[Freesurfer] adding volume to aparc aseg

External Email - Use Caution Hi there, I have extracted an ROI mask for the subthalamic nucleus from MNI space and registered this with the subject's native space orig.mgz I would like to append this to the subject's automated segmentation from aparc+aseg.mgz. So I can use this s

[Freesurfer] mri_concat killed

External Email - Use Caution Hi there, I am attempting to concat a number of volume files that are filled cortical ribbons from a series of label files. My workflow is to take the following steps: *Convert overlay file to label file* mri_vol2label --i ${inDir}/Indi_Matched_ROIs/

Re: [Freesurfer] mri_aparc2aseg bad incorrect ROIs

rchive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg56796.html Any ideas? On Tue, Jun 21, 2022 at 1:48 PM Benjamin Deck wrote: > Hi Doug, > > Thanks for getting back to me. > > Yes, it's very weird. My LUT doesn't contain any subcortical structures > but when

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi Yujing, It seems that this did not solve the issue. Are there any other reasons why this would occur? Ben On Fri, Jun 17, 2022 at 2:59 PM Benjamin Deck wrote: > Hi Yujing, > > Thank you. I will give it a try! Can documentation b

Re: [Freesurfer] mri_aparc2aseg bad incorrect ROIs

aseg.presurf.hypos > If you need more help,make sure to include the full terminal output > > On 6/13/2022 4:49 PM, Benjamin Deck wrote: > > External Email - Use Caution > Hi Freesurfer experts, > > I am attempting to turn my surface-based parcellation into a segmentat

Re: [Freesurfer] mris_label2annot seed not set

fe > > On 6/16/2022 9:58 AM, Benjamin Deck wrote: > > External Email - Use Caution > Hi Freesurfer experts, > > While trying to create a custom annotation file I get the following > warning: > > mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab > sub-D

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

0 0’ in your LUT, I’m not > sure you should use ‘--no-unknown’ for mris_label2annot. It will cause your > annotation off by one. > > > > Yujing > > > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvar

Re: [Freesurfer] mri_label2vol fill-ribbon segmentation fault

sure what > the right action is to work around this. > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Benjamin Deck > *Sent:* Friday, June 10, 2022 11:47 AM > *To:* Fr

[Freesurfer] mris_label2annot seed not set

External Email - Use Caution Hi Freesurfer experts, While trying to create a custom annotation file I get the following warning: mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_lab

[Freesurfer] mri_aparc2aseg bad incorrect ROIs

External Email - Use Caution Hi Freesurfer experts, I am attempting to turn my surface-based parcellation into a segmentation file using the following command: mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask Howev

[Freesurfer] mri_label2vol fill-ribbon segmentation fault

External Email - Use Caution Hi there, Having issues with the following command: mri_label2vol --annot lh.yeo_2011.annot --temp /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/mri/orig.mgz --hemi lh --fill-ribbon --identity --subject sub-DAEK --o lh.sub-DAEK_annot_nat.nii.gz pro

Re: [Freesurfer] vertex out of range mris_label2annot

> Yujing > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > On Behalf Of Benjamin Deck > Sent: Thursday, June 9, 2022 2:41 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] vertex out of range mris_label2annot > > External Email - Use Cautio

Re: [Freesurfer] vertex out of range mris_label2annot

. > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Benjamin Deck > *Sent:* Thursday, June 9, 2022 11:11 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] vertex out of ran

Re: [Freesurfer] vertex out of range mris_label2annot

-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Thu, Jun 9, 2022 at 11:08 AM Huang, Yujing wrote: > Sorry, I meant the command that you ran with --ldir flag and generated > empty annotation file. > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard

Re: [Freesurfer] vertex out of range mris_label2annot

> > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Benjamin Deck > *Sent:* Thursday, June 9, 2022 10:11 AM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] vertex out of ra

Re: [Freesurfer] vertex out of range mris_label2annot

eated those label files. > > > > Best, > > > > Yujing > > > > > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Benjamin Deck > *Sent:* Monday, June 6, 2022 4:06 PM &g

[Freesurfer] vertex out of range mris_label2annot

External Email - Use Caution Hi freesurfer experts, I am attempting to create a custom annotation file with the following LUT and call: mris_label2annot --s sub-DAEK --hemi lh \ --ctab sub-DAEK_yeoLUT.txt \ --a yeo2011nodes \ --maxstatwinner \ --l Net_10_ROIs_1_lh_native_dil2.l

Re: [Freesurfer] Custom LUT

Greve wrote: > No, there is a problem with your LUT (for the default, there might not be > entries for all of your segs which is why you are not seeing them). I don't > know what the problem is. Try making it a different way or doing it by hand > in linux. > > On 6/3/2022

[Freesurfer] Custom LUT

External Email - Use Caution Responding re: Douglas Greve How exactly did you create the LUT? Eg, in windows using notepad? I'm thinking that there might be some hidden characters in there as the color is wrong. I did notice that your first entry had a value of 5 in the last colu

[Freesurfer] convert surface overlays to atlas

External Email - Use Caution Hi there freesurfer experts, I am fairly new to freesurfer. I am attempting to convert freesurfer overlay files and eventually create individual-specific annotation files which will then be used to create a segmentation file to be used for drawing whit