[Freesurfer] stats t test

[jiahui]

External Email - Use Caution

Hello FreeSurfer Developers,
I'm attempting to compute  gray matter volume average thickness.Can I use them 
from stats file to compare two groups (HC and diesease) through t test?1) 
FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
figure1.png: see attached



 





 





 





 





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Re: [Freesurfer] sig.cluster.summary and sig.cluster.mgh of mri_glmfit-sim

[Douglas N. Greve]

but when you click on the vertex, is the value in the freeview the same 
value in the summary file? Note, you must load the sig.mgh file, not the 
corrected map.


On 5/5/2020 4:58 PM, Xiaojiang Yang wrote:


External Email - Use Caution

Hi Douglas,

Not only vertex 10738. For all vertexeslisted in the summary file, 
they all have a very big Max value (absolute) that is out of the 
visual range. Please see the video I grabbed from my screen: 
https://imgur.com/a/kkSO7sT


***Thank you for your time to help this.*

***Xiaojiang*

*
*


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Re: [Freesurfer] Get Atlas surfaces in subject space

[Ian Hardingham]

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Thank you both.

I've made edits and these are the current commands:

mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white 
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz 
--trgsurfval {output_dir}/registered_lh.white
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white 
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz 
--trgsurfval {output_dir}/registered_rh.white
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial 
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz 
--trgsurfval {output_dir}/registered_lh.pial
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial 
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz 
--trgsurfval {output_dir}/registered_rh.pial


These execute successfully and the file size looks about right, but 
after using mris_convert to convert to Gifti format nibabel crashes on 
trying to load them - is there anything obviously wrong in my commands?


I'll also take a look at mris_apply_reg.

On 05/05/2020 18:01, Douglas N. Greve wrote:

Don't specify a --trg_type. But add --tval-xyz
mris_apply_reg will do the same thing, but the interface might be a 
little easier


On 5/5/2020 12:49 PM, Bruce Fischl wrote:
no definitely not "w" format, which we don't use for anything 
anymore. YOu should use tval-xyz also I think

On Tue, 5 May 2020, Ian Hardingham wrote:



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It would appear not, as I'm getting an error on my pial output files 
but not

my white ones.  Here are my commands:

mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white 
--trgsubject

fs_target --trgsurfval ./registered_lh.white --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white 
--trgsubject

fs_target --trgsurfval ./registered_rh.white --trg_type w
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial 
--trgsubject

fs_target --trgsurfval ./registered_lh.pial --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial 
--trgsubject

fs_target --trgsurfval ./registered_rh.pial --trg_type w

The white calls output seems to be fine, but the pial ones aren't.  I
somewhat naively trued trg_type pial but that wasn't correct.

On 05/05/2020 17:33, Ian Hardingham wrote:

  Thanks Bruce, extremely helpful.

  Can I just check that the "w" format is what is used by both the
  lh/rh.pial and the lh/rh.white files?  I only ask because my
  surf2surf command outputs the exact output filename if the end
  is ".white", but if it's ".pial" it outputs ".pial.w", which I
  find a little curious.

  Ian

  On 05/05/2020 16:34, Bruce Fischl wrote:
  yes, check out options like:
  --sval-xyz

  if you need further help though I'll have to defer to Doug
  :)
  Bruce


  On Tue, 5 May 2020, Ian Hardingham wrote:


    External Email - Use Caution

    Bruce, I've read the docs on mri_surf2surf - I
    wish to get surface files out
    (again, lh.pial, rh.pial, lh.white, and
    rh.white) rather than values for
    something such as thickness - is there an
    option for mri_surf2surf to allow
    this?

    On 05/05/2020 14:43, Bruce Fischl wrote:
      Hi Ian

      you can use mri_surf2surf to map
    surfaces between subjects, but
      our atlas isn't really a surface. You
    can use the surfaces in
      the fsaverage dir, but they are meant
    for visualization and are
      much smoother than individuals

      cheers
      Bruce


      On Tue, 5 May 2020, Ian wrote:


        External Email - Use
    Caution

        Hi Freesurfers.

        I have a subject S with recon-all
    having been run on
        it.

        I have the subject-specific
    surface files
        /surf/lh.pial, rh.pial, lh.white,
        and rh.white.

