[Freesurfer] Qdec - thickness-age correlation - Interpretation
Dear Freesurfer Experts, We have two groups at similar ages and the thickness-age correlation shows many cluster of significant values. Pointing to this maximum the plots present similar regressions coefficients for both groups. Actually it would be intresting to have the regions were the thickness – age correlation differ. Or what is the physiological meening of this kind of correlations ?? Sincerely, Sergiu, Alex. ___ 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.
Re: [Freesurfer] mri_mask problem
Hello Nick
I'm wondering if you're able to verify my data today,
I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked,
I'm guessing you'll need my data, to see if there is something wrong on it, but
I think is gonna be hard to send it to through the e-mail.
Bests,
Gabriel.
Subject: RE: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Date: Thu, 10 Mar 2011 21:38:50 -0500
i'd have to try to replicate this myself, although it will have to wait
till monday (i'm with the freesurfer group three days a week).
i wonder if you can use the brain.mgz as your mask instead of
brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their
actually not there (zeroed).
n.
On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
Hello Nick,
good mornig for you, when you read this, Now I have tryed the flag in
the mri_mask command but it seems too similar to what was doing
before, it says that will transfer 1 voxel edits to dst vol, but there
many more voxels edited, I have also tryed mri_vol2vol in the
brainmask.mgz intead of brain.mgz but the result is exactly the same
(the output from mri_vol2vol has the voxel 'deletions', but the
mri_mask ignore them. Now i have no idea how to solve this, do you?
Bests,
Gabriel
Subject: RE: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Date: Wed, 9 Mar 2011 18:00:37 -0500
we've improved some of the help text for the next version (5.1),
which
is the only reason i noticed it this time.
On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote:
Than you Nick,
Actually that was exactly what i did, delete some voxels from the
brainmask, I will try adding the flag and let you know, I dind't
saw
that this option exist in the mri_mask.
thank you again,
Gabriel
Subject: Re: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 9 Mar 2011 17:52:34 -0500
hi, not sure what you are trying to do, as the commands below
seem
to do
what i expect them to do, which is to create a masked
(skull-stripped)
version of rawavg.mgz. what do you mean by 'manual segmentation
changes'?, and what exactly is going wrong?
if you deleted voxels in brainmask.mgz, then perhaps you need to
add
the
flag -keep_mask_deletion_edits to mri_mask to transfer those
voxels
('deleted' voxels actually have a special value to indicate
deleted).
n.
On Wed, 2011-03-09 at 22:28 +, Gabriel Go.Es. wrote:
Hello everybody,
Sorry for the insistance, but I need to solve this...
I'm making some manual segmentation changes in the
brainmask.mgz
and
using mri_vol2vol and mri_mask commands to apply these changes
to
the
rawavg.mgz, the output from the mri_vol2vol looks perfectly
normal,and
retains all changed made by me, but when I use the mri_mask
command
over the rawavg.mgz no segmentation seems to be donne in the
final
output file.
Does any one has an idea of what could be wrong?
the commands after manual corrections are:
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out
brain2raw.mgz
--regheader
mri_mask rawavg.mgz brain2raw.mgz outbrain.mgz
Thanks in advanced,
Gabriel
___
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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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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
Re: [Freesurfer] mri_mask problem
Hi Gabriel,
did you convert the brain.mgz so it is in the same space as the
rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you can try
mri_mask -t threshold. The default is 1e-10 so pretty much anything
non-zero is dept. Try changing it to 2 (voxels edited to be turned off are
1).
cheers
Bruce
On Mon, 14 Mar 2011,
Gabriel Go.Es. wrote:
Hello Nick
I'm wondering if you're able to verify my data today,
I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked,
I'm guessing you'll need my data, to see if there is something wrong on it,
but I think is gonna be hard to send it to through the e-mail.
Bests,
Gabriel.
Subject: RE: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Date: Thu, 10 Mar 2011 21:38:50 -0500
i'd have to try to replicate this myself, although it will have to wait
till monday (i'm with the freesurfer group three days a week).
i wonder if you can use the brain.mgz as your mask instead of
brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their
actually not there (zeroed).
n.
On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
Hello Nick,
good mornig for you, when you read this, Now I have tryed the flag in
the mri_mask command but it seems too similar to what was doing
before, it says that will transfer 1 voxel edits to dst vol, but there
many more voxels edited, I have also tryed mri_vol2vol in the
brainmask.mgz intead of brain.mgz but the result is exactly the same
(the output from mri_vol2vol has the voxel 'deletions', but the
mri_mask ignore them. Now i have no idea how to solve this, do you?
