[Freesurfer] multiple overlay - tksurfer

old based on intensity / only voxels which are overlaid by atleast half of the subjects ?? >tksurfer #Sub_ID lh inflated -annot aparc.annot -ov 1.nii -ovreg register.dat -fthresh 0.3 -fmid 0.3 -fslope 1 - How I can overlay multiple regions, in specific colours, with 50% thr. ? , Than

Re: [Freesurfer] multiple overlay - tksurfer

HOME/**FreeSurferColorLUT.txt. > You list your regions and give them the colors you want. > > doug > > vin . wrote: > >> Hi Doug, >> sorry for confusing names. >> >> - 1.nii is name of the cluster, which I want to overlay. it's a >> coritical

Re: [Freesurfer] multiple overlay - tksurfer

Thanx Bruce for quick reply. you are right, it's surface based file after mri_vol2surf. yeah, tried with following command. >tksurfer Sub_ID lh inflated -annot lh.seg.annot -ov lh.seg.mgh -fthresh 0.01 -fmid 0.3 -fslope 1 On Wed, Dec 14, 2011 at 3:33 AM, Bruce Fischl wrote: > Hi

Re: [Freesurfer] multiple overlay - tksurfer

no, in tksurfer, just inflated lh appears (no overlay). so, I viewed lh.seg.mgh in freeview and converted it to .nii and viewed in fslview. On Wed, Dec 14, 2011 at 3:37 AM, Bruce Fischl wrote: > oh, so you mean you see a line on the surface? > > On Wed, 14 Dec 2011, vin . wrote: &

[Freesurfer] segmentation region export

...Mid anterior and Anterior. How I can get these sub regions. In which files they are stored, and How I can extract them as NIFTI format. any suggestion would be great !! thank you very much , vin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] segmentation region export

nErode3d 0 nErode2d 0 output thalamus_nuclei_fs.nii Binarizing based on matching values nMatch 1 0 8001 binval1 binvalnot 0 Found 0 values in range mri_binarize done should I choose some other file expect aseg.nii.gz ? to get thalamic nuclie . thank you very much

Re: [Freesurfer] segmentation region export

o get these regions. regards, vin On Tue, Nov 11, 2008 at 12:37 AM, Bruce Fischl <[EMAIL PROTECTED]>wrote: no, the aparc+aseg.mgz has some as does the wmparc.mgz. You should send these questions to the list so Doug, Nick et al. can answer > > >> On Mon, Nov 10, 2008 at 11:46 PM,

[Freesurfer] Re: free surfer error

hi, i am new to freesurfer. I tried reconstruction three times, autorecon1 works fine, but autorecon2 gives same error. *recon-all -autorecon1 -subjid your_subject_name % worked fine. :) **recon-all -autorecon2 -subjid your_subject_name* % this gives following error came in 11/ 12 hours. e

[Freesurfer] exporting label/segmented regions in diffusion space

understand registeration( diffusion to freesurfer image) and than take the segmented regions and convert them in NIFTI format for example for FSL probtrack. Thank you, vin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] Thalamus Anatomy and Connectomics Conference (October 30 – 31 in Tübingen)

External Email - Use Caution Dear Esteemed Researchers, Greetings! We are thrilled to invite you to the upcoming Thalamus Anatomy and Connectomics Conference, funded by the SPP-2041. The conference aims to dive deep into the fascinating and intricate thalamus. This event promises

[Freesurfer] MICCAI Workshop on Machine Learning in Clinical NeuroImaging: Paper Submissions

External Email - Use Caution Dear Researchers! We are excited to announce that the paper submissions for the #MICCAI Workshop on Machine Learning in Clinical NeuroImaging are now open! This workshop aims to bring together experts from the fields of machine learning and clinical

[Freesurfer] Freeview Crashes!!

Dear FS Experts, While using updated Freeview in ubuntu 16.04, I reproducibly get two following errors: 1st Crash (While selecting color for the volume): Volume - Colormap -Lookup Table option: 0�freeview.bin: symbol lookup error: freeview.bin: undefined symbol: _ZN6QMutex12lockInternalEv 2nd

[Freesurfer] fs on GPU? Segmentation fault error!

External Email - Use Caution Freesurfer Wizards, Any thoughts on this? Thanks in advance ## *I renamed:* /usr/local/cuda-8.0/lib64$ sudo cp libcudart.so.8.0 libcudart.so.5.0 *in the next step:* recon-all -i $sub_dir/$i/"$i".nii -all -sd $output_dir $i -use-gpu . . Testing for CUD

[Freesurfer] mni152reg ends with (ERROR: flirt)

External Email - Use Caution Dear Freesurfer Experts! The idea is to transform freesurfer output in to the MNI 1mm space using following command: mni152reg --s subject_id --1 But mni152reg crashes with following error: flirt.newdefault.20080811.sch terminate called after throwi

[Freesurfer] Error running recon-all

External Email - Use Caution Dear Freesurfer experts, Greetings! In the first minute of recon-all, we are getting following error: mghRead(/media/results/mri/rawavg.mgz): could not read 262144 bytes at slice 0 T1 data type is int16, data type 4 (looked using fslinfo) Looking

Re: [Freesurfer] Error running recon-all

External Email - Use Caution Please also find recon-all.log file. Thanks! On Thu, Jul 25, 2019 at 6:50 AM vin rasa wrote: > Dear Freesurfer experts, > Greetings! > > > In the first minute of recon-all, we are getting following error: > > mghRead(/media/r

[Freesurfer] Extract ThickAvg ThickStd from rh/lh.aparc.stats of a specific structure for group of subjects

External Email - Use Caution Dear Freesurfer experts, Is there a shortcut to extract mean thickness(ThickAvg) and std (ThickStd) from rh/lh.aparc.stats for let's say 4 structures only. I found aparcstats2table command, which seems to extract all the segmented regions. https://sur

[Freesurfer] recon-all ends in 4 seconds without error!!

External Email - Use Caution Dear Freesurfer Experts, Greetings! I am trying to run freesurfer on Synthetic T1 data (see in snapshot: *''Simulated T1 image', last sentence in the snapshot*') from Brainweb ( https://secure-web.cisco.com/1M8y2jTKqcaZLr3pWIX9ajloxBQ00by9kyM5AmTJvStE6

Re: [Freesurfer] recon-all ends in 4 seconds without error!!

5DVJ6nRs2V4QwQZXulUxg2M2_GqOROHWi-TB9KyiBcPWmc4JGUIhhIGtJ6o3uCFNb6kCnhApPYc-Y4O-LPm1SacVHfhu2Ed2QzkGUtwgxu8u5MqaBpajJz7zSqpwpiURhxidPnsAAQhOMyMO5-qsvqwIExnTA9maNlw/http%3A%2F%2Fwww.jeiglesias.com > > On Aug 25, 2021, at 12:04, vin rasa wrote: > > External Email - Use Caution > > Dear Free