        I would like an Atlas's lh.pial,
    rh.pial, lh.white,
        and rh.white in subject
        space.

        Any helpers on how to achieve
    this?

        Thanks,
        Ian

        --

        Ian Hardingham





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Re: [Freesurfer] sig.cluster.summary and sig.cluster.mgh of mri_glmfit-sim

[Xiaojiang Yang]

External Email - Use Caution

Hi Douglas,

 Not only vertex 10738. For all vertexes listed in the summary file, they
all have a very big Max value (absolute) that is out of the visual range.
Please see the video I grabbed from my screen: https://imgur.com/a/kkSO7sT

 *Thank you for your time to help this.*

 *Xiaojiang*
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Re: [Freesurfer] Get Atlas surfaces in subject space

[Ian Hardingham]

   External Email - Use Caution

It would appear not, as I'm getting an error on my pial output files but 
not my white ones.  Here are my commands:


mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white 
--trgsubject fs_target --trgsurfval ./registered_lh.white --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white 
--trgsubject fs_target --trgsurfval ./registered_rh.white --trg_type w
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial 
--trgsubject fs_target --trgsurfval ./registered_lh.pial --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial 
--trgsubject fs_target --trgsurfval ./registered_rh.pial --trg_type w


The white calls output seems to be fine, but the pial ones aren't.  I 
somewhat naively trued trg_type pial but that wasn't correct.


On 05/05/2020 17:33, Ian Hardingham wrote:


Thanks Bruce, extremely helpful.

Can I just check that the "w" format is what is used by both the 
lh/rh.pial and the lh/rh.white files?  I only ask because my surf2surf 
command outputs the exact output filename if the end is ".white", but 
if it's ".pial" it outputs ".pial.w", which I find a little curious.


Ian

On 05/05/2020 16:34, Bruce Fischl wrote:

yes, check out options like:
--sval-xyz

if you need further help though I'll have to defer to Doug :)
Bruce


On Tue, 5 May 2020, Ian Hardingham wrote:



External Email - Use Caution

Bruce, I've read the docs on mri_surf2surf - I wish to get surface 
files out
(again, lh.pial, rh.pial, lh.white, and rh.white) rather than values 
for
something such as thickness - is there an option for mri_surf2surf 
to allow

this?

On 05/05/2020 14:43, Bruce Fischl wrote:
  Hi Ian

  you can use mri_surf2surf to map surfaces between subjects, but
  our atlas isn't really a surface. You can use the surfaces in
  the fsaverage dir, but they are meant for visualization and are
  much smoother than individuals

  cheers
  Bruce


  On Tue, 5 May 2020, Ian wrote:


    External Email - Use Caution

    Hi Freesurfers.

    I have a subject S with recon-all having been run on
    it.

    I have the subject-specific surface files
    /surf/lh.pial, rh.pial, lh.white,
    and rh.white.

    I would like an Atlas's lh.pial, rh.pial, lh.white,
    and rh.white in subject
    space.

    Any helpers on how to achieve this?

    Thanks,
    Ian

    --

    Ian Hardingham





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Re: [Freesurfer] Get Atlas surfaces in subject space

[Ian Hardingham]

   External Email - Use Caution


Thanks Bruce, extremely helpful.

Can I just check that the "w" format is what is used by both the 
lh/rh.pial and the lh/rh.white files?  I only ask because my surf2surf 
command outputs the exact output filename if the end is ".white", but if 
it's ".pial" it outputs ".pial.w", which I find a little curious.


Ian

On 05/05/2020 16:34, Bruce Fischl wrote:

yes, check out options like:
--sval-xyz

if you need further help though I'll have to defer to Doug :)
Bruce


On Tue, 5 May 2020, Ian Hardingham wrote:



External Email - Use Caution

Bruce, I've read the docs on mri_surf2surf - I wish to get surface 
files out

(again, lh.pial, rh.pial, lh.white, and rh.white) rather than values for
something such as thickness - is there an option for mri_surf2surf to 
allow

this?

On 05/05/2020 14:43, Bruce Fischl wrote:
  Hi Ian

  you can use mri_surf2surf to map surfaces between subjects, but
  our atlas isn't really a surface. You can use the surfaces in
  the fsaverage dir, but they are meant for visualization and are
  much smoother than individuals

  cheers
  Bruce


  On Tue, 5 May 2020, Ian wrote:


    External Email - Use Caution

    Hi Freesurfers.

