[Freesurfer] Segmentation Algo

Hello Freesurfer expert, I am new to freesurfer. I wanted to know which algorithm is used for segmentation in freesurfer. Thanks in advanced, cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvar

[Freesurfer] Freeview not working

Hi all, My freeview is not working. //=// saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ freeview freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or direc

[Freesurfer] scuba running problem.

Hello Friends, I m facing problem in freeview and scuba. can anyone help me in this matter. //==// saurabh@saurabh-Precision-WorkStation-T3500:/$ cd $FREESURFER_HOME saurabh@saurabh-Precision-WorkStation-T3500:/usr/local/freesurfer$ saurabh

Re: [Freesurfer] Segmentation Algo

Hi Saurabh there are a number of different segmentatons in FreeSurfer (cortical, subcortical, hippocampal), all of which are documenented at: http://surfer.nmr.mgh.harvard.edu/fswiki cheers Bruce On Mon, 10 Feb 2014, Saurabh Thakur wrote: > Hello Freesurfer expert, > > I am new to freesurfer

Re: [Freesurfer] scuba running problem.

Hi Saurabh scuba is deprecated - we haven't used it in years. Ruopeng or someone will answer your freeview question when they get a chance. cheers Bruce On Mon, 10 Feb 2014, Saurabh Thakur wrote: Hello Friends, I m facing problem in freeview and scuba. can anyone help me in this matter.

Re: [Freesurfer] scuba running problem.

Oh...is it so Bruce Thanks a lot for info. cheers Saurabh Thakur, On Mon, Feb 10, 2014 at 6:55 PM, Bruce Fischl wrote: > Hi Saurabh > > scuba is deprecated - we haven't used it in years. Ruopeng or someone will > answer your freeview question when they get a chance. > > cheers > Bruce

[Freesurfer] How to combine attached commands into one run

Dear Freesufers, I want to use the following commands in my recon-all to try to improve my output some difficult images: -gentle to mri_normalize and -min_border_white 85 -min_gray_at_white_border 80 So far I only managed to do this by making one step at a time. I was wondering if there is a

[Freesurfer] QDEC Error

Hi FS community, After I open QDEC, when I try to load my qdec data table, QDEC crashes for some reason. The error message that comes out at the terminal is: Returned Error on line 1: missing close-brace Stack trace: missing close-brace while executing ".vtkKWLoadSaveDialog5.vtkKWFileBrowserW

Re: [Freesurfer] Freeview not working

Saurabh, What is the output when you type "locate libXss.so.1" (without quotes) on the command line? -Zeke On 02/10/2014 05:17 AM, Saurabh Thakur wrote: > Hi all, > > My freeview is not working. > > //=// > > saurabh@saurabh-Precision-

[Freesurfer] Erasing, adding voxels in Freeview

Hi all, This is probably a very elementary error in my use of Freeview, but I have been having trouble adding voxels to scans. I set the eraser value to "0", but when I draw, the voxel still shows up as a black box instead of grey. Am I not setting the right values or am I just in the wrong vie

[Freesurfer] Fwd: Edit hyperintense regions in aseg.mgz file in long or base?

-- Forwarded message -- From: Linn Christin Bonaventure Norbom Date: Mon, Feb 10, 2014 at 4:06 PM Subject: Edit hyperintense regions in aseg.mgz file in long or base? To: Bruce Fischl Hi everyone, I am registering hyperintense lesions as "lh-lesion" or "rh-lesion" and I was won

Re: [Freesurfer] setting the useRealRAS bit

Doug, mris_convert does not read / write that information either. On Sun, 9 Feb 2014, Bruce Fischl wrote: > really? I didn't realize that as I don't use them much. Doug: do you have > something like MRISread? > > On Sun, 9 Feb 2014, Lilla Zollei wrote: > >> >> Those .m files only give me a set

[Freesurfer] Color Bar options

Hi all, Would someone kindly point me toward color bar options, specifically for thickness maps. The color bar that appears by default includes negative values, and the bit with positive thickness values is very compressed. For reference I’m looking at surfaces in freeview brought up by freev

Re: [Freesurfer] Color Bar options

Hi Jon, The range of color bar is automatically set by the internal color bar component that is used to display it. There is no option to change it at this point. I'll take note on that for future update. Best, Ruopeng On 02/10/2014 11:49 AM, Jonathan Holt wrote: > Hi all, > > Would someone ki

[Freesurfer] Fwd: OHBM Glass Brain Award: Call for Nominations

FYI Original Message Subject:OHBM Glass Brain Award: Call for Nominations Date: Mon, 10 Feb 2014 11:18:43 -0600 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu *ORGA

