Hi Bruce,

Thank you for your response. I tried it many times and I kept getting the same error like at the bottom of this email. Why do you put the -s in there? and what exactly is the subject ID? FYI, I was already in the folder where the .nii.gz is located. And by your answer I assume I can do it only one patient at a time?

Thanks,

Marja

--- Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all

ERROR: Flag -001 unrecognized.

-001 -i AD_TM001.nii.gz -all

Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri Feb 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64

recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016

For more details, see the log file

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin ---

On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Marja

can you send us the actual command and screen output you ran? It should be something like:

recon-all -all -s <subject id> -i <path to input .nii.gz file>

Depending on your hardware it will take hours to finish, but it will do pretty much everything (segmentation, surface reconstruction, template registration, thickness measurement, parcellation, etc...)

cheers Bruce

On Thu, 26 May 2016, Marja Caverlé wrote:

Hi All,

...

I am new to Freesurfer and I would like to use it for a project I am working on right now. For this project I have two patient groups of which I have structural MRI scans and a lot of other measures. I hope to get cortical thickness numbers from the scans and compare these with the other measures.

Anyway, I am trying to get something done in Freesurfer and it does not really seem to work. I assume I have to do a recon-all -all, but when I try this, I get an error saying that the flag is unrecognised. It probably is a small error, easy to solve, but I already get stuck on it since I am totally new to Freesurfer.

Could anyone help me out? Some of my questions are;

• Am I correct that recon-all -all already coregisters the scans to

template?

• What will be the outcome? Will I get pictures, or a table with numbers,

and if it is a table, which area's are specified? I have a list of ROIs, but how do I let Freesurfer know I am interested in those areas?

• Can I do recon-all -all on a folder with all my patients, or do I have

to do it one by one? (There not that much, approximately 12 scans)

• Can I do recon-all -all on .nii.gz files? The originals are DICOM, but

the problem is that there is just one large DICOM folder, which does not specify which files are part of which scan. I have converted them to .nii.gz since I am a bit familiar with FSL, but I do not know whether this actually works in Freesurfer.

• Why do I get the unrecognised flag error?

I apologise for these questions, they are probably very easy to answer, but I just don't have a clue yet.

Thank you guys.

Best,

Marja

---

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Thanks Bruce,

001 was indeed the subject id, but I did not know it needed -s. If I don't specify the output directory, where will it be put?

Best,

Marja

On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

the subject id is something you make up. What is 001 in your example? Maybe it is the subject ID? If so, preface it with -s. You probably also want to specify the location of your output directory with -sd <directory where you will put each subject>

cheers Bruce

On Fri, 27 May 2016, Marja Caverlé wrote:

Hi Bruce,

...

Thank you for your response. I tried it many times and I kept getting the same error like at the bottom of this email. Why do you put the -s in there? and what exactly is the subject ID? FYI, I was already in the folder where the .nii.gz is located. And by your answer I assume I can do it only one patient at a time?

Thanks,

Marja

---

Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i AD_TM001.nii.gz -all

ERROR: Flag -001 unrecognized.

-001 -i AD_TM001.nii.gz -all

Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel Version 15.4.0: Fri Feb 26 22:08:05 PST 2016; root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64

recon-all -s exited with ERRORS at Thu May 26 14:40:06 AEST 2016

For more details, see the log file

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin

---

On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Marja

  can you send us the actual command and screen output you ran? It
  should be something like:

  recon-all -all -s <subject id> -i <path to input .nii.gz file>

  Depending on your hardware it will take hours to finish, but it
  will do pretty much everything (segmentation, surface
  reconstruction, template registration, thickness measurement,
  parcellation, etc...)

   cheers
  Bruce

  On Thu, 26 May 2016, Marja Caverlé wrote:

        Hi All,

        I am new to Freesurfer and I would like to use it
        for a project I am working
        on right now. For this project I have two patient
        groups of which I have
        structural MRI scans and a lot of other measures. I
        hope to get cortical
        thickness numbers from the scans and compare these
        with the other measures.

        Anyway, I am trying to get something done in
        Freesurfer and it does not
        really seem to work. I assume I have to do a
        recon-all -all, but when I try
        this, I get an error saying that the flag is
        unrecognised. It probably is a
        small error, easy to solve, but I already get stuck
        on it since I am totally
        new to Freesurfer.