    I have a subject S with recon-all having been run on
    it.

    I have the subject-specific surface files
    /surf/lh.pial, rh.pial, lh.white,
    and rh.white.

    I would like an Atlas's lh.pial, rh.pial, lh.white,
    and rh.white in subject
    space.

    Any helpers on how to achieve this?

    Thanks,
    Ian

    --

    Ian Hardingham





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Re: [Freesurfer] Get Atlas surfaces in subject space

[Ian Hardingham]

   External Email - Use Caution

Bruce, I've read the docs on mri_surf2surf - I wish to get surface files 
out (again, lh.pial, rh.pial, lh.white, and rh.white) rather than values 
for something such as thickness - is there an option for mri_surf2surf 
to allow this?


On 05/05/2020 14:43, Bruce Fischl wrote:

Hi Ian

you can use mri_surf2surf to map surfaces between subjects, but our 
atlas isn't really a surface. You can use the surfaces in the 
fsaverage dir, but they are meant for visualization and are much 
smoother than individuals


cheers
Bruce


On Tue, 5 May 2020, Ian wrote:



External Email - Use Caution

Hi Freesurfers.

I have a subject S with recon-all having been run on it.

I have the subject-specific surface files /surf/lh.pial, rh.pial, 
lh.white,

and rh.white.

I would like an Atlas's lh.pial, rh.pial, lh.white, and rh.white in 
subject

space.

Any helpers on how to achieve this?

Thanks,
Ian

--

Ian Hardingham






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Re: [Freesurfer] Get Atlas surfaces in subject space

[Douglas N. Greve]

You should load the surfaces in FV. If it load in FV ok but nibable is 
crashing, you should contact them.


On 5/5/2020 1:05 PM, Ian Hardingham wrote:


External Email - Use Caution

Thank you both.

I've made edits and these are the current commands:

mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white 
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz 
--trgsurfval {output_dir}/registered_lh.white
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white 
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz 
--trgsurfval {output_dir}/registered_rh.white
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial 
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz 
--trgsurfval {output_dir}/registered_lh.pial
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial 
--trgsubject fs_target --tval-xyz {input_dir}/T1_nifti.nii.gz 
--trgsurfval {output_dir}/registered_rh.pial


These execute successfully and the file size looks about right, but 
after using mris_convert to convert to Gifti format nibabel crashes on 
trying to load them - is there anything obviously wrong in my commands?


I'll also take a look at mris_apply_reg.

On 05/05/2020 18:01, Douglas N. Greve wrote:

Don't specify a --trg_type. But add --tval-xyz
mris_apply_reg will do the same thing, but the interface might be a 
little easier


On 5/5/2020 12:49 PM, Bruce Fischl wrote:
no definitely not "w" format, which we don't use for anything 
anymore. YOu should use tval-xyz also I think

On Tue, 5 May 2020, Ian Hardingham wrote:



External Email - Use Caution

It would appear not, as I'm getting an error on my pial output 
files but not

my white ones.  Here are my commands:

mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white 
--trgsubject

fs_target --trgsurfval ./registered_lh.white --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white 
--trgsubject

fs_target --trgsurfval ./registered_rh.white --trg_type w
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial 
--trgsubject

fs_target --trgsurfval ./registered_lh.pial --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial 
--trgsubject

fs_target --trgsurfval ./registered_rh.pial --trg_type w

The white calls output seems to be fine, but the pial ones aren't.  I
somewhat naively trued trg_type pial but that wasn't correct.

On 05/05/2020 17:33, Ian Hardingham wrote:

  Thanks Bruce, extremely helpful.

  Can I just check that the "w" format is what is used by both the
  lh/rh.pial and the lh/rh.white files?  I only ask because my
  surf2surf command outputs the exact output filename if the end
  is ".white", but if it's ".pial" it outputs ".pial.w", which I
  find a little curious.

