you can try recon-all -make all for that subject and and see if it doesn anything. But run mris_euler_number on those surfaces and see if they match. They should all have the same number of faces/edges/vertices (for one hemisphere in the same subject)

On Tue, 22 Mar 2016, Ji Won Bang wrote:

Dear. Bruce.

Thank you for your advice. I think I misunderstood what you meant.

What I did is this. I showed the contrast result on a surface by using the command: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast HorVer

Then I cut line, and then plane (occipital plane) and save it(3d) as lh.oc.patch.3d under $SUBJECTS_DIR/$SUBJECT/surf/

I'm not sure if I regenerated the surface files correctly but I believe I created the surface($SUBJECTS_DIR/$SUBJECT/surf directory) from recon-all process.

Should I do something else to regenerate the surface?

Thank you.

Best, Ji Won

2016-03-22 11:39 GMT-04:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: what surface did you recut it from? Can you run mris_euler_number on that surface (presumably the inflated) and also on the white/orig/pial surfaces? They should all have the same number of vertices, but I suspect some of them won't, meaning that they need to be regenerated.

  cheers
  Bruce




  On Tue, 22 Mar 2016, Ji Won Bang wrote:

  > Dear. Freesurfer experts.
  >
  > Hi. How are you?
  >
  > I'm trying to flatten the visual cortex using the command mris_flatten
  (freesurfer
  > version 5.3.0).
  >
  > The command line is:
  > mris_flatten -w 0 -distances 12 7
  $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
  > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat
  >
  > The error I get is:
  > using write iterations = 0
  > sampling 7 neighbors out to a distance of 12 mm
  > reading patch
  /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d with
  > 27964 vertices (19.0% of total)
  > MRISreadPatch: bad vertex # (147220) found in patch file
  > No such file or directory
  >
  > Previously, Bruce advised me to recut it, so I deleted the
  lh.oc.patch.3d and recut
  > it. However, freesurfer gives me the same error message...
  >
  > Could you please help me fix it?
  >
  > Thank you so much.
  >
  > Best,
  > Ji Won
  >
  >

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no, for all surfaces for the same hemi (lh and rh). lh.inflated.K is not a surface - it's a scalar field over the surface. The ones that should be the same are:

lh.inflated lh.white lh.pial lh.orig lh.sphere lh.sphere.reg

and same for the rh (but different from the lh ones)

cheers Bruce

On Tue, 22 Mar 2016, Ji Won Bang wrote:

Dear. Bruce.

Thanks for your help.

When I tried: mris_euler_number rh.inflated.K

It gave me: nquads=15728644,  nvertices=574 ERROR: MRISread: file 'rh.inflated.K' has many more faces than vertices! Probably trying to use a scalar data file as a surface!

When I tried: mris_euler_number lh.inflated

It gave me: euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes       F =2V-4:          289950 = 289954-4 (0)       2E=3F:            869850 = 869850 (0)

When I tried: mris_euler_number rh.inflated

It gave me: euler # = v-e+f = 2g-2: 147184 - 441546 + 294364 = 2 --> 0 holes       F =2V-4:          294364 = 294368-4 (0)       2E=3F:            883092 = 883092 (0)

So if everything is correct, I should see the same numbers for all surfaces, but since it's not the case, I should run recon again...

Thanks, Ji Won

2016-03-22 12:24 GMT-04:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: you can try recon-all -make all for that subject and and see if it doesn anything. But run mris_euler_number on those surfaces and see if they match. They should all have the same number of faces/edges/vertices (for one hemisphere in the same subject)

  On Tue, 22 Mar 2016,
  Ji Won Bang wrote:

  > Dear. Bruce.
  >
  > Thank you for your advice.
  > I think I misunderstood what you meant.
  >
  > What I did is this.
  > I showed the contrast result on a surface by using the command:
  > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
  -contrast HorVer
  >
  > Then I cut line, and then plane (occipital plane) and save it(3d) as
  lh.oc.patch.3d
  > under $SUBJECTS_DIR/$SUBJECT/surf/
  >
  > I'm not sure if I regenerated the surface files correctly but I believe
  I created the
  > surface($SUBJECTS_DIR/$SUBJECT/surf directory) from recon-all process.
  >
  >
  > Should I do something else to regenerate the surface?
  >
  > Thank you.
  >
  > Best,
  > Ji Won
  >
  >
  >
  >
  >
  > 2016-03-22 11:39 GMT-04:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
  >       what surface did you recut it from? Can you run mris_euler_number
  on that
  >       surface (presumably the inflated) and also on the white/orig/pial
  >       surfaces? They should all have the same number of vertices, but I
  suspect
  >       some of them won't, meaning that they need to be regenerated.
  >
  >       cheers
  >       Bruce
  >
  >
  >
  >
  >       On Tue, 22 Mar 2016, Ji Won Bang wrote:
  >
  >       > Dear. Freesurfer experts.
  >       >
  >       > Hi. How are you?
  >       >
  >       > I'm trying to flatten the visual cortex using the command
  mris_flatten
  >       (freesurfer
  >       > version 5.3.0).
  >       >
  >       > The command line is:
  >       > mris_flatten -w 0 -distances 12 7
  >       $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
  >       > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat
  >       >
  >       > The error I get is:
  >       > using write iterations = 0
  >       > sampling 7 neighbors out to a distance of 12 mm
  >       > reading patch
  >       /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d
  with
  >       > 27964 vertices (19.0% of total)
  >       > MRISreadPatch: bad vertex # (147220) found in patch file
  >       > No such file or directory
  >       >
  >       > Previously, Bruce advised me to recut it, so I deleted the
  >       lh.oc.patch.3d and recut
  >       > it. However, freesurfer gives me the same error message...
  >       >
  >       > Could you please help me fix it?
  >       >
  >       > Thank you so much.
  >       >
  >       > Best,
  >       > Ji Won
  >       >
  >       >
  > _______________________________________________
  > 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

then you must not have cut the patch from those surfaces. The error is about a vertex # in the patch (147220), which is larger than the total number of vertices in those surfaces (144977), so it's out of bounds. How did you do the cutting?

On Tue, 22 Mar 2016, Ji Won Bang wrote:

Oh, I see.

When I run all of these surfaces, it gave me the exactly same numbers...

[jbang@cpu156 surf]$ mris_euler_number lh.inflated euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes       F =2V-4:          289950 = 289954-4 (0)       2E=3F:            869850 = 869850 (0)

total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.white euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes       F =2V-4:          289950 = 289954-4 (0)       2E=3F:            869850 = 869850 (0)

total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.pial euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes       F =2V-4:          289950 = 289954-4 (0)       2E=3F:            869850 = 869850 (0)

total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.orig euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes       F =2V-4:          289950 = 289954-4 (0)       2E=3F:            869850 = 869850 (0)

total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.sphere euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes       F =2V-4:          289950 = 289954-4 (0)       2E=3F:            869850 = 869850 (0)

total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.sphere.reg euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes       F =2V-4:          289950 = 289954-4 (0)       2E=3F:            869850 = 869850 (0)

total defect index = 0

Thanks, Ji Won

2016-03-22 12:59 GMT-04:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: no, for all surfaces for the same hemi (lh and rh). lh.inflated.K is not a surface - it's a scalar field over the surface. The ones that should be the same are:

  lh.inflated
  lh.white
  lh.pial
  lh.orig
  lh.sphere
  lh.sphere.reg



  and same for the rh (but different from the lh ones)

  cheers
  Bruce


  On Tue, 22 Mar 2016, Ji Won Bang wrote:

        Dear. Bruce.

        Thanks for your help.

        When I tried:
        mris_euler_number rh.inflated.K

        It gave me:
        nquads=15728644,  nvertices=574
        ERROR: MRISread: file 'rh.inflated.K' has many more faces
        than vertices!
        Probably trying to use a scalar data file as a surface!

        When I tried:
        mris_euler_number lh.inflated

        It gave me:
        euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0
        holes
              F =2V-4:          289950 = 289954-4 (0)
              2E=3F:            869850 = 869850 (0)

        When I tried:
        mris_euler_number rh.inflated

        It gave me:
        euler # = v-e+f = 2g-2: 147184 - 441546 + 294364 = 2 --> 0
        holes
              F =2V-4:          294364 = 294368-4 (0)
              2E=3F:            883092 = 883092 (0)

        So if everything is correct, I should see the same numbers
        for all surfaces, but
        since it's not the case, I should run recon again...

        Thanks,
        Ji Won

        2016-03-22 12:24 GMT-04:00 Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>:
              you can try recon-all -make all for that subject and
        and see if it doesn
              anything. But run mris_euler_number on those surfaces
        and see if they
              match. They should all have the same number of
        faces/edges/vertices (for
              one hemisphere in the same subject)

              On Tue, 22 Mar 2016,
              Ji Won Bang wrote:

              > Dear. Bruce.
              >
              > Thank you for your advice.
              > I think I misunderstood what you meant.
              >
              > What I did is this.
              > I showed the contrast result on a surface by using
        the command:
              > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh
        -analysis retino
              -contrast HorVer
              >
              > Then I cut line, and then plane (occipital plane) and
        save it(3d) as
              lh.oc.patch.3d
              > under $SUBJECTS_DIR/$SUBJECT/surf/
              >
              > I'm not sure if I regenerated the surface files
        correctly but I believe
              I created the
              > surface($SUBJECTS_DIR/$SUBJECT/surf directory) from
        recon-all process.
              >
              >
              > Should I do something else to regenerate the surface?
              >
              > Thank you.
              >
              > Best,
              > Ji Won
              >
              >
              >
              >
              >
              > 2016-03-22 11:39 GMT-04:00 Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>:
              >       what surface did you recut it from? Can you run
        mris_euler_number
              on that
              >       surface (presumably the inflated) and also on
        the white/orig/pial
              >       surfaces? They should all have the same number
        of vertices, but I
              suspect
              >       some of them won't, meaning that they need to
        be regenerated.
              >
              >       cheers
              >       Bruce
              >
              >
              >
              >
              >       On Tue, 22 Mar 2016, Ji Won Bang wrote:
              >
              >       > Dear. Freesurfer experts.
              >       >
              >       > Hi. How are you?
              >       >
              >       > I'm trying to flatten the visual cortex using
        the command
              mris_flatten
              >       (freesurfer
              >       > version 5.3.0).
              >       >
              >       > The command line is:
              >       > mris_flatten -w 0 -distances 12 7
              >       $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
              >       > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat
              >       >
              >       > The error I get is:
              >       > using write iterations = 0
              >       > sampling 7 neighbors out to a distance of 12
        mm
              >       > reading patch
              >     
         /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d
              with
              >       > 27964 vertices (19.0% of total)
              >       > MRISreadPatch: bad vertex # (147220) found in
        patch file
              >       > No such file or directory
              >       >
              >       > Previously, Bruce advised me to recut it, so
        I deleted the
              >       lh.oc.patch.3d and recut
              >       > it. However, freesurfer gives me the same
        error message...
              >       >
              >       > Could you please help me fix it?
              >       >
              >       > Thank you so much.
              >       >
              >       > Best,
              >       > Ji Won
              >       >
              >       >
              > _______________________________________________
              > Freesurfer mailing list
              > Freesurfer@nmr.mgh.harvard.edu
              >
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
              >
              >
              > The information in this e-mail is intended only for
        the person to whom
              it is
              > addressed. If you believe this e-mail was sent to you
        in error and the
              e-mail
              > contains patient information, please contact the
        Partners Compliance
              HelpLine
              > at
              > http://www.partners.org/complianceline . If the
        e-mail was sent to you
              in error
              > but does not contain patient information, please
        contact the sender and
              > properly
              > dispose of the e-mail.
              >
              >
              >
              >
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              Freesurfer mailing list
              Freesurfer@nmr.mgh.harvard.edu
             
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Dear. All.

I tried tksurfer and it works.. It's still very strange why tksurfer-sess does not work.

The command line that worked successfully is: tksurfer replay06 lh inflated -curv -gray

Then I overlayed the contrast result sig.nii.gz and the registration file.

Then I cut the plane and then flattenr the cortex.

The command that did not work well is: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower

For some reason, it calls fsaverage map and when I cut the plane, it seems like the vertex is off the surface that I created... Probably, this cutting work was done in other surface that I did not intend...

If anyone knows why it's happening, let me know.

Thank you!

Best, Ji Won

2016-03-22 13:18 GMT-04:00 Ji Won Bang kirstens03@gmail.com:

Oh, I see.

I showed the contrast results on a surface using the command: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower

Then I select 3 points along a boundary between upper and lower visual fields (near calcarine sulcus) and press "Cut line". Then, select 4 points to define the cutting plane: 1 on lower side of the line, 2 on upper side of the line, 3 on the opposite surface (use rotation tool), and 4 to specify which portion of surface is kept, and press "Cur plane". File->Patch->Save Patch As {lh, rh}.oc.patch.3d

This is the usual way that I've been doing...

1 thing that's weird is when I run: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower It calls fsaverage..such as: Reading source surface reg /home/jbang/Projects/replay/mri//replay06/surf/lh.sphere.reg Loading source data Reading target surface reg /home/jbang/Projects/replay/mri//fsaverage/surf/lh.sphere.reg Done

Previously when everything went smooth, I think it did not call fsaverage.

Is it normal?

Thank you.

Best, Ji Won

2016-03-22 13:06 GMT-04:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

then you must not have cut the patch from those surfaces. The error is about a vertex # in the patch (147220), which is larger than the total number of vertices in those surfaces (144977), so it's out of bounds. How did you do the cutting?

On Tue, 22 Mar 2016, Ji Won Bang wrote:

Oh, I see.

