Dear Dr. Fischl,
Thank you for offering to look at our data.
I have used the FTP server to upload a zip archive, based on the website instructions (http://freesurfer.net/fswiki/FtpFileExchange)
The file is in:
transfer/incoming/1353.zip (using anonymous and my email address for the user/password)
Please let us know if you have any thoughts on how we can improve our temporal lobe pial reconstruction.
Sincerely,
Las
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Today's Topics:
1. Re: mni152reg error (JacobML@nmr.mgh.harvard.edu)
2. template replacement (Ilwoo Lyu)
3. unit of each index (thickness, volume, sulc, curv) after
mri_glmfit-sim (wang kangcheng)
4. Re: unit of each index (thickness, volume, sulc, curv) after
mri_glmfit-sim (Douglas Greve)
5. Re: mni152reg error (Douglas Greve)
6. Re: unit of each index (thickness, volume, sulc, curv) after
mri_glmfit-sim (wang kangcheng)
7. Re: unit of each index (thickness, volume, sulc, curv) after
mri_glmfit-sim (Douglas Greve)
8. Spatial smoothing in Matlab (Reza Rajimehr)
9. Re: unit of each index (thickness, volume, sulc, curv) after
mri_glmfit-sim (wang kangcheng)
10. Re: Anterior Temporal Lobe / Pial Reconstruc?tion Troubles -
part 1 (Las Blawimo)
11. Re: selxavg3-sess error in ==> fast_selxavg3 at 434
(pfannmoelj@uni-greifswald.de)
12. Errors in Mapping of Brodmann Areas (pfannmoelj@uni-greifswald.de)
13. Re: mni152reg error (JacobML@nmr.mgh.harvard.edu)
14. Re: Errors in Mapping of Brodmann Areas (Bruce Fischl)
15. Re: Errors in Mapping of Brodmann Areas
(pfannmoelj@uni-greifswald.de)
16. Re: Anterior Temporal Lobe / Pial Reconstruc?tion Troubles -
part 1 (Bruce Fischl)
17. Thickness measurements on longitudinal data set (Bastian Cheng)
----------------------------------------------------------------------
Message: 1
Date: Thu, 17 Jul 2014 13:14:43 -0400 (EDT)
From: "JacobML@nmr.mgh.harvard.edu" <jacobml@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mni152reg error
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<44065.172.20.147.36.1405617283.squirrel@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
Hello again Doug,
Thank you for sending the updated version of mri152reg. It ran without
error and generated the reg.mni152.2mm.dat registration matrix.
Unfortunately though, when I tried to apply the transformation to the same
subject's t_000.bfloat, the registration is not correct (command below).
mri_vol2vol --inv --targ /.../t_000.bfloat --mov
$FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o
CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg
/.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
On a positive note, I was able to load the output image and
MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to be
shifted too far anterior.
With my next attempt, I used mri_convert to make the t_000.bfloat into a
.mgz and than ran mri_vol2vol, but the same misalignment occurred (see
attached photo).
Using tkmedit, I have confirmed that this file aligns properly on this
subject's native structural image, so I am not quite sure why the
registration matrix may be off. Given that the reg.mni152.2mm.dat file
reflects the transformation of the native struc to MNI, I wonder if I need
to account for the reg file between the func data and the native struc?
Can you please let me know what I may be doing incorrectly?
As always, your help is very appreciated.
Jacob
>
> Yea, i fixed this problem. I've attached a new version with the fix. doug
>
> On 07/17/2014 10:35 AM, JacobML@nmr.mgh.harvard.edu wrote:
>> Hello Freesurfer Experts,
>> I am trying to view stats generated with FsFast in fslview/MNIspace,
and
>> in doing so I have run mni152reg to generate the registration matrix.
That said, mni152reg did not complete correctly and below I have pasted
the terminal output:
>> Thu Jul 17 09:58:10 EDT 2014
>> setenv SUBJECTS_DIR
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
>> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
/usr/local/freesurfer/stable5_3_0/bin/mni152reg --s
>> CD_cerv_pat4_sess1_recon
>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
UTC
>> 2014 x86_64 x86_64 x86_64 GNU/Linux
>> fslregister --mov
>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
--s CD_cerv_pat4_sess1_recon --reg
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
--dof 12
>> mkdir: cannot create directory
>> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833':
Permission denied
>> Log file is
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log
Thu Jul 17 09:58:11 EDT 2014
>> --mov
>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
--s CD_cerv_pat4_sess1_recon --reg
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
--dof 12
>> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
>> purkinje
>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
UTC
>> 2014 x86_64 x86_64 x86_64 GNU/Linux
>> nIters 1
>> --------------------------------------
>> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
>> mri_convert
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
mri_convert
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
niiWrite(): error opening file
>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from
>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz...
TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00
>> i_ras = (-1, 0, 0)
>> j_ras = (-0, -0, -1)
>> k_ras = (0, 1, 0)
>> writing to
>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii...
ERROR: failure writing
>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
I tried to run the fslregister command from within the subject's
directory
>> (in hopes to possible correct what may be a permissions issue), but
this
>> produces the same final error, "ERROR: failure writing
>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii."
Lastly, probably to no surprise, the
>> /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any
ideas how I may be able to correct these errors?
>> Thank you for the help!
