[Freesurfer] R: LGI value aberrant high

External Email - Use Caution Dear expert I am trying to calculate LGI for a subject. Now with some of your suggestions it runs, but after one hour and half it gives me this errors remeasuring lGI value for vertex iV = 29501. It may take a few minutes.WARNING -- Problem for verte

[Freesurfer] Problems with GM segmentation -- How to solve it

External Email - Use Caution Dear Free Surfer team and Bruce, I have been doing well editing the skull stripping, and using control points to improve white matter segmentation. Furthermore, the few participants I had problems with due to large ventricles were solved using the flag

[Freesurfer] Version 6.0.0 or 6.0.1?

External Email - Use Caution Hi Freesurfer team, On the download website version 6.0.0 is linked: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall But on this list there has been discussion of version 6.0.1 which can be downloaded from https://surfer.nmr.mgh.harvard.e

[Freesurfer] Power analysis

External Email - Use Caution Hi, I want to perform a power analysis and I read that I need 3 of 4 things: 1. Effect size (mean/std) 2. False positive rate 3. Number of subjects 4. True positive rate I also read that the effect size can be calculated using gamma.mgh and gammavar.

Re: [Freesurfer] Increasing the Number of a non-FreeSurfer Parcellation

External Email - Use Caution Dear Bruce The parcellation I have is not on surface, it is volumetric. I wanna increase the number of its ROIs, I thought maybe I can change it into an annotation file and then use "mris_divide_parcellation". Hope it is clear enough now. Best Maedeh__

Re: [Freesurfer] Increasing the Number of a non-FreeSurfer Parcellation

can you include previous emails so that we know what you are talking about? On 12/11/18 7:15 AM, Maedeh Khalilian wrote: External Email - Use Caution Dear Bruce The parcellation I have is not on surface, it is volumetric. I wanna increase the number of its ROIs, I thought maybe I can cha

Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices

That all looks like it would work to me. Another thing you can try is the way we create the wmparc.mgz using mri_aparc2aseg. You can find the commandline in the recon-all.log file (make sure to set the output name so that you don't overwrite wmparc.mgz). You can specify the max distance away fro

Re: [Freesurfer] R: LGI value aberrant high

Sorry, the lGI code is not being maintained anymore On 12/11/18 4:00 AM, Lorenzo Ferri wrote: External Email - Use Caution Dear expert I am trying to calculate LGI for a subject. Now with some of your suggestions it runs, but after one hour and half it gives me this errors remeasuring

Re: [Freesurfer] fdr correction problem

do you mean that nothing survived threshold? That happens sometimes. On 12/10/18 8:03 AM, 1013364183 wrote: External Email - Use Caution Dear Bruce?? I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected graphs are all 0. Why is this, the instructions and the run

Re: [Freesurfer] Power analysis

The gamma and gammavar files are vertex-wise values. You can load them in matlab with something like g = MRIread('gamma.mgh'); gv = MRIread('gammavar.mgz'); but you will need the vertex that you are interested in (or do for all vertices). You can use fast_glm_power.m in the FSFAST toolbox to comp

Re: [Freesurfer] glm analysis

That matrix will test for an effect of group regressing out the effect of age. I would first test for an interaction between group and age with 0 0 0 1 -1 0 0 0 0 1 0 -1 Assuming that there is no effect, then I would re-run with DOSS (different-offset, same-slope) with a contrast like 1 -1 0 0 1

Re: [Freesurfer] GLM multiple comparison correction

That is not normal. Are you sure you are looking at the different maps that are created? Also, we are recommending that people not use MCZ (especially with such a low threshold). Permutation is more accurate. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm?high

Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices {Disarmed}

External Email - Use Caution Hi Doug, Thanks a lot for getting back to me and your helpful comments! Good that you mention the mri_aparc2aseg option. I had tried that and registered the resulting volume aparc.250+2mm.nii.gz to DTI space (bbregister and mri_vol2vol). Yet, extract

Re: [Freesurfer] Error in running make_average_subject

Sorry, the disk that held that patch failed and we did not have a backup so not everything was restored. I just put this file there: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/make_average_surface Copy it to $FREESURFER_HOME/bin. Let me know how it goes On 12/10/18 12:4