Bests,
Gabriel
Subject: RE: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Date: Wed, 9 Mar 2011 18:00:37 -0500
we've improved some of the help text for the next version (5.1),
which
is the only reason i noticed it this time.
On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote:
Than you Nick,
Actually that was exactly what i did, delete some voxels from the
brainmask, I will try adding the flag and let you know, I dind't
saw
that this option exist in the mri_mask.
thank you again,
Gabriel
Subject: Re: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 9 Mar 2011 17:52:34 -0500
hi, not sure what you are trying to do, as the commands below
seem
to do
what i expect them to do, which is to create a masked
(skull-stripped)
version of rawavg.mgz. what do you mean by 'manual segmentation
changes'?, and what exactly is going wrong?
if you deleted voxels in brainmask.mgz, then perhaps you need to
add
the
flag -keep_mask_deletion_edits to mri_mask to transfer those
voxels
('deleted' voxels actually have a special value to indicate
deleted).
n.
On Wed, 2011-03-09 at 22:28 +, Gabriel Go.Es. wrote:
Hello everybody,
Sorry for the insistance, but I need to solve this...
I'm making some manual segmentation changes in the
brainmask.mgz
and
using mri_vol2vol and mri_mask commands to apply these changes
to
the
rawavg.mgz, the output from the mri_vol2vol looks perfectly
normal,and
retains all changed made by me, but when I use the mri_mask
command
over the rawavg.mgz no segmentation seems to be donne in the
final
output file.
Does any one has an idea of what could be wrong?
the commands after manual corrections are:
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out
brain2raw.mgz
--regheader
mri_mask rawavg.mgz brain2raw.mgz outbrain.mgz
Thanks in advanced,
Gabriel
___
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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
Re: [Freesurfer] question about the capability of qdec and using non normal distributed subjects
QDEC can do analyses with as many as two discrete variables (two levels each) and two continuous variables. More general analyses are possible with the mri_glmfit command-line. If data are not normally distributed, then you can use our permutation program (not available in QDEC but possible in mri_glmfit). doug Knut J Bjuland wrote: Hi I am beginner in using Freesurfer. What can of statical analyze is Qdec cable of doing? Can I use data that are not normal distributed since my data sample contains subjects with neuronal damage? Cheers Knut J Bjuland DMV ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] Qdec - thickness-age correlation - Interpretation
Hi Alex, you can compute the difference in those slopes using an appropriate contrast matrix passed to mri_glmfit. QDEC should do so autotmatically (this would be an interaction between group and age). doug Alex Hanganu wrote: Dear Freesurfer Experts, We have two groups at similar ages and the thickness-age correlation shows many cluster of significant values. Pointing to this maximum the plots present similar regressions coefficients for both groups. Actually it would be intresting to have the regions were the thickness – age correlation differ. Or what is the physiological meening of this kind of correlations ?? Sincerely, Sergiu, Alex. ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] mri_mask problem
Helo Bruce, I've tryed these options you said and still not working, I must say
that is not in all my subjects,
I've tryed both brain.mgz and brainmask.mgz.
The commands I've used are:
A1) mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz
--regheader
A2) mri_mask flag -keep_mask_deletion_edits rawavg.mgz brain2raw.mgz
outbrain.mgz
after mri_vol2vol the brain2raw.mgz look perfecty fine, but when apply the
mri_mask the image apperars with no edits.
B1) mri_convert -rl rawavg.mgz brainmask.mgz brainmask2raw.mgz
B2) mri_mask flag -T 2 -keep_mask_deletion_edits rawavg.mgz brainmask2raw.mgz
outbrain2.mgz
I've ran the mri_mask command with and without the -keep_mask_deletion_edits
flag
and again appears to be the mri_mask command the one that is not doing the
work, actually the outputs from mri_convert and mri_vol2vol, looks pretty
similar, any ideas?
Bests
Gabriel
Date: Mon, 14 Mar 2011 08:57:16 -0400
From: fis...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
CC: ni...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_mask problem
Hi Gabriel,
did you convert the brain.mgz so it is in the same space as the
rawavg.mgz using either mri_convert -rl or mri_vol2vol? If so, you can try
mri_mask -t threshold. The default is 1e-10 so pretty much anything
non-zero is dept. Try changing it to 2 (voxels edited to be turned off are
1).
cheers
Bruce
On Mon, 14 Mar 2011,
Gabriel Go.Es. wrote:
Hello Nick
I'm wondering if you're able to verify my data today,
I did try using brainmask.mgz to mask the rawavg.mgz, and didn't worked,
I'm guessing you'll need my data, to see if there is something wrong on it,
but I think is gonna be hard to send it to through the e-mail.