  Ian

  On 05/05/2020 16:34, Bruce Fischl wrote:
  yes, check out options like:
  --sval-xyz

  if you need further help though I'll have to defer to Doug
  :)
  Bruce


  On Tue, 5 May 2020, Ian Hardingham wrote:


    External Email - Use Caution

    Bruce, I've read the docs on mri_surf2surf - I
    wish to get surface files out
    (again, lh.pial, rh.pial, lh.white, and
    rh.white) rather than values for
    something such as thickness - is there an
    option for mri_surf2surf to allow
    this?

    On 05/05/2020 14:43, Bruce Fischl wrote:
      Hi Ian

      you can use mri_surf2surf to map
    surfaces between subjects, but
      our atlas isn't really a surface. You
    can use the surfaces in
      the fsaverage dir, but they are meant
    for visualization and are
      much smoother than individuals

      cheers
      Bruce


      On Tue, 5 May 2020, Ian wrote:


        External Email - Use
    Caution

        Hi Freesurfers.

        I have a subject S with recon-all
    having been run on
        it.

        I have the subject-specific
    surface files
        /surf/lh.pial, rh.pial, lh.white,
        and rh.white.

        I would like an Atlas's lh.pial,
    rh.pial, lh.white,
        and rh.white in subject
        space.

        Any helpers on how to achieve
    this?

        Thanks,
        Ian

        --

        Ian Hardingham





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Re: [Freesurfer] T1 recon -all error "XL defect detected"

[Douglas N. Greve]

You should load that volume along with the orig.nofix hemisphere that is 
giving you problems and look for a large area that should not be within 
the surface


On 5/5/2020 1:23 PM, Zeng, Qi wrote:


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Hi Douglas,

The cerebrum is removed and with no skull attached.
However, compared to others that run normally,  it may have problems 
with white matter segmentation and missing brainstem (no clear). 
Attached the comparison below. Can you help figure it out?




Thank you so much!
Best,
Qi

On Tue, May 5, 2020 at 11:36 AM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


You should look at the wm.mgz to see where the defect is. Probably
cerebellum is still attached or maybe a big piece of skull.

On 5/4/2020 11:19 PM, Zeng, Qi wrote:


External Email - Use Caution

Hi,

I've conducted longitudinal T1 recon-all. One subject's last-scan
ran into error in the first independent recon all step: "
recon-all -s SUBJ1 -SUBJ1.nii -all'.
Error: "CORRECTING DEFECT 0 (vertices=14101, convex hull=2297,
v0=1419) XL defect detected...". Log file attached below.

I've increased the memory usage limit as some suggestions did,
but no help. Also T1.nii looks fine, same parameter setting as
first scan, also attached below. Subject first scan and all the
other subjects were finished without errors. Can you help figure
out what has caused it?

Thank you so much!
Best,
Qi

-- 


Ph.D. candidate
Icahn School of Medicine at Mount Sinai


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--

Ph.D. candidate
Icahn School of Medicine at Mount Sinai


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Re: [Freesurfer] Get Atlas surfaces in subject space

[Douglas N. Greve]

Don't specify a --trg_type. But add --tval-xyz
mris_apply_reg will do the same thing, but the interface might be a 
little easier


On 5/5/2020 12:49 PM, Bruce Fischl wrote:
no definitely not "w" format, which we don't use for anything anymore. 
YOu should use tval-xyz also I think

On Tue, 5 May 2020, Ian Hardingham wrote:



External Email - Use Caution

It would appear not, as I'm getting an error on my pial output files 
but not

my white ones.  Here are my commands:

mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white 
--trgsubject

fs_target --trgsurfval ./registered_lh.white --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white 
--trgsubject

fs_target --trgsurfval ./registered_rh.white --trg_type w
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial 
--trgsubject

fs_target --trgsurfval ./registered_lh.pial --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial 
--trgsubject

fs_target --trgsurfval ./registered_rh.pial --trg_type w

The white calls output seems to be fine, but the pial ones aren't.  I
somewhat naively trued trg_type pial but that wasn't correct.

On 05/05/2020 17:33, Ian Hardingham wrote:

  Thanks Bruce, extremely helpful.

  Can I just check that the "w" format is what is used by both the
  lh/rh.pial and the lh/rh.white files?  I only ask because my
  surf2surf command outputs the exact output filename if the end
  is ".white", but if it's ".pial" it outputs ".pial.w", which I
  find a little curious.

