Hey Bruce.

Thanks for the response. How do I go about uploading the subject?

On Monday, July 28, 2014, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Matt

certainly something is wrong, but it's hard to tell why from the single slice. You have big topological defects that are being fixed incorrectly. Can you upload the subject and we will take a look? cheers Bruce On Mon, 28 Jul 2014, Walton, Matt wrote:

Hello Freesurfer team,

...

I've used freesurfer to segment (recon-all) approximately 30 different subjects from a study. I've noticed that a large number of these subjects have a misclassification of the white and pial boundaries in the occipital lobe (such that grey matter is being classified as white matter). I believe this problem is originating from my scanner and original data. I'm acquiring a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a 32 channel phased array head coil. For many subjects, this acquistion gives intensity inhomogeneity in the occipital lobe. I've begun using a GE based correction technique (PURE) on the images, and it appears to improve the intensity in the occipital lobe, but Freesurfer is still frequently misclassifying.

I'm wondering what would be the best way to edit the data. I've often tried to edit the wm.vol, but this doesn't seem to fix anything. For the most part, the wm.vol is correct to begin with, but the wm cutting line isn't segmenting with the wm.vol. I've also tried to add control points but this doesn't seem to improve anything either.

I've attached an image which I hope will further explain my problems.

Thanks for any help

Hey Bruce.

I've sent one of my subjects in which I noticed the segmentation problems in the occipital lobe. Sagittal slice 115 provides a good example. I've also noticed that with my subjects I frequently have problems with segmentation of the temporal lobes, although adding control points usually fixes this quite well.

Thanks for your help

Matt

On Mon, Jul 28, 2014 at 3:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Matt

there are instructions on our wiki. You can either ftp or use the filedrop, although ftp is probably best if you are uploading an entire subject

cheers Bruce On Mon, 28 Jul 2014, Walton, Matt wrote:

Hey Bruce.

...

Thanks for the response. How do I go about uploading the subject?

On Monday, July 28, 2014, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Matt

  certainly something is wrong, but it's hard to tell why from the
  single slice. You have big topological defects that are being
  fixed incorrectly. Can you upload the subject and we will take a
  look?
  cheers
  Bruce
  On Mon, 28 Jul 2014, Walton, Matt wrote:

        Hello Freesurfer team,
        I've used freesurfer to segment (recon-all)
         approximately 30 different
        subjects from a study. I've noticed that a large
        number of these subjects
        have a misclassification of the white and pial
        boundaries in the occipital
        lobe (such that grey matter is being classified as
        white matter). I believe
        this problem is originating from my scanner and
        original data. I'm acquiring
        a T1W BRAVO sequence on a GE Discovery 750w 3T
        scanner, using a 32 channel
        phased array head coil. For many subjects, this
        acquistion gives intensity
        inhomogeneity in the occipital lobe.  I've begun
        using a GE based correction
        technique (PURE) on the images, and it appears to
        improve the intensity in
        the occipital lobe, but Freesurfer is still
        frequently misclassifying.

        I'm wondering what would be the best way to edit the
        data. I've often tried
        to edit the wm.vol, but this doesn't seem to fix
        anything. For the most
        part, the wm.vol is correct to begin with, but the
        wm cutting line isn't
        segmenting with the wm.vol. I've also tried to add
        control points but this
        doesn't seem to improve anything either.

        I've attached an image which I hope will further
        explain my problems.

        Thanks for any help

---

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.

Hi Matt,

I've taken a look at the subject that you uploaded. I initially deleted portions of the skull from the brainmask that weren't removed from coronal slices 101-109 (see screenshot), which led to some improvement. I also edited the wm volume by deleting areas that were obviously not white matter, even if it didn't effect the white matter surface. However, this didn't lead to much improvement. The segmentation isn't as bad in this subject as in the screenshot that you sent originally, so this strategy may help in worse cases.

I am going to take another look at it now to try to improve the segmentation further.

Best, Lee

On 07/30/2014 12:21 PM, Walton, Matt wrote: Hey Bruce,

I uploaded a subject that you requested a few days ago (problems with segmentation in the occipital lobe). I just wanted to make sure the file transferred successfully, and if you have had a change to analyze.

Thanks,

Matt

On Mon, Jul 28, 2014 at 5:48 PM, Walton, Matt <mt.walton@alumni.uleth.camailto:mt.walton@alumni.uleth.ca> wrote: Hey Bruce.

I've sent one of my subjects in which I noticed the segmentation problems in the occipital lobe. Sagittal slice 115 provides a good example. I've also noticed that with my subjects I frequently have problems with segmentation of the temporal lobes, although adding control points usually fixes this quite well.

Thanks for your help

Matt

On Mon, Jul 28, 2014 at 3:22 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Matt

there are instructions on our wiki. You can either ftp or use the filedrop, although ftp is probably best if you are uploading an entire subject

cheers Bruce On Mon, 28 Jul 2014, Walton, Matt wrote:

Hey Bruce. Thanks for the response. How do I go about uploading the subject?

On Monday, July 28, 2014, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Matt

certainly something is wrong, but it's hard to tell why from the single slice. You have big topological defects that are being fixed incorrectly. Can you upload the subject and we will take a look? cheers Bruce On Mon, 28 Jul 2014, Walton, Matt wrote:

Hello Freesurfer team, I've used freesurfer to segment (recon-all) approximately 30 different subjects from a study. I've noticed that a large number of these subjects have a misclassification of the white and pial boundaries in the occipital lobe (such that grey matter is being classified as white matter). I believe this problem is originating from my scanner and original data. I'm acquiring a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a 32 channel phased array head coil. For many subjects, this acquistion gives intensity inhomogeneity in the occipital lobe. I've begun using a GE based correction technique (PURE) on the images, and it appears to improve the intensity in the occipital lobe, but Freesurfer is still frequently misclassifying.

I'm wondering what would be the best way to edit the data. I've often tried to edit the wm.vol, but this doesn't seem to fix anything. For the most part, the wm.vol is correct to begin with, but the wm cutting line isn't segmenting with the wm.vol. I've also tried to add control points but this doesn't seem to improve anything either.

I've attached an image which I hope will further explain my problems.

Thanks for any help

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

Hi Matt,

Overall, I've made the following changes that have led to some improvements: - Remove excess dura from the brainmask that hasn't been stripped away - Erasing voxels from wm in areas where white matter should be, even if the voxels don't show up as what on the wm mask. (If you view the wm volume with the heat color map, and lower the mid parameter to zero, areas that you have deleted show up in red) - Control points to push out the pial surface

Specifically for the case I sent you, I added control points near 115, 89, 82 (+/- a few slices in the sagittal view) to move the pial surface out further. The wm intensity is decreasing as it moves out along that strand, so adding control points in these areas will increase the values to help Freesurfer recognize it as part of the white matter surface.

Also, near 141, 116, 45 (sagittal view) there is a problem with the wm surface. I tried deleting wm voxels as mentioned above, but I don't think I was aggressive enough on the first attempt so it didn't help much. I will try this again to see if it leads to further improvements.

Best, Lee

On 08/06/2014 11:54 AM, Walton, Matt wrote: Hey Bruce,

Thanks so much. If it would help, I could upload another subject, perhaps one with worse segmentation in the occipital lobe. I could also upload a raw T1 image sequence (Nifiti)

Matt

On Wed, Aug 6, 2014 at 9:48 AM, Tirrell, Lee <LTIRRELL@mgh.harvard.edumailto:LTIRRELL@mgh.harvard.edu> wrote: Hi Matt,

I've taken a look at the subject that you uploaded. I initially deleted portions of the skull from the brainmask that weren't removed from coronal slices 101-109 (see screenshot), which led to some improvement. I also edited the wm volume by deleting areas that were obviously not white matter, even if it didn't effect the white matter surface. However, this didn't lead to much improvement. The segmentation isn't as bad in this subject as in the screenshot that you sent originally, so this strategy may help in worse cases.

I am going to take another look at it now to try to improve the segmentation further.

Best, Lee

On 07/30/2014 12:21 PM, Walton, Matt wrote: Hey Bruce,

I uploaded a subject that you requested a few days ago (problems with segmentation in the occipital lobe). I just wanted to make sure the file transferred successfully, and if you have had a change to analyze.

Thanks,

Matt

On Mon, Jul 28, 2014 at 5:48 PM, Walton, Matt <mt.walton@alumni.uleth.camailto:mt.walton@alumni.uleth.ca> wrote: Hey Bruce.

I've sent one of my subjects in which I noticed the segmentation problems in the occipital lobe. Sagittal slice 115 provides a good example. I've also noticed that with my subjects I frequently have problems with segmentation of the temporal lobes, although adding control points usually fixes this quite well.

Thanks for your help

Matt

On Mon, Jul 28, 2014 at 3:22 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Matt

there are instructions on our wiki. You can either ftp or use the filedrop, although ftp is probably best if you are uploading an entire subject

cheers Bruce On Mon, 28 Jul 2014, Walton, Matt wrote:

Hey Bruce. Thanks for the response. How do I go about uploading the subject?

On Monday, July 28, 2014, Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> wrote: Hi Matt

certainly something is wrong, but it's hard to tell why from the single slice. You have big topological defects that are being fixed incorrectly. Can you upload the subject and we will take a look? cheers Bruce On Mon, 28 Jul 2014, Walton, Matt wrote:

Hello Freesurfer team, I've used freesurfer to segment (recon-all) approximately 30 different subjects from a study. I've noticed that a large number of these subjects have a misclassification of the white and pial boundaries in the occipital lobe (such that grey matter is being classified as white matter). I believe this problem is originating from my scanner and original data. I'm acquiring a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a 32 channel phased array head coil. For many subjects, this acquistion gives intensity inhomogeneity in the occipital lobe. I've begun using a GE based correction technique (PURE) on the images, and it appears to improve the intensity in the occipital lobe, but Freesurfer is still frequently misclassifying.

I'm wondering what would be the best way to edit the data. I've often tried to edit the wm.vol, but this doesn't seem to fix anything. For the most part, the wm.vol is correct to begin with, but the wm cutting line isn't segmenting with the wm.vol. I've also tried to add control points but this doesn't seem to improve anything either.

I've attached an image which I hope will further explain my problems.

Thanks for any help

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.

Hi Matt

the young age is probably why you are having to do extra work - incomplete myelination.

cheers Bruce On Thu, 7 Aug 2014, Walton, Matt wrote:

Thanks for your help. It is most appreciated. I thought I would mention that these subjects are  quite young (3-4 years old). I've read a few posts that free surfer is not ideal for analyzing young subjects, so I am wondering if this might be causing some errors. Maybe there is a way to register to a paediatric template, or something?

As well the raw T1w images always have an intensity bias in the occipital lobe. I'm not sure if this is from the coil itself (32 channel phased array), or just from the young subject age. Do you think ramping up the normalization procedures in freesurfer would result in an improvement?

Thought I would just let you know this, incase it helps you.

Matt

On Thu, Aug 7, 2014 at 10:12 AM, Tirrell, Lee LTIRRELL@mgh.harvard.edu wrote: Hi Matt,

  Overall, I've made the following changes that have led to some
  improvements:
  - Remove excess dura from the brainmask that hasn't been
  stripped away
  - Erasing voxels from wm in areas where white matter should be,
  even if the voxels don't show up as what on the wm mask. (If you
  view the wm volume with the heat color map, and lower the mid
  parameter to zero, areas that you have deleted show up in red) 
  - Control points to push out the pial surface

  Specifically for the case I sent you, I added control points
  near 115, 89, 82 (+/- a few slices in the sagittal view) to move
  the pial surface out further.  The wm intensity is decreasing as
  it moves out along that strand, so adding control points in
  these areas will increase the values to help Freesurfer
  recognize it as part of the white matter surface.

  Also, near 141, 116, 45 (sagittal view) there is a problem with
  the wm surface. I tried deleting wm voxels as mentioned above,
  but I don't think I was aggressive enough on the first attempt
  so it didn't help much.  I will try this again to see if it
  leads to further improvements.

  Best,
  Lee

  On 08/06/2014 11:54 AM, Walton, Matt wrote:
  Hey Bruce,

Thanks so much. If it would help, I could upload another subject, perhaps one with worse segmentation in the occipital lobe. I could also upload a raw T1 image sequence (Nifiti)

Matt

On Wed, Aug 6, 2014 at 9:48 AM, Tirrell, Lee LTIRRELL@mgh.harvard.edu wrote: Hi Matt,

  I've taken a look at the subject that you uploaded. 
  I initially deleted portions of the skull from the
  brainmask that weren't removed from coronal slices
  101-109 (see screenshot), which led to some
  improvement.  I also edited the wm volume by
  deleting areas that were obviously not white matter,
  even if it didn't effect the white matter surface. 
  However, this didn't lead to much improvement.  The
  segmentation isn't as bad in this subject as in the
  screenshot that you sent originally, so this
  strategy may help in worse cases. 

  I am going to take another look at it now to try to
  improve the segmentation further.

  Best,
  Lee
       
  On 07/30/2014 12:21 PM, Walton, Matt wrote:
  Hey Bruce,

I uploaded a subject that you requested a few days ago (problems with segmentation in the occipital lobe). I just wanted to make sure the file transferred successfully, and if you have had a change to analyze.

Thanks,

Matt

On Mon, Jul 28, 2014 at 5:48 PM, Walton, Matt mt.walton@alumni.uleth.ca wrote: Hey Bruce.  I've sent one of my subjects in which I noticed the segmentation problems in the occipital lobe. Sagittal slice 115 provides a good example. I've also noticed that with my subjects I frequently have problems with segmentation of the temporal lobes, although adding control points usually fixes this quite well.

Thanks for your help

Matt

On Mon, Jul 28, 2014 at 3:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Matt

  there are instructions on our
  wiki. You can either ftp or use
  the filedrop, although ftp is
  probably best if you are uploading
  an entire subject

  cheers
  Bruce
  On Mon, 28 Jul 2014, Walton, Matt
  wrote:

        Hey Bruce.
        Thanks for the
        response. How do I go
        about uploading the
        subject?

        On Monday, July 28,
        2014, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Matt

              certainly
        something is wrong,
        but it's hard to tell
        why from the
              single slice.
        You have big
        topological defects
        that are being
              fixed
        incorrectly. Can you
        upload the subject and
        we will take a
              look?
              cheers
              Bruce
              On Mon, 28 Jul
        2014, Walton, Matt
        wrote:

                    Hello
        Freesurfer team,
                    I've used
        freesurfer to segment
        (recon-all)
                   
         approximately 30
        different
                    subjects
        from a study. I've
        noticed that a large
                    number of
        these subjects
                    have a
        misclassification of
        the white and pial
                    boundaries
        in the occipital
                    lobe (such
        that grey matter is
        being classified as
                    white
        matter). I believe
                    this
        problem is originating
        from my scanner and
                    original
        data. I'm acquiring
                    a T1W
        BRAVO sequence on a GE
        Discovery 750w 3T
                    scanner,
        using a 32 channel
                    phased
        array head coil. For
        many subjects, this
                    acquistion
        gives intensity
                   
        inhomogeneity in the
        occipital lobe.  I've
        begun
                    using a GE
        based correction
                    technique
        (PURE) on the images,
        and it appears to
                    improve
        the intensity in
                    the
        occipital lobe, but
        Freesurfer is still
                    frequently
        misclassifying. 