Re: [Freesurfer] Problems with GM segmentation -- How to solve it

Hi Rosalia if you upload an example with voxel coordinates of where you see problems we will take a look cheers Bruce On Tue, 11 Dec 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Dear Free Surfer team and Bruce, I have been doing well editing the skull s

Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices {Disarmed}

It might be that the mri_aparc2aseg route requires two transformations (one to 1mm, then one to your DTI). On 12/11/18 11:09 AM, Winkelbeiner, Stephanie A wrote: External Email - Use Caution Hi Doug, Thanks a lot for getting back to me and your helpful comments! Good that you mention th

Re: [Freesurfer] Increasing the Number of a non-FreeSurfer Parcellation

I see. You will need to sample it onto the surface before you can use mris_divide_parcellation. cheers Bruce On Tue, 11 Dec 2018, Maedeh Khalilian wrote: External Email - Use Caution Dear Bruce The parcellation I have is not on surface, it is volumetric. I wanna increase the

Re: [Freesurfer] Command to convert subcortical values into subcortical segmentation

not sure that you are trying to do. An annot is usually used for cortical segmentation, not subcortical On 12/9/18 5:57 PM, Conchy PF wrote: External Email - Use Caution Hello FS experts, I was wondering if there is a command similar to annotval2surfoverlay.m that allows converting su

Re: [Freesurfer] aparc regions misclassified

Hi Simon what FS version are you using? Some of these are fixed in 6.0. If you are already using 6.0 and still having this problem, it can be corrected but probably the easiest thing is if you updated your data and I take a look. cheers Bruce On Tue, 11 Dec 2018, Simon Jones wrote:   

Re: [Freesurfer] [EXTERNAL] Re: mri_surf2vol: has many more faces than vertices {Disarmed} {Disarmed}

External Email - Use Caution Great - I gonna try that straight away! Thanks a lot! From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, Douglas N.,Ph.D. Sent: Tuesday, December 11, 2018 11:16 AM To: freesurfer@nmr.mgh.h

Re: [Freesurfer] Command to convert subcortical values into subcortical segmentation

External Email - Use Caution Dear Greve, I would like to represent the r values (correlations calculated in Matlab) from specific subcortical regions (hippocampus, for example) in a subcortical segmentation (aseg.mgz), so I can load the aseg.mgz and visualise it using Freeview. S

[Freesurfer] Recon command with T1 and T2

Dear Experts, I am planning to run "recon" using T1 and T2 images, and was wondering if you wouldn't mind confirming whether this is the right command with recon: recon-all -s ${subject} -i T1.nii -T2 T2.nii -all I have seen a slightly different variation in the mailing archives, but this w

Re: [Freesurfer] Power analysis

External Email - Use Caution Dear Douglas, I performed the statistical analysis using stats files so I do not have vertex information, I assume it will be cortical regions information. Is the approach to read them the same? Thank you, Laura > El 11 dic 2018, a las 16:54, Gre

Re: [Freesurfer] Power analysis

yes, same approach On 12/11/2018 12:21 PM, Laura Ferrero wrote: > External Email - Use Caution > > Dear Douglas, > > I performed the statistical analysis using stats files so I do not have > vertex information, I assume it will be cortical regions information. Is the > approach to read

Re: [Freesurfer] Command to convert subcortical values into subcortical segmentation

yea, you can do something like a = MRIread('aseg.mgz'); rhovol= a; rhovol.vol = zeros(size(rhovol.vol)); lhip = find(a.vol==17); rhovol.vol(lhip) = left_hippo_rho; MRIwrite(rhovol,'rhovol.mgh'); On 12/11/2018 11:41 AM, Conchy PF wrote: > > External Email - Use Caution > > Dear Greve, > >

Re: [Freesurfer] Recon command with T1 and T2

Yes, include the -T2pial flag On 12/11/2018 12:06 PM, Maksimovskiy, Arkadiy wrote: > > Dear Experts, > > > I am planning to run "recon" using T1 and T2 images, and was wondering > if you wouldn't mind confirming whether this is the right command with > recon: > > > recon-all -s ${subject} -i T1.

Re: [Freesurfer] Recon command with T1 and T2

Thank you Doug. Much appreciated. -arkadiy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Freeview Scrolling through slices on a Mac

External Email - Use Caution Maybe I am missing something, but how can I scroll through slices with keyboard or mouse in Freeview on a Mac? Nothing I’ve tried works thus far. Any typical key ( cmd, ctrl, shift ) with scroll just zooms. Up/down moves the image up and down … sh

Re: [Freesurfer] Version 6.0.0 or 6.0.1?