  Ian

  On 05/05/2020 16:34, Bruce Fischl wrote:
  yes, check out options like:
  --sval-xyz

  if you need further help though I'll have to defer to Doug
  :)
  Bruce


  On Tue, 5 May 2020, Ian Hardingham wrote:


    External Email - Use Caution

    Bruce, I've read the docs on mri_surf2surf - I
    wish to get surface files out
    (again, lh.pial, rh.pial, lh.white, and
    rh.white) rather than values for
    something such as thickness - is there an
    option for mri_surf2surf to allow
    this?

    On 05/05/2020 14:43, Bruce Fischl wrote:
      Hi Ian

      you can use mri_surf2surf to map
    surfaces between subjects, but
      our atlas isn't really a surface. You
    can use the surfaces in
      the fsaverage dir, but they are meant
    for visualization and are
      much smoother than individuals

      cheers
      Bruce


      On Tue, 5 May 2020, Ian wrote:


        External Email - Use
    Caution

        Hi Freesurfers.

        I have a subject S with recon-all
    having been run on
        it.

        I have the subject-specific
    surface files
        /surf/lh.pial, rh.pial, lh.white,
        and rh.white.

        I would like an Atlas's lh.pial,
    rh.pial, lh.white,
        and rh.white in subject
        space.

        Any helpers on how to achieve
    this?

        Thanks,
        Ian

        --

        Ian Hardingham





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    Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Get Atlas surfaces in subject space

[Bruce Fischl]

no definitely not "w" format, which we don't use for anything anymore. 
YOu should use tval-xyz also I think
On Tue, 5 May 2020, Ian Hardingham 
wrote:




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It would appear not, as I'm getting an error on my pial output files but not
my white ones.  Here are my commands:

mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white --trgsubject
fs_target --trgsurfval ./registered_lh.white --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz white --trgsubject
fs_target --trgsurfval ./registered_rh.white --trg_type w
mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz pial --trgsubject
fs_target --trgsurfval ./registered_lh.pial --trg_type w
mri_surf2surf --hemi rh --srcsubject fsaverage --sval-xyz pial --trgsubject
fs_target --trgsurfval ./registered_rh.pial --trg_type w

The white calls output seems to be fine, but the pial ones aren't.  I
somewhat naively trued trg_type pial but that wasn't correct.

On 05/05/2020 17:33, Ian Hardingham wrote:

  Thanks Bruce, extremely helpful.

  Can I just check that the "w" format is what is used by both the
  lh/rh.pial and the lh/rh.white files?  I only ask because my
  surf2surf command outputs the exact output filename if the end
  is ".white", but if it's ".pial" it outputs ".pial.w", which I
  find a little curious.

  Ian

  On 05/05/2020 16:34, Bruce Fischl wrote:
  yes, check out options like:
  --sval-xyz

  if you need further help though I'll have to defer to Doug
  :)
  Bruce


  On Tue, 5 May 2020, Ian Hardingham wrote:


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Bruce, I've read the docs on mri_surf2surf - I
wish to get surface files out
(again, lh.pial, rh.pial, lh.white, and
rh.white) rather than values for
something such as thickness - is there an
option for mri_surf2surf to allow
this?

On 05/05/2020 14:43, Bruce Fischl wrote:
  Hi Ian

  you can use mri_surf2surf to map
surfaces between subjects, but
  our atlas isn't really a surface. You
can use the surfaces in
  the fsaverage dir, but they are meant
for visualization and are
  much smoother than individuals

  cheers
  Bruce


  On Tue, 5 May 2020, Ian wrote:


    External Email - Use
Caution

    Hi Freesurfers.

    I have a subject S with recon-all
having been run on
    it.

    I have the subject-specific
surface files
    /surf/lh.pial, rh.pial, lh.white,
    and rh.white.

    I would like an Atlas's lh.pial,
rh.pial, lh.white,
    and rh.white in subject
    space.

    Any helpers on how to achieve
this?

    Thanks,
    Ian

    --

    Ian Hardingham





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Re: [Freesurfer] samseg with subfields {Disarmed}

[Sneha Pandya]

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Dear Dough,

No worries, this was helpful too. Probably, I will test it on a subset of 
subjects and compare the two for possible discrepancies.