                    I'm
        wondering what would
        be the best way to
        edit the
                    data. I've
        often tried
                    to edit
        the wm.vol, but this
        doesn't seem to fix
                    anything.
        For the most
                    part, the
        wm.vol is correct to
        begin with, but the
                    wm cutting
        line isn't
                    segmenting
        with the wm.vol. I've
        also tried to add
                    control
        points but this
                    doesn't
        seem to improve
        anything either.

                    I've
        attached an image
        which I hope will
        further
                    explain my
        problems. 

                    Thanks for
        any help

---

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.

---

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.

---

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.

Hi Matt Not really. Is the white matter in those regions already 110? Bruce

On Aug 12, 2014, at 8:21 PM, "Walton, Matt" mt.walton@alumni.uleth.ca wrote:

Hey Bruce,

Is there anyway I can make edits to the grey matter to help with the segmentation errors (i.e reclassify grey matter in the brainmask with voxel edit so they are included in the pial layer). Even with the addition of control points and wm edits I'm still not getting a proper segmentation, especially in areas like the temporal lobes and central grey matter where signal is lower.

Thanks,

Matt

...

On Thu, Aug 7, 2014 at 1:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Matt

the young age is probably why you are having to do extra work - incomplete myelination.

cheers Bruce

On Thu, 7 Aug 2014, Walton, Matt wrote:

...

Thanks for your help. It is most appreciated. I thought I would mention that these subjects are quite young (3-4 years old). I've read a few posts that free surfer is not ideal for analyzing young subjects, so I am wondering if this might be causing some errors. Maybe there is a way to register to a paediatric template, or something?

As well the raw T1w images always have an intensity bias in the occipital lobe. I'm not sure if this is from the coil itself (32 channel phased array), or just from the young subject age. Do you think ramping up the normalization procedures in freesurfer would result in an improvement?

Thought I would just let you know this, incase it helps you.

Matt

On Thu, Aug 7, 2014 at 10:12 AM, Tirrell, Lee LTIRRELL@mgh.harvard.edu wrote: Hi Matt,

  Overall, I've made the following changes that have led to some
  improvements:
  - Remove excess dura from the brainmask that hasn't been
  stripped away
  - Erasing voxels from wm in areas where white matter should be,
  even if the voxels don't show up as what on the wm mask. (If you
  view the wm volume with the heat color map, and lower the mid
  parameter to zero, areas that you have deleted show up in red) 
  - Control points to push out the pial surface

  Specifically for the case I sent you, I added control points
  near 115, 89, 82 (+/- a few slices in the sagittal view) to move
  the pial surface out further.  The wm intensity is decreasing as
  it moves out along that strand, so adding control points in
  these areas will increase the values to help Freesurfer
  recognize it as part of the white matter surface.

  Also, near 141, 116, 45 (sagittal view) there is a problem with
  the wm surface. I tried deleting wm voxels as mentioned above,
  but I don't think I was aggressive enough on the first attempt
  so it didn't help much.  I will try this again to see if it
  leads to further improvements.

  Best,
  Lee

  On 08/06/2014 11:54 AM, Walton, Matt wrote:
  Hey Bruce,

Thanks so much. If it would help, I could upload another subject, perhaps one with worse segmentation in the occipital lobe. I could also upload a raw T1 image sequence (Nifiti)

Matt

On Wed, Aug 6, 2014 at 9:48 AM, Tirrell, Lee LTIRRELL@mgh.harvard.edu wrote: Hi Matt,

  I've taken a look at the subject that you uploaded. 
  I initially deleted portions of the skull from the
  brainmask that weren't removed from coronal slices
  101-109 (see screenshot), which led to some
  improvement.  I also edited the wm volume by
  deleting areas that were obviously not white matter,
  even if it didn't effect the white matter surface. 
  However, this didn't lead to much improvement.  The
  segmentation isn't as bad in this subject as in the
  screenshot that you sent originally, so this
  strategy may help in worse cases. 

  I am going to take another look at it now to try to
  improve the segmentation further.

  Best,
  Lee

  On 07/30/2014 12:21 PM, Walton, Matt wrote:
  Hey Bruce,

I uploaded a subject that you requested a few days ago (problems with segmentation in the occipital lobe). I just wanted to make sure the file transferred successfully, and if you have had a change to analyze.

Thanks,

Matt

On Mon, Jul 28, 2014 at 5:48 PM, Walton, Matt mt.walton@alumni.uleth.ca wrote: Hey Bruce. I've sent one of my subjects in which I noticed the segmentation problems in the occipital lobe. Sagittal slice 115 provides a good example. I've also noticed that with my subjects I frequently have problems with segmentation of the temporal lobes, although adding control points usually fixes this quite well.

Thanks for your help

Matt

On Mon, Jul 28, 2014 at 3:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Matt

  there are instructions on our
  wiki. You can either ftp or use
  the filedrop, although ftp is
  probably best if you are uploading
  an entire subject

  cheers
  Bruce
  On Mon, 28 Jul 2014, Walton, Matt
  wrote:

        Hey Bruce.
        Thanks for the
        response. How do I go
        about uploading the
        subject?

        On Monday, July 28,
        2014, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Matt

              certainly
        something is wrong,
        but it's hard to tell
        why from the
              single slice.
        You have big
        topological defects
        that are being
              fixed
        incorrectly. Can you
        upload the subject and
        we will take a
              look?
              cheers
              Bruce
              On Mon, 28 Jul
        2014, Walton, Matt
        wrote:

                    Hello
        Freesurfer team,
                    I've used
        freesurfer to segment
        (recon-all)

         approximately 30
        different
                    subjects
        from a study. I've
        noticed that a large
                    number of
        these subjects
                    have a
        misclassification of
        the white and pial
                    boundaries
        in the occipital
                    lobe (such
        that grey matter is
        being classified as
                    white
        matter). I believe
                    this
        problem is originating
        from my scanner and
                    original
        data. I'm acquiring
                    a T1W
        BRAVO sequence on a GE
        Discovery 750w 3T
                    scanner,
        using a 32 channel
                    phased
        array head coil. For
        many subjects, this
                    acquistion
        gives intensity

        inhomogeneity in the
        occipital lobe.  I've
        begun
                    using a GE
        based correction
                    technique
        (PURE) on the images,
        and it appears to
                    improve
        the intensity in
                    the
        occipital lobe, but
        Freesurfer is still
                    frequently
        misclassifying. 

                    I'm
        wondering what would
        be the best way to
        edit the
                    data. I've
        often tried
                    to edit
        the wm.vol, but this
        doesn't seem to fix
                    anything.
        For the most
                    part, the
        wm.vol is correct to
        begin with, but the
                    wm cutting
        line isn't
                    segmenting
        with the wm.vol. I've
        also tried to add
                    control
        points but this
                    doesn't
        seem to improve
        anything either.

                    I've
        attached an image
        which I hope will
        further
                    explain my
        problems. 

                    Thanks for
        any help

---

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If you upload the subject and send us the voxel coords we will have a look Bruce

On Aug 12, 2014, at 10:55 PM, "Walton, Matt" mt.walton@alumni.uleth.ca wrote:

Hey,

Bruce, yes WM is already classified as 110 in the regions, but grey matter is still being excluded.

Matt

...

On Tue, Aug 12, 2014 at 2:08 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Matt Not really. Is the white matter in those regions already 110? Bruce

...

On Aug 12, 2014, at 8:21 PM, "Walton, Matt" mt.walton@alumni.uleth.ca wrote:

Hey Bruce,

Is there anyway I can make edits to the grey matter to help with the segmentation errors (i.e reclassify grey matter in the brainmask with voxel edit so they are included in the pial layer). Even with the addition of control points and wm edits I'm still not getting a proper segmentation, especially in areas like the temporal lobes and central grey matter where signal is lower.

Thanks,

Matt

...

On Thu, Aug 7, 2014 at 1:20 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Matt

the young age is probably why you are having to do extra work - incomplete myelination.

cheers Bruce

On Thu, 7 Aug 2014, Walton, Matt wrote:

...

Thanks for your help. It is most appreciated. I thought I would mention that these subjects are quite young (3-4 years old). I've read a few posts that free surfer is not ideal for analyzing young subjects, so I am wondering if this might be causing some errors. Maybe there is a way to register to a paediatric template, or something?

As well the raw T1w images always have an intensity bias in the occipital lobe. I'm not sure if this is from the coil itself (32 channel phased array), or just from the young subject age. Do you think ramping up the normalization procedures in freesurfer would result in an improvement?

Thought I would just let you know this, incase it helps you.

Matt

On Thu, Aug 7, 2014 at 10:12 AM, Tirrell, Lee LTIRRELL@mgh.harvard.edu wrote: Hi Matt,

  Overall, I've made the following changes that have led to some
  improvements:
  - Remove excess dura from the brainmask that hasn't been
  stripped away
  - Erasing voxels from wm in areas where white matter should be,
  even if the voxels don't show up as what on the wm mask. (If you
  view the wm volume with the heat color map, and lower the mid
  parameter to zero, areas that you have deleted show up in red) 
  - Control points to push out the pial surface

  Specifically for the case I sent you, I added control points
  near 115, 89, 82 (+/- a few slices in the sagittal view) to move
  the pial surface out further.  The wm intensity is decreasing as
  it moves out along that strand, so adding control points in
  these areas will increase the values to help Freesurfer
  recognize it as part of the white matter surface.

  Also, near 141, 116, 45 (sagittal view) there is a problem with
  the wm surface. I tried deleting wm voxels as mentioned above,
  but I don't think I was aggressive enough on the first attempt
  so it didn't help much.  I will try this again to see if it
  leads to further improvements.

  Best,
  Lee

  On 08/06/2014 11:54 AM, Walton, Matt wrote:
  Hey Bruce,

Thanks so much. If it would help, I could upload another subject, perhaps one with worse segmentation in the occipital lobe. I could also upload a raw T1 image sequence (Nifiti)

Matt

On Wed, Aug 6, 2014 at 9:48 AM, Tirrell, Lee LTIRRELL@mgh.harvard.edu wrote: Hi Matt,

  I've taken a look at the subject that you uploaded. 
  I initially deleted portions of the skull from the
  brainmask that weren't removed from coronal slices
  101-109 (see screenshot), which led to some
  improvement.  I also edited the wm volume by
  deleting areas that were obviously not white matter,
  even if it didn't effect the white matter surface. 
  However, this didn't lead to much improvement.  The
  segmentation isn't as bad in this subject as in the
  screenshot that you sent originally, so this
  strategy may help in worse cases. 

  I am going to take another look at it now to try to
  improve the segmentation further.

  Best,
  Lee

  On 07/30/2014 12:21 PM, Walton, Matt wrote:
  Hey Bruce,

I uploaded a subject that you requested a few days ago (problems with segmentation in the occipital lobe). I just wanted to make sure the file transferred successfully, and if you have had a change to analyze.

Thanks,

Matt

On Mon, Jul 28, 2014 at 5:48 PM, Walton, Matt mt.walton@alumni.uleth.ca wrote: Hey Bruce. I've sent one of my subjects in which I noticed the segmentation problems in the occipital lobe. Sagittal slice 115 provides a good example. I've also noticed that with my subjects I frequently have problems with segmentation of the temporal lobes, although adding control points usually fixes this quite well.

Thanks for your help

Matt

On Mon, Jul 28, 2014 at 3:22 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Matt

  there are instructions on our
  wiki. You can either ftp or use
  the filedrop, although ftp is
  probably best if you are uploading
  an entire subject

  cheers
  Bruce
  On Mon, 28 Jul 2014, Walton, Matt
  wrote:

        Hey Bruce.
        Thanks for the
        response. How do I go
        about uploading the
        subject?

        On Monday, July 28,
        2014, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Matt

              certainly
        something is wrong,
        but it's hard to tell
        why from the
              single slice.
        You have big
        topological defects
        that are being
              fixed
        incorrectly. Can you
        upload the subject and
        we will take a
              look?
              cheers
              Bruce
              On Mon, 28 Jul
        2014, Walton, Matt
        wrote:

                    Hello
        Freesurfer team,
                    I've used
        freesurfer to segment
        (recon-all)

         approximately 30
        different
                    subjects
        from a study. I've
        noticed that a large
                    number of
        these subjects
                    have a
        misclassification of
        the white and pial
                    boundaries
        in the occipital
                    lobe (such
        that grey matter is
        being classified as
                    white
        matter). I believe
                    this
        problem is originating
        from my scanner and
                    original
        data. I'm acquiring
                    a T1W
        BRAVO sequence on a GE
        Discovery 750w 3T
                    scanner,
        using a 32 channel
                    phased
        array head coil. For
        many subjects, this
                    acquistion
        gives intensity

        inhomogeneity in the
        occipital lobe.  I've
        begun
                    using a GE
        based correction
                    technique
        (PURE) on the images,
        and it appears to
                    improve
        the intensity in
                    the
        occipital lobe, but
        Freesurfer is still
                    frequently
        misclassifying. 

                    I'm
        wondering what would
        be the best way to
        edit the
                    data. I've
        often tried
                    to edit
        the wm.vol, but this
        doesn't seem to fix
                    anything.
        For the most
                    part, the
        wm.vol is correct to
        begin with, but the
                    wm cutting
        line isn't
                    segmenting
        with the wm.vol. I've
        also tried to add
                    control
        points but this
                    doesn't
        seem to improve
        anything either.

                    I've
        attached an image
        which I hope will
        further
                    explain my
        problems. 

                    Thanks for
        any help

---

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What is the command line that is failing and what is the full terminal output? doug

On 07/29/2014 05:55 AM, angela.favaro@unipd.it wrote:

Hi all, I am now working with the 5.3 version and performing interhemispheric registration (building my own atlas)

after running for all subjects: xhemireg --s subj001.... surfreg --s subj001 --t fsaverage_sym --lh surfreg --s subj001 --t fsaverage_sym --xhemi --lh

I have tried first iteration, but the following error occurs:

processing subject subj001 (1 of 194) reading spherical surface /Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/Angela/studyfree/subj002/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface

how can I get the rh.fsaverage_sym.sphere.reg file?

thank you!

Angela

...

Hi Matt

certainly something is wrong, but it's hard to tell why from the single slice. You have big topological defects that are being fixed incorrectly. Can you upload the subject and we will take a look? cheers Bruce On Mon, 28 Jul 2014, Walton, Matt wrote:

...

Hello Freesurfer team, I've used freesurfer to segment (recon-all) approximately 30 different subjects from a study. I've noticed that a large number of these subjects have a misclassification of the white and pial boundaries in the occipital lobe (such that grey matter is being classified as white matter). I believe this problem is originating from my scanner and original data. I'm acquiring a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a 32 channel phased array head coil. For many subjects, this acquistion gives intensity inhomogeneity in the occipital lobe. I've begun using a GE based correction technique (PURE) on the images, and it appears to improve the intensity in the occipital lobe, but Freesurfer is still frequently misclassifying.

I'm wondering what would be the best way to edit the data. I've often tried to edit the wm.vol, but this doesn't seem to fix anything. For the most part, the wm.vol is correct to begin with, but the wm cutting line isn't segmenting with the wm.vol. I've also tried to add control points but this doesn't seem to improve anything either.

I've attached an image which I hope will further explain my problems.