Hi Kirstie, sorry for the lack of documentation – there’s practically no difference between 6.0.0 and 6.0.1. The only update in 6.0.1 is the ability to point to an external license using the FS_LICENSE environment variable. What kind of issues are you having with 6.0.0? Best, Andrew From: on

Re: [Freesurfer] Freeview Scrolling through slices on a Mac

What version of freesurfer are you running? I think in 6.0, up/down arrow keys will scroll through slices. If not, the latest dev build should have it. You can get the latest freeview build here: https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview Best, Ruopeng On 12/11/2018 01:23 PM, Ch

Re: [Freesurfer] Version 6.0.0 or 6.0.1?

External Email - Use Caution Thank you for clarifying. One big problem was the error in the make file and I think I'm still somewhat suffering from that even though I've replaced the file. The short answer is that if I run recon-all -make all on the same subject twice it will re-r

Re: [Freesurfer] Freeview Scrolling through slices on a Mac

External Email - Use Caution Dear Chris, We're actually working on control points in our group as well - on Mac you have to press the 'fn' (very left bottom key) along with the up-down arrow keys. Hope that helps, Cheers, Barbara On 11/12/2018 18:36, Ruopeng Wang wrote: > Wh

[Freesurfer] segmentHA_T2 newbie questions

External Email - Use Caution Hi, Trying to run the HippoAmig segmentation with T1-w and T2-w files for the first time and I have a few basic questions I could not resolve looking on the FS wiki: 1. Does the T2-w image need to be first recon-all processed like the T1-w? On the

Re: [Freesurfer] segmentHA_T2 newbie questions

External Email - Use Caution Dear K 1. No 2. No, just the subject name; the subjects directory is specified separately. 3. Points at a file. 4. Yes. Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University C

[Freesurfer] Conversion of registration files

External Email - Use Caution Dear Freesurfer experts, I was wondering if there is any way to convert the .dat file output from spmregister (generated using Freesurfer version 5.3) to a .lta file? Thank you! Best wishes, Jane ___ Freesur

Re: [Freesurfer] Conversion of registration files

Try lta_convert On 12/11/2018 03:46 PM, Jane Tseng wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I was wondering if there is any way to convert the .dat file output > from spmregister (generated using Freesurfer version 5.3) to a .lta > file? Thank you! > > Be

Re: [Freesurfer] Fwd: fcseedcor output

External Email - Use Caution hi, I don't have matlab in my freesurfer path, instead I download Matlab Runtime as described in following link: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime as my freesurfer version is "freesurfer-linux-centos6_x86_64_stable_pub-v6", so I

Re: [Freesurfer] Fwd: fcseedcor output

sorry, I don't have a matlab binary for fast_fcseedcor On 12/11/2018 05:07 PM, Sara Jafakesh wrote: > > External Email - Use Caution > > hi, I don't have matlab in my freesurfer path, instead I download > Matlab Runtime as described in following link: > https://surfer.nmr.mgh.harvard.edu/

[Freesurfer] Extracting both the GM and WM ROIs

External Email - Use Caution Hello, I've been trying to extract ROIs directly from the Desikan atlas by using the mri_annotation2label and the aparc.annot files from the fsaverage folder. I noticed that this pulls out the grey matter portion for these regions but was wondering i

Re: [Freesurfer] Extracting both the GM and WM ROIs

what do you mean by the white matter region? The aparc only labels cortex, which is, of course, GM. If you mean the WM adjacent to the aparc, have you looked at the wmparc.mgz file? On 12/11/2018 05:16 PM, Song, Da-Yea wrote: > > External Email - Use Caution > > Hello, > > I’ve been tryi

Re: [Freesurfer] Classification of amygdala subregions using Freesurfers new Algorithm

External Email - Use Caution Dear Sally, As you've mentioned, different approaches have been used in the literature comprising different nuclei into different groups. The exact details are in the paper, but what you wrote sounds about right. Cheers, /Eugenio -- Juan Eugenio Igles

Re: [Freesurfer] aparc regions misclassified

External Email - Use Caution Hi Bruce, It's freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c I uploaded it I think. Thanks, Simon -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: 11 December 2018 16:20 To: Frees