Bests,
Gabriel.
Subject: RE: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Date: Thu, 10 Mar 2011 21:38:50 -0500
i'd have to try to replicate this myself, although it will have to wait
till monday (i'm with the freesurfer group three days a week).
i wonder if you can use the brain.mgz as your mask instead of
brainmask.mgz. i think brain.mgz doesnt have 'deleted' voxels but their
actually not there (zeroed).
n.
On Thu, 2011-03-10 at 08:42 +, Gabriel Go.Es. wrote:
Hello Nick,
good mornig for you, when you read this, Now I have tryed the flag in
the mri_mask command but it seems too similar to what was doing
before, it says that will transfer 1 voxel edits to dst vol, but there
many more voxels edited, I have also tryed mri_vol2vol in the
brainmask.mgz intead of brain.mgz but the result is exactly the same
(the output from mri_vol2vol has the voxel 'deletions', but the
mri_mask ignore them. Now i have no idea how to solve this, do you?
Bests,
Gabriel
Subject: RE: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
Date: Wed, 9 Mar 2011 18:00:37 -0500
we've improved some of the help text for the next version (5.1),
which
is the only reason i noticed it this time.
On Wed, 2011-03-09 at 22:58 +, Gabriel Go.Es. wrote:
Than you Nick,
Actually that was exactly what i did, delete some voxels from the
brainmask, I will try adding the flag and let you know, I dind't
saw
that this option exist in the mri_mask.
thank you again,
Gabriel
Subject: Re: [Freesurfer] mri_mask problem
From: ni...@nmr.mgh.harvard.edu
To: gabriel...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Date: Wed, 9 Mar 2011 17:52:34 -0500
hi, not sure what you are trying to do, as the commands below
seem
to do
what i expect them to do, which is to create a masked
(skull-stripped)
version of rawavg.mgz. what do you mean by 'manual segmentation
changes'?, and what exactly is going wrong?
if you deleted voxels in brainmask.mgz, then perhaps you need to
add
the
flag -keep_mask_deletion_edits to mri_mask to transfer those
voxels
('deleted' voxels actually have a special value to indicate
deleted).
n.
On Wed, 2011-03-09 at 22:28 +, Gabriel Go.Es. wrote:
Hello everybody,
Sorry for the insistance, but I need to solve this...
I'm making some manual segmentation changes in the
brainmask.mgz
and
using mri_vol2vol and mri_mask commands to apply these changes
to
the
rawavg.mgz, the output from the mri_vol2vol looks perfectly
normal,and
retains all changed made by me, but when I use the mri_mask
command
over the rawavg.mgz no segmentation seems to be donne in the
final
output file.
Does any one has an idea of what could be wrong?
the commands after manual corrections are:
mri_vol2vol --mov brain.mgz --targ rawavg.mgz --out
brain2raw.mgz
--regheader
mri_mask rawavg.mgz brain2raw.mgz outbrain.mgz
Thanks in advanced,
Gabriel
[Freesurfer] mri_convert Siemens Allegra Dicom problem
Hi everybody, We're doing a structural VBM bicentric cross cultural study, using Freesurfer v5.0.0. on 2 computers : FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 Kernel info: Darwin 9.8.0 i386 FREESURFER_HOME: /home/scnlab/Desktop/ freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 Debian version: squeeze/sid Kernel info: Linux 2.6.32-29-generic i686 freesurfer@nmr.mgh.harvard.edu Successful reconstructions have been realized for some of the subjects from one of the 2 centers, using their DICOMS (Siemens Trio), but we seem to be unable to use any DICOM from the other center (Siemens Allegra). It seems that the same problem has already been submitted to the mailing list, without any available solution : http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01354.html We get the following error messages (same on both computers): [wireless-XXX-XXX-XXX-XXX:/OK-J-01/structural] SPLab% mri_convert 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz mri_convert 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz file not found or unknown file type for file 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm [wireless-XXX-XXX-XXX-XXX:/OK-J-01/structural] SPLab% mri_convert --in_type siemens_dicom 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz mri_convert --in_type siemens_dicom 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm... ERROR (ScanSiemensSeries): /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm is not a Siemens DICOM file ERROR: could not find any files (SeriesList==NULL) [wireless-XXX-XXX-XXX-XXX:fMRI/OK-J-01/structural] SPLab% mri_convert --in_type dicom 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgzmri_convert --in_type dicom 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm... Starting DICOMRead2() dcmfile = /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm dcmdir = /Users/SPLab/Desktop/OK-J-01/structural