Sorry, I don't see any files attached. Also, please just respond to the email that I sent you so that I have the previous emails.
On 8/10/2020 4:10 AM, 真 我 wrote:
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Hi, Dr. Greve. I am sorry to reply so late.
The version of FS I used is v6.0.0. Here are the dt_recon and recon_all file.
Thanks.
Bo Tao
------------------ Original ------------------ *From:* "freesurfer" freesurfer-request@nmr.mgh.harvard.edu; *Date:* Fri, Aug 7, 2020 10:18 PM *To:* "freesurfer"freesurfer@nmr.mgh.harvard.edu; *Subject:* Freesurfer Digest, Vol 198, Issue 11
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Today's Topics:
1. Re: labels in .nii file (Douglas N. Greve) 2. Re: high pass filter cutoff (Douglas N. Greve) 3. Re: Recon-all Soft Errors (Douglas N. Greve) 4. Re: mri_vol2vol and diffusion issue (Douglas N. Greve)
Message: 1 Date: Fri, 7 Aug 2020 10:10:43 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] labels in .nii file To: freesurfer@nmr.mgh.harvard.edu Message-ID: 95d0a55e-80c2-915c-caf3-e45af6c8a9c1@mgh.harvard.edu Content-Type: text/plain; charset="utf-8"
The hemi just refers to either lh or rh to load the proper surface. The command have no idea what you are transferring to the surface.
Before the mri_vol2label stage, try loading surf.MDROI? onto the surface as an overlay and see if the ROIs are showing up in the right place
On 8/6/2020 11:41 AM, Eleni Nikalexi wrote:
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Dear Freesurfer developers, We have a volume that assigns unique numerical labels to each of the ROIs it contains, in NIFTI format. I want to register it to MNI152 (1mm) space, so that I can map it on my subjects and use mris_anatomical_stats. I have tried the following command:
- tkregisterfv --mov MDROI.nii --s MNI_1mm --regheader --reg
registrationMD/MDROI.lta
to get : ?"LTA input is not RAS to RAS...converting...". Then I run:
????????2. mri_vol2surf --src MDROI.nii --src_type nii --out registrationMD/surf.MDROI.mgh --reg ????????????registrationMD/MDROI.lta --hemi lh?--surf white --projdist-max 0 1 0.1 ? ? ?3. mri_vol2surf --src MDROI.nii --src_type nii --out registrationMD/surf.MDROI_rh.mgh --reg ????????????registrationMD/MDROI.lta --hemi rh?--surf white --projdist-max 0 1 0.1 The 2 commands above demand the --hemi argument, but I wasn't sure what to put, as the ROIs are mixed and are in both hemispheres. Thus I run the command once for the left and once for the right hemisphere, creating different .mgh files. Last, I continued with:
? ? ? ? 4. mri_vol2label --i registrationMD/surf.MDROI.mgh --id 1 --l lab.MDROI_lh.label --surf MNI_1mm l
which failed, as I get "ERROR: found no voxels matching id 1"
Could you please tell me, if the commands make sense, and if I should change something?
Thank you so much for your help!
Best regards, Eleni
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