No, we have not talked
On 4/16/2021 12:20 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:
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So yes running it from scratch would work. But I was trying to
implement fmriprep approach in which they have chosen the optimal
approaches for skull-stripping or intensity normalization via other
applications like ANTs or FSL and they imported those to be used in
Freesurfer instead of internally calculated skull-strip brain mask
(brainmask.mgz). The last step of autorecon-1 is where the skull
stripping needs to be off and that’s where it fails, cause its waiting
for that brainmask.mgz and cant find it. Has there been any
collaboration between freesurfer and fmriprep people on this matter?
Thanks
Shervin
*From: *"Douglas N. Greve" <dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Date: *Friday, April 16, 2021 at 11:08 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] Autorecon1 failure
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:
* External Email - Use Caution *
Hi Douglas, Sure, here is the copy of recon-all.log
*From: *"Douglas N. Greve" <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Wednesday, April 14, 2021 at 10:32 AM
*To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu>
<mailto: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.abdoll...@nih.gov> <mailto:shervin.abdoll...@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
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