Greve
On 9/25/2022 5:06 AM, Mikolaj Pawlak wrote: External Email - Use Caution On Fri, Sep 23, 2022 at 4:05 PM Douglas N. Greve wrote: On 9/22/2022 8:59 AM, Mikolaj Pawlak wrote: External Email - Use Caution Would providing better manual segmentations of

Re: [Freesurfer] Sclimbic segmentation error

2022-09-25 Thread Douglas N. Greve
This is a bug. I've attached a new version. You can copy it to $FREESURFER/python/scripts/mri_sclimbic_seg doug On 9/23/2022 5:29 PM, bar gen wrote: External Email - Use Caution Hi all, I am receiving this error when trying to run sclimbic module. mri_sclimbic_seg --i

Re: [Freesurfer] SAMSEG - modification of the template files

2022-09-25 Thread Mikolaj Pawlak
External Email - Use Caution On Fri, Sep 23, 2022 at 4:05 PM Douglas N. Greve wrote: > > > On 9/22/2022 8:59 AM, Mikolaj Pawlak wrote: > > External Email - Use Caution > Would providing better manual segmentations of those structures of > interest help you in building