[Freesurfer] Recon-all error

External Email - Use Caution I am trying to debug why all of our T1's are failing Freesurfer recon-all. It seems that most of the files are being created but it isn't getting to the stats steps to output those files. In the recon-all log it does say "recon-all -s 13265 exited with

Re: [Freesurfer] Recon-all error

Hi Courtney Can you send us your command line and a recon-all.log? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Courtney Haswell Sent: Wednesday, December 2, 2020 9:24 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Recon-all error External Email

Re: [Freesurfer] Aligning functional and structural scans with FsFast

Sure, try the bbregister tool Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Karan Desai Sent: Tuesday, December 1, 2020 10:46 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Aligning functional and structural scans with FsFast External Email - Use

Re: [Freesurfer] About mri_vol2surf {Disarmed}

Yes On 11/30/2020 10:45 AM, Alberto Del Cerro Leon wrote: External Email - Use Caution Then, now that I have the AAL in the surface I should make a label for every region in the AAL_surface image with mri_vol2label with surf option and run mri_label2label for every label and every subj

Re: [Freesurfer] Fwd: Issue with custom label

Try --i mri/aparc+aseg.mgz instead of --c On 11/30/2020 7:28 PM, Catherine Tallman wrote: External Email - Use Caution Hello, I was wondering if there were any updates on this question? Thank you, Catherine -- Forwarded message - From: Catherine Tallman mailto:ctall...

Re: [Freesurfer] mri_surf2surf lh.area does not match surface (148208, 146833)

It looks like you edited the subject but did not fully re-run it. Try recon-all -s HLN-12-2 -autorecon3 On 12/1/2020 4:01 AM, 1248742467 wrote: External Email - Use Caution Hello, Fs When I run the following command: mri_surf2surf --srcsubject HLN-12-2 --sval area --src_type curv --trg

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

What are you using to compute the significance of the difference using the ROI average? On 11/30/2020 7:59 PM, 李梦君 wrote: External Email - Use Caution Yes, what should I do if there is something wrong -原始邮件- 发件人:"Greve, Douglas N.,Ph.D." 发送时间:2

Re: [Freesurfer] Aligning functional and structural scans with FsFast

Do you mean you want to register the fMRI data to the anatomical? If so, use bbregister. If you've run the fMRI through FEAT, then pass the template to the --mov flag On 12/1/2020 10:46 PM, Karan Desai wrote: External Email - Use Caution Hi FreeSurfer developers, I have Freesurfer ana

[Freesurfer] Fwd: extracting mask for basal ganglia, deep grey, and centrum semiovale

External Email - Use Caution Any help with this will be greatly appreciated. Thanks. -- Forwarded message - From: miracle ozzoude Date: Fri, Nov 27, 2020 at 9:28 AM Subject: extracting mask for basal ganglia, deep grey, and centrum semiovale To: Douglas N Greve

Re: [Freesurfer] extracting mask for basal ganglia, deep grey, and centrum semiovale

External Email - Use Caution Nevermind. I didn't see your initial reply Doug. Thanks alot. Best, Paul On Wed, Dec 2, 2020 at 1:35 PM miracle ozzoude wrote: > Any help with this will be greatly appreciated. > Thanks. > > -- Forwarded message - > From: miracle ozz

Re: [Freesurfer] Fwd: extracting mask for basal ganglia, deep grey, and centrum semiovale

Hi Paul Have you tried using the wmseg? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of miracle ozzoude Sent: Wednesday, December 2, 2020 1:35 PM To: Douglas N Greve Subject: [Freesurfer] Fwd: extracting mask for basal ganglia, deep grey, and centrum semiovale

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

External Email - Use Caution I extracted the value of the ROI average in each subject in the standard space and imported into the SPSS 26.0 to compute the significance of the difference. -原始邮件- 发件人:"Greve, Douglas N.,Ph.D." 发送时间:2020-12-02 23:31:26 (星期三) 收件人: "freesurfe

Re: [Freesurfer] tkregister issue with reg-feat2anat

External Email - Use Caution Hi, thought I would try one last time to see if there any ideas for troubleshooting? Not sure what to do at this point to run reg-feat2anat without error. Thanks again. Erin From: Walsh, Erin Sent: Wednesday, Novemb

Re: [Freesurfer] mri_watershed error: problem in the COG calcuation

Have you looked at the T1.mgz? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Julia Yang Sent: Wednesday, December 2, 2020 8:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_watershed error: problem in the COG calcuation External Email - Use Caution Hi, Wh