[Freesurfer] hippocampal subfields

Dear all, 1. Which is the suggested resolution for hippocampal subfields segmentation with freesurfer? I've seen articles with 0.5*0.5*0.5mm^3 and with 1.0*1.0*1.0mm^3 as well. Does the hippocampal subfields segmentation really work with 1.0*1.0*1.0 resolution? 2. The article Automated

[Freesurfer] How to define a new label for aparc+aseg.mgz in FreeView

Hello, I want to define a new label in aparc+aseg.mgz (to mark certain brainstem structures); I would appreciate it if you help me with how I have to do it. Lots of thanks, Emad Emad Ahmadi, MD --- Postdoc Research Fellow Department of Radiology

[Freesurfer] Convert expert segmentation to FreeSurfer space

Hi all, I've performed FS subcortical segmentation and my purpose is to use these segmentations as seeds to another method. As FS uses GCA atlas to perform subcortical segmentation, I want to know if the *aseg.mgz* output is in GCA atlas space, or in original space except that the dimensions are

Re: [Freesurfer] How to define a new label for aparc+aseg.mgz in FreeView

Hi Emad do you mean draw one manually or add it so it is automatically labeled in new subjects? If the latter it requires manually labeling a training set and rebuilding a classifer, etc..., so it is far from trivial cheers Bruce On Mon, 3 Mar 2014, Emad Ahmadi wrote: Hello, I want to

Re: [Freesurfer] Convert expert segmentation to FreeSurfer space

Hi Mohamed the segmentations are in the individual subject conformed space. The talairach.m3z is what is used to transform GCA to the conformed coords cheers Bruce On Mon, 3 Mar 2014, Mohamed Oualid Benkarim wrote: Hi all, I've performed FS subcortical segmentation and my purpose is to

Re: [Freesurfer] Problematic dilated ventricles

I think that it should. To be safe, I would cp aseg.auto.mgz aseg.mgz otherwise aseg.mgz will not change (any differences will be interpreted as manual changes) doug On 03/02/2014 10:07 AM, Bruce Fischl wrote: Hi Victor hmmm, I'm not sure why that didn't work. Perhaps someone else can

Re: [Freesurfer] Fw: Re: error in mri_glmfit-sim when using --bg and doss

Try sending me another file (even junk.mgh). Until I get a valid file, I cannot do much doug On 03/01/2014 02:14 AM, charujing123 wrote: Hi doug, Thanks very much doug for your help all the time. I try mri_convert rh.38sb_score.10.mgh junk.mgh,and it display this:

Re: [Freesurfer] WM vol as measure

Dear all, I notice that there is a file called wmparc_stats.txt http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#Tableofwhitematterparcellationvolumes Is it possible to get corresponding WM info for a given label? Best, Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral

Re: [Freesurfer] WM vol as measure

That is the jacobian of the white matter surface when it is registered to fsaverage (not related to the actual white matter). On 03/02/2014 08:40 PM, Yang, Daniel wrote: Hi FreeSurfers, A related question (I can't find the answers on the FS website): what's jacobian_white (as a measure)?

Re: [Freesurfer] WM vol as measure

you can just add them into your qdec file (from wmparc.stats) doug On 03/02/2014 07:18 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, FS provides thickness as the DV in qdec and mri-glmfit. Do you know how I can have WM vol as the DV in these tools with the same GLM model? For example, I

Re: [Freesurfer] WM vol as measure

Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel: (203) 737-5454 E-mail: yung-jui.y...@yale.edu On 3/3/14

Re: [Freesurfer] WM vol as measure

It should be there if the recon did not fail. The file is called wmparc.stats (not wmparc_stats.txt) On 03/03/2014 01:07 PM, Yang, Daniel wrote: Thanks, Doug! But that is about using wmparc.stats as IV or continuous/covariate variables. I would like to use WM vol as the DV (measure). --

[Freesurfer] fsgd plots 2 Class

Hi, What is the best way for me to either generate fsgd plots or at least extract the data when I have 5 classes in my fsgd file (using FS 5.3.0)? I have tried the Plot fsgd option in freeview, when viewing results, but I get a segmentation fault (I assume this means that it isn't supported, but