Thanks for any help

---

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Try adding --lh to the make_average_subject command line. Let me know if that works and I'll change the docs doug

On 07/29/2014 05:13 PM, angela.favaro@unipd.it wrote:

Hi Doug, this the command and output (here with only five subjects). thank you!

make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

/Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

$Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $ Mar 29 Lug 2014 23:09:30 CEST /Users/angelafavaro/Desktop/risonanze/studyfree setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/risonanze/studyfree output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree uid=501(angelafavaro) gid=20(staff) groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) ==================== make_average_surface ==================== Mar 29 Lug 2014 23:09:31 CEST /Users/angelafavaro/Desktop/risonanze/studyfree /Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only input subjects: subj001 subj002 subj003 subj004 subj005 output subject: myatlas.i1 mri_add_xform_to_header -c auto /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz INFO: extension is mgz

#@# Making lh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc lh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... curvature mean = -0.028, std = 0.969 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm...

processing subject subj001/xhemi (2 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.586 curvature mean = -0.082, std = 0.795 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... curvature mean = -0.026, std = 1.007 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm...

processing subject subj002 (3 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.593 curvature mean = -0.071, std = 1.122 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... curvature mean = -0.025, std = 0.999 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm...

processing subject subj002/xhemi (4 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.597 curvature mean = -0.059, std = 1.231 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... curvature mean = -0.032, std = 0.973 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm...

processing subject subj003 (5 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.603 curvature mean = -0.062, std = 0.880 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... curvature mean = -0.035, std = 0.995 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm...

processing subject subj003/xhemi (6 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.572 curvature mean = -0.070, std = 2.235 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... curvature mean = -0.039, std = 0.991 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm...

processing subject subj004 (7 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.586 curvature mean = -0.097, std = 4.940 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... curvature mean = -0.028, std = 1.002 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm...

processing subject subj004/xhemi (8 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.603 curvature mean = -0.069, std = 1.134 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... curvature mean = -0.025, std = 1.004 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm...

processing subject subj005 (9 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.622 curvature mean = -0.067, std = 0.915 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... curvature mean = -0.038, std = 0.967 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm...

processing subject subj005/xhemi (10 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.591 curvature mean = -0.078, std = 0.997 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... curvature mean = -0.030, std = 0.984 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... writing updated template with 10 subjects to lh.reg.template.tif... curvature mean = 0.003, std = 0.598 curvature mean = -0.080, std = 0.911

#@# Making rh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface [host-002:~/Desktop/

...

What is the command line that is failing and what is the full terminal output? doug

On 07/29/2014 05:55 AM, angela.favaro@unipd.it wrote:

...

Hi all, I am now working with the 5.3 version and performing interhemispheric registration (building my own atlas)

after running for all subjects: xhemireg --s subj001.... surfreg --s subj001 --t fsaverage_sym --lh surfreg --s subj001 --t fsaverage_sym --xhemi --lh

I have tried first iteration, but the following error occurs:

processing subject subj001 (1 of 194) reading spherical surface /Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/Angela/studyfree/subj002/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface

how can I get the rh.fsaverage_sym.sphere.reg file?

thank you!

Angela

...

Hi Matt

certainly something is wrong, but it's hard to tell why from the single slice. You have big topological defects that are being fixed incorrectly. Can you upload the subject and we will take a look? cheers Bruce On Mon, 28 Jul 2014, Walton, Matt wrote:

...

Hello Freesurfer team, I've used freesurfer to segment (recon-all) approximately 30 different subjects from a study. I've noticed that a large number of these subjects have a misclassification of the white and pial boundaries in the occipital lobe (such that grey matter is being classified as white matter). I believe this problem is originating from my scanner and original data. I'm acquiring a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a 32 channel phased array head coil. For many subjects, this acquistion gives intensity inhomogeneity in the occipital lobe. I've begun using a GE based correction technique (PURE) on the images, and it appears to improve the intensity in the occipital lobe, but Freesurfer is still frequently misclassifying.

I'm wondering what would be the best way to edit the data. I've often tried to edit the wm.vol, but this doesn't seem to fix anything. For the most part, the wm.vol is correct to begin with, but the wm cutting line isn't segmenting with the wm.vol. I've also tried to add control points but this doesn't seem to improve anything either.

I've attached an image which I hope will further explain my problems.

Thanks for any help

---

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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Is that all it prints out? What version of FS are you using?

On 07/29/2014 05:26 PM, angela.favaro@unipd.it wrote:

ERROR: Flag --lh unrecognized.

...

Try adding --lh to the make_average_subject command line. Let me know if that works and I'll change the docs doug

On 07/29/2014 05:13 PM, angela.favaro@unipd.it wrote:

...

Hi Doug, this the command and output (here with only five subjects). thank you!

make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

/Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

$Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $ Mar 29 Lug 2014 23:09:30 CEST /Users/angelafavaro/Desktop/risonanze/studyfree setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/risonanze/studyfree output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree uid=501(angelafavaro) gid=20(staff) groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) ==================== make_average_surface ==================== Mar 29 Lug 2014 23:09:31 CEST /Users/angelafavaro/Desktop/risonanze/studyfree /Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only input subjects: subj001 subj002 subj003 subj004 subj005 output subject: myatlas.i1 mri_add_xform_to_header -c auto /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz INFO: extension is mgz

#@# Making lh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc lh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... curvature mean = -0.028, std = 0.969 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm...

processing subject subj001/xhemi (2 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.586 curvature mean = -0.082, std = 0.795 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... curvature mean = -0.026, std = 1.007 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm...

processing subject subj002 (3 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.593 curvature mean = -0.071, std = 1.122 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... curvature mean = -0.025, std = 0.999 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm...

processing subject subj002/xhemi (4 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.597 curvature mean = -0.059, std = 1.231 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... curvature mean = -0.032, std = 0.973 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm...

processing subject subj003 (5 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.603 curvature mean = -0.062, std = 0.880 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... curvature mean = -0.035, std = 0.995 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm...

processing subject subj003/xhemi (6 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.572 curvature mean = -0.070, std = 2.235 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... curvature mean = -0.039, std = 0.991 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm...

processing subject subj004 (7 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.586 curvature mean = -0.097, std = 4.940 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... curvature mean = -0.028, std = 1.002 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm...

processing subject subj004/xhemi (8 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.603 curvature mean = -0.069, std = 1.134 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... curvature mean = -0.025, std = 1.004 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm...

processing subject subj005 (9 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.622 curvature mean = -0.067, std = 0.915 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... curvature mean = -0.038, std = 0.967 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm...

processing subject subj005/xhemi (10 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.591 curvature mean = -0.078, std = 0.997 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... curvature mean = -0.030, std = 0.984 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... writing updated template with 10 subjects to lh.reg.template.tif... curvature mean = 0.003, std = 0.598 curvature mean = -0.080, std = 0.911

#@# Making rh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface [host-002:~/Desktop/

...

What is the command line that is failing and what is the full terminal output? doug

On 07/29/2014 05:55 AM, angela.favaro@unipd.it wrote:

...

Hi all, I am now working with the 5.3 version and performing interhemispheric registration (building my own atlas)

after running for all subjects: xhemireg --s subj001.... surfreg --s subj001 --t fsaverage_sym --lh surfreg --s subj001 --t fsaverage_sym --xhemi --lh

I have tried first iteration, but the following error occurs:

processing subject subj001 (1 of 194) reading spherical surface /Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/Angela/studyfree/subj002/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface

how can I get the rh.fsaverage_sym.sphere.reg file?

thank you!

Angela

...

Hi Matt

certainly something is wrong, but it's hard to tell why from the single slice. You have big topological defects that are being fixed incorrectly. Can you upload the subject and we will take a look? cheers Bruce On Mon, 28 Jul 2014, Walton, Matt wrote:

> Hello Freesurfer team, > I've used freesurfer to segment (recon-all) approximately 30 > different > subjects from a study. I've noticed that a large number of these > subjects > have a misclassification of the white and pial boundaries in the > occipital > lobe (such that grey matter is being classified as white matter). I > believe > this problem is originating from my scanner and original data. I'm > acquiring > a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a 32 > channel > phased array head coil. For many subjects, this acquistion gives > intensity > inhomogeneity in the occipital lobe. I've begun using a GE based > correction > technique (PURE) on the images, and it appears to improve the > intensity > in > the occipital lobe, but Freesurfer is still frequently > misclassifying. > > I'm wondering what would be the best way to edit the data. I've > often > tried > to edit the wm.vol, but this doesn't seem to fix anything. For the > most > part, the wm.vol is correct to begin with, but the wm cutting line > isn't > segmenting with the wm.vol. I've also tried to add control points > but > this > doesn't seem to improve anything either. > > I've attached an image which I hope will further explain my > problems. > > Thanks for any help > > _______________________________________________ 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.

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Copy this file into $FREESURFER_HOME/bin (make a backup of the existing one) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface

let me know if that works doug

On 07/29/2014 05:37 PM, angela.favaro@unipd.it wrote:

I am using 5.3

make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh ERROR: Flag --lh unrecognized. --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh ERROR: make_average_surface

...

Is that all it prints out? What version of FS are you using?

On 07/29/2014 05:26 PM, angela.favaro@unipd.it wrote:

...

ERROR: Flag --lh unrecognized.

...

Try adding --lh to the make_average_subject command line. Let me know if that works and I'll change the docs doug

On 07/29/2014 05:13 PM, angela.favaro@unipd.it wrote:

...

Hi Doug, this the command and output (here with only five subjects). thank you!

make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

/Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

$Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $ Mar 29 Lug 2014 23:09:30 CEST /Users/angelafavaro/Desktop/risonanze/studyfree setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/risonanze/studyfree output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree uid=501(angelafavaro) gid=20(staff) groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) ==================== make_average_surface ==================== Mar 29 Lug 2014 23:09:31 CEST /Users/angelafavaro/Desktop/risonanze/studyfree /Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only input subjects: subj001 subj002 subj003 subj004 subj005 output subject: myatlas.i1 mri_add_xform_to_header -c auto /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz INFO: extension is mgz

#@# Making lh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc lh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... curvature mean = -0.028, std = 0.969 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm...

processing subject subj001/xhemi (2 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.586 curvature mean = -0.082, std = 0.795 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... curvature mean = -0.026, std = 1.007 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm...

processing subject subj002 (3 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.593 curvature mean = -0.071, std = 1.122 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... curvature mean = -0.025, std = 0.999 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm...

processing subject subj002/xhemi (4 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.597 curvature mean = -0.059, std = 1.231 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... curvature mean = -0.032, std = 0.973 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm...

processing subject subj003 (5 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.603 curvature mean = -0.062, std = 0.880 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... curvature mean = -0.035, std = 0.995 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm...

processing subject subj003/xhemi (6 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.572 curvature mean = -0.070, std = 2.235 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... curvature mean = -0.039, std = 0.991 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm...

processing subject subj004 (7 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.586 curvature mean = -0.097, std = 4.940 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... curvature mean = -0.028, std = 1.002 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm...

processing subject subj004/xhemi (8 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.603 curvature mean = -0.069, std = 1.134 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... curvature mean = -0.025, std = 1.004 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm...

processing subject subj005 (9 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.622 curvature mean = -0.067, std = 0.915 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... curvature mean = -0.038, std = 0.967 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm...

processing subject subj005/xhemi (10 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.591 curvature mean = -0.078, std = 0.997 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... curvature mean = -0.030, std = 0.984 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... writing updated template with 10 subjects to lh.reg.template.tif... curvature mean = 0.003, std = 0.598 curvature mean = -0.080, std = 0.911

#@# Making rh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface [host-002:~/Desktop/

...

What is the command line that is failing and what is the full terminal output? doug

On 07/29/2014 05:55 AM, angela.favaro@unipd.it wrote: > Hi all, > I am now working with the 5.3 version and performing > interhemispheric > registration (building my own atlas) > > after running for all subjects: > xhemireg --s subj001.... > surfreg --s subj001 --t fsaverage_sym --lh > surfreg --s subj001 --t fsaverage_sym --xhemi --lh > > I have tried first iteration, but the following error occurs: > > processing subject subj001 (1 of 194) > reading spherical surface > /Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... > MRISread(/Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): > could not open file > No such file or directory > mris_make_template: could not read surface file > /Users/angelafavaro/Desktop/Angela/studyfree/subj002/surf/rh.fsaverage_sym.sphere.reg > No such file or directory > ERROR: make_average_surface > > how can I get the rh.fsaverage_sym.sphere.reg file? > > thank you! > > Angela > > > > > >> Hi Matt >> >> certainly something is wrong, but it's hard to tell why from the >> single >> slice. You have big topological defects that are being fixed >> incorrectly. >> Can you upload the subject and we will take a look? >> cheers >> Bruce >> On Mon, 28 Jul 2014, >> Walton, Matt wrote: >> >>> Hello Freesurfer team, >>> I've used freesurfer to segment (recon-all) approximately 30 >>> different >>> subjects from a study. I've noticed that a large number of these >>> subjects >>> have a misclassification of the white and pial boundaries in the >>> occipital >>> lobe (such that grey matter is being classified as white matter). >>> I >>> believe >>> this problem is originating from my scanner and original data. I'm >>> acquiring >>> a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a 32 >>> channel >>> phased array head coil. For many subjects, this acquistion gives >>> intensity >>> inhomogeneity in the occipital lobe. I've begun using a GE based >>> correction >>> technique (PURE) on the images, and it appears to improve the >>> intensity >>> in >>> the occipital lobe, but Freesurfer is still frequently >>> misclassifying. >>> >>> I'm wondering what would be the best way to edit the data. I've >>> often >>> tried >>> to edit the wm.vol, but this doesn't seem to fix anything. For the >>> most >>> part, the wm.vol is correct to begin with, but the wm cutting line >>> isn't >>> segmenting with the wm.vol. I've also tried to add control points >>> but >>> this >>> doesn't seem to improve anything either. >>> >>> I've attached an image which I hope will further explain my >>> problems. >>> >>> Thanks for any help >>> >>> _______________________________________________ >> 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. >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

>

Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

can you send the full terminal output On 07/29/2014 06:00 PM, angela.favaro@unipd.it wrote:

Hi Doug, unfortunately the same error message appear... it looks for rh.fsaverage_sym.sphere.reg

.... #@# Making rh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface

...

Copy this file into $FREESURFER_HOME/bin (make a backup of the existing one) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface

let me know if that works doug

On 07/29/2014 05:37 PM, angela.favaro@unipd.it wrote:

...

I am using 5.3

make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh ERROR: Flag --lh unrecognized. --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh ERROR: make_average_surface

...

Is that all it prints out? What version of FS are you using?

On 07/29/2014 05:26 PM, angela.favaro@unipd.it wrote:

...

ERROR: Flag --lh unrecognized.

...