...

When I run all of these surfaces, it gave me the exactly same numbers...

[jbang@cpu156 surf]$ mris_euler_number lh.inflated euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F: 869850 = 869850 (0)

total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.white euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F: 869850 = 869850 (0)

total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.pial euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F: 869850 = 869850 (0)

total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.orig euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F: 869850 = 869850 (0)

total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.sphere euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F: 869850 = 869850 (0)

total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.sphere.reg euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F: 869850 = 869850 (0)

total defect index = 0

Thanks, Ji Won

2016-03-22 12:59 GMT-04:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: no, for all surfaces for the same hemi (lh and rh). lh.inflated.K is not a surface - it's a scalar field over the surface. The ones that should be the same are:

  lh.inflated
  lh.white
  lh.pial
  lh.orig
  lh.sphere
  lh.sphere.reg



  and same for the rh (but different from the lh ones)

  cheers
  Bruce


  On Tue, 22 Mar 2016, Ji Won Bang wrote:

        Dear. Bruce.

        Thanks for your help.

        When I tried:
        mris_euler_number rh.inflated.K

        It gave me:
        nquads=15728644,  nvertices=574
        ERROR: MRISread: file 'rh.inflated.K' has many more faces
        than vertices!
        Probably trying to use a scalar data file as a surface!

        When I tried:
        mris_euler_number lh.inflated

        It gave me:
        euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0
        holes
              F =2V-4:          289950 = 289954-4 (0)
              2E=3F:            869850 = 869850 (0)

        When I tried:
        mris_euler_number rh.inflated

        It gave me:
        euler # = v-e+f = 2g-2: 147184 - 441546 + 294364 = 2 --> 0
        holes
              F =2V-4:          294364 = 294368-4 (0)
              2E=3F:            883092 = 883092 (0)

        So if everything is correct, I should see the same numbers
        for all surfaces, but
        since it's not the case, I should run recon again...

        Thanks,
        Ji Won

        2016-03-22 12:24 GMT-04:00 Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>:
              you can try recon-all -make all for that subject and
        and see if it doesn
              anything. But run mris_euler_number on those surfaces
        and see if they
              match. They should all have the same number of
        faces/edges/vertices (for
              one hemisphere in the same subject)

              On Tue, 22 Mar 2016,
              Ji Won Bang wrote:

              > Dear. Bruce.
              >
              > Thank you for your advice.
              > I think I misunderstood what you meant.
              >
              > What I did is this.
              > I showed the contrast result on a surface by using
        the command:
              > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh
        -analysis retino
              -contrast HorVer
              >
              > Then I cut line, and then plane (occipital plane) and
        save it(3d) as
              lh.oc.patch.3d
              > under $SUBJECTS_DIR/$SUBJECT/surf/
              >
              > I'm not sure if I regenerated the surface files
        correctly but I believe
              I created the
              > surface($SUBJECTS_DIR/$SUBJECT/surf directory) from
        recon-all process.
              >
              >
              > Should I do something else to regenerate the surface?
              >
              > Thank you.
              >
              > Best,
              > Ji Won
              >
              >
              >
              >
              >
              > 2016-03-22 11:39 GMT-04:00 Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>:
              >       what surface did you recut it from? Can you run
        mris_euler_number
              on that
              >       surface (presumably the inflated) and also on
        the white/orig/pial
              >       surfaces? They should all have the same number
        of vertices, but I
              suspect
              >       some of them won't, meaning that they need to
        be regenerated.
              >
              >       cheers
              >       Bruce
              >
              >
              >
              >
              >       On Tue, 22 Mar 2016, Ji Won Bang wrote:
              >
              >       > Dear. Freesurfer experts.
              >       >
              >       > Hi. How are you?
              >       >
              >       > I'm trying to flatten the visual cortex using
        the command
              mris_flatten
              >       (freesurfer
              >       > version 5.3.0).
              >       >
              >       > The command line is:
              >       > mris_flatten -w 0 -distances 12 7
              >       $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d
              >       > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat
              >       >
              >       > The error I get is:
              >       > using write iterations = 0
              >       > sampling 7 neighbors out to a distance of 12
        mm
              >       > reading patch
              >

/home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d with > > 27964 vertices (19.0% of total) > > MRISreadPatch: bad vertex # (147220) found in patch file > > No such file or directory > > > > Previously, Bruce advised me to recut it, so I deleted the > lh.oc.patch.3d and recut > > it. However, freesurfer gives me the same error message... > > > > Could you please help me fix it? > > > > Thank you so much. > > > > Best, > > Ji Won > > > > > _______________________________________________ > 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

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