[Freesurfer] Freeview crashes xterm

Hi, I am running freesurfer on a RedHat v6.5 machine (Santiago). I think the installation was successful and the paths are set correctly. However, my xterm crashes when I try to launch freeview. Strangely, the program works as expected when launched remotely via NX. Has anyone encountered this

Re: [Freesurfer] fsgd plots 2 Class

Hi Dan, I have not tried the FSGD plot in freeview yet. You can certainly do the matlab/python thing. The order is the same as in the fsgd file. doug On 03/03/2014 01:17 PM, dgw wrote: Hi, What is the best way for me to either generate fsgd plots or at least extract the data when I have 5

Re: [Freesurfer] Freeview crashes xterm

My apologies, I meant the X server crashes, not the xterm. Thanks. - Archana -Original Message- From: Venkataraman, Archana Sent: Monday, March 3, 2014 1:19 PM To: 'freesurfer@nmr.mgh.harvard.edu' Subject: Freeview crashes xterm Hi, I am running freesurfer on a RedHat v6.5

Re: [Freesurfer] WM vol as measure

Hi Doug, I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs. However, do you know how can we generate corresponding WM vol for a given label (not the D-K ROIs)? I'd like to use WM vol as DV but are limited to pre-defined ROIs. Best, Daniel -- Daniel

Re: [Freesurfer] WM vol as measure

I don't understand. What label do you have? Do you mean a WM label or a cortical label that you want to find the WM under? On 03/03/2014 02:12 PM, Yang, Daniel wrote: Hi Doug, I am able to find wmparc.stats in stats. It shows WM vol based on pre-defined ROIs. However, do you know how can

Re: [Freesurfer] Resting State Networks on Cortical Surface

you will need to create a registration between your volume (maps) and the anatomical. You can do this with bbregister. Then use mri_vol2surf to map your ICs to the surface doug On 03/02/2014 04:21 AM, Xuelong Zhao wrote: Hi, I am trying to display the 20 ICA components in this nifti file

Re: [Freesurfer] WM vol as measure

Sorry, I wasn't clear. It's a cortical label that I manually created, based on the pial surface. Is it possible to generate the corresponding WM vol based on a new label (not pre-defined)? -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral Researcher Yale Child Study Center New Haven, CT Tel:

Re: [Freesurfer] WM vol as measure

yes, but not easily. You will have to create an annotation with your new label in it (and any other label for the other parts of cortex) (probably using mris_label2annot), then run mri_aparc2aseg to generate a new wmparc-style volume, then run mri_segstats. You can look in the recon-all.log

Re: [Freesurfer] WM vol as measure

Sounds like a lot of work, but thanks for your reply. By the way, the wm vol generated this way is 5mm from white surface into the center of the brain, correct? Thus, it is not necessarily the complete WM vol underneath the label? Daniel -- Daniel (Yung-Jui) Yang, Ph.D. Postdoctoral

Re: [Freesurfer] Group Analysis Questions

Hi Doug, I was wondering about something. If I have an fsgd file that has no variable set (just the 2 groups: Diseased and Control) do I need to include the DefaultVariable line at the end of the file? Thanks, Panos That's great. Thanks a lot for your help, Doug! Those are the same things.

Re: [Freesurfer] WM vol as measure

Right. How do you define the complete WM vol underneath the label? On 03/03/2014 03:01 PM, Yang, Daniel wrote: Sounds like a lot of work, but thanks for your reply. By the way, the wm vol generated this way is 5mm from white surface into the center of the brain, correct? Thus, it is not

Re: [Freesurfer] Group Analysis Questions

no, that is only for plotting On 03/03/2014 03:18 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, I was wondering about something. If I have an fsgd file that has no variable set (just the 2 groups: Diseased and Control) do I need to include the DefaultVariable line at the end of the file?