Try adding --lh to the make_average_subject command line. Let me know if that works and I'll change the docs doug

On 07/29/2014 05:13 PM, angela.favaro@unipd.it wrote: > Hi Doug, this the command and output (here with only five subjects). > thank you! > > make_average_subject --out myatlas.i1 --surf-reg > fsaverage_sym.sphere.reg > --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol > --template-only > make_average_surface --out myatlas.i1 --surf-reg > fsaverage_sym.sphere.reg > --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol > --template-only > > /Applications/freesurfer/bin/make_average_surface > --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects > subj001 > subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only > > $Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $ > Mar 29 Lug 2014 23:09:30 CEST > /Users/angelafavaro/Desktop/risonanze/studyfree > setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/risonanze/studyfree > output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree > uid=501(angelafavaro) gid=20(staff) > groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) > ==================== > make_average_surface > ==================== > Mar 29 Lug 2014 23:09:31 CEST > /Users/angelafavaro/Desktop/risonanze/studyfree > /Applications/freesurfer/bin/make_average_surface > --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects > subj001 > subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only > input subjects: subj001 subj002 subj003 subj004 subj005 > output subject: myatlas.i1 > mri_add_xform_to_header -c auto > /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz > /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz > INFO: extension is mgz > > > #@# Making lh registration template --------- > /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 > mris_make_template -norot -annot aparc lh fsaverage_sym.sphere.reg > subj001 > subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 > subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif > not aligning hemispheres before averaging. > zeroing medial wall in aparc > creating new parameterization... > > processing subject subj001 (1 of 10) > reading spherical surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > ripping medial wall... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... > curvature mean = -0.028, std = 0.969 > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm... > > processing subject subj001/xhemi (2 of 10) > reading spherical surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... > curvature mean = 0.003, std = 0.586 > curvature mean = -0.082, std = 0.795 > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > ripping medial wall... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... > curvature mean = -0.026, std = 1.007 > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm... > > processing subject subj002 (3 of 10) > reading spherical surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... > curvature mean = 0.003, std = 0.593 > curvature mean = -0.071, std = 1.122 > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > ripping medial wall... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... > curvature mean = -0.025, std = 0.999 > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm... > > processing subject subj002/xhemi (4 of 10) > reading spherical surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... > curvature mean = 0.002, std = 0.597 > curvature mean = -0.059, std = 1.231 > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > ripping medial wall... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... > curvature mean = -0.032, std = 0.973 > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm... > > processing subject subj003 (5 of 10) > reading spherical surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... > curvature mean = 0.003, std = 0.603 > curvature mean = -0.062, std = 0.880 > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > ripping medial wall... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... > curvature mean = -0.035, std = 0.995 > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm... > > processing subject subj003/xhemi (6 of 10) > reading spherical surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... > curvature mean = 0.000, std = 0.572 > curvature mean = -0.070, std = 2.235 > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > ripping medial wall... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... > curvature mean = -0.039, std = 0.991 > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm... > > processing subject subj004 (7 of 10) > reading spherical surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... > curvature mean = 0.000, std = 0.586 > curvature mean = -0.097, std = 4.940 > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > ripping medial wall... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... > curvature mean = -0.028, std = 1.002 > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm... > > processing subject subj004/xhemi (8 of 10) > reading spherical surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... > curvature mean = 0.002, std = 0.603 > curvature mean = -0.069, std = 1.134 > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > ripping medial wall... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... > curvature mean = -0.025, std = 1.004 > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm... > > processing subject subj005 (9 of 10) > reading spherical surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... > curvature mean = 0.003, std = 0.622 > curvature mean = -0.067, std = 0.915 > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > ripping medial wall... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... > curvature mean = -0.038, std = 0.967 > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm... > > processing subject subj005/xhemi (10 of 10) > reading spherical surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... > curvature mean = 0.002, std = 0.591 > curvature mean = -0.078, std = 0.997 > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > ripping medial wall... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... > curvature mean = -0.030, std = 0.984 > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... > computing parameterization for surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... > writing updated template with 10 subjects to lh.reg.template.tif... > curvature mean = 0.003, std = 0.598 > curvature mean = -0.080, std = 0.911 > > > #@# Making rh registration template --------- > /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 > mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg > subj001 > subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 > subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif > not aligning hemispheres before averaging. > zeroing medial wall in aparc > creating new parameterization... > > processing subject subj001 (1 of 10) > reading spherical surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... > MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): > could not open file > No such file or directory > mris_make_template: could not read surface file > /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg > No such file or directory > ERROR: make_average_surface > [host-002:~/Desktop/ > > > > > > > > > >> What is the command line that is failing and what is the full >> terminal >> output? >> doug >> >> >> On 07/29/2014 05:55 AM, angela.favaro@unipd.it wrote: >>> Hi all, >>> I am now working with the 5.3 version and performing >>> interhemispheric >>> registration (building my own atlas) >>> >>> after running for all subjects: >>> xhemireg --s subj001.... >>> surfreg --s subj001 --t fsaverage_sym --lh >>> surfreg --s subj001 --t fsaverage_sym --xhemi --lh >>> >>> I have tried first iteration, but the following error occurs: >>> >>> processing subject subj001 (1 of 194) >>> reading spherical surface >>> /Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... >>> MRISread(/Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): >>> could not open file >>> No such file or directory >>> mris_make_template: could not read surface file >>> /Users/angelafavaro/Desktop/Angela/studyfree/subj002/surf/rh.fsaverage_sym.sphere.reg >>> No such file or directory >>> ERROR: make_average_surface >>> >>> how can I get the rh.fsaverage_sym.sphere.reg file? >>> >>> thank you! >>> >>> Angela >>> >>> >>> >>> >>> >>>> Hi Matt >>>> >>>> certainly something is wrong, but it's hard to tell why from the >>>> single >>>> slice. You have big topological defects that are being fixed >>>> incorrectly. >>>> Can you upload the subject and we will take a look? >>>> cheers >>>> Bruce >>>> On Mon, 28 Jul 2014, >>>> Walton, Matt wrote: >>>> >>>>> Hello Freesurfer team, >>>>> I've used freesurfer to segment (recon-all) approximately 30 >>>>> different >>>>> subjects from a study. I've noticed that a large number of these >>>>> subjects >>>>> have a misclassification of the white and pial boundaries in the >>>>> occipital >>>>> lobe (such that grey matter is being classified as white >>>>> matter). >>>>> I >>>>> believe >>>>> this problem is originating from my scanner and original data. >>>>> I'm >>>>> acquiring >>>>> a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using a >>>>> 32 >>>>> channel >>>>> phased array head coil. For many subjects, this acquistion gives >>>>> intensity >>>>> inhomogeneity in the occipital lobe. I've begun using a GE >>>>> based >>>>> correction >>>>> technique (PURE) on the images, and it appears to improve the >>>>> intensity >>>>> in >>>>> the occipital lobe, but Freesurfer is still frequently >>>>> misclassifying. >>>>> >>>>> I'm wondering what would be the best way to edit the data. I've >>>>> often >>>>> tried >>>>> to edit the wm.vol, but this doesn't seem to fix anything. For >>>>> the >>>>> most >>>>> part, the wm.vol is correct to begin with, but the wm cutting >>>>> line >>>>> isn't >>>>> segmenting with the wm.vol. I've also tried to add control >>>>> points >>>>> but >>>>> this >>>>> doesn't seem to improve anything either. >>>>> >>>>> I've attached an image which I hope will further explain my >>>>> problems. >>>>> >>>>> Thanks for any help >>>>> >>>>> _______________________________________________ >>>> 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. >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

>

Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

when you run make_average_subject, you will still need the --lh doug

On 07/29/2014 06:07 PM, angela.favaro@unipd.it wrote:

ftp ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 331 Please specify the password. 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. 200 Switching to Binary mode. 250 Directory successfully changed. 250 Directory successfully changed. 250 Directory successfully changed. 250 Directory successfully changed. local: make_average_surface remote: make_average_surface 229 Entering Extended Passive Mode (|||37856|). 150 Opening BINARY mode data connection for make_average_surface (19641 bytes). 100% |***********************************| 19641 95.79 KiB/s 00:00 ETA 226 Transfer complete. 19641 bytes received in 00:00 (54.68 KiB/s) 221 Goodbye. [host-002:~/Desktop/risonanze/studyfree] angelafavaro% cp make_average_surface $FREESURFER_HOME/bin/make_average_surface cp: /Applications/freesurfer/bin/make_average_surface: Permission denied [host-002:~/Desktop/risonanze/studyfree] angelafavaro% sudo cp make_average_surface $FREESURFER_HOME/bin/make_average_surface Password: [host-002:~/Desktop/risonanze/studyfree] angelafavaro% make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

/Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

$Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $ Mar 29 Lug 2014 23:57:25 CEST /Users/angelafavaro/Desktop/risonanze/studyfree setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/risonanze/studyfree output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree uid=501(angelafavaro) gid=20(staff) groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) ==================== make_average_surface ==================== Mar 29 Lug 2014 23:57:27 CEST /Users/angelafavaro/Desktop/risonanze/studyfree /Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only input subjects: subj001 subj002 subj003 subj004 subj005 output subject: myatlas.i1 mri_add_xform_to_header -c auto /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz INFO: extension is mgz

#@# Making lh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc lh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... curvature mean = -0.028, std = 0.969 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm...

processing subject subj001/xhemi (2 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.586 curvature mean = -0.082, std = 0.795 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... curvature mean = -0.026, std = 1.007 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm...

processing subject subj002 (3 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.593 curvature mean = -0.071, std = 1.122 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... curvature mean = -0.025, std = 0.999 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm...

processing subject subj002/xhemi (4 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.597 curvature mean = -0.059, std = 1.231 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... curvature mean = -0.032, std = 0.973 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm...

processing subject subj003 (5 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.603 curvature mean = -0.062, std = 0.880 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... curvature mean = -0.035, std = 0.995 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm...

processing subject subj003/xhemi (6 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.572 curvature mean = -0.070, std = 2.235 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... curvature mean = -0.039, std = 0.991 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm...

processing subject subj004 (7 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.586 curvature mean = -0.097, std = 4.940 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... curvature mean = -0.028, std = 1.002 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm...

processing subject subj004/xhemi (8 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.603 curvature mean = -0.069, std = 1.134 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... curvature mean = -0.025, std = 1.004 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm...

processing subject subj005 (9 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.622 curvature mean = -0.067, std = 0.915 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... curvature mean = -0.038, std = 0.967 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm...

processing subject subj005/xhemi (10 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.591 curvature mean = -0.078, std = 0.997 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... curvature mean = -0.030, std = 0.984 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... writing updated template with 10 subjects to lh.reg.template.tif... curvature mean = 0.003, std = 0.598 curvature mean = -0.080, std = 0.911

#@# Making rh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface

...

can you send the full terminal output On 07/29/2014 06:00 PM, angela.favaro@unipd.it wrote:

...

Hi Doug, unfortunately the same error message appear... it looks for rh.fsaverage_sym.sphere.reg

.... #@# Making rh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface

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Copy this file into $FREESURFER_HOME/bin (make a backup of the existing one) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface

let me know if that works doug

On 07/29/2014 05:37 PM, angela.favaro@unipd.it wrote:

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I am using 5.3

make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh ERROR: Flag --lh unrecognized. --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh ERROR: make_average_surface

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Is that all it prints out? What version of FS are you using?