        Could anyone help me out?
        Some of my questions are;

        - Am I correct that recon-all -all already
        coregisters the scans to
        template?
        - What will be the outcome? Will I get pictures, or
        a table with numbers,
        and if it is a table, which area's are specified? I
        have a list of ROIs, but
        how do I let Freesurfer know I am interested in
        those areas?
        - Can I do recon-all -all on a folder with all my
        patients, or do I have to
        do it one by one? (There not that much,
        approximately 12 scans)
        - Can I do recon-all -all on .nii.gz files? The
        originals are DICOM, but the
        problem is that there is just one large DICOM
        folder, which does not specify
        which files are part of which scan. I have converted
        them to .nii.gz since I
        am a bit familiar with FSL, but I do not know
        whether this actually works in
        Freesurfer.
        - Why do I get the unrecognised flag error?

        I apologise for these questions, they are probably
        very easy to answer, but
        I just don't have a clue yet.

        Thank you guys.

        Best,

        Marja

---

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

---

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

run them separately

On 5/26/16 11:01 AM, Marja Caverlé wrote:

Thanks! It runs now. But that still leaves me with the question whether I can do all the patients in one run or that I have to run them separately.

Best,

Marja

On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé <marja.caverle@gmail.com mailto:marja.caverle@gmail.com> wrote:

Thanks Bruce,

001 was indeed the subject id, but I did not know it needed -s.
If I don't specify the output directory, where will it be put?

Best,

Marja

On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>
wrote:

    the subject id is something you make up. What is 001 in your
    example? Maybe it is the subject ID? If so, preface it with
    -s. You probably also want to specify the location of your
    output directory with -sd <directory where you will put each
    subject>

    cheers
    Bruce


    On Fri, 27 May 2016, Marja Caverlé wrote:

        Hi Bruce,

        Thank you for your response. I tried it many times and I
        kept getting the
        same error like at the bottom of this email.
        Why do you put the -s in there? and what exactly is the
        subject ID? FYI, I
        was already in the folder where the .nii.gz is located. 
        And by your answer
        I assume I can do it only one patient at a time?

        Thanks,

        Marja

        ---
        Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001 -i
        AD_TM001.nii.gz -all

        ERROR: Flag -001 unrecognized.

        -001 -i AD_TM001.nii.gz -all

        Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel
        Version 15.4.0: Fri Feb
        26 22:08:05 PST 2016;
        root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64


        recon-all -s  exited with ERRORS at Thu May 26 14:40:06
        AEST 2016


        For more details, see the log file

        To report a problem, see
        http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
        ---


        On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu
        <mailto:fischl@nmr.mgh.harvard.edu>>
        wrote:
              Hi Marja

              can you send us the actual command and screen output
        you ran? It
              should be something like:

              recon-all -all -s <subject id> -i <path to input
        .nii.gz file>

              Depending on your hardware it will take hours to
        finish, but it
              will do pretty much everything (segmentation, surface
              reconstruction, template registration, thickness
        measurement,
              parcellation, etc...)

               cheers
              Bruce

              On Thu, 26 May 2016, Marja Caverlé wrote:

                    Hi All,

                    I am new to Freesurfer and I would like to use it
                    for a project I am working
                    on right now. For this project I have two patient
                    groups of which I have
                    structural MRI scans and a lot of other
        measures. I
                    hope to get cortical
                    thickness numbers from the scans and compare these
                    with the other measures.

                    Anyway, I am trying to get something done in
                    Freesurfer and it does not
                    really seem to work. I assume I have to do a
                    recon-all -all, but when I try
                    this, I get an error saying that the flag is
                    unrecognised. It probably is a
                    small error, easy to solve, but I already get
        stuck
                    on it since I am totally
                    new to Freesurfer.

                    Could anyone help me out?
                    Some of my questions are;

                    - Am I correct that recon-all -all already
                    coregisters the scans to
                    template?
                    - What will be the outcome? Will I get
        pictures, or
                    a table with numbers,
                    and if it is a table, which area's are
        specified? I
                    have a list of ROIs, but
                    how do I let Freesurfer know I am interested in
                    those areas?
                    - Can I do recon-all -all on a folder with all my
                    patients, or do I have to
                    do it one by one? (There not that much,
                    approximately 12 scans)
                    - Can I do recon-all -all on .nii.gz files? The
                    originals are DICOM, but the
                    problem is that there is just one large DICOM
                    folder, which does not specify
                    which files are part of which scan. I have
        converted
                    them to .nii.gz since I
                    am a bit familiar with FSL, but I do not know
                    whether this actually works in
                    Freesurfer.
                    - Why do I get the unrecognised flag error?