Thank you,
Sneha

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Tuesday, May 5, 2020 11:39 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields

sorry, did not see this before I responded. Ignore what I said
On 5/5/2020 11:13 AM, Iglesias Gonzalez, Juan E. wrote:
Dear Sneha,
We use cortical and white matter parcels in the hippocampal subfields, which is 
more reliable than using the whole white / gray matter to compute parameters. 
But it could be hacked, albeit it would be a bit less reliable. I’ll add this 
to the wishlist / to-do list (unfortunately it isn’t likely I’ll be able to 
look at it any time soon…)
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From: 

 on behalf of Sneha Pandya 

Reply-To: Freesurfer support list 

Date: Tuesday, May 5, 2020 at 10:46
To: "freesurfer@nmr.mgh.harvard.edu" 

Subject: Re: [Freesurfer] samseg with subfields


External Email - Use Caution
Dear experts,

I want to revisit if anyone has ran subfield analysis just by running samseg? 
If it is possible is it as reliable as from running regular routine with “-all” 
recon-all flag?

Thank you,

Sneha

From: Sneha Pandya
Sent: Thursday, April 30, 2020 4:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: samseg with subfields

Dear experts,

Is it possible to run subfield analysis (hippcampal subfields, amygdalar, 
thalamic nuclei, and brainstem structures) when we only run samseg on our 
dataset?

Thank you,
Sneha



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Re: [Freesurfer] samseg with subfields

[Douglas N. Greve]

sorry, did not see this before I responded. Ignore what I said

On 5/5/2020 11:13 AM, Iglesias Gonzalez, Juan E. wrote:


Dear Sneha,

We use cortical and white matter parcels in the hippocampal subfields, 
which is more reliable than using the whole white / gray matter to 
compute parameters. But it could be hacked, albeit it would be a bit 
less reliable. I’ll add this to the wishlist / to-do list 
(unfortunately it isn’t likely I’ll be able to look at it any time soon…)


Cheers,

/Eugenio

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: * on behalf of Sneha 
Pandya 

*Reply-To: *Freesurfer support list 
*Date: *Tuesday, May 5, 2020 at 10:46
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] samseg with subfields

*External Email - Use Caution *

Dear experts,

I want to revisit if anyone has ran subfield analysis just by running 
samseg? If it is possible is it as reliable as from running regular 
routine with “-all” recon-all flag?


Thank you,

Sneha

*From:* Sneha Pandya
*Sent:* Thursday, April 30, 2020 4:15 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* samseg with subfields

Dear experts,

Is it possible to run subfield analysis (hippcampal subfields, 
amygdalar, thalamic nuclei, and brainstem structures) when we only run 
samseg on our dataset?


Thank you,

Sneha


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Re: [Freesurfer] samseg with subfields

[Douglas N. Greve]

In theory it is possible, though I don't know if it is better or worse. 
You can run samseg, then run samseg2recon (this creates a folder that 
looks like it was created by recon-all), then run subfields on that folder


On 5/5/2020 10:45 AM, Sneha Pandya wrote:


External Email - Use Caution

Dear experts,

I want to revisit if anyone has ran subfield analysis just by running 
samseg? If it is possible is it as reliable as from running regular 
routine with “-all” recon-all flag?


Thank you,

Sneha

*From:* Sneha Pandya
*Sent:* Thursday, April 30, 2020 4:15 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* samseg with subfields

Dear experts,

Is it possible to run subfield analysis (hippcampal subfields, 
amygdalar, thalamic nuclei, and brainstem structures) when we only run 
samseg on our dataset?


Thank you,

Sneha


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Re: [Freesurfer] T1 recon -all error "XL defect detected"

[Douglas N. Greve]

You should look at the wm.mgz to see where the defect is. Probably 
cerebellum is still attached or maybe a big piece of skull.


On 5/4/2020 11:19 PM, Zeng, Qi wrote:


External Email - Use Caution

Hi,

I've conducted longitudinal T1 recon-all. One subject's last-scan ran 
into error in the first independent recon all step: " recon-all -s 
SUBJ1 -SUBJ1.nii -all'.
Error: "CORRECTING DEFECT 0 (vertices=14101, convex hull=2297, 
v0=1419) XL defect detected...". Log file attached below.


I've increased the memory usage limit as some suggestions did, but no 
help. Also T1.nii looks fine, same parameter setting as first scan, 
also attached below. Subject first scan and all the other subjects 
were finished without errors. Can you help figure out what has caused it?