On 07/29/2014 05:26 PM, angela.favaro@unipd.it wrote: > ERROR: Flag --lh unrecognized. > >> Try adding --lh to the make_average_subject command line. Let me >> know >> if >> that works and I'll change the docs >> doug >> >> >> On 07/29/2014 05:13 PM, angela.favaro@unipd.it wrote: >>> Hi Doug, this the command and output (here with only five >>> subjects). >>> thank you! >>> >>> make_average_subject --out myatlas.i1 --surf-reg >>> fsaverage_sym.sphere.reg >>> --subjects subj001 subj002 subj003 subj004 subj005 --xhemi >>> --no-vol >>> --template-only >>> make_average_surface --out myatlas.i1 --surf-reg >>> fsaverage_sym.sphere.reg >>> --subjects subj001 subj002 subj003 subj004 subj005 --xhemi >>> --no-vol >>> --template-only >>> >>> /Applications/freesurfer/bin/make_average_surface >>> --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects >>> subj001 >>> subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only >>> >>> $Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp >>> $ >>> Mar 29 Lug 2014 23:09:30 CEST >>> /Users/angelafavaro/Desktop/risonanze/studyfree >>> setenv SUBJECTS_DIR >>> /Users/angelafavaro/Desktop/risonanze/studyfree >>> output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree >>> uid=501(angelafavaro) gid=20(staff) >>> groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) >>> ==================== >>> make_average_surface >>> ==================== >>> Mar 29 Lug 2014 23:09:31 CEST >>> /Users/angelafavaro/Desktop/risonanze/studyfree >>> /Applications/freesurfer/bin/make_average_surface >>> --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects >>> subj001 >>> subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only >>> input subjects: subj001 subj002 subj003 subj004 subj005 >>> output subject: myatlas.i1 >>> mri_add_xform_to_header -c auto >>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz >>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz >>> INFO: extension is mgz >>> >>> >>> #@# Making lh registration template --------- >>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 >>> mris_make_template -norot -annot aparc lh fsaverage_sym.sphere.reg >>> subj001 >>> subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 >>> subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif >>> not aligning hemispheres before averaging. >>> zeroing medial wall in aparc >>> creating new parameterization... >>> >>> processing subject subj001 (1 of 10) >>> reading spherical surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... >>> reading colortable from annotation file... >>> colortable with 36 entries read (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>> ripping medial wall... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... >>> curvature mean = -0.028, std = 0.969 >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm... >>> >>> processing subject subj001/xhemi (2 of 10) >>> reading spherical surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>> curvature mean = 0.003, std = 0.586 >>> curvature mean = -0.082, std = 0.795 >>> reading colortable from annotation file... >>> colortable with 36 entries read (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>> ripping medial wall... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... >>> curvature mean = -0.026, std = 1.007 >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm... >>> >>> processing subject subj002 (3 of 10) >>> reading spherical surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... >>> curvature mean = 0.003, std = 0.593 >>> curvature mean = -0.071, std = 1.122 >>> reading colortable from annotation file... >>> colortable with 36 entries read (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>> ripping medial wall... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... >>> curvature mean = -0.025, std = 0.999 >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm... >>> >>> processing subject subj002/xhemi (4 of 10) >>> reading spherical surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>> curvature mean = 0.002, std = 0.597 >>> curvature mean = -0.059, std = 1.231 >>> reading colortable from annotation file... >>> colortable with 36 entries read (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>> ripping medial wall... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... >>> curvature mean = -0.032, std = 0.973 >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm... >>> >>> processing subject subj003 (5 of 10) >>> reading spherical surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... >>> curvature mean = 0.003, std = 0.603 >>> curvature mean = -0.062, std = 0.880 >>> reading colortable from annotation file... >>> colortable with 36 entries read (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>> ripping medial wall... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... >>> curvature mean = -0.035, std = 0.995 >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm... >>> >>> processing subject subj003/xhemi (6 of 10) >>> reading spherical surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>> curvature mean = 0.000, std = 0.572 >>> curvature mean = -0.070, std = 2.235 >>> reading colortable from annotation file... >>> colortable with 36 entries read (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>> ripping medial wall... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... >>> curvature mean = -0.039, std = 0.991 >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm... >>> >>> processing subject subj004 (7 of 10) >>> reading spherical surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... >>> curvature mean = 0.000, std = 0.586 >>> curvature mean = -0.097, std = 4.940 >>> reading colortable from annotation file... >>> colortable with 36 entries read (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>> ripping medial wall... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... >>> curvature mean = -0.028, std = 1.002 >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm... >>> >>> processing subject subj004/xhemi (8 of 10) >>> reading spherical surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>> curvature mean = 0.002, std = 0.603 >>> curvature mean = -0.069, std = 1.134 >>> reading colortable from annotation file... >>> colortable with 36 entries read (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>> ripping medial wall... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... >>> curvature mean = -0.025, std = 1.004 >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm... >>> >>> processing subject subj005 (9 of 10) >>> reading spherical surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... >>> curvature mean = 0.003, std = 0.622 >>> curvature mean = -0.067, std = 0.915 >>> reading colortable from annotation file... >>> colortable with 36 entries read (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>> ripping medial wall... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... >>> curvature mean = -0.038, std = 0.967 >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm... >>> >>> processing subject subj005/xhemi (10 of 10) >>> reading spherical surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>> curvature mean = 0.002, std = 0.591 >>> curvature mean = -0.078, std = 0.997 >>> reading colortable from annotation file... >>> colortable with 36 entries read (originally >>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>> ripping medial wall... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... >>> curvature mean = -0.030, std = 0.984 >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... >>> computing parameterization for surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... >>> writing updated template with 10 subjects to >>> lh.reg.template.tif... >>> curvature mean = 0.003, std = 0.598 >>> curvature mean = -0.080, std = 0.911 >>> >>> >>> #@# Making rh registration template --------- >>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 >>> mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg >>> subj001 >>> subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 >>> subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif >>> not aligning hemispheres before averaging. >>> zeroing medial wall in aparc >>> creating new parameterization... >>> >>> processing subject subj001 (1 of 10) >>> reading spherical surface >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... >>> MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): >>> could not open file >>> No such file or directory >>> mris_make_template: could not read surface file >>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg >>> No such file or directory >>> ERROR: make_average_surface >>> [host-002:~/Desktop/ >>> >>> >>> >>> >>> >>> >>> >>> >>> >>>> What is the command line that is failing and what is the full >>>> terminal >>>> output? >>>> doug >>>> >>>> >>>> On 07/29/2014 05:55 AM, angela.favaro@unipd.it wrote: >>>>> Hi all, >>>>> I am now working with the 5.3 version and performing >>>>> interhemispheric >>>>> registration (building my own atlas) >>>>> >>>>> after running for all subjects: >>>>> xhemireg --s subj001.... >>>>> surfreg --s subj001 --t fsaverage_sym --lh >>>>> surfreg --s subj001 --t fsaverage_sym --xhemi --lh >>>>> >>>>> I have tried first iteration, but the following error occurs: >>>>> >>>>> processing subject subj001 (1 of 194) >>>>> reading spherical surface >>>>> /Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... >>>>> MRISread(/Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): >>>>> could not open file >>>>> No such file or directory >>>>> mris_make_template: could not read surface file >>>>> /Users/angelafavaro/Desktop/Angela/studyfree/subj002/surf/rh.fsaverage_sym.sphere.reg >>>>> No such file or directory >>>>> ERROR: make_average_surface >>>>> >>>>> how can I get the rh.fsaverage_sym.sphere.reg file? >>>>> >>>>> thank you! >>>>> >>>>> Angela >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> Hi Matt >>>>>> >>>>>> certainly something is wrong, but it's hard to tell why from >>>>>> the >>>>>> single >>>>>> slice. You have big topological defects that are being fixed >>>>>> incorrectly. >>>>>> Can you upload the subject and we will take a look? >>>>>> cheers >>>>>> Bruce >>>>>> On Mon, 28 Jul 2014, >>>>>> Walton, Matt wrote: >>>>>> >>>>>>> Hello Freesurfer team, >>>>>>> I've used freesurfer to segment (recon-all) approximately 30 >>>>>>> different >>>>>>> subjects from a study. I've noticed that a large number of >>>>>>> these >>>>>>> subjects >>>>>>> have a misclassification of the white and pial boundaries in >>>>>>> the >>>>>>> occipital >>>>>>> lobe (such that grey matter is being classified as white >>>>>>> matter). >>>>>>> I >>>>>>> believe >>>>>>> this problem is originating from my scanner and original data. >>>>>>> I'm >>>>>>> acquiring >>>>>>> a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, using >>>>>>> a >>>>>>> 32 >>>>>>> channel >>>>>>> phased array head coil. For many subjects, this acquistion >>>>>>> gives >>>>>>> intensity >>>>>>> inhomogeneity in the occipital lobe. I've begun using a GE >>>>>>> based >>>>>>> correction >>>>>>> technique (PURE) on the images, and it appears to improve the >>>>>>> intensity >>>>>>> in >>>>>>> the occipital lobe, but Freesurfer is still frequently >>>>>>> misclassifying. >>>>>>> >>>>>>> I'm wondering what would be the best way to edit the data. >>>>>>> I've >>>>>>> often >>>>>>> tried >>>>>>> to edit the wm.vol, but this doesn't seem to fix anything. For >>>>>>> the >>>>>>> most >>>>>>> part, the wm.vol is correct to begin with, but the wm cutting >>>>>>> line >>>>>>> isn't >>>>>>> segmenting with the wm.vol. I've also tried to add control >>>>>>> points >>>>>>> but >>>>>>> this >>>>>>> doesn't seem to improve anything either. >>>>>>> >>>>>>> I've attached an image which I hope will further explain my >>>>>>> problems. >>>>>>> >>>>>>> Thanks for any help >>>>>>> >>>>>>> _______________________________________________ >>>>>> 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. >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

>

Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

Hi Doug, I am having a problem with the last step of building my own symmetric atlas. I am using the make_average_surface you gave me and adding the --lh flag in the first two iteration. However in the third iteration the command 'make_average_subject' did not recognize neither the --hemi lh flag (indicated in the wiki guide) neither the --lh flag (you suggested to add in the first two iterations)

the error message was immediate in the first case: ERROR: Flag --hemi unrecognized.

and after two hours in the second... ERROR: Flag --lh unrecognized. --out myatlas.i3 --surf-reg myatlas.i2.sphere.reg --subjects subj001 subj002 .... --xhemi --lh ERROR: make_average_volume

Do you think I need a 'special' make_average_volume? or I need to use the 'old' 'make_average_surface'?

the log of make_average_surface in the script folder of my atlas.i3 indicates no error... (attached)

thank you for any help!!

Angela

when you run make_average_subject, you will still need the --lh doug

On 07/29/2014 06:07 PM, angela.favaro@unipd.it wrote:

...

ftp ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 331 Please specify the password. 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. 200 Switching to Binary mode. 250 Directory successfully changed. 250 Directory successfully changed. 250 Directory successfully changed. 250 Directory successfully changed. local: make_average_surface remote: make_average_surface 229 Entering Extended Passive Mode (|||37856|). 150 Opening BINARY mode data connection for make_average_surface (19641 bytes). 100% |***********************************| 19641 95.79 KiB/s 00:00 ETA 226 Transfer complete. 19641 bytes received in 00:00 (54.68 KiB/s) 221 Goodbye. [host-002:~/Desktop/risonanze/studyfree] angelafavaro% cp make_average_surface $FREESURFER_HOME/bin/make_average_surface cp: /Applications/freesurfer/bin/make_average_surface: Permission denied [host-002:~/Desktop/risonanze/studyfree] angelafavaro% sudo cp make_average_surface $FREESURFER_HOME/bin/make_average_surface Password: [host-002:~/Desktop/risonanze/studyfree] angelafavaro% make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

/Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

$Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $ Mar 29 Lug 2014 23:57:25 CEST /Users/angelafavaro/Desktop/risonanze/studyfree setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/risonanze/studyfree output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree uid=501(angelafavaro) gid=20(staff) groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) ==================== make_average_surface ==================== Mar 29 Lug 2014 23:57:27 CEST /Users/angelafavaro/Desktop/risonanze/studyfree /Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only input subjects: subj001 subj002 subj003 subj004 subj005 output subject: myatlas.i1 mri_add_xform_to_header -c auto /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz INFO: extension is mgz

#@# Making lh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc lh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... curvature mean = -0.028, std = 0.969 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm...

processing subject subj001/xhemi (2 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.586 curvature mean = -0.082, std = 0.795 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... curvature mean = -0.026, std = 1.007 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm...

processing subject subj002 (3 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.593 curvature mean = -0.071, std = 1.122 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... curvature mean = -0.025, std = 0.999 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm...

processing subject subj002/xhemi (4 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.597 curvature mean = -0.059, std = 1.231 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... curvature mean = -0.032, std = 0.973 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm...

processing subject subj003 (5 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.603 curvature mean = -0.062, std = 0.880 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... curvature mean = -0.035, std = 0.995 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm...

processing subject subj003/xhemi (6 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.572 curvature mean = -0.070, std = 2.235 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... curvature mean = -0.039, std = 0.991 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm...

processing subject subj004 (7 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.586 curvature mean = -0.097, std = 4.940 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... curvature mean = -0.028, std = 1.002 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm...

processing subject subj004/xhemi (8 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.603 curvature mean = -0.069, std = 1.134 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... curvature mean = -0.025, std = 1.004 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm...

processing subject subj005 (9 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.622 curvature mean = -0.067, std = 0.915 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... curvature mean = -0.038, std = 0.967 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm...

processing subject subj005/xhemi (10 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.591 curvature mean = -0.078, std = 0.997 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... curvature mean = -0.030, std = 0.984 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... writing updated template with 10 subjects to lh.reg.template.tif... curvature mean = 0.003, std = 0.598 curvature mean = -0.080, std = 0.911

#@# Making rh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface

...

can you send the full terminal output On 07/29/2014 06:00 PM, angela.favaro@unipd.it wrote:

...

Hi Doug, unfortunately the same error message appear... it looks for rh.fsaverage_sym.sphere.reg

.... #@# Making rh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface

...

Copy this file into $FREESURFER_HOME/bin (make a backup of the existing one) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface

let me know if that works doug

On 07/29/2014 05:37 PM, angela.favaro@unipd.it wrote:

...

I am using 5.3

make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh ERROR: Flag --lh unrecognized. --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only --lh ERROR: make_average_surface

> Is that all it prints out? What version of FS are you using? > > > On 07/29/2014 05:26 PM, angela.favaro@unipd.it wrote: >> ERROR: Flag --lh unrecognized. >> >>> Try adding --lh to the make_average_subject command line. Let me >>> know >>> if >>> that works and I'll change the docs >>> doug >>> >>> >>> On 07/29/2014 05:13 PM, angela.favaro@unipd.it wrote: >>>> Hi Doug, this the command and output (here with only five >>>> subjects). >>>> thank you! >>>> >>>> make_average_subject --out myatlas.i1 --surf-reg >>>> fsaverage_sym.sphere.reg >>>> --subjects subj001 subj002 subj003 subj004 subj005 --xhemi >>>> --no-vol >>>> --template-only >>>> make_average_surface --out myatlas.i1 --surf-reg >>>> fsaverage_sym.sphere.reg >>>> --subjects subj001 subj002 subj003 subj004 subj005 --xhemi >>>> --no-vol >>>> --template-only >>>> >>>> /Applications/freesurfer/bin/make_average_surface >>>> --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects >>>> subj001 >>>> subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only >>>> >>>> $Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve >>>> Exp >>>> $ >>>> Mar 29 Lug 2014 23:09:30 CEST >>>> /Users/angelafavaro/Desktop/risonanze/studyfree >>>> setenv SUBJECTS_DIR >>>> /Users/angelafavaro/Desktop/risonanze/studyfree >>>> output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree >>>> uid=501(angelafavaro) gid=20(staff) >>>> groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) >>>> ==================== >>>> make_average_surface >>>> ==================== >>>> Mar 29 Lug 2014 23:09:31 CEST >>>> /Users/angelafavaro/Desktop/risonanze/studyfree >>>> /Applications/freesurfer/bin/make_average_surface >>>> --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects >>>> subj001 >>>> subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only >>>> input subjects: subj001 subj002 subj003 subj004 subj005 >>>> output subject: myatlas.i1 >>>> mri_add_xform_to_header -c auto >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz >>>> INFO: extension is mgz >>>> >>>> >>>> #@# Making lh registration template --------- >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 >>>> mris_make_template -norot -annot aparc lh >>>> fsaverage_sym.sphere.reg >>>> subj001 >>>> subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi >>>> subj004 >>>> subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif >>>> not aligning hemispheres before averaging. >>>> zeroing medial wall in aparc >>>> creating new parameterization... >>>> >>>> processing subject subj001 (1 of 10) >>>> reading spherical surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... >>>> reading colortable from annotation file... >>>> colortable with 36 entries read (originally >>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>> ripping medial wall... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... >>>> curvature mean = -0.028, std = 0.969 >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm... >>>> >>>> processing subject subj001/xhemi (2 of 10) >>>> reading spherical surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>> curvature mean = 0.003, std = 0.586 >>>> curvature mean = -0.082, std = 0.795 >>>> reading colortable from annotation file... >>>> colortable with 36 entries read (originally >>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>> ripping medial wall... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... >>>> curvature mean = -0.026, std = 1.007 >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm... >>>> >>>> processing subject subj002 (3 of 10) >>>> reading spherical surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... >>>> curvature mean = 0.003, std = 0.593 >>>> curvature mean = -0.071, std = 1.122 >>>> reading colortable from annotation file... >>>> colortable with 36 entries read (originally >>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>> ripping medial wall... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... >>>> curvature mean = -0.025, std = 0.999 >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm... >>>> >>>> processing subject subj002/xhemi (4 of 10) >>>> reading spherical surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>> curvature mean = 0.002, std = 0.597 >>>> curvature mean = -0.059, std = 1.231 >>>> reading colortable from annotation file... >>>> colortable with 36 entries read (originally >>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>> ripping medial wall... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... >>>> curvature mean = -0.032, std = 0.973 >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm... >>>> >>>> processing subject subj003 (5 of 10) >>>> reading spherical surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... >>>> curvature mean = 0.003, std = 0.603 >>>> curvature mean = -0.062, std = 0.880 >>>> reading colortable from annotation file... >>>> colortable with 36 entries read (originally >>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>> ripping medial wall... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... >>>> curvature mean = -0.035, std = 0.995 >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm... >>>> >>>> processing subject subj003/xhemi (6 of 10) >>>> reading spherical surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>> curvature mean = 0.000, std = 0.572 >>>> curvature mean = -0.070, std = 2.235 >>>> reading colortable from annotation file... >>>> colortable with 36 entries read (originally >>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>> ripping medial wall... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... >>>> curvature mean = -0.039, std = 0.991 >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm... >>>> >>>> processing subject subj004 (7 of 10) >>>> reading spherical surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... >>>> curvature mean = 0.000, std = 0.586 >>>> curvature mean = -0.097, std = 4.940 >>>> reading colortable from annotation file... >>>> colortable with 36 entries read (originally >>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>> ripping medial wall... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... >>>> curvature mean = -0.028, std = 1.002 >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm... >>>> >>>> processing subject subj004/xhemi (8 of 10) >>>> reading spherical surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>> curvature mean = 0.002, std = 0.603 >>>> curvature mean = -0.069, std = 1.134 >>>> reading colortable from annotation file... >>>> colortable with 36 entries read (originally >>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>> ripping medial wall... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... >>>> curvature mean = -0.025, std = 1.004 >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm... >>>> >>>> processing subject subj005 (9 of 10) >>>> reading spherical surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... >>>> curvature mean = 0.003, std = 0.622 >>>> curvature mean = -0.067, std = 0.915 >>>> reading colortable from annotation file... >>>> colortable with 36 entries read (originally >>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>> ripping medial wall... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... >>>> curvature mean = -0.038, std = 0.967 >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm... >>>> >>>> processing subject subj005/xhemi (10 of 10) >>>> reading spherical surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>> curvature mean = 0.002, std = 0.591 >>>> curvature mean = -0.078, std = 0.997 >>>> reading colortable from annotation file... >>>> colortable with 36 entries read (originally >>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>> ripping medial wall... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... >>>> curvature mean = -0.030, std = 0.984 >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... >>>> computing parameterization for surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... >>>> writing updated template with 10 subjects to >>>> lh.reg.template.tif... >>>> curvature mean = 0.003, std = 0.598 >>>> curvature mean = -0.080, std = 0.911 >>>> >>>> >>>> #@# Making rh registration template --------- >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 >>>> mris_make_template -norot -annot aparc rh >>>> fsaverage_sym.sphere.reg >>>> subj001 >>>> subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi >>>> subj004 >>>> subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif >>>> not aligning hemispheres before averaging. >>>> zeroing medial wall in aparc >>>> creating new parameterization... >>>> >>>> processing subject subj001 (1 of 10) >>>> reading spherical surface >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... >>>> MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): >>>> could not open file >>>> No such file or directory >>>> mris_make_template: could not read surface file >>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg >>>> No such file or directory >>>> ERROR: make_average_surface >>>> [host-002:~/Desktop/ >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>>> What is the command line that is failing and what is the full >>>>> terminal >>>>> output? >>>>> doug >>>>> >>>>> >>>>> On 07/29/2014 05:55 AM, angela.favaro@unipd.it wrote: >>>>>> Hi all, >>>>>> I am now working with the 5.3 version and performing >>>>>> interhemispheric >>>>>> registration (building my own atlas) >>>>>> >>>>>> after running for all subjects: >>>>>> xhemireg --s subj001.... >>>>>> surfreg --s subj001 --t fsaverage_sym --lh >>>>>> surfreg --s subj001 --t fsaverage_sym --xhemi --lh >>>>>> >>>>>> I have tried first iteration, but the following error occurs: >>>>>> >>>>>> processing subject subj001 (1 of 194) >>>>>> reading spherical surface >>>>>> /Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... >>>>>> MRISread(/Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): >>>>>> could not open file >>>>>> No such file or directory >>>>>> mris_make_template: could not read surface file >>>>>> /Users/angelafavaro/Desktop/Angela/studyfree/subj002/surf/rh.fsaverage_sym.sphere.reg >>>>>> No such file or directory >>>>>> ERROR: make_average_surface >>>>>> >>>>>> how can I get the rh.fsaverage_sym.sphere.reg file? >>>>>> >>>>>> thank you! >>>>>> >>>>>> Angela >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Hi Matt >>>>>>> >>>>>>> certainly something is wrong, but it's hard to tell why from >>>>>>> the >>>>>>> single >>>>>>> slice. You have big topological defects that are being fixed >>>>>>> incorrectly. >>>>>>> Can you upload the subject and we will take a look? >>>>>>> cheers >>>>>>> Bruce >>>>>>> On Mon, 28 Jul 2014, >>>>>>> Walton, Matt wrote: >>>>>>> >>>>>>>> Hello Freesurfer team, >>>>>>>> I've used freesurfer to segment (recon-all) approximately >>>>>>>> 30 >>>>>>>> different >>>>>>>> subjects from a study. I've noticed that a large number of >>>>>>>> these >>>>>>>> subjects >>>>>>>> have a misclassification of the white and pial boundaries in >>>>>>>> the >>>>>>>> occipital >>>>>>>> lobe (such that grey matter is being classified as white >>>>>>>> matter). >>>>>>>> I >>>>>>>> believe >>>>>>>> this problem is originating from my scanner and original >>>>>>>> data. >>>>>>>> I'm >>>>>>>> acquiring >>>>>>>> a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, >>>>>>>> using >>>>>>>> a >>>>>>>> 32 >>>>>>>> channel >>>>>>>> phased array head coil. For many subjects, this acquistion >>>>>>>> gives >>>>>>>> intensity >>>>>>>> inhomogeneity in the occipital lobe. I've begun using a GE >>>>>>>> based >>>>>>>> correction >>>>>>>> technique (PURE) on the images, and it appears to improve >>>>>>>> the >>>>>>>> intensity >>>>>>>> in >>>>>>>> the occipital lobe, but Freesurfer is still frequently >>>>>>>> misclassifying. >>>>>>>> >>>>>>>> I'm wondering what would be the best way to edit the data. >>>>>>>> I've >>>>>>>> often >>>>>>>> tried >>>>>>>> to edit the wm.vol, but this doesn't seem to fix anything. >>>>>>>> For >>>>>>>> the >>>>>>>> most >>>>>>>> part, the wm.vol is correct to begin with, but the wm >>>>>>>> cutting >>>>>>>> line >>>>>>>> isn't >>>>>>>> segmenting with the wm.vol. I've also tried to add control >>>>>>>> points >>>>>>>> but >>>>>>>> this >>>>>>>> doesn't seem to improve anything either. >>>>>>>> >>>>>>>> I've attached an image which I hope will further explain my >>>>>>>> problems. >>>>>>>> >>>>>>>> Thanks for any help >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>> 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. >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve@nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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