                    I apologise for these questions, they are probably
                    very easy to answer, but
                    I just don't have a clue yet.

                    Thank you guys.

                    Best,

                    Marja







        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
        <mailto:Freesurfer@nmr.mgh.harvard.edu>
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


        The information in this e-mail is intended only for the
        person to whom
        it is
        addressed. If you believe this e-mail was sent to you in
        error and the
        e-mail
        contains patient information, please contact the Partners
        Compliance
        HelpLine at
        http://www.partners.org/complianceline . If the e-mail was
        sent to you
        in error
        but does not contain patient information, please contact
        the sender
        and properly
        dispose of the e-mail.




    _______________________________________________
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    Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


    The information in this e-mail is intended only for the person
    to whom it is
    addressed. If you believe this e-mail was sent to you in error
    and the e-mail
    contains patient information, please contact the Partners
    Compliance HelpLine at
    http://www.partners.org/complianceline . If the e-mail was
    sent to you in error
    but does not contain patient information, please contact the
    sender and properly
    dispose of the e-mail.

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you have to run them separately On Fri, 27 May 2016, Marja Caverlé wrote:

Thanks! It runs now. But that still leaves me with the question whether I can do all the patients in one run or that I have to run them separately.

Best,

Marja

On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé marja.caverle@gmail.com wrote: Thanks Bruce,

  001 was indeed the subject id, but I did not know it needed -s.
  If I don't specify the output directory, where will it be put?

  Best,

  Marja

On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: the subject id is something you make up. What is 001 in your example? Maybe it is the subject ID? If so, preface it with -s. You probably also want to specify the location of your output directory with -sd <directory where you will put each subject>

  cheers
  Bruce

  On Fri, 27 May 2016, Marja Caverlé wrote:

        Hi Bruce,

        Thank you for your response. I tried it many
        times and I kept getting the
        same error like at the bottom of this email.
        Why do you put the -s in there? and what
        exactly is the subject ID? FYI, I
        was already in the folder where the .nii.gz is
        located.  And by your answer
        I assume I can do it only one patient at a
        time?

        Thanks,

        Marja

        ---
        Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all
        -001 -i AD_TM001.nii.gz -all

        ERROR: Flag -001 unrecognized.

        -001 -i AD_TM001.nii.gz -all

        Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin
        Kernel Version 15.4.0: Fri Feb
        26 22:08:05 PST 2016;
        root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64


        recon-all -s  exited with ERRORS at Thu May 26
        14:40:06 AEST 2016


        For more details, see the log file 

        To report a problem, see
        http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
        ---


        On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Marja

              can you send us the actual command and
        screen output you ran? It
              should be something like:

              recon-all -all -s <subject id> -i <path
        to input .nii.gz file>

              Depending on your hardware it will take
        hours to finish, but it
              will do pretty much everything
        (segmentation, surface
              reconstruction, template registration,
        thickness measurement,
              parcellation, etc...)

               cheers
              Bruce

              On Thu, 26 May 2016, Marja Caverlé
        wrote:

                    Hi All,

                    I am new to Freesurfer and I would
        like to use it
                    for a project I am working
                    on right now. For this project I
        have two patient
                    groups of which I have
                    structural MRI scans and a lot of
        other measures. I
                    hope to get cortical
                    thickness numbers from the scans
        and compare these
                    with the other measures.

                    Anyway, I am trying to get
        something done in
                    Freesurfer and it does not
                    really seem to work. I assume I
        have to do a
                    recon-all -all, but when I try
                    this, I get an error saying that
        the flag is
                    unrecognised. It probably is a
                    small error, easy to solve, but I
        already get stuck
                    on it since I am totally
                    new to Freesurfer.

                    Could anyone help me out?
                    Some of my questions are;

                    - Am I correct that recon-all -all
        already
                    coregisters the scans to
                    template?
                    - What will be the outcome? Will I
        get pictures, or
                    a table with numbers,
                    and if it is a table, which area's
        are specified? I
                    have a list of ROIs, but
                    how do I let Freesurfer know I am
        interested in
                    those areas?
                    - Can I do recon-all -all on a
        folder with all my
                    patients, or do I have to
                    do it one by one? (There not that
        much,
                    approximately 12 scans)
                    - Can I do recon-all -all on
        .nii.gz files? The
                    originals are DICOM, but the
                    problem is that there is just one
        large DICOM
                    folder, which does not specify
                    which files are part of which
        scan. I have converted
                    them to .nii.gz since I
                    am a bit familiar with FSL, but I
        do not know
                    whether this actually works in
                    Freesurfer.
                    - Why do I get the unrecognised
        flag error?