ERROR: /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm is not a dicom file [wireless-XXX-XXX-XXX-XXX:fMRI/OK-J-01/structural] SPLab% mri_convert --in_type siemens --out_type mgz 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz mri_convert --in_type siemens --out_type mgz 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm... ERROR: could not parse /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm ERROR: siemensRead(): /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm - When trying to convert them with the MRI Convert software I get the following error message : Unable to find series UID - I can however convert them to nifti using SPM8 and MIPAV, and then successfully run mri_convert and auto-recon1. I also tried to save as dicoms in MIPAV, but it didn't change anything. Here are headers as given by MIPAV : Dimension 256 Dimension 256 Dimension 192 Type Unsigned Short Min 0.0 Max 1654.0 Orientation Axial Pixel resolution 0 0.75 Pixel resolution 1 0.75 Pixel resolution 2 1.0 Unit of measure Millimeters per pixel Transformation Matrix 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. (0002,) File Meta Information Group Length 206 (0002,0001) File Meta Information Version 1 (0002,0002) Media Storage SOP Class UID 1.2.840.10008.5.1.4.1.1.4 (0002,0003) Media Storage SOP Instance UID 1.3.12.2.1107.5.2.7.20409.300703080442501872322 (0002,0010) Transfer Syntax UID 1.2.840.10008.1.2 (0002,0012) Implementation Class UID 1.2.804.114118.3 (0002,0013) Implementation Version Name eFilm/UCDavisLib (0002,0016) Source Application Entity Title (0008,0005) Specific Character Set ISO_IR 100 (0008,0008) Image Type ORIGINAL, PRIMARY, M, ND (0008,0016) SOP Class UID 1.2.840.10008.5.1.4.1.1.4 (0008,0018) SOP Instance UID 1.3.12.2.1107.5.2.7.20409.300703080442501872322 (0008,0020) Study Date 20070308 (0008,0021) Series Date 20070308 (0008,0022) Acquisition Date 20070308 (0008,0023) Content (formerly Image) Date 20070308 (0008,0030) Study Time 142430.328000 (0008,0031) Series Time 153343.484000 (0008,0032) Acquisition Time 152244.074999 (0008,0033) Content (formerly Image) Time 153344.937000 (0008,0050) Accession Number 06H17
Re: [Freesurfer] mri_convert Siemens Allegra Dicom problem
Can you drop 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm to me at the file drop below? doug Myriam Siefert wrote: Hi everybody, We're doing a structural VBM bicentric cross cultural study, using Freesurfer v5.0.0. on 2 computers : FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 Kernel info: Darwin 9.8.0 i386 FREESURFER_HOME: /home/scnlab/Desktop/ freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v5.0.0 Debian version: squeeze/sid Kernel info: Linux 2.6.32-29-generic i686 mailto:freesurfer@nmr.mgh.harvard.edu Successful reconstructions have been realized for some of the subjects from one of the 2 centers, using their DICOMS (Siemens Trio), but we seem to be unable to use any DICOM from the other center (Siemens Allegra). It seems that the same problem has already been submitted to the mailing list, without any available solution : http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01354.html We get the following error messages (same on both computers): [wireless-XXX-XXX-XXX-XXX:/OK-J-01/structural] SPLab% mri_convert 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz mri_convert 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz file not found or unknown file type for file 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm [wireless-XXX-XXX-XXX-XXX:/OK-J-01/structural] SPLab% mri_convert --in_type siemens_dicom 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz mri_convert --in_type siemens_dicom 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm... ERROR (ScanSiemensSeries): /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm is not a Siemens DICOM file ERROR: could not find any files (SeriesList==NULL) [wireless-XXX-XXX-XXX-XXX:fMRI/OK-J-01/structural] SPLab% mri_convert --in_type dicom 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgzmri_convert --in_type dicom 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm... Starting DICOMRead2() dcmfile = /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm dcmdir = /Users/SPLab/Desktop/OK-J-01/structural ERROR: /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm is not a dicom file [wireless-XXX-XXX-XXX-XXX:fMRI/OK-J-01/structural] SPLab% mri_convert --in_type siemens --out_type mgz 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz mri_convert --in_type siemens --out_type mgz 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm 001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm... ERROR: could not parse /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm ERROR: siemensRead(): /Users/SPLab/Desktop/OK-J-01/structural/1.3.12.2.1107.5.2.7.20409.300703080442501872322.dcm - When trying to convert them with the MRI Convert software I get the following error message : Unable to find series UID - I can however convert them to nifti using SPM8 and MIPAV, and then successfully run mri_convert and auto-recon1. I also tried to save as dicoms in MIPAV, but it didn't change anything. Here are headers as given by MIPAV : Dimension 256 Dimension 256 Dimension 192 Type Unsigned Short Min 0.0 Max 1654.0 Orientation Axial Pixel resolution 0 0.75 Pixel resolution 1 0.75 Pixel resolution 2 1.0 Unit of measure Millimeters per pixel Transformation Matrix 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. (0002,) File Meta Information Group Length 206 (0002,0001) File Meta Information Version 1 (0002,0002) Media Storage SOP Class UID 1.2.840.10008.5.1.4.1.1.4 (0002,0003) Media Storage SOP Instance UID 1.3.12.2.1107.5.2.7.20409.300703080442501872322 (0002,0010) Transfer Syntax UID 1.2.840.10008.1.2 (0002,0012) Implementation Class UID 1.2.804.114118.3 (0002,0013) Implementation Version Name eFilm/UCDavisLib (0002,0016) Source Application Entity Title (0008,0005) Specific Character Set ISO_IR 100 (0008,0008) Image Type ORIGINAL, PRIMARY, M, ND (0008,0016) SOP Class UID 1.2.840.10008.5.1.4.1.1.4 (0008,0018) SOP Instance UID 1.3.12.2.1107.5.2.7.20409.300703080442501872322 (0008,0020) Study Date 20070308 (0008,0021) Series Date 20070308
Re: [Freesurfer] normal vector in gm
Thank you ! I successfully projected the pial surface normals in the volume. Now I wanted to project the normals in the inner gm boundary voxels (i.e. gm boundary voxels with wm). What I tried is scaling up the wm surface by mris_convert -s 1.01 lh.white lh.white101 and then projected the normals on the volume by mri_surf2surf -- hemi lh --sval-nxyz white101 --tval wn101.mgz mri_surf2vol --surfval wn101.mgz --hemi lh --surf white101 --volreg reg2ana.dat --template vol.mgz --outvol wn101_b.mgz However, the projection seemed not in the scaled-up layers, but in the original wm layers. The scaling seemed not effective. Would you have any ideas what could project normals in the gm boundary voxels with wm? Eventually what I wanted to do is assign normal vectors in all gm voxels somehow. Thanks, Seok On Mar 9, 2011, at 5:44 PM, Douglas N Greve wrote: That is the file created by registering your orig.mgz to the mni152 brain (assuming you are using the 152). You can create this registration file with the mni152reg script. doug Seok Lew wrote: Thanks, first of all. I tried with the following scripts, but ended up with an error. I am not sure which format or file is required for the --volreg. # mri_surf2surf --s FS --hemi lh --sval-nxyz pial --tval ./ttt.mgz # mri_surf2vol --surfval ttt.mgz --hemi lh --volreg mri/transforms/ talairach.xfm --outvol ooo.mgz --template mri/T1.mgz gdiagno = -1 regio_read_register(): No such file or directory Error reading inplaneres from mri/transforms/talairach.xfm Thanks, Seok On Mar 9, 2011, at 2:00 PM, Douglas N Greve wrote: Try using mri_surf2surf with the --sval-nxyz. The output have 3- frame, one for each component in the normal. Then use mri_surf2vol to stuff this back into a volume. doug Seok Lew wrote: Hello users, My colleagues and I are trying to create a gray matter electric conduction model where a preferable conduction direction is aligned with the normal direction induced from the pial and white surface normals. Freesurfer reconstruction already gives pial and white matter surface normals and correspondences between them. Now I want to have the freesurfer surface normals projected on the mri volumes and interpolated for gray matter voxels (regions between the pial surface and the white surface), such that each voxel of gray matter can have a normal direction. Is it possible to do the job with freesurfer scripts ? If so, what scripts might work for this? Thanks in advance, Seok ___ 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Seok Lew, Ph.D. MEG Core Laboratory Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School s...@nmr.mgh.harvard.edu -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Seok Lew, Ph.D. MEG Core Laboratory Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School s...@nmr.mgh.harvard.edu ___ 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] Homologous Right Left ROIs
Hi all I have a ROI label on left hemisphere - I need to map this ROI onto right hemisphere to get a homologous region (for testing hemispheric differences). What is the best way for doing this? Cheers Lena -- Lena Palaniyappan Clinical Lecturer Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.___ 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.