thank you!

sorry, I should have given you a new make_average_volume.

you can get it from here

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_volume

On 08/11/2014 07:52 AM, angela.favaro@unipd.it wrote:

...

Hi Doug, I am having a problem with the last step of building my own symmetric atlas. I am using the make_average_surface you gave me and adding the --lh flag in the first two iteration. However in the third iteration the command 'make_average_subject' did not recognize neither the --hemi lh flag (indicated in the wiki guide) neither the --lh flag (you suggested to add in the first two iterations)

the error message was immediate in the first case: ERROR: Flag --hemi unrecognized.

and after two hours in the second... ERROR: Flag --lh unrecognized. --out myatlas.i3 --surf-reg myatlas.i2.sphere.reg --subjects subj001 subj002 .... --xhemi --lh ERROR: make_average_volume

Do you think I need a 'special' make_average_volume? or I need to use the 'old' 'make_average_surface'?

the log of make_average_surface in the script folder of my atlas.i3 indicates no error... (attached)

thank you for any help!!

Angela

...

when you run make_average_subject, you will still need the --lh doug

On 07/29/2014 06:07 PM, angela.favaro@unipd.it wrote:

...

ftp ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 331 Please specify the password. 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. 200 Switching to Binary mode. 250 Directory successfully changed. 250 Directory successfully changed. 250 Directory successfully changed. 250 Directory successfully changed. local: make_average_surface remote: make_average_surface 229 Entering Extended Passive Mode (|||37856|). 150 Opening BINARY mode data connection for make_average_surface (19641 bytes). 100% |***********************************| 19641 95.79 KiB/s 00:00 ETA 226 Transfer complete. 19641 bytes received in 00:00 (54.68 KiB/s) 221 Goodbye. [host-002:~/Desktop/risonanze/studyfree] angelafavaro% cp make_average_surface $FREESURFER_HOME/bin/make_average_surface cp: /Applications/freesurfer/bin/make_average_surface: Permission denied [host-002:~/Desktop/risonanze/studyfree] angelafavaro% sudo cp make_average_surface $FREESURFER_HOME/bin/make_average_surface Password: [host-002:~/Desktop/risonanze/studyfree] angelafavaro% make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

/Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

$Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $ Mar 29 Lug 2014 23:57:25 CEST /Users/angelafavaro/Desktop/risonanze/studyfree setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/risonanze/studyfree output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree uid=501(angelafavaro) gid=20(staff) groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) ==================== make_average_surface ==================== Mar 29 Lug 2014 23:57:27 CEST /Users/angelafavaro/Desktop/risonanze/studyfree /Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only input subjects: subj001 subj002 subj003 subj004 subj005 output subject: myatlas.i1 mri_add_xform_to_header -c auto /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz INFO: extension is mgz

#@# Making lh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc lh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... curvature mean = -0.028, std = 0.969 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm...

processing subject subj001/xhemi (2 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.586 curvature mean = -0.082, std = 0.795 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... curvature mean = -0.026, std = 1.007 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm...

processing subject subj002 (3 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.593 curvature mean = -0.071, std = 1.122 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... curvature mean = -0.025, std = 0.999 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm...

processing subject subj002/xhemi (4 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.597 curvature mean = -0.059, std = 1.231 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... curvature mean = -0.032, std = 0.973 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm...

processing subject subj003 (5 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.603 curvature mean = -0.062, std = 0.880 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... curvature mean = -0.035, std = 0.995 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm...

processing subject subj003/xhemi (6 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.572 curvature mean = -0.070, std = 2.235 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... curvature mean = -0.039, std = 0.991 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm...

processing subject subj004 (7 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.586 curvature mean = -0.097, std = 4.940 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... curvature mean = -0.028, std = 1.002 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm...

processing subject subj004/xhemi (8 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.603 curvature mean = -0.069, std = 1.134 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... curvature mean = -0.025, std = 1.004 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm...

processing subject subj005 (9 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.622 curvature mean = -0.067, std = 0.915 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... curvature mean = -0.038, std = 0.967 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm...

processing subject subj005/xhemi (10 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.591 curvature mean = -0.078, std = 0.997 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... curvature mean = -0.030, std = 0.984 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... writing updated template with 10 subjects to lh.reg.template.tif... curvature mean = 0.003, std = 0.598 curvature mean = -0.080, std = 0.911

#@# Making rh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface

...

can you send the full terminal output On 07/29/2014 06:00 PM, angela.favaro@unipd.it wrote:

...

Hi Doug, unfortunately the same error message appear... it looks for rh.fsaverage_sym.sphere.reg

