It is not a segmentation in the sense that a probablistic atlas is fit the the data. It exclusively relies on the registration.
On 5/9/2021 3:31 PM, Tanrada Pansuwan wrote:
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Dear Douglas,
I think my previous reply got lost…
Could you possibly elaborate more on how this method will only reflectthe registration in that area instead of volume? I got this methodfrom freesurfer tutorial on obtaining custom anatomical ROI analysis.And do you have any suggestion on an alternative method to accuratelyobtain sub thalamic nucleus volume?
Note: these were our original messages
>> Message: 9 >> Date: Mon, 5 Apr 2021 09:54:24 -0400 >> From: "Douglas N. Greve" <dgreve@mgh.harvard.edu >> mailto:dgreve@mgh.harvard.edu> >> Subject: Re: [Freesurfer] Subthalamic nucleus volume >> To: freesurfer@nmr.mgh.harvard.edu >> mailto:freesurfer@nmr.mgh.harvard.edu >> Message-ID: >> <2737d6a7-618b-cd97-b4a2-fe29f4c1ce49@mgh.harvard.edu >> mailto:2737d6a7-618b-cd97-b4a2-fe29f4c1ce49@mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> If you want the volume in the native space, then why not just >> register >> your volume to mni space, then map the label back to the >> individual? You >> could probably do that all with FSL (or SPM). BTW, the "volume" >> you get >> is not at all likely to be accurate. It will just reflect the >> registration in that area. >> >> On 3/30/2021 4:28 PM, T. Pansuwan wrote: >>> >>> ????????External Email - Use Caution >>> >>> ????????External Email - Use Caution >>> >>> Dear Freesurfer experts, >>> >>> As part of my project, I would need to have subthalamic >>> nucleus as one >>> of my ROIs in which this is not available by Freesurfer. I found a >>> probabilistic subthalamic nucleus atlas in FSL atlases (in MNI152 >>> space) and thought I would convert this to fsaverage space. I have >>> attempted: >>> >>> mri_label2vol ?reg >>> $FREESURFER_HOME/average/mni152.register.dat ?seg >>> STN-maxprob-thr25-0.5mm.nii.gz ?temp >>> $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz ?o >>> STN_mni152_in_mni305.nii.gz >>> >>> But the location was much more dorsal than original, >>> 1) I was wondering if there are alternative methods I should >>> try and >>> what could have been the problem? >>> >>> At the end, I hope to obtain individual subject?s subthalamic >>> nucleus >>> volume, >>> 2) I was wondering how to convert volume in fsaverage space to >>> labels >>> in fsaverage space so that I can convert the labels to native >>> space? >>> >>> >>> Thank you so much! >>> >>> Tanrada Pansuwan
Best wishes, Tanrada
On 15 Apr 2021, at 15:10, freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
1. Re: Skull stripping with T2 (Douglas N. Greve) 2. Re: Regarding xhemi comparison of hemispheres of the same subject (Douglas N. Greve) 3. Re: Decompressed problem during reconall (Douglas N. Greve) 4. Re: Freesurfer Digest, Vol 206, Issue 6 (Douglas N. Greve) 5. Re: Surface registration problem (Douglas N. Greve) 6. Re: aparc+aseg to native space issue (Douglas N. Greve) 7. Re: mkcontrast2 typo in 7.1.1 (Douglas N. Greve) 8. Re: mri_segstats to report empty and non-empty segmentation (Douglas N. Greve) 9. Re: Subthalamic nucleus volume (Douglas N. Greve) (Douglas N. Greve)
Message: 1 Date: Thu, 15 Apr 2021 09:49:23 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Skull stripping with T2 To: freesurfer@nmr.mgh.harvard.edu Message-ID: cedcfba5-f488-2cb9-87eb-f8e778e5384d@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
It looks like you are running a T2 through recon-all, which won't work. recon-all only takes T1-weighted. You can run it through samseg, eg, samseg --i T2_age_reg_bias.nii.gz --o samseg You can then binarize the seg.mgz to get everything inside the skull
On 4/7/2021 2:17 PM, Rohan Bareja wrote:
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Hello,
I am doing skull stripping with free surfer v6.0, and have tried various watershed cut-offs to do skull stripping on T2 scans. But, it removes a lot of brain portion.
Here are my commands:
mri_convert /Applications/freesurfer/subjects/patient_20_t2/mri/T2_age_reg_bias.nii.gz
/Applications/freesurfer/subjects/patient_20_t2/mri/001.mgz
recon-all -s patient_20_t2 -autorecon1
## to be used only when increasing or decreasing threshold of skull stripping. recon-all -skullstrip -wsthresh 25 -clean-bm -s patient_12_t2
Is there any way that I can improve?upon this and get better results if I am missing something?
Thanks, Rohan
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