[Freesurfer] missing brain

Hi, I am currently in the process of reconstructing my brains after edits. However, the brains keep being reconstructed with large portions of brain missing/cerebellum missing; ie they are much worse than before I edited them. However, I am sure that I have only put control points in white matter

[Freesurfer] aseg.stats

Dear freesurfers. I'm using freesurfer for two weeks. I'm currently trying to make a script to get asegstats resultats for >100 patients. I did this script in tcsh : foreach filename (t1_) asegstats2table --subjects ${filename} \ --segno 12 18 14\ --tablefile asegstats.txt end The p

Re: [Freesurfer] freeview

On Sunday, December 02, 2012 23:56:38 Yaniv Kaufman wrote: > Dear Freesurfer experts, > > I am trying to display DTI using freeview, however, every time I attempt to > run freeview from the command line (I am using Ubuntu 12.4), I receive the > following error: > > "freeview.bin: error whil

Re: [Freesurfer] aseg.stats

On Monday, December 03, 2012 13:46:11 charles laidi wrote: > Dear freesurfers. > > I'm using freesurfer for two weeks. I'm currently trying to make a script > to get asegstats resultats for >100 patients. > > I did this script in tcsh : > > foreach filename (t1_) > asegstats2table --subj

[Freesurfer] Calculatin​g the mean intensity ratio in one specific region

Hello everyone, I got grey matter/ white matter intensity ratio at each vertex across the cortex. I would like to know the mean intensity ratio in one region (ex, superior temporal gyrus). Anyone knows how to get it? Thanks in advance! Li ___ Fre

Re: [Freesurfer] missing brain

Hi Cathy What version are you running? If 5.1 you will need Nick's updated recon-all Cheers Bruce On Dec 3, 2012, at 5:33 AM, Catherine Bois wrote: > Hi, > > I am currently in the process of reconstructing my brains after edits. > However, the brains keep being reconstructed with large port

Re: [Freesurfer] VOI

Hi Octavian it's hard to say. I would think you could get a bunch of it automatically by looking for places that are significantly different between the two timpoints, but that will depend on how well they register. You can certainly do it manually in freeview. cheers Bruce On Sun, 2 Dec 201

Re: [Freesurfer] recon-all unable to make pial and white surfaces

Hi Negar perhaps Nick or PPJ can comment on how much a virtual box needs? In any case, try increasing the ram and see what happens as the error message is pretty clear. Also, if you can run "top" or something similar (/usr/bin/free) to see how memory is actually available on the system that w

Re: [Freesurfer] Calculatin​g the mean intensity ratio in one specific region

Hi Li save it as a .mgz volume and use mris_anatomical_stats with the parcellation you want. cheers Bruce On Mon, 3 Dec 2012, Kong, Li wrote: Hello everyone,     I got grey matter/ white matter intensity ratio at each vertex across the cortex. I would like to know the mean intensity rat

Re: [Freesurfer] TRACULA tract path failure

Dear Anastasia, Thanks for the suggestions. The new control point didn't help. Therefore I uploaded remaining images. It would be great if you could have a look again. All the best, Arman On Sat, Dec 1, 2012 at 1:45 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Arman - On

Re: [Freesurfer] Calculatin​g the mean intensity ratio in one specific region

Hi Bruce, Thanks for your answer! I tried mris_anatomical_stats command, but I met problems: (1) I would like to get the mean intensity ratio of the superior temporal, so I need a label of this region. I first used mri_annotation2label to get lh.superiortemporal.label file. (2) Then I used

[Freesurfer] Insula missing

Dear experts, I am registering cortical labels from Talairach coordinates to my native T1. For doing this, I have run the next script lines: tkregister --targ brainmask.mgz --mov highres_brain.nii.gz --reg T1FS2Highres.dat --regheader --noedit mri_label2vol --annot rh.aparc.annot --temp highres

[Freesurfer] hippocampal subfield segmentation

Dear FS team, I would like to know if there is any options to get the hippocampal subfield segmentation so I can get the volume for each segmentation if I was running only recon-all for all my subjects or I need to re-run recon-all but with a hippocampal subfield segmentation option this tim

Re: [Freesurfer] hippocampal subfield segmentation

Hi Antonella, Just run recon-all with the flag "-hippo-subfields" but without the flag "-all" (otherwise you'll be rerunning a lot of stuff you do not need to rerun): DO: recon-all -s bert -hippo-subfields DON'T DO: recon-all -s bert -all -hippo-subfields Kind regards, /Eugenio On Mon, 2012-12-03

[Freesurfer] Reducing pial and main surfaces

I have not seen a lot of documentation on how to do this. I've attached two images of specific areas where I'd like to have the pial and main surfaces follow the actual surface of the brain. The aux volume OK in both of these cases. The empty space is segmented as white matter. In the past I have t

Re: [Freesurfer] Insula missing

For the missing insula problem, try using a newer version of mri_label2vol ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol The 2nd problem is not so easy to fix. You might be better off using aparc+aseg.mgz as input to mri_label2vol instead of

Re: [Freesurfer] Reducing pial and main surfaces

Hi Jon those are probably due to topological defects, the fixing of which forces the surfaces to enclose those spaces. See if you can find the source of the defect - I think fixing it will remove these problems. You can verify they are defects by looking at the filled.mgz. If the spaces aren't

Re: [Freesurfer] Calculatin​g the mean intensity ratio in one specific region

Hi Li, they should not have been identical. The data under the "ThickAvg" column should be the value you want. This and other columns are mislabeled when thickness is not the actual input (eg, GrayVol is meaningless). You might prefer to use mri_segstats, something like mri_segstats --slabel s

[Freesurfer] wmparc 2 wmsurf

I'm running FSv5.1.0 on RHEL6. 1) My goal is to run a glm-fit on White Matter aparc regions for a "between group" surf-based analysis and evaluate spatial maps of significant differences. 2) I noticed that fsaverage does not have a wmparc.mgz file, so I'm currently working with bert