.... #@# Making rh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface

> Copy this file into $FREESURFER_HOME/bin (make a backup of the > existing > one) > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface > > let me know if that works > doug > > On 07/29/2014 05:37 PM, angela.favaro@unipd.it wrote: >> I am using 5.3 >> >> make_average_subject --out myatlas.i1 --surf-reg >> fsaverage_sym.sphere.reg >> --subjects subj001 subj002 subj003 subj004 subj005 --xhemi >> --no-vol >> --template-only --lh >> make_average_surface --out myatlas.i1 --surf-reg >> fsaverage_sym.sphere.reg >> --subjects subj001 subj002 subj003 subj004 subj005 --xhemi >> --no-vol >> --template-only --lh >> ERROR: Flag --lh unrecognized. >> --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects >> subj001 >> subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only >> --lh >> ERROR: make_average_surface >> >> >> >> >>> Is that all it prints out? What version of FS are you using? >>> >>> >>> On 07/29/2014 05:26 PM, angela.favaro@unipd.it wrote: >>>> ERROR: Flag --lh unrecognized. >>>> >>>>> Try adding --lh to the make_average_subject command line. Let >>>>> me >>>>> know >>>>> if >>>>> that works and I'll change the docs >>>>> doug >>>>> >>>>> >>>>> On 07/29/2014 05:13 PM, angela.favaro@unipd.it wrote: >>>>>> Hi Doug, this the command and output (here with only five >>>>>> subjects). >>>>>> thank you! >>>>>> >>>>>> make_average_subject --out myatlas.i1 --surf-reg >>>>>> fsaverage_sym.sphere.reg >>>>>> --subjects subj001 subj002 subj003 subj004 subj005 --xhemi >>>>>> --no-vol >>>>>> --template-only >>>>>> make_average_surface --out myatlas.i1 --surf-reg >>>>>> fsaverage_sym.sphere.reg >>>>>> --subjects subj001 subj002 subj003 subj004 subj005 --xhemi >>>>>> --no-vol >>>>>> --template-only >>>>>> >>>>>> /Applications/freesurfer/bin/make_average_surface >>>>>> --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg >>>>>> --subjects >>>>>> subj001 >>>>>> subj002 subj003 subj004 subj005 --xhemi --no-vol >>>>>> --template-only >>>>>> >>>>>> $Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve >>>>>> Exp >>>>>> $ >>>>>> Mar 29 Lug 2014 23:09:30 CEST >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree >>>>>> setenv SUBJECTS_DIR >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree >>>>>> output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree >>>>>> uid=501(angelafavaro) gid=20(staff) >>>>>> groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) >>>>>> ==================== >>>>>> make_average_surface >>>>>> ==================== >>>>>> Mar 29 Lug 2014 23:09:31 CEST >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree >>>>>> /Applications/freesurfer/bin/make_average_surface >>>>>> --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg >>>>>> --subjects >>>>>> subj001 >>>>>> subj002 subj003 subj004 subj005 --xhemi --no-vol >>>>>> --template-only >>>>>> input subjects: subj001 subj002 subj003 subj004 subj005 >>>>>> output subject: myatlas.i1 >>>>>> mri_add_xform_to_header -c auto >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz >>>>>> INFO: extension is mgz >>>>>> >>>>>> >>>>>> #@# Making lh registration template --------- >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 >>>>>> mris_make_template -norot -annot aparc lh >>>>>> fsaverage_sym.sphere.reg >>>>>> subj001 >>>>>> subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi >>>>>> subj004 >>>>>> subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif >>>>>> not aligning hemispheres before averaging. >>>>>> zeroing medial wall in aparc >>>>>> creating new parameterization... >>>>>> >>>>>> processing subject subj001 (1 of 10) >>>>>> reading spherical surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... >>>>>> reading colortable from annotation file... >>>>>> colortable with 36 entries read (originally >>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>> ripping medial wall... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... >>>>>> curvature mean = -0.028, std = 0.969 >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm... >>>>>> >>>>>> processing subject subj001/xhemi (2 of 10) >>>>>> reading spherical surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>>>> curvature mean = 0.003, std = 0.586 >>>>>> curvature mean = -0.082, std = 0.795 >>>>>> reading colortable from annotation file... >>>>>> colortable with 36 entries read (originally >>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>> ripping medial wall... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... >>>>>> curvature mean = -0.026, std = 1.007 >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm... >>>>>> >>>>>> processing subject subj002 (3 of 10) >>>>>> reading spherical surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... >>>>>> curvature mean = 0.003, std = 0.593 >>>>>> curvature mean = -0.071, std = 1.122 >>>>>> reading colortable from annotation file... >>>>>> colortable with 36 entries read (originally >>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>> ripping medial wall... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... >>>>>> curvature mean = -0.025, std = 0.999 >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm... >>>>>> >>>>>> processing subject subj002/xhemi (4 of 10) >>>>>> reading spherical surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>>>> curvature mean = 0.002, std = 0.597 >>>>>> curvature mean = -0.059, std = 1.231 >>>>>> reading colortable from annotation file... >>>>>> colortable with 36 entries read (originally >>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>> ripping medial wall... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... >>>>>> curvature mean = -0.032, std = 0.973 >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm... >>>>>> >>>>>> processing subject subj003 (5 of 10) >>>>>> reading spherical surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... >>>>>> curvature mean = 0.003, std = 0.603 >>>>>> curvature mean = -0.062, std = 0.880 >>>>>> reading colortable from annotation file... >>>>>> colortable with 36 entries read (originally >>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>> ripping medial wall... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... >>>>>> curvature mean = -0.035, std = 0.995 >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm... >>>>>> >>>>>> processing subject subj003/xhemi (6 of 10) >>>>>> reading spherical surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>>>> curvature mean = 0.000, std = 0.572 >>>>>> curvature mean = -0.070, std = 2.235 >>>>>> reading colortable from annotation file... >>>>>> colortable with 36 entries read (originally >>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>> ripping medial wall... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... >>>>>> curvature mean = -0.039, std = 0.991 >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm... >>>>>> >>>>>> processing subject subj004 (7 of 10) >>>>>> reading spherical surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... >>>>>> curvature mean = 0.000, std = 0.586 >>>>>> curvature mean = -0.097, std = 4.940 >>>>>> reading colortable from annotation file... >>>>>> colortable with 36 entries read (originally >>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>> ripping medial wall... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... >>>>>> curvature mean = -0.028, std = 1.002 >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm... >>>>>> >>>>>> processing subject subj004/xhemi (8 of 10) >>>>>> reading spherical surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>>>> curvature mean = 0.002, std = 0.603 >>>>>> curvature mean = -0.069, std = 1.134 >>>>>> reading colortable from annotation file... >>>>>> colortable with 36 entries read (originally >>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>> ripping medial wall... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... >>>>>> curvature mean = -0.025, std = 1.004 >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm... >>>>>> >>>>>> processing subject subj005 (9 of 10) >>>>>> reading spherical surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... >>>>>> curvature mean = 0.003, std = 0.622 >>>>>> curvature mean = -0.067, std = 0.915 >>>>>> reading colortable from annotation file... >>>>>> colortable with 36 entries read (originally >>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>> ripping medial wall... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... >>>>>> curvature mean = -0.038, std = 0.967 >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm... >>>>>> >>>>>> processing subject subj005/xhemi (10 of 10) >>>>>> reading spherical surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>>>> curvature mean = 0.002, std = 0.591 >>>>>> curvature mean = -0.078, std = 0.997 >>>>>> reading colortable from annotation file... >>>>>> colortable with 36 entries read (originally >>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>> ripping medial wall... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... >>>>>> curvature mean = -0.030, std = 0.984 >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... >>>>>> computing parameterization for surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... >>>>>> writing updated template with 10 subjects to >>>>>> lh.reg.template.tif... >>>>>> curvature mean = 0.003, std = 0.598 >>>>>> curvature mean = -0.080, std = 0.911 >>>>>> >>>>>> >>>>>> #@# Making rh registration template --------- >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 >>>>>> mris_make_template -norot -annot aparc rh >>>>>> fsaverage_sym.sphere.reg >>>>>> subj001 >>>>>> subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi >>>>>> subj004 >>>>>> subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif >>>>>> not aligning hemispheres before averaging. >>>>>> zeroing medial wall in aparc >>>>>> creating new parameterization... >>>>>> >>>>>> processing subject subj001 (1 of 10) >>>>>> reading spherical surface >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... >>>>>> MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): >>>>>> could not open file >>>>>> No such file or directory >>>>>> mris_make_template: could not read surface file >>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg >>>>>> No such file or directory >>>>>> ERROR: make_average_surface >>>>>> [host-002:~/Desktop/ >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> What is the command line that is failing and what is the full >>>>>>> terminal >>>>>>> output? >>>>>>> doug >>>>>>> >>>>>>> >>>>>>> On 07/29/2014 05:55 AM, angela.favaro@unipd.it wrote: >>>>>>>> Hi all, >>>>>>>> I am now working with the 5.3 version and performing >>>>>>>> interhemispheric >>>>>>>> registration (building my own atlas) >>>>>>>> >>>>>>>> after running for all subjects: >>>>>>>> xhemireg --s subj001.... >>>>>>>> surfreg --s subj001 --t fsaverage_sym --lh >>>>>>>> surfreg --s subj001 --t fsaverage_sym --xhemi --lh >>>>>>>> >>>>>>>> I have tried first iteration, but the following error >>>>>>>> occurs: >>>>>>>> >>>>>>>> processing subject subj001 (1 of 194) >>>>>>>> reading spherical surface >>>>>>>> /Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... >>>>>>>> MRISread(/Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): >>>>>>>> could not open file >>>>>>>> No such file or directory >>>>>>>> mris_make_template: could not read surface file >>>>>>>> /Users/angelafavaro/Desktop/Angela/studyfree/subj002/surf/rh.fsaverage_sym.sphere.reg >>>>>>>> No such file or directory >>>>>>>> ERROR: make_average_surface >>>>>>>> >>>>>>>> how can I get the rh.fsaverage_sym.sphere.reg file? >>>>>>>> >>>>>>>> thank you! >>>>>>>> >>>>>>>> Angela >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> Hi Matt >>>>>>>>> >>>>>>>>> certainly something is wrong, but it's hard to tell why >>>>>>>>> from >>>>>>>>> the >>>>>>>>> single >>>>>>>>> slice. You have big topological defects that are being >>>>>>>>> fixed >>>>>>>>> incorrectly. >>>>>>>>> Can you upload the subject and we will take a look? >>>>>>>>> cheers >>>>>>>>> Bruce >>>>>>>>> On Mon, 28 Jul 2014, >>>>>>>>> Walton, Matt wrote: >>>>>>>>> >>>>>>>>>> Hello Freesurfer team, >>>>>>>>>> I've used freesurfer to segment (recon-all) approximately >>>>>>>>>> 30 >>>>>>>>>> different >>>>>>>>>> subjects from a study. I've noticed that a large number of >>>>>>>>>> these >>>>>>>>>> subjects >>>>>>>>>> have a misclassification of the white and pial boundaries >>>>>>>>>> in >>>>>>>>>> the >>>>>>>>>> occipital >>>>>>>>>> lobe (such that grey matter is being classified as white >>>>>>>>>> matter). >>>>>>>>>> I >>>>>>>>>> believe >>>>>>>>>> this problem is originating from my scanner and original >>>>>>>>>> data. >>>>>>>>>> I'm >>>>>>>>>> acquiring >>>>>>>>>> a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, >>>>>>>>>> using >>>>>>>>>> a >>>>>>>>>> 32 >>>>>>>>>> channel >>>>>>>>>> phased array head coil. For many subjects, this acquistion >>>>>>>>>> gives >>>>>>>>>> intensity >>>>>>>>>> inhomogeneity in the occipital lobe. I've begun using a >>>>>>>>>> GE >>>>>>>>>> based >>>>>>>>>> correction >>>>>>>>>> technique (PURE) on the images, and it appears to improve >>>>>>>>>> the >>>>>>>>>> intensity >>>>>>>>>> in >>>>>>>>>> the occipital lobe, but Freesurfer is still frequently >>>>>>>>>> misclassifying. >>>>>>>>>> >>>>>>>>>> I'm wondering what would be the best way to edit the data. >>>>>>>>>> I've >>>>>>>>>> often >>>>>>>>>> tried >>>>>>>>>> to edit the wm.vol, but this doesn't seem to fix anything. >>>>>>>>>> For >>>>>>>>>> the >>>>>>>>>> most >>>>>>>>>> part, the wm.vol is correct to begin with, but the wm >>>>>>>>>> cutting >>>>>>>>>> line >>>>>>>>>> isn't >>>>>>>>>> segmenting with the wm.vol. I've also tried to add control >>>>>>>>>> points >>>>>>>>>> but >>>>>>>>>> this >>>>>>>>>> doesn't seem to improve anything either. >>>>>>>>>> >>>>>>>>>> I've attached an image which I hope will further explain >>>>>>>>>> my >>>>>>>>>> problems. >>>>>>>>>> >>>>>>>>>> Thanks for any help >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>> 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. >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>> -- >>>>>>> Douglas N. Greve, Ph.D. >>>>>>> MGH-NMR Center >>>>>>> greve@nmr.mgh.harvard.edu >>>>>>> Phone Number: 617-724-2358 >>>>>>> Fax: 617-726-7422 >>>>>>> >>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>> Outgoing: >>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve@nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> Outgoing: >>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

You can inflate it more with something like mris_inflate -dist .01 -f .001 -no-save-sulc 20 lh.smoothwm lh.inflated

20 is the number of iterations (default is 15) so play with that number

On 08/13/2014 11:25 AM, angela.favaro@unipd.it wrote:

Hi Doug, a further question: my final symmetric atlas seems to be not inflated enough, but still have important sulcations. Do I have to perform further iterations (myatlas.i4, myatlas.i5 ....) until the resulting volume is good enough? Or which is the correct method (other than performing asymmetry analyses on fsaverage_sym, that I will do) in this case?

thank you!

Angela

...

sorry, I should have given you a new make_average_volume. you can get it from here

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_volume

On 08/11/2014 07:52 AM, angela.favaro@unipd.it wrote:

...

Hi Doug, I am having a problem with the last step of building my own symmetric atlas. I am using the make_average_surface you gave me and adding the --lh flag in the first two iteration. However in the third iteration the command 'make_average_subject' did not recognize neither the --hemi lh flag (indicated in the wiki guide) neither the --lh flag (you suggested to add in the first two iterations)

the error message was immediate in the first case: ERROR: Flag --hemi unrecognized.

and after two hours in the second... ERROR: Flag --lh unrecognized. --out myatlas.i3 --surf-reg myatlas.i2.sphere.reg --subjects subj001 subj002 .... --xhemi --lh ERROR: make_average_volume

Do you think I need a 'special' make_average_volume? or I need to use the 'old' 'make_average_surface'?

the log of make_average_surface in the script folder of my atlas.i3 indicates no error... (attached)

thank you for any help!!

Angela

...

when you run make_average_subject, you will still need the --lh doug

On 07/29/2014 06:07 PM, angela.favaro@unipd.it wrote:

...

ftp ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface Connected to surfer.nmr.mgh.harvard.edu. 220-This is the Martinos Center Anonymous FTP service. Use of this site 220-shows implicit consent to our Acceptable Use Policy outlined at 220-http://www.nmr.mgh.harvard.edu/martinos/userInfo/computer/nmr-aup.php 220- 220-OPERATIONAL NOTE: If, when doing a GET or PUT, you encounter either 220- 220-229 Entering Extended Passive Mode 220- 220- and nothing happens OR 220- 220-229 Entering Extended Passive Mode 220-500 Bad EPRT protocol. 220- 220- try issuing the EPSV command prior to GET or PUT. 220- 220 331 Please specify the password. 230 Login successful. Remote system type is UNIX. Using binary mode to transfer files. 200 Switching to Binary mode. 250 Directory successfully changed. 250 Directory successfully changed. 250 Directory successfully changed. 250 Directory successfully changed. local: make_average_surface remote: make_average_surface 229 Entering Extended Passive Mode (|||37856|). 150 Opening BINARY mode data connection for make_average_surface (19641 bytes). 100% |***********************************| 19641 95.79 KiB/s 00:00 ETA 226 Transfer complete. 19641 bytes received in 00:00 (54.68 KiB/s) 221 Goodbye. [host-002:~/Desktop/risonanze/studyfree] angelafavaro% cp make_average_surface $FREESURFER_HOME/bin/make_average_surface cp: /Applications/freesurfer/bin/make_average_surface: Permission denied [host-002:~/Desktop/risonanze/studyfree] angelafavaro% sudo cp make_average_surface $FREESURFER_HOME/bin/make_average_surface Password: [host-002:~/Desktop/risonanze/studyfree] angelafavaro% make_average_subject --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

/Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only

$Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve Exp $ Mar 29 Lug 2014 23:57:25 CEST /Users/angelafavaro/Desktop/risonanze/studyfree setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/risonanze/studyfree output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree uid=501(angelafavaro) gid=20(staff) groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) ==================== make_average_surface ==================== Mar 29 Lug 2014 23:57:27 CEST /Users/angelafavaro/Desktop/risonanze/studyfree /Applications/freesurfer/bin/make_average_surface --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects subj001 subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only input subjects: subj001 subj002 subj003 subj004 subj005 output subject: myatlas.i1 mri_add_xform_to_header -c auto /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz INFO: extension is mgz

#@# Making lh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc lh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... curvature mean = -0.028, std = 0.969 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm...

processing subject subj001/xhemi (2 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.586 curvature mean = -0.082, std = 0.795 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... curvature mean = -0.026, std = 1.007 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm...

processing subject subj002 (3 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.593 curvature mean = -0.071, std = 1.122 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... curvature mean = -0.025, std = 0.999 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm...

processing subject subj002/xhemi (4 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.597 curvature mean = -0.059, std = 1.231 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... curvature mean = -0.032, std = 0.973 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm...

processing subject subj003 (5 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.603 curvature mean = -0.062, std = 0.880 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... curvature mean = -0.035, std = 0.995 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm...

processing subject subj003/xhemi (6 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.572 curvature mean = -0.070, std = 2.235 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... curvature mean = -0.039, std = 0.991 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm...

processing subject subj004 (7 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.000, std = 0.586 curvature mean = -0.097, std = 4.940 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... curvature mean = -0.028, std = 1.002 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm...

processing subject subj004/xhemi (8 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.603 curvature mean = -0.069, std = 1.134 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... curvature mean = -0.025, std = 1.004 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm...

processing subject subj005 (9 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.003, std = 0.622 curvature mean = -0.067, std = 0.915 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... curvature mean = -0.038, std = 0.967 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm...

processing subject subj005/xhemi (10 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... curvature mean = 0.002, std = 0.591 curvature mean = -0.078, std = 0.997 reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) ripping medial wall... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... curvature mean = -0.030, std = 0.984 computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... computing parameterization for surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... writing updated template with 10 subjects to lh.reg.template.tif... curvature mean = 0.003, std = 0.598 curvature mean = -0.080, std = 0.911

#@# Making rh registration template --------- /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg subj001 subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif not aligning hemispheres before averaging. zeroing medial wall in aparc creating new parameterization...

processing subject subj001 (1 of 10) reading spherical surface /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): could not open file No such file or directory mris_make_template: could not read surface file /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg No such file or directory ERROR: make_average_surface

...