Thank you so much!
Best,
Qi

--

Ph.D. candidate
Icahn School of Medicine at Mount Sinai


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Re: [Freesurfer] sig.cluster.summary and sig.cluster.mgh of mri_glmfit-sim

[Douglas N. Greve]

Not sure. Are you visiting vertex 10738 ?

On 5/4/2020 10:01 PM, Xiaojiang Yang wrote:


External Email - Use Caution

Hi FS developers,

I have used mri_glmfit-sim to do multiple comparison like below:

mri_glmfit-sim --glmdir lh.thickness.0.glmdir --cache 3 abs --cwp  
0.05 --2spaces


and in the lh.thickness.0.glmdir/group.diff directory, I got some 
output files, some of which were:


    cache.th30.abs.sig.cluster.summary

cache.th30.abs.sig.cluster.mgh

When I open the file cache.th30.abs.sig.cluster.summary, I see its 
content like below:


# ClusterNo  Max   VtxMax   Size(mm^2) MNIX   MNIY   MNIZ    CWP    
CWPLow    CWPHi   NVtxs WghtVtx   Annot


   1   -7.090   10738 37.13 -4.6   48.8  -22.0  0.00020  
0.0  0.00040 75 -296.47  medialorbitofrontal


   2    6.620   27279 32.15 -43.2   32.8    8.6  0.00060  
0.00020  0.00100 35 148.52  parstriangularis


   3    7.006  144024 25.30 -26.8  -69.9   -4.5  0.00300  
0.00200  0.00400 40 172.77  lingual


   4   -4.688    4845 23.24   -22.5   52.4  -12.6  0.00579  
0.00440  0.00719 28 -99.88  rostralmiddlefrontal


   5    5.796  123246 17.35 -25.1   33.2   26.4  0.04019  
0.03666  0.04371 30 109.79  rostralmiddlefrontal


My question is: what are the values of the Max column? I thing they 
are –log10(p), and the file cache.th30.abs.sig.cluster.mgh should also 
have this kind of values saved. But when I use freeview to view the 
lh.inflated surface with overlay file cache.th30.abs.sig.cluster.mgh, 
and use the “configure” button to configure the “Overlay” threshold, I 
cannot find the Max value of overlay displayed on the inflated surface.


Could you please explain to me why I cannot see the Max values (shown 
in the summary file) as the overlay on the lh.inflated surface?


BTW, in another experiment where I use mri_surfcluster to generate 
both summary file and overlay file, this problem does NOT exist.


Thanks!

Xiaojiang


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Re: [Freesurfer] Get Atlas surfaces in subject space

[Bruce Fischl]

yes, check out options like:
--sval-xyz

if you need further help though I'll have to defer to Doug :)
Bruce


On Tue, 5 May 2020, Ian Hardingham wrote:



External Email - Use Caution

Bruce, I've read the docs on mri_surf2surf - I wish to get surface files out
(again, lh.pial, rh.pial, lh.white, and rh.white) rather than values for
something such as thickness - is there an option for mri_surf2surf to allow
this?

On 05/05/2020 14:43, Bruce Fischl wrote:
  Hi Ian

  you can use mri_surf2surf to map surfaces between subjects, but
  our atlas isn't really a surface. You can use the surfaces in
  the fsaverage dir, but they are meant for visualization and are
  much smoother than individuals

  cheers
  Bruce


  On Tue, 5 May 2020, Ian wrote:


External Email - Use Caution

Hi Freesurfers.

I have a subject S with recon-all having been run on
it.

I have the subject-specific surface files
/surf/lh.pial, rh.pial, lh.white,
and rh.white.

I would like an Atlas's lh.pial, rh.pial, lh.white,
and rh.white in subject
space.

Any helpers on how to achieve this?

Thanks,
Ian

--

Ian Hardingham





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Re: [Freesurfer] samseg with subfields {Disarmed}

[Sneha Pandya]

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Dear Eugenio,

Thank you for quick response. That will be great if we could achieve it with 
whole-head segmentation too, considering its shorter run time, but can 
understand that it could be less reliable. If implemented, is it something that 
will be included as a patch to current release or will it part of next big 
release?