Re: [Freesurfer] error at spmregister

So I'm running spmregister from a new computer now, and I'm still not getting a successful output. I am not longer getting a matlab error, but after I run spmregister, I then run tkregister2 but get an error that it couldn't open spm.reg.dat. It wasn't created in the spmregister I guess. What

Re: [Freesurfer] asegstats2table error

All aseg.stats seems to have volume of 45 ROIs with some hypointensities value =0. Also, I checked aseg.mgz and looks fine with these subjects. I extracted values with asegstats2table with --all-seg flag. I hope that is okay? On Sunday, March 2, 2014 11:28 AM, Douglas Greve

Re: [Freesurfer] Group Analysis Questions

I see. Thank you no, that is only for plotting On 03/03/2014 03:18 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, I was wondering about something. If I have an fsgd file that has no variable set (just the 2 groups: Diseased and Control) do I need to include the DefaultVariable line at

Re: [Freesurfer] How to define a new label for aparc+aseg.mgz in FreeView

Hi Bruce, Thank you for your response. I just want to draw manually the region of the new label on the images of few subjects. What I am about to do is to define a new label for the trigeminal nerve sensory nucleus (just roughly as the region that the nerve enters the brainstem); I

Re: [Freesurfer] hippocampal subfields

Dear Gabor, the segmentation benefits to some extent from higher resolution data, but produces decent estimates of the subfields at 1x1x1. We are working on a new atlas that will incorporate much more detail, and will more effectively take advantage of high-resolution images. Kind regards, Juan

Re: [Freesurfer] hippocampal subfields

Hi, just wondering if you have a guesstimate on the ETA of the new atlas ? thanks On 03/03/14, Juan Eugenio Iglesias wrote: Dear Gabor, the segmentation benefits to some extent from higher resolution data, but produces decent estimates of the subfields at 1x1x1. We are working on a new

[Freesurfer] How to create a figure for a scientific article

Dear Freesurfers, I have just performed cerebellar segmentation with freesurfer. I checked the segmentation was correct using freeview : freeview -v t1_xxx/mri/aseg.mgz:colormap=lut:opacity=0.2 I would like to create a figure for my article. However, I'm not able to find a way to highlight only

Re: [Freesurfer] How to create a figure for a scientific article

not sure if it can be done in fv, but you can create a mask of just the cerebellum cortex and wm with mri_binarize (use --match A B, where A and B are the segids for the two ROIs), then use mri_mask to mask everything else out of your segmentation On 03/03/2014 06:01 PM, charles laidi wrote:

Re: [Freesurfer] Export freesurfer data

Dear Bruce and Doug, Thank you very much! Would you please tell me more about what freesurfer data actually is? Is it composed of pixel positions and intensities? If that's the case, how do you calculate cortical thickness? Thank you very much! Sincerely, Ye On Fri, Feb 28, 2014 at 10:21

Re: [Freesurfer] Resting State Networks on Cortical Surface

Hi Doug, thanks for the quick reply. I've been playing around with the commands you suggested and managed to get what seemed like a good registration by inspecting the green lines in tkregister. However, I wasn't actually sure if I put the correct input: bbregister --s colin --mov

Re: [Freesurfer] Compute DTI metrics in NAWM in Tracula

Hi Anastasia I have finally managed to coregister and resample all lesion masks on DTI images :-), and as you suggested I set the lesion voxels to 0 in dtifit_FA.nii.gz (as well as L1 L2 L3 and MD volumes) Then the command I found in the trac-all log was the one below (where TRACT is the full

[Freesurfer] Matlab help

Hello Freesurfer, I am trying to runs MRIread.m file in matlab. But it is not reading the brain.mgz or any other format. Can u help in this regards. Thanks in advance, cheers Saurabh Thakur, ___ Freesurfer mailing list

Re: [Freesurfer] Matlab help

Hi! Can you specify what happens when you try to read the files? On 4 mars 2014, at 06:44, Saurabh Thakur srbht...@gmail.com wrote: Hello Freesurfer, I am trying to runs MRIread.m file in matlab. But it is not reading the brain.mgz or any other format. Can u help in this regards.

Re: [Freesurfer] Matlab help

Hi Markus Gschwind, I am using Matlab 7.12.0.635 (R2011a), I am not able to read the dicom image neither brain.mgz file nor the surface file in matlab. I have added these file in matlab directory. Comment or error i m getting is : for example : * load_dicom_fl(IM_0001)??? Undefined

Re: [Freesurfer] Matlab help

Hi Saurabh, On Mar 4, 2014, at 07:56 , Saurabh Thakur srbht...@gmail.com wrote: Hi Markus Gschwind, I am using Matlab 7.12.0.635 (R2011a), I am not able to read the dicom image neither brain.mgz file nor the surface file in matlab. I have added these file in matlab directory.