                    I apologise for these questions,
        they are probably
                    very easy to answer, but
                    I just don't have a clue yet.

                    Thank you guys.

                    Best,

                    Marja







        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


        The information in this e-mail is intended
        only for the person to whom
        it is
        addressed. If you believe this e-mail was sent
        to you in error and the
        e-mail
        contains patient information, please contact
        the Partners Compliance
        HelpLine at
        http://www.partners.org/complianceline . If
        the e-mail was sent to you
        in error
        but does not contain patient information,
        please contact the sender
        and properly
        dispose of the e-mail.

---

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

whatever then environment variable SUBJECTS_DIR points to On Fri, 27 May 2016, Marja Caverlé wrote:

Thanks Bruce,

001 was indeed the subject id, but I did not know it needed -s. If I don't specify the output directory, where will it be put?

Best,

Marja

On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: the subject id is something you make up. What is 001 in your example? Maybe it is the subject ID? If so, preface it with -s. You probably also want to specify the location of your output directory with -sd <directory where you will put each subject>

  cheers
  Bruce

  On Fri, 27 May 2016, Marja Caverlé wrote:

        Hi Bruce,

        Thank you for your response. I tried it many times
        and I kept getting the
        same error like at the bottom of this email.
        Why do you put the -s in there? and what exactly is
        the subject ID? FYI, I
        was already in the folder where the .nii.gz is
        located.  And by your answer
        I assume I can do it only one patient at a time?

        Thanks,

        Marja

        ---
        Marjas-MacBook-Pro:mri MarjaCaverle$ recon-all -001
        -i AD_TM001.nii.gz -all

        ERROR: Flag -001 unrecognized.

        -001 -i AD_TM001.nii.gz -all

        Darwin Marjas-MacBook-Pro.local 15.4.0 Darwin Kernel
        Version 15.4.0: Fri Feb
        26 22:08:05 PST 2016;
        root:xnu-3248.40.184~3/RELEASE_X86_64 x86_64


        recon-all -s  exited with ERRORS at Thu May 26
        14:40:06 AEST 2016


        For more details, see the log file 

        To report a problem, see
        http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportin
        ---


        On Thu, May 26, 2016 at 10:56 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Marja

              can you send us the actual command and screen
        output you ran? It
              should be something like:

              recon-all -all -s <subject id> -i <path to
        input .nii.gz file>

              Depending on your hardware it will take hours
        to finish, but it
              will do pretty much everything (segmentation,
        surface
              reconstruction, template registration,
        thickness measurement,
              parcellation, etc...)

               cheers
              Bruce

              On Thu, 26 May 2016, Marja Caverlé wrote:

                    Hi All,

                    I am new to Freesurfer and I would like
        to use it
                    for a project I am working
                    on right now. For this project I have
        two patient
                    groups of which I have
                    structural MRI scans and a lot of other
        measures. I
                    hope to get cortical
                    thickness numbers from the scans and
        compare these
                    with the other measures.

                    Anyway, I am trying to get something
        done in
                    Freesurfer and it does not
                    really seem to work. I assume I have to
        do a
                    recon-all -all, but when I try
                    this, I get an error saying that the
        flag is
                    unrecognised. It probably is a
                    small error, easy to solve, but I
        already get stuck
                    on it since I am totally
                    new to Freesurfer.

                    Could anyone help me out?
                    Some of my questions are;

                    - Am I correct that recon-all -all
        already
                    coregisters the scans to
                    template?
                    - What will be the outcome? Will I get
        pictures, or
                    a table with numbers,
                    and if it is a table, which area's are
        specified? I
                    have a list of ROIs, but
                    how do I let Freesurfer know I am
        interested in
                    those areas?
                    - Can I do recon-all -all on a folder
        with all my
                    patients, or do I have to
                    do it one by one? (There not that much,
                    approximately 12 scans)
                    - Can I do recon-all -all on .nii.gz
        files? The
                    originals are DICOM, but the
                    problem is that there is just one large
        DICOM
                    folder, which does not specify
                    which files are part of which scan. I
        have converted
                    them to .nii.gz since I
                    am a bit familiar with FSL, but I do not
        know
                    whether this actually works in
                    Freesurfer.
                    - Why do I get the unrecognised flag
        error?

                    I apologise for these questions, they
        are probably
                    very easy to answer, but
                    I just don't have a clue yet.

                    Thank you guys.

                    Best,

                    Marja







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