Re: [Freesurfer] ROI center of gravity

Tyler, you can use mri_surfcluster with the (hidden) --centroid option doug On 7/16/13 8:39 PM, Tyler Manning wrote: Hi, I'd like to use freesurfer to determine the center of gravity of an ROI from a functional overlay in surface space. I've tried looking for some sequence of commands to do

Re: [Freesurfer] convert DK atlas ROI to .nii.gz in MNI space

use $FREESURFER_HOME/average/mni152.register.dat doug On 7/16/13 8:36 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am interested in a specific ROI in the DK atlas, and I know that I can use tkregister2 to obtain a register.dat, and then mri_annotation2label + mri_label2vol to convert

[Freesurfer] ROI center of gravity

Hi, I'd like to use freesurfer to determine the center of gravity of an ROI from a functional overlay in surface space. I've tried looking for some sequence of commands to do this with no luck. Any suggestions? Thanks in advance for your help. All the best, Tyler

[Freesurfer] convert DK atlas ROI to .nii.gz in MNI space

Dear FreeSurfer Experts, I am interested in a specific ROI in the DK atlas, and I know that I can use tkregister2 to obtain a register.dat, and then mri_annotation2label + mri_label2vol to convert the annotation of the ROI to an .nii.gz. However, it seems that the end product is in the TAL spac

Re: [Freesurfer] freesurfer does not recognize white matter or the brain

Hi Christine why don't you upload the subject and we'll take a look cheers Bruce On Tue, 16 Jul 2013, Christine Smith wrote: I have a subject for whom we have had consistent difficulties within freesurfer. The difficulties existed for a single scan from 2008 and also for a pair of scans (ave

Re: [Freesurfer] motion dependent resolution: bbr vs flt

the QC on the T1 data gives no obvious clue. We edit the brainmask when there are surface issues However, we have not quantified this data yet - a closer look may indeed tell us more. Thanks Gerit On 16 July 2013 20:52, Pfuhl, Gerit wrote: > > > Von: Ana

Re: [Freesurfer] motion dependent resolution: bbr vs flt

> > Hi, > > we have more motion in the anatomical data between the groups (healthy > controls vs patients). > The difference between 5.1 using flt and 5.2. using bbr is not extreme. > If I understood correctly, since we use first recon-all and thatis > independent of flt or bbr, any difference must

Re: [Freesurfer] Freesurfer faster with CUDA or I7 3770k ?

On 07/12/2013 12:15 PM, Dorian P. wrote: > Dear list, > > We are buying a computer dedicated mostly to Freesurfer. Initially we > thought an I7 3770k a bit overclocked (about 4.5ghz) should be a good > choice. However, I noticed that Freesurfer seem better tuned to use > CUDA. Many of the messages

Re: [Freesurfer] Motion correction in recon-all

Hi Louis, Thanks again for your help! In addition, I was wondering: Would it be ok to follow the exact same procedure/pipeline (that is the mri_robust template command, followed by the mri_convert and mri_add_xform_to_header commands) if I only have one movable volume (for the mri_robust_templa

[Freesurfer] Fwd: subcortical segmentation

-- Forwarded message -- From: Bruce Fischl Date: Tue, Jul 16, 2013 at 12:44 PM Subject: Re: [Freesurfer] subcortical segmentation To: Liane Hunter Hi Liane can you cc the list so others can answer? You will get better and faster answers that way, and also others will be able to

Re: [Freesurfer] Button Press Regressor

can you send the X.mat file? On 07/16/2013 12:04 PM, Nicholas Paul Denisuk wrote: > Dear Freesurfer Users, > > I have opened up the X.mat file from the analysis. I think that the > button regressor is the third column in the file, but I am not 100% > sure. Do you know which column the button r

Re: [Freesurfer] Segfault error

I support what Marcos found. Freesurfer does not work on CentOS in VirtualBox because of the 3D error in the VirtualBox driver for graphics under CentOS. I solved the problem by using Vmware player instead. It seems more mature in the 3D driver. If others would like to use freesurfer on a virtualma

[Freesurfer] Button Press Regressor

Dear Freesurfer Users, I have opened up the X.mat file from the analysis. I think that the button regressor is the third column in the file, but I am not 100% sure. Do you know which column the button regressor is? Below is the background info to this question. >>I am trying to regress out th

[Freesurfer] mritotal vs. talairach_avi scripts

Hello, I have a quick question about talairach transform. I know that FreeSurfer previously used mritotal to create the linear talairach transform. You could check the "final objective function value" in the mritotal.log file. I think the ideal value was in the ballpark of 0.06. Is there a

Re: [Freesurfer] Articles regarding using FreeSurfer manual interventions

I think Xiao Han or Jorge Jovicich did a reliability study and found no detectable inter-rater effects, but I can't remember if they published it. Maybe Jorge will chime in? cheers Bruce On Tue, 16 Jul 2013, Douglas N Greve wrote: > I don't know of any, though I'm doing such a study right now.