Thank you,
Sneha

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Iglesias Gonzalez, Juan E.
Sent: Tuesday, May 5, 2020 11:14 AM
To: Freesurfer support list 
Subject: [EXTERNAL] Re: [Freesurfer] samseg with subfields

Dear Sneha,
We use cortical and white matter parcels in the hippocampal subfields, which is 
more reliable than using the whole white / gray matter to compute parameters. 
But it could be hacked, albeit it would be a bit less reliable. I’ll add this 
to the wishlist / to-do list (unfortunately it isn’t likely I’ll be able to 
look at it any time soon…)
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Sneha Pandya 
mailto:snp2...@med.cornell.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, May 5, 2020 at 10:46
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] samseg with subfields


External Email - Use Caution
Dear experts,

I want to revisit if anyone has ran subfield analysis just by running samseg? 
If it is possible is it as reliable as from running regular routine with “-all” 
recon-all flag?

Thank you,

Sneha

From: Sneha Pandya
Sent: Thursday, April 30, 2020 4:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: samseg with subfields

Dear experts,

Is it possible to run subfield analysis (hippcampal subfields, amygdalar, 
thalamic nuclei, and brainstem structures) when we only run samseg on our 
dataset?

Thank you,
Sneha
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Re: [Freesurfer] samseg with subfields

[Iglesias Gonzalez, Juan E.]

Dear Sneha,
We use cortical and white matter parcels in the hippocampal subfields, which is 
more reliable than using the whole white / gray matter to compute parameters. 
But it could be hacked, albeit it would be a bit less reliable. I’ll add this 
to the wishlist / to-do list (unfortunately it isn’t likely I’ll be able to 
look at it any time soon…)
Cheers,
/Eugenio


Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com



From:  on behalf of Sneha Pandya 

Reply-To: Freesurfer support list 
Date: Tuesday, May 5, 2020 at 10:46
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] samseg with subfields


External Email - Use Caution
Dear experts,

I want to revisit if anyone has ran subfield analysis just by running samseg? 
If it is possible is it as reliable as from running regular routine with “-all” 
recon-all flag?

Thank you,

Sneha

From: Sneha Pandya
Sent: Thursday, April 30, 2020 4:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: samseg with subfields

Dear experts,

Is it possible to run subfield analysis (hippcampal subfields, amygdalar, 
thalamic nuclei, and brainstem structures) when we only run samseg on our 
dataset?

Thank you,
Sneha
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Re: [Freesurfer] samseg with subfields

[Sneha Pandya]

External Email - Use Caution

Dear experts,

I want to revisit if anyone has ran subfield analysis just by running samseg? 
If it is possible is it as reliable as from running regular routine with "-all" 
recon-all flag?

Thank you,

Sneha

From: Sneha Pandya
Sent: Thursday, April 30, 2020 4:15 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: samseg with subfields

Dear experts,

Is it possible to run subfield analysis (hippcampal subfields, amygdalar, 
thalamic nuclei, and brainstem structures) when we only run samseg on our 
dataset?

Thank you,
Sneha
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[Freesurfer] Get Atlas surfaces in subject space

[Ian]

   External Email - Use Caution


Hi Freesurfers.

I have a subject S with recon-all having been run on it.

I have the subject-specific surface files /surf/lh.pial, rh.pial, 
lh.white, and rh.white.


I would like an Atlas's lh.pial, rh.pial, lh.white, and rh.white in 
subject space.


Any helpers on how to achieve this?

Thanks,
Ian

--

*Ian Hardingham*


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Re: [Freesurfer] Get Atlas surfaces in subject space

[Bruce Fischl]

Hi Ian

you can use mri_surf2surf to map surfaces between subjects, but our atlas 
isn't really a surface. You can use the surfaces in the fsaverage dir, but 
they are meant for visualization and are much smoother than individuals


cheers
Bruce


On Tue, 5 May 
2020, Ian wrote:




External Email - Use Caution

Hi Freesurfers.

I have a subject S with recon-all having been run on it.

I have the subject-specific surface files /surf/lh.pial, rh.pial, lh.white,
and rh.white.

I would like an Atlas's lh.pial, rh.pial, lh.white, and rh.white in subject
space.

Any helpers on how to achieve this?

Thanks,
Ian

--

Ian Hardingham



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