Re: [Freesurfer] Running autorecon2-wm after wm edits makes no difference in final surface

Your ‘recon-all -autorecon2-wm -autorecon3’ finished without errors. ‘unknown-args.txt’ is created to filter out arguments not in recon-config.yaml. It doesn’t mean those flags are not recognized. I don’t know why new surfaces are not created after your editing of wm.mgz. Can you re-send your c

[Freesurfer] Fwd: About Mean LGI value

External Email - Use CautionDear Dr. Greve,I trust this message finds you well. I wanted to follow up on the inquiry I posted to the FreeSurfer mailing list a while back regarding "About Mean LGI value" as below.I understand you are busy, and I appreciate your dedication to the comm

[Freesurfer] Large discrepancy in left and right volumes of perirhinal/entorhinal cortices on FreeSurfer 7.1

External Email - Use Caution Dear FreeSurfer developers, Our research group used the FreeSurfer's recon-all tool to reconstruct 74 anatomical images from cognitively healthy older individuals and parcellate the cortex based on the Desikan-Killiany atlas. However, we are running

Re: [Freesurfer] How many regions does "aparc.DKTatlas+aseg.mgz" have?

Hi Kei, Here is my calculation: 198 aparc.a2005s+aseg.mgz 192 aparc.a2009s+aseg.mgz 114 aparc+aseg.mgz I can't find aparc.DKTatlas+aseg.mgz in Freesurfer distribution directory. Is it the same as aparc+aseg.mgz? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of K

[Freesurfer] Errors in recon-all command

External Email - Use Caution Hello Freesurfer Developers I'm attempting to apply preprocess and segment to my data that consist of 24 subjects by recon-all syntax, as described on the FreeSurfer wiki on macOs software https://secure-web.cisco.com/1sL0UR9IcjyzN-iiFPRBpUbos_zcdbT2W0

Re: [Freesurfer] How many regions does "aparc.DKTatlas+aseg.mgz" have?

External Email - Use Caution Hi, Yujing Thank you for reply. It is likely that the version of freesurfer is different. The latest version (7.4.1) output results based on three atlases. https://secure-web.cisco.com/16kyFKZBTTmJxzWlCpHckTWKfW7NeWPN9nduq80zrB4veUgSnqf_Yxf0V4hYrnX-id0

Re: [Freesurfer] Transformation of volume images

External Email - Use Caution Hi Yujing, thank you for your help! But I think, this is only the affine registration? Is it possible that I can use the same transformation, by which e.g. aseg.mgz-atlas is transformed into the native space of a given subject? The volume-dataset of the

Re: [Freesurfer] recon-all error

NaNs are in your original input image. They are replaced with 0 in the output mri/orig/001.mgz. Doug mentioned “Sometimes SPM will put NaNs in the image to indicate a mask.”. Is that your case? Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Carlos Alcocer Sent: Tuesday, Nov

Re: [Freesurfer] Boundary based registration on partial FoV to MNI space

Is MRS_201_MT_tfl_stripped.mgz  correctly oriented when you view it in freeview? Also, bbr is meant to be used for within subject registration. For something like registering to the mni152, try mri_coreg and specify --dof 12 On 11/20/2023 10:00 AM, Spapens, Jeltje (NP) wrote: Extern

Re: [Freesurfer] Doubts about GLM contrasts

yes, it is the same contrast On 11/20/2023 3:30 PM, Laura Willers de Souza wrote: External Email - Use Caution Great, thanks so much! But I am having difficulty understanding how to construct the contrast to answer the following question "Is the interaction between group (CU/CI) and

Re: [Freesurfer] Large discrepancy in left and right volumes of perirhinal/entorhinal cortices on FreeSurfer 7.1

Do you see the same thing in the source BA data (in fsaverage)? On 11/21/2023 10:22 AM, Marawi, Tulip wrote: External Email - Use Caution Dear FreeSurfer developers, Our research group used the FreeSurfer’s recon-all tool to reconstruct 74 anatomical images from cognitively healthy o

Re: [Freesurfer] How many regions does "aparc.DKTatlas+aseg.mgz" have?

I see now that recon-all produces aparc.DKTatlas+aseg.mgz aparc.a2009s+aseg.mgz aparc+aseg.mgz Just to clarify, my calculation is based on fsaverage/mri/aparc*.mgz Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Kei Nishimaki Sent: Tuesday, November 21, 2023 11:02 AM To: Free

Re: [Freesurfer] Distance Measurement After recon-all

External Email - Use Caution Dear Freesurfer Experts, I would like to inquire if there is a FreeSurfer command that allows me to measure the distance (in voxels or mm) between a lesion mask (output of samseg) and the closest voxels in the ribbon after applying "recon-all" to T1 ima

Re: [Freesurfer] Errors in recon-all command

Assuming 1. NIFTI files for your subjects are 1.nii, 2.nii, …, 300.nii 2. To name the subjects as sub1, sub2, …, sub300 In bash shell, you can do the batch submission as following at prompt: for i in {1..300}; \ do \ echo “recon-all -all -s sub${i} -i ${i}.nii” \ recon-all -all -s sub${i} -

[Freesurfer] recon-all error - MRISlabel2Mask()

External Email - Use Caution Dear Freesurfer experts, Hi. Hoping someone can give me some guidance in how to proceed with this error in recon-all (at the moment, was running autorecon-wm, but not sure that's relevant). Just pasting the last few commands which were successfully r