[Freesurfer] TRACULA longitudinal stream - length of Center variable

Dear TRACULA experts, I have used the longitudinal version and find that for some subjects' tracts Len_Min is larger than Len_Center. How is this possible? (An extreme example is Len_Min: 36, Len_Max: 75, Len_Center: 4.) Best, Vincent --- This email is free from viruses and malware because ava

Re: [Freesurfer] Subcortical segmentation for PAG

no, not yet. Sorry. We have been talking about it Bruce On Thu, 3 Apr 2014, Jeni Chen wrote: > Hi, > > Just wondering if the periaqueductal gray is part of the automatic > segmentation process and if we can obtain the volume. I checked the aseg > table but didn't see it, however, I somehow

[Freesurfer] Subcortical segmentation for PAG

Hi, Just wondering if the periaqueductal gray is part of the automatic segmentation process and if we can obtain the volume. I checked the aseg table but didn't see it, however, I somehow remember seeing it before... Was it ever included? Thanks. Jeni __

Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

Hi Laura, I am facing the same problem when using freeview. Can you tell me what was your commandline that solved the problem in tksurfer? How did you get the ctab file and did you edit it using the RGB color codes? Thanks in advance. Shantanu On Thu, April 3, 2014 6:55 pm, Laura Taylor wrote: >

Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

Hi Again Doug, I was able to get what I was looking for after I modified my ctab file slightly and used tksurfer instead of freeview to display the images. I am hoping, however, that it is still possible to get things to work in freeview. For the ctab file, I put my 6 parcellated ROI's at the st

[Freesurfer] Converting a volume from MNI152 to subject space

Hi Freesurfers, I am trying to convert a volume from MNI152 to subject space. I tried to do what this previous question suggested: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-December/034722.html I tried to create a registration matrix from subject space to MNI152: mni152reg --s

[Freesurfer] Standard surface tessellation

Dear FreeSurfer, I am a beginner in FreeSurfer and wonder if it is possible in FreeSurfer to apply the same triangulation across multiple subjects, i.e. the same number of vertices and triangles at the anatomically identical locations. For instance, I have 10 subjects and want to have pial (or whi

Re: [Freesurfer] missing Freesurfer wiki pages

Hi Gabor, Thanks, should be fixed now. Any of the links with the _tktools suffix can be replaced with _freeview to view an alternate version of the wiki page using freeview commands. -Louis On Tue, 1 Apr 2014, Gabor Perlaki wrote: > Dear all, > > Most of the links on > https://surfer.nmr.mgh.h

Re: [Freesurfer] preprocessing question

Hi, I seem to have even less files: Eran-Harels-MacBook-Pro:/applications/freesurfer] eiran% which $FREESURFER_HOME/bin/*.fsl /Applications/freesurfer/bin/epidewarp.fsl [Eran-Harels-MacBook-Pro:/applications/freesurfer] eiran% which $FREESURFER_HOME/bin/fsl* /Applications/freesurfer/bin/fsl_lab

Re: [Freesurfer] FW: registration difficulty

Hi Doug, I managed to get the subfield volumes aligned at last. I used bbregister to get the dat file for the No_diff2orig transform. Then used tkregister2 to get the dat for my subfield volume to orig. Used mdi_vol2vol to align my subfield vol to the orig.mgz. Finally aligned the subfieldalign

Re: [Freesurfer] Display tkmedit image of surface after mri_vol2surf with projfrac or projdist

Hi Ruthger! Use mris_expand to create a surf inside or outside of white e.g. mris_expand surf/lh.white -1 surf/lh.white_1mm_inside # use positive values for outside ?h.white border mris_expand -thickness surf/lh.white -1 surf/lh.white_in100%_thickness # this samples in % of GM thickness, use po

[Freesurfer] Display tkmedit image of surface after mri_vol2surf with projfrac or projdist

Hi All, mri_vol2surf has the flags --projfrac and --projdist. If I understand these flags correctly, the volume is sampled inbetween the white-matter surface and the pial surface (for ex. --projfrac 0.5 is midway). Is there a possibility in tkmedit/Freeview to display with a colored line for e

[Freesurfer] reading colorized labels in tcl file to tksurfer...

Hi all -- I have a process that generates a list of ROIs (from aparc.annot) based on some cost condition. I wanted to view these labeled ROIs in 'tksurfer'. I created the following rough tcl script: 'label_load.tcl' set label lh.bankssts.label ; read_and_color_labeled_vertices 255 255 0 set la

Re: [Freesurfer] preprocessing question

Hi Eiran and Doug, I do not have bet.fsl neither (c.f. previous mail with the list of what I had). It seems that there is quite some more missing in the mac build... This is what I find on my ubuntu installation freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 $ ls $FREESURFER_HOME/bin/*.fsl /

Re: [Freesurfer] mri_vol2surf --projopt

it sounds cool! I wonder what it does? Actually, this uses mri_compute_volume_fractions and mri_compute_intensities to build partial-volume models of the tissue and then estimate them with projopt. I haven't tried this code in a few years so you are somewhat on your own. We are hoping to clean

Re: [Freesurfer] preprocessing question

Hi Doug, I changed the file permissions to be executable and it passed this stage. It then gets stuck when looking for bet.fsl: # -- Using FSL's BET to Extract Brain-- # /applications/freesurfer/BSMT_project/bsmt103/bold bet.fsl /tmp/mkbrainmask_76128/in.nii /tmp/mkbrainmas

Re: [Freesurfer] CWP values

Dear FreeSurfer list, When reporting coordinates of significant clusters found with Qdec, should one report 1) the Talairach coordinates displayed immediately after running the MonteCarlo correction (which I imagine are the center of gravity (CoG) coordinates?!) or 2) the max vertex Talairach coor

Re: [Freesurfer] FW: registration difficulty

Hi Doug, Thanks for that, I will give that a shot and see how it looks. As for my highres hippo images, I ran the recon-all with the -hippo-subfields setting on my T1 highres whole brain anatomy file. This gave me the usual FS outputs and the extra hippo subfield volumes. I can look at these wi

Re: [Freesurfer] LGI - Statistical Analysis

Hi Kenza, (I added the freesurfer mailing list in copy, please post there) You have to set the min threshold at 1 when you overlay the lGI, then you should not see any gray regions anymore. Not sure I understood your problem with the statistical analyses, maybe there is simply no significant

[Freesurfer] mri_surcluster and centroid option

Hi, I am trying to compute centroid coordinates of maps for functional activation obtained from fsfast with mri_surfcluster. The command is: mri_surfcluster --in /.../sig.nii.gz --thmin 3 --thmax infinity--sign pos --subject subjid --hemi rh --surf white --annot aparc --frame 0 --minarea 0