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 *Date: *Thursday, March 18, 2021 at 12:42 PM *To: *"freesurfer@nmr.mgh.harvard.edu" 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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" 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



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No, we have not talked

On 4/16/2021 12:20 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

External Email - Use Caution

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" dgreve@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" <dgreve@MGH.HARVARD.EDU>
<mailto:dgreve@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.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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

You should talk to them

On 4/19/2021 7:52 AM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

External Email - Use Caution

What is your advice for me now? Should I abandon the approach or is there anyway to dig deeper into it and solve the error?

*From: *"Douglas N. Greve" dgreve@MGH.HARVARD.EDU *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Sunday, April 18, 2021 at 10:21 PM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Autorecon1 failure

No, we have not talked

On 4/16/2021 12:20 PM, Abdollahi, Shervin (NIH/NINDS) [C] wrote:

*        External Email - Use Caution *

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" <dgreve@mgh.harvard.edu>
<mailto:dgreve@mgh.harvard.edu>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Friday, April 16, 2021 at 11:08 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

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" <dgreve@MGH.HARVARD.EDU>
    <mailto:dgreve@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.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





        _______________________________________________

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        Freesurfer@nmr.mgh.harvard.edu  <mailto:Freesurfer@nmr.mgh.harvard.edu>

        *MailScanner has detected a possible fraud attempt from
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