If you run it from scratch (recon-all -s subject -all), does it work? If you are going to pick and chose which options to apply, then there is a high risk of missing steps
On 4/14/2021 2:23 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:
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Hi Douglas, Sure, here is the copy of recon-all.log
*From: *"Douglas N. Greve" dgreve@MGH.HARVARD.EDU *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, April 14, 2021 at 10:32 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Autorecon1 failure
Sorry, can you resend the recon-all.log file?
On 4/7/2021 8:45 AM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:
* External Email - Use Caution * *From: *"Abdollahi, Shervin (NIH/NINDS) [C]" <shervin.abdollahi@nih.gov> <mailto:shervin.abdollahi@nih.gov> *Date: *Thursday, March 18, 2021 at 12:42 PM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Autorecon1 failure Hello Freesurfer Developers, am trying to use run freesurfer that is configured inside smriprep.workflow.anatomical.py under init_anat_preproc_wf pipeline. this workflow, does the following: 1. T1w reference: realigning and then averaging T1w images 2. Brain Extraction and INU (bias field) correction (antsBrainExtraction.sh) 3. Brian tissue segmentation (@fsl_fast) 4. Spatial normalization to standard space (antsRegistration) 5. Surface reconstruction with Freesurfer When it gets to step 5, it takes skull-stripped t1, ants_segm, and bias_corrected image to use in freesurfer recon-all command. In the surface reconstruction section, it starts by running the following command: recon-all -autorecon1 -i /path-to /sub-03_ses-20140624_T1w.nii -T2 /path-to/sub-03_ses-20140624_T2w.nii -noskullstrip -hires -openmp 1 -subjid sub-03 -sd /Users/abdollahis2/Desktop/fcd_nipype/derivatives/freesurfer -expert /Users/abdollahis2/Desktop/fcd_nipype/single_subject_03/anat_preproc_wf/surface_recon_wf/_subject_id_03/autorecon1/expert.opts And surely soon, it gives me an error that it can not read mgh file (brainmask.mgz). looking into freesurfer/sub-03/mri directory I can see that brainmask.mgz is not created and I am not sure if this is because the option -noskullstrip was used? I have attached the recon-all.log file. I would appreciate any suggestion on how to debug this problem. 1. Freesurfer version: 7.1.1 (freesurfer-darwin-macOS-7.1.1-20200811-8b40551) 2. Platform: macOS Catalina, Version 10.15.7 3. uname -a: Darwin ndsd-eeg-cedar 19.6.0 Darwin Kernel Version 19.6.0: Tue Jan 12 22:13:05 PST 2021; root:xnu-6153.141.16~1/RELEASE_X86_64 x86_64 4. Recon-all.log: see attached _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/115Jn5Kp-nlZp91e4_mPnlZmATS7hnUW_kV4dk5Gio39h8QD6rzuMP462I8XUGQ_HwhY9HHFl3eJow-BztTdT0Ej9T3GWYZtVKrVQDY0Uvo2O-yErwwwZcX9vt-Gii3S9mvaURnxe8u8plvSNnKrg4Ms5GKlUQEKTApWiDt3UcwQJTMDYZ3-2Uwgosj0SSdnPK76k8UH0W3Q7GtvOTMLhgQINg78aM-ITrd25tVvTwmYGXhijlRoRKtzjycDnVrfo/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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