Re: [Freesurfer] PET Partial volume correction

I can when I have a beta version! I'm actively working on putting the programs together into a package. Check back in a month or so. doug On 02/08/2014 03:41 PM, Jonathan DuBois wrote: > Hi Doug, > > Thanks for replying. We are currently working on this analysis, is > there anyway you could

Re: [Freesurfer] Erasing, adding voxels in Freeview

Hi Alexander, Eraser value is used for erasing. Brush value is used for drawing. To erase, just hold shift key and press left mouse button. Best, Ruopeng On 02/10/2014 10:23 AM, Denker, Alexander (NIH/NIMH) [F] wrote: > Hi all, > > This is probably a very elementary error in my use of Freeview,

Re: [Freesurfer] Erasing, adding voxels in Freeview

Hi Alexander, If you are editing FS recons, then you should keep the eraser value set to "1" so that the edits can be detected by recon-all. -Louis On Mon, 10 Feb 2014, Ruopeng Wang wrote: > Hi Alexander, > > Eraser value is used for erasing. Brush value is used for drawing. To > erase, just hol

Re: [Freesurfer] Erasing, adding voxels in Freeview

So if I keep the value of the eraser at "1" then what do I need to change to add the voxels? It seems that no matter what value I put for drawing/erasing, I click and get a black box drawn on the screen. It seems that I am not combining button-clicks or values for the eraser and adding correctly

Re: [Freesurfer] Erasing, adding voxels in Freeview

In terms of FS editing, you should be only adding voxels which have a value of 255 to the wm.mgz (or cloning voxels into the brainmask.mgz). If you are segmenting or drawing labels then select the color LUT for the colormap and then select the name of the structure you are segmenting. Are you

Re: [Freesurfer] FDR question

Hi FS community, I was wondering if anyone had a chance to give this a look. Thanks in advance, Panos > Hi FS community, > > I am doing a cortical thickness comparison between a diseased and a > healthy group. After running the mri_glmfit command for both hemispheres, > I project the uncorrecte

Re: [Freesurfer] Fwd: trac-all -path error

Hi Anastasia, thanks for the information.we are able to process the DTI data successfully. we had 24 subjects which crashed during either the -perp or -path stage. I viewed the alignments between the FA and the alignement segmentations (flirt and bbr alignments),  which ever alignment is better.

[Freesurfer] creating specific files

Hi Freesurfers, I was wondering if there was a way to kind of fill in the blanks for a Surfer Output folder. I am working with an old data set, and it seem that some of the files are empty (0 bytes), "rh.pial" for example. Is there a way to pass the SurferOutput folder in and recreate what's mi

Re: [Freesurfer] creating specific files

Hi Mia delete the 0 length files and run recon-all -make all -s cheers Bruce On Mon, 10 Feb 2014, Borzello, Mia wrote: Hi Freesurfers,  I was wondering if there was a way to kind of fill in the blanks for a Surfer Output folder. I am working with an old data set, and it seem that some of th

Re: [Freesurfer] Tracula version and download problem

Hi Clive - These are not stats in the volume or on the surface, so mri_glmfit doesn't apply. If you want to do group analyses along a tract on a table produced by trac-all -stat, you should import the table in any software that you use for statistics (matlab, SPSS, etc). Best, a.y On Mon, 1

Re: [Freesurfer] Fwd: trac-all -path error

Hi Jon - Glad to hear you could get around the registration issue. If the anatomical images are poor, then it makes sense that you'd encounter issues with bbregister, as bbregister relies on the surfaces that are derived exactly from those anatomical images. Best, a.y On Mon, 10 Feb 2014, J

Re: [Freesurfer] Tracula version and download problem

Thanks Anastasia. I ask that because in the tracula stat page, it saids *"Measures can be extracted from these files to be analyzed further, e.g., for tract-based group analysis. Specifically, the text files can be converted into a table using the command tractstats2table and then used for doing GL

Re: [Freesurfer] Freeview not working

Hello Zeke, There was some packages missing. I have updated it,so now its working. Really thanks for the your help. cheers Saurabh Thakur, On Mon, Feb 10, 2014 at 8:50 PM, Z K wrote: > Saurabh, > > What is the output when you type "locate libXss.so.1" (without quotes) > on the command l

Re: [Freesurfer] Choi's parcellation expansion inquiry

Hi Sooyun, It is possible that tri-linear might work better, but I have to caution that you will get non-integer values. Have you tried mri_label2vol? According to Doug in the last email, mri_label2vol might work better than mri_vol2vol. My suggestion is to first verify whether the transformation