can you send the full terminal output On 07/29/2014 06:00 PM, angela.favaro@unipd.it wrote: > Hi Doug, > unfortunately the same error message appear... it looks for > rh.fsaverage_sym.sphere.reg > > .... > #@# Making rh registration template --------- > /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 > mris_make_template -norot -annot aparc rh fsaverage_sym.sphere.reg > subj001 > subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi subj004 > subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif > not aligning hemispheres before averaging. > zeroing medial wall in aparc > creating new parameterization... > > processing subject subj001 (1 of 10) > reading spherical surface > /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... > MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): > could not open file > No such file or directory > mris_make_template: could not read surface file > /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg > No such file or directory > ERROR: make_average_surface > > > > >> Copy this file into $FREESURFER_HOME/bin (make a backup of the >> existing >> one) >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface >> >> let me know if that works >> doug >> >> On 07/29/2014 05:37 PM, angela.favaro@unipd.it wrote: >>> I am using 5.3 >>> >>> make_average_subject --out myatlas.i1 --surf-reg >>> fsaverage_sym.sphere.reg >>> --subjects subj001 subj002 subj003 subj004 subj005 --xhemi >>> --no-vol >>> --template-only --lh >>> make_average_surface --out myatlas.i1 --surf-reg >>> fsaverage_sym.sphere.reg >>> --subjects subj001 subj002 subj003 subj004 subj005 --xhemi >>> --no-vol >>> --template-only --lh >>> ERROR: Flag --lh unrecognized. >>> --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg --subjects >>> subj001 >>> subj002 subj003 subj004 subj005 --xhemi --no-vol --template-only >>> --lh >>> ERROR: make_average_surface >>> >>> >>> >>> >>>> Is that all it prints out? What version of FS are you using? >>>> >>>> >>>> On 07/29/2014 05:26 PM, angela.favaro@unipd.it wrote: >>>>> ERROR: Flag --lh unrecognized. >>>>> >>>>>> Try adding --lh to the make_average_subject command line. Let >>>>>> me >>>>>> know >>>>>> if >>>>>> that works and I'll change the docs >>>>>> doug >>>>>> >>>>>> >>>>>> On 07/29/2014 05:13 PM, angela.favaro@unipd.it wrote: >>>>>>> Hi Doug, this the command and output (here with only five >>>>>>> subjects). >>>>>>> thank you! >>>>>>> >>>>>>> make_average_subject --out myatlas.i1 --surf-reg >>>>>>> fsaverage_sym.sphere.reg >>>>>>> --subjects subj001 subj002 subj003 subj004 subj005 --xhemi >>>>>>> --no-vol >>>>>>> --template-only >>>>>>> make_average_surface --out myatlas.i1 --surf-reg >>>>>>> fsaverage_sym.sphere.reg >>>>>>> --subjects subj001 subj002 subj003 subj004 subj005 --xhemi >>>>>>> --no-vol >>>>>>> --template-only >>>>>>> >>>>>>> /Applications/freesurfer/bin/make_average_surface >>>>>>> --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg >>>>>>> --subjects >>>>>>> subj001 >>>>>>> subj002 subj003 subj004 subj005 --xhemi --no-vol >>>>>>> --template-only >>>>>>> >>>>>>> $Id: make_average_surface,v 1.53.2.1 2011/05/25 20:53:44 greve >>>>>>> Exp >>>>>>> $ >>>>>>> Mar 29 Lug 2014 23:09:30 CEST >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree >>>>>>> setenv SUBJECTS_DIR >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree >>>>>>> output ddir is /Users/angelafavaro/Desktop/risonanze/studyfree >>>>>>> uid=501(angelafavaro) gid=20(staff) >>>>>>> groups=20(staff),204(_developer),100(_lpoperator),98(_lpadmin),81(_appserveradm),80(admin),79(_appserverusr),61(localaccounts),12(everyone),402(com.apple.sharepoint.group.1),401(com.apple.access_screensharing) >>>>>>> ==================== >>>>>>> make_average_surface >>>>>>> ==================== >>>>>>> Mar 29 Lug 2014 23:09:31 CEST >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree >>>>>>> /Applications/freesurfer/bin/make_average_surface >>>>>>> --out myatlas.i1 --surf-reg fsaverage_sym.sphere.reg >>>>>>> --subjects >>>>>>> subj001 >>>>>>> subj002 subj003 subj004 subj005 --xhemi --no-vol >>>>>>> --template-only >>>>>>> input subjects: subj001 subj002 subj003 subj004 subj005 >>>>>>> output subject: myatlas.i1 >>>>>>> mri_add_xform_to_header -c auto >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1/mri/mni305.cor.mgz >>>>>>> INFO: extension is mgz >>>>>>> >>>>>>> >>>>>>> #@# Making lh registration template --------- >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 >>>>>>> mris_make_template -norot -annot aparc lh >>>>>>> fsaverage_sym.sphere.reg >>>>>>> subj001 >>>>>>> subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi >>>>>>> subj004 >>>>>>> subj004/xhemi subj005 subj005/xhemi lh.reg.template.tif >>>>>>> not aligning hemispheres before averaging. >>>>>>> zeroing medial wall in aparc >>>>>>> creating new parameterization... >>>>>>> >>>>>>> processing subject subj001 (1 of 10) >>>>>>> reading spherical surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.fsaverage_sym.sphere.reg... >>>>>>> reading colortable from annotation file... >>>>>>> colortable with 36 entries read (originally >>>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>>> ripping medial wall... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.inflated.H... >>>>>>> curvature mean = -0.028, std = 0.969 >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.sulc... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/lh.smoothwm... >>>>>>> >>>>>>> processing subject subj001/xhemi (2 of 10) >>>>>>> reading spherical surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>>>>> curvature mean = 0.003, std = 0.586 >>>>>>> curvature mean = -0.082, std = 0.795 >>>>>>> reading colortable from annotation file... >>>>>>> colortable with 36 entries read (originally >>>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>>> ripping medial wall... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.inflated.H... >>>>>>> curvature mean = -0.026, std = 1.007 >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.sulc... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/xhemi/surf/lh.smoothwm... >>>>>>> >>>>>>> processing subject subj002 (3 of 10) >>>>>>> reading spherical surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.fsaverage_sym.sphere.reg... >>>>>>> curvature mean = 0.003, std = 0.593 >>>>>>> curvature mean = -0.071, std = 1.122 >>>>>>> reading colortable from annotation file... >>>>>>> colortable with 36 entries read (originally >>>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>>> ripping medial wall... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.inflated.H... >>>>>>> curvature mean = -0.025, std = 0.999 >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.sulc... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/surf/lh.smoothwm... >>>>>>> >>>>>>> processing subject subj002/xhemi (4 of 10) >>>>>>> reading spherical surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>>>>> curvature mean = 0.002, std = 0.597 >>>>>>> curvature mean = -0.059, std = 1.231 >>>>>>> reading colortable from annotation file... >>>>>>> colortable with 36 entries read (originally >>>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>>> ripping medial wall... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.inflated.H... >>>>>>> curvature mean = -0.032, std = 0.973 >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.sulc... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj002/xhemi/surf/lh.smoothwm... >>>>>>> >>>>>>> processing subject subj003 (5 of 10) >>>>>>> reading spherical surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.fsaverage_sym.sphere.reg... >>>>>>> curvature mean = 0.003, std = 0.603 >>>>>>> curvature mean = -0.062, std = 0.880 >>>>>>> reading colortable from annotation file... >>>>>>> colortable with 36 entries read (originally >>>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>>> ripping medial wall... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.inflated.H... >>>>>>> curvature mean = -0.035, std = 0.995 >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.sulc... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/surf/lh.smoothwm... >>>>>>> >>>>>>> processing subject subj003/xhemi (6 of 10) >>>>>>> reading spherical surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>>>>> curvature mean = 0.000, std = 0.572 >>>>>>> curvature mean = -0.070, std = 2.235 >>>>>>> reading colortable from annotation file... >>>>>>> colortable with 36 entries read (originally >>>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>>> ripping medial wall... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.inflated.H... >>>>>>> curvature mean = -0.039, std = 0.991 >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.sulc... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj003/xhemi/surf/lh.smoothwm... >>>>>>> >>>>>>> processing subject subj004 (7 of 10) >>>>>>> reading spherical surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.fsaverage_sym.sphere.reg... >>>>>>> curvature mean = 0.000, std = 0.586 >>>>>>> curvature mean = -0.097, std = 4.940 >>>>>>> reading colortable from annotation file... >>>>>>> colortable with 36 entries read (originally >>>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>>> ripping medial wall... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.inflated.H... >>>>>>> curvature mean = -0.028, std = 1.002 >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.sulc... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/surf/lh.smoothwm... >>>>>>> >>>>>>> processing subject subj004/xhemi (8 of 10) >>>>>>> reading spherical surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>>>>> curvature mean = 0.002, std = 0.603 >>>>>>> curvature mean = -0.069, std = 1.134 >>>>>>> reading colortable from annotation file... >>>>>>> colortable with 36 entries read (originally >>>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>>> ripping medial wall... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.inflated.H... >>>>>>> curvature mean = -0.025, std = 1.004 >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.sulc... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj004/xhemi/surf/lh.smoothwm... >>>>>>> >>>>>>> processing subject subj005 (9 of 10) >>>>>>> reading spherical surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.fsaverage_sym.sphere.reg... >>>>>>> curvature mean = 0.003, std = 0.622 >>>>>>> curvature mean = -0.067, std = 0.915 >>>>>>> reading colortable from annotation file... >>>>>>> colortable with 36 entries read (originally >>>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>>> ripping medial wall... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.inflated.H... >>>>>>> curvature mean = -0.038, std = 0.967 >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.sulc... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/surf/lh.smoothwm... >>>>>>> >>>>>>> processing subject subj005/xhemi (10 of 10) >>>>>>> reading spherical surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.fsaverage_sym.sphere.reg... >>>>>>> curvature mean = 0.002, std = 0.591 >>>>>>> curvature mean = -0.078, std = 0.997 >>>>>>> reading colortable from annotation file... >>>>>>> colortable with 36 entries read (originally >>>>>>> /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) >>>>>>> ripping medial wall... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.inflated.H... >>>>>>> curvature mean = -0.030, std = 0.984 >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.sulc... >>>>>>> computing parameterization for surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj005/xhemi/surf/lh.smoothwm... >>>>>>> writing updated template with 10 subjects to >>>>>>> lh.reg.template.tif... >>>>>>> curvature mean = 0.003, std = 0.598 >>>>>>> curvature mean = -0.080, std = 0.911 >>>>>>> >>>>>>> >>>>>>> #@# Making rh registration template --------- >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/myatlas.i1 >>>>>>> mris_make_template -norot -annot aparc rh >>>>>>> fsaverage_sym.sphere.reg >>>>>>> subj001 >>>>>>> subj001/xhemi subj002 subj002/xhemi subj003 subj003/xhemi >>>>>>> subj004 >>>>>>> subj004/xhemi subj005 subj005/xhemi rh.reg.template.tif >>>>>>> not aligning hemispheres before averaging. >>>>>>> zeroing medial wall in aparc >>>>>>> creating new parameterization... >>>>>>> >>>>>>> processing subject subj001 (1 of 10) >>>>>>> reading spherical surface >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... >>>>>>> MRISread(/Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): >>>>>>> could not open file >>>>>>> No such file or directory >>>>>>> mris_make_template: could not read surface file >>>>>>> /Users/angelafavaro/Desktop/risonanze/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg >>>>>>> No such file or directory >>>>>>> ERROR: make_average_surface >>>>>>> [host-002:~/Desktop/ >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> What is the command line that is failing and what is the full >>>>>>>> terminal >>>>>>>> output? >>>>>>>> doug >>>>>>>> >>>>>>>> >>>>>>>> On 07/29/2014 05:55 AM, angela.favaro@unipd.it wrote: >>>>>>>>> Hi all, >>>>>>>>> I am now working with the 5.3 version and performing >>>>>>>>> interhemispheric >>>>>>>>> registration (building my own atlas) >>>>>>>>> >>>>>>>>> after running for all subjects: >>>>>>>>> xhemireg --s subj001.... >>>>>>>>> surfreg --s subj001 --t fsaverage_sym --lh >>>>>>>>> surfreg --s subj001 --t fsaverage_sym --xhemi --lh >>>>>>>>> >>>>>>>>> I have tried first iteration, but the following error >>>>>>>>> occurs: >>>>>>>>> >>>>>>>>> processing subject subj001 (1 of 194) >>>>>>>>> reading spherical surface >>>>>>>>> /Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg... >>>>>>>>> MRISread(/Users/angelafavaro/Desktop/Angela/studyfree/subj001/surf/rh.fsaverage_sym.sphere.reg): >>>>>>>>> could not open file >>>>>>>>> No such file or directory >>>>>>>>> mris_make_template: could not read surface file >>>>>>>>> /Users/angelafavaro/Desktop/Angela/studyfree/subj002/surf/rh.fsaverage_sym.sphere.reg >>>>>>>>> No such file or directory >>>>>>>>> ERROR: make_average_surface >>>>>>>>> >>>>>>>>> how can I get the rh.fsaverage_sym.sphere.reg file? >>>>>>>>> >>>>>>>>> thank you! >>>>>>>>> >>>>>>>>> Angela >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> Hi Matt >>>>>>>>>> >>>>>>>>>> certainly something is wrong, but it's hard to tell why >>>>>>>>>> from >>>>>>>>>> the >>>>>>>>>> single >>>>>>>>>> slice. You have big topological defects that are being >>>>>>>>>> fixed >>>>>>>>>> incorrectly. >>>>>>>>>> Can you upload the subject and we will take a look? >>>>>>>>>> cheers >>>>>>>>>> Bruce >>>>>>>>>> On Mon, 28 Jul 2014, >>>>>>>>>> Walton, Matt wrote: >>>>>>>>>> >>>>>>>>>>> Hello Freesurfer team, >>>>>>>>>>> I've used freesurfer to segment (recon-all) approximately >>>>>>>>>>> 30 >>>>>>>>>>> different >>>>>>>>>>> subjects from a study. I've noticed that a large number of >>>>>>>>>>> these >>>>>>>>>>> subjects >>>>>>>>>>> have a misclassification of the white and pial boundaries >>>>>>>>>>> in >>>>>>>>>>> the >>>>>>>>>>> occipital >>>>>>>>>>> lobe (such that grey matter is being classified as white >>>>>>>>>>> matter). >>>>>>>>>>> I >>>>>>>>>>> believe >>>>>>>>>>> this problem is originating from my scanner and original >>>>>>>>>>> data. >>>>>>>>>>> I'm >>>>>>>>>>> acquiring >>>>>>>>>>> a T1W BRAVO sequence on a GE Discovery 750w 3T scanner, >>>>>>>>>>> using >>>>>>>>>>> a >>>>>>>>>>> 32 >>>>>>>>>>> channel >>>>>>>>>>> phased array head coil. For many subjects, this acquistion >>>>>>>>>>> gives >>>>>>>>>>> intensity >>>>>>>>>>> inhomogeneity in the occipital lobe. I've begun using a >>>>>>>>>>> GE >>>>>>>>>>> based >>>>>>>>>>> correction >>>>>>>>>>> technique (PURE) on the images, and it appears to improve >>>>>>>>>>> the >>>>>>>>>>> intensity >>>>>>>>>>> in >>>>>>>>>>> the occipital lobe, but Freesurfer is still frequently >>>>>>>>>>> misclassifying. >>>>>>>>>>> >>>>>>>>>>> I'm wondering what would be the best way to edit the data. >>>>>>>>>>> I've >>>>>>>>>>> often >>>>>>>>>>> tried >>>>>>>>>>> to edit the wm.vol, but this doesn't seem to fix anything. >>>>>>>>>>> For >>>>>>>>>>> the >>>>>>>>>>> most >>>>>>>>>>> part, the wm.vol is correct to begin with, but the wm >>>>>>>>>>> cutting >>>>>>>>>>> line >>>>>>>>>>> isn't >>>>>>>>>>> segmenting with the wm.vol. I've also tried to add control >>>>>>>>>>> points >>>>>>>>>>> but >>>>>>>>>>> this >>>>>>>>>>> doesn't seem to improve anything either. >>>>>>>>>>> >>>>>>>>>>> I've attached an image which I hope will further explain >>>>>>>>>>> my >>>>>>>>>>> problems. >>>>>>>>>>> >>>>>>>>>>> Thanks for any help >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>> 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. >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve@nmr.mgh.harvard.edu >>>>>>>> Phone Number: 617-724-2358 >>>>>>>> Fax: 617-726-7422 >>>>>>>> >>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> Outgoing: >>>>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>> -- >>>>>> Douglas N. Greve, Ph.D. >>>>>> MGH-NMR Center >>>>>> greve@nmr.mgh.harvard.edu >>>>>> Phone Number: 617-724-2358 >>>>>> Fax: 617-726-7422 >>>>>> >>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>> Outgoing: >>>>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>> -- >>>> Douglas N. Greve, Ph.D. >>>> MGH-NMR Center >>>> greve@nmr.mgh.harvard.edu >>>> Phone Number: 617-724-2358 >>>> Fax: 617-726-7422 >>>> >>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>> Outgoing: >>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

>

Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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