Re: [Freesurfer] Articles regarding using FreeSurfer manual interventions

I don't know of any, though I'm doing such a study right now. doug On 07/16/2013 11:00 AM, Liane Hunter wrote: > Hello, > I wanted to inquire if anyone knows of any articles in the literature > that quantify the differences between using FreeSurfer with and > without manual intervention. > Than

Re: [Freesurfer] subcortical segmentation

Hi Liane the brainmask is not for subcortical segmentation - use the norm.mgz if you want to visualize subcortical structures cheers Bruce On Tue, 16 Jul 2013, Liane Hunter wrote: Hello,  I noticed that when I am checking the subcortical segmentation the brainmask does not accurately disp

[Freesurfer] subcortical segmentation

Hello, I noticed that when I am checking the subcortical segmentation the brainmaskdoes not accurately display the subcortical structures ( ie. the putamen is too small). The segmentation appears to be correct when I compare it to the original file. Does anyone know why this is the case? Also, if I

Re: [Freesurfer] bvecs error from Tracula

Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia,  I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul

Re: [Freesurfer] Xhemi question

I must have misunderstood the previous emails then. I though you suggested smoothing the anatomical data prior to registration to avoid the noisy numbers. Glad that is now cleared up, thank you. Is there a way to find out how many vertices are on the fsaverage_sym surface? Thank you again, Dari

[Freesurfer] Articles regarding using FreeSurfer manual interventions

Hello, I wanted to inquire if anyone knows of any articles in the literature that quantify the differences between using FreeSurfer with and without manual intervention. Thank you Liane -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine _

Re: [Freesurfer] ROI info in the DK atlas

Thanks a lot! It works! -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 7/16/13 10:37 AM, "Bruce Fischl" mailto:fis...@nmr.mgh.harvard.edu>> wrote: I think in freeview the syntax would be: freeview -f lh.inflated:label=lh.your_ROI.

Re: [Freesurfer] bvecs error from Tracula

Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Amirhossein - Are

Re: [Freesurfer] ROI info in the DK atlas

I think in freeview the syntax would be: freeview -f lh.inflated:label=lh.your_ROI.label cheers Bruce On Tue, 16 Jul 2013, Yang, Daniel wrote: Hi Bruce, Sorry for so many responses. I figured it out that I can visualize it using tksurfer.  Besides this, can I visualize it in freeview, CAR

Re: [Freesurfer] ROI info in the DK atlas

Hi Bruce, Sorry for so many responses. I figured it out that I can visualize it using tksurfer. Besides this, can I visualize it in freeview, CARET, or some other tools? My goal is to display the ROI on a fsaverage inflated surface. If it can be done in freeview, could you give me some instruc

Re: [Freesurfer] Xhemi question

Couple of quick things in regards to smoothing prior to calculating the LI. I'm just trying to use the fsaverage_sym atlas and improve my xhemi registration, not conduct a thickness asymmetry analysis. Should the smoothing be done before the xhemi registration? If so, do you have a recommendatio

Re: [Freesurfer] ROI info in the DK atlas

Hi Bruce, Thanks so much! So I ran the following and obtained all the DK ROI labels. mri_annotation2label --subject fsaverage --hemi rh --outdir Then, I am wondering how I can use the label files. For example, can I overlay it on a brain in fslview? The label file has many lines. Could you su

Re: [Freesurfer] Segfault error

Hi, Rune and Zeke I have posted some time ago my experience with VirtualBox. I also got similar segfaults. The only way I could run FreeSurfer without problems was installing CentOS64 on a second hard disk so I have a dual boot system and skipped VirtualBox. Freesurfer 5.3 also solved some proble

Re: [Freesurfer] ROI info in the DK atlas

Hi Daniel you could use the DK annotation of the fsaverage brain, which I think we supply. The atlas itself is a compilation of multiple statistics and not easily visualizable (except for the prior probability I guess). cheers Bruce On Tue, 16 Jul 2013, Yang, Daniel wrote: Hi Bruce, I am

Re: [Freesurfer] ROI info in the DK atlas

Hi Bruce, I am sorry, I mean, is there a DK atlas on a standard template brain (like MNI 152)? sorry, I don't know how DK atlas works. Is it a probabilistic atlas, or dependent on the exact folding pattern of the unique individual? (I guess it's the latter). I'd like to generate a ROI brain ma

Re: [Freesurfer] rtview.sh & fsig

Hi Doug, Thanks for your help. I think the most important thing for me was to know that the vertices are thresholded by default at p < .01. So that is good news! I was just a little worried that the thresholding I see was arbitrary and might even be inconsistent across subjects. In that case