Re: [Freesurfer] Creating and analyzing combined ROIs, combining different FreeSurfer versions
Thank you for the reply,
1. Once each participant's aparc has been broken and we've created the desired new label for each participant, should we create this, the desired label, for fsaverage and follow the remaining steps of the ROI-tutorial (e.g resample with mris_label2label using fsaverage as the srcsubject)? Sorry didn't quite understand this part.
3. We can't seem to get mris_register and mri_ca_label working with FS711 or 720, it's running fine with 732 and the dev-version (attaching a simple montage to show the output we're getting; we've tried to force FreeSurfer to use a manually designated central sulcus to move the pre and post central gyri "forward"). I think there was a mention that mris_register wasn't running as intended prior to 732https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg73308.html. Thank you for the clarification!
Kind regards,
Carl
Message: 7 Date: Mon, 12 Dec 2022 10:34:15 -0500 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Creating and analyzing combined ROIs, combining different FreeSurfer versions To: freesurfer@nmr.mgh.harvard.edu Message-ID: 8e7e390b-bbef-00cd-29c6-bda799bfd81e@mgh.harvard.edu Content-Type: text/plain; charset="utf-8" On 12/2/2022 12:35 PM, Trolle, Carl wrote:
Dear FreeSurfer team,
- We're trying to focus our cortical analysis following suggestions here https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23939.html.?T... FS ROI tutorial page?mentions that labels should be drawn or registered on the fsaverage template; could we then break the fsaverage aparc_annot atlas and combine the fsaverage labels of interest into our new label or should we break each individual subjects aparc_annot atlas and then create the combined ROI from the subject specific labels? I'm assuming that we either way will have to resample the combined label to each subject using mri_label2label?
You should break each subject aparc and then combine.
When running the mri_glmfit-sim analysis later on, the thread above mentions not using the --cache option. Can we use "--mczsim 3 pos" instead for a one-sided test?
Yes
- We've had some success in correcting incorrect parcellations using the mris_register and mri_ca_label functions. As we had some issues with mris_register in 7.1.1, we used the developer version for these steps, but 7.1.1 when re-running recon-all as this is the version we used for our study. Is it ok to combine versions like this?
probably ok in this case, but what is the problem?
Thank you for your time!
Kind regards,
Carl Trolle Research fellow Spaulding Neuroimaging Lab
Platform:?linux-centos7_x86_64-7.1.1-20200723-8b40551 FreeSurfer version: 7.1.1
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
On 12/12/2022 6:14 PM, Trolle, Carl wrote:
Thank you for the reply,
- Once each participant's aparc has been broken and we've created the desired new label for each participant, should we create this, the desired label, for fsaverage and follow the remaining steps of the ROI-tutorial (e.g resample with mris_label2label using fsaverage as the srcsubject)? Sorry didn't quite understand this part.
Nope, once you have the ROI you want in the native subject space, just use it, no need to go to fsaverage at all. That was only for if you were going to draw your own label. Instead of drawing it on 10s or 100s of subjects you would draw it once on fsaverage then transfer it to all your subjects. But you don't need to do that.
3. We can't seem to get mris_register and mri_ca_label working with FS711 or 720, it's running fine with 732 and the dev-version (attaching a simple montage to show the output we're getting; we've tried to force FreeSurfer to use a manually designated central sulcus to move the pre and post central gyri "forward"). I think there was a mention that mris_register wasn't running as intended prior to 732 https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg73308.html. Thank you for the clarification!
Unfortunately, I don't remember what I was referring to. As far as I know mris_register and mri_ca_label were working normally pre 732.
Kind regards,
Carl
Message: 7 Date: Mon, 12 Dec 2022 10:34:15 -0500 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Creating and analyzing combined ROIs, combining different FreeSurfer versions To: freesurfer@nmr.mgh.harvard.edu Message-ID: 8e7e390b-bbef-00cd-29c6-bda799bfd81e@mgh.harvard.edu Content-Type: text/plain; charset="utf-8" On 12/2/2022 12:35 PM, Trolle, Carl wrote:
Dear FreeSurfer team,
1. We're trying to focus our cortical analysis following suggestions here
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23939.html.?T... https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23939.html.?The
FS ROI tutorial page?mentions that labels should be drawn or registered on the fsaverage template; could we then break the fsaverage aparc_annot atlas and combine the fsaverage labels of interest into our new label or should we break each individual subjects aparc_annot atlas and then create the combined ROI from the subject specific labels? I'm assuming that we either way will have to resample the combined label to each subject using mri_label2label?
You should break each subject aparc and then combine.
2. When running the mri_glmfit-sim analysis later on, the thread above mentions not using the --cache option. Can we use "--mczsim 3 pos" instead for a one-sided test?
Yes
3. We've had some success in correcting incorrect parcellations using the mris_register and mri_ca_label functions. As we had some issues with mris_register in 7.1.1, we used the developer version for these steps, but 7.1.1 when re-running recon-all as this is the version we used for our study. Is it ok to combine versions like this?
probably ok in this case, but what is the problem?
Thank you for your time!
Kind regards,
Carl Trolle Research fellow Spaulding Neuroimaging Lab
Platform:?linux-centos7_x86_64-7.1.1-20200723-8b40551 FreeSurfer version: 7.1.1
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N. Greve -
Trolle, Carl