>> Jacob
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 2
Date: Thu, 17 Jul 2014 19:51:54 -0400
From: Ilwoo Lyu <ilwoolyu@email.unc.edu>
Subject: [Freesurfer] template replacement
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAKi6891Ve6HYHH70eOyjo54cdrDHoaUSAuUxQx+zm0=1Srp+2w@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear FS experts,
I am trying to adapt a macaque template (dim: 250 by 300 by 300, voxel
size: 0.8202 mm).
I changed voxel spacing and dimensions to be the same as the MNI305
template in freesurfer,
but it seems not to work correctly for the affine transformation in the
Talairach space.
Here are my questions:
1) Should I change the voxel size and dimensions of the macaque template?
2) Should I change the original coordinate system of the
macaque template into the Talairach space? If so, how can I do that (eg,
roughly aligned to (or registration) the MNI template)?
Thank you!
Ilwoo
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Message: 3
Date: Fri, 18 Jul 2014 10:55:07 +0800
From: "wang kangcheng" <kangchengwang0808@gmail.com>
Subject: [Freesurfer] unit of each index (thickness, volume, sulc,
curv) after mri_glmfit-sim
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2014071810550526177611@gmail.com>
Content-Type: text/plain; charset="us-ascii"
Dear freesurfer experts
After using the command of mri_glmfit-sim (mri_glmfit-sim --glmdir aaa.thickness(or thickness, volume, sulc, curv ).lh.10 --cache 1.3 pos --cwp 1 --2spaces). I check the data in the fie of cache.th13.pos.y.ocn.dat and found that the data of volume was so small ( e.g 1.39463 1.50616 2.53250).Data of thickness was same as volume (e.g 1.83629 3.01648 2.16078).
Could you tell the unit of each index? And could the data be used as further analysis, e.g correlation with IQ or other behaviors?
Thank you
Wang kangcheng
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Message: 4
Date: Thu, 17 Jul 2014 22:59:12 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] unit of each index (thickness, volume, sulc,
curv) after mri_glmfit-sim
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <53C88D80.6010504@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
where are you getting those numbers? Thickness will be between 0 and 5,
so those numbers look ok.
doug
On 7/17/14 10:55 PM, wang kangcheng wrote:
> Dear freesurfer experts
> After using the command of mri_glmfit-sim (mri_glmfit-sim --glmdir
> aaa.thickness(or thickness, volume, sulc, curv ).lh.10 --cache 1.3 pos
> --cwp 1 --2spaces). I check the data in the fie
> ofcache.th13.pos.y.ocn.dat and found that the data of volume was so
> small (e.g 1.39463 1.50616 2.53250).Data of thickness was same as
> volume (e.g 1.83629 3.01648 2.16078).
> Could you tell the unit of each index? And could the data be used as
> further analysis, e.g correlation with IQ or other behaviors?
>
> Thank you
>
> Wang kangcheng
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 5
Date: Thu, 17 Jul 2014 23:05:54 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mni152reg error
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <53C88F12.1000809@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
I'm not sure what you are trying to do, but that command line looks like
things are not set up properly. What is t_000.bfloat? (And why are you
using bfloats?)
doug
On 7/17/14 1:14 PM, JacobML@nmr.mgh.harvard.edu wrote:
> Hello again Doug,
>
> Thank you for sending the updated version of mri152reg. It ran without
> error and generated the reg.mni152.2mm.dat registration matrix.
>
> Unfortunately though, when I tried to apply the transformation to the same
> subject's t_000.bfloat, the registration is not correct (command below).
>
> mri_vol2vol --inv --targ /.../t_000.bfloat --mov
> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o
> CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg
> /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
>
> On a positive note, I was able to load the output image and
> MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to be
> shifted too far anterior.
>
> With my next attempt, I used mri_convert to make the t_000.bfloat into a
> .mgz and than ran mri_vol2vol, but the same misalignment occurred (see
> attached photo).
>
> Using tkmedit, I have confirmed that this file aligns properly on this
> subject's native structural image, so I am not quite sure why the
> registration matrix may be off. Given that the reg.mni152.2mm.dat file
> reflects the transformation of the native struc to MNI, I wonder if I need
> to account for the reg file between the func data and the native struc?
>
> Can you please let me know what I may be doing incorrectly?
>
> As always, your help is very appreciated.
>
> Jacob
>
>
>
>> Yea, i fixed this problem. I've attached a new version with the fix. doug
>>
>> On 07/17/2014 10:35 AM, JacobML@nmr.mgh.harvard.edu wrote:
>>> Hello Freesurfer Experts,
>>> I am trying to view stats generated with FsFast in fslview/MNIspace,
> and
>>> in doing so I have run mni152reg to generate the registration matrix.
> That said, mni152reg did not complete correctly and below I have pasted
> the terminal output:
>>> Thu Jul 17 09:58:10 EDT 2014
>>> setenv SUBJECTS_DIR
>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
>>> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
> /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s
>>> CD_cerv_pat4_sess1_recon
>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
> UTC
>>> 2014 x86_64 x86_64 x86_64 GNU/Linux
>>> fslregister --mov
>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
> --s CD_cerv_pat4_sess1_recon --reg
>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
> --dof 12
>>> mkdir: cannot create directory
>>> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833':
> Permission denied
>>> Log file is
>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log
> Thu Jul 17 09:58:11 EDT 2014
>>> --mov
>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
> --s CD_cerv_pat4_sess1_recon --reg
>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
> --dof 12
>>> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
>>> purkinje
>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
> UTC
>>> 2014 x86_64 x86_64 x86_64 GNU/Linux
>>> nIters 1
>>> --------------------------------------
>>> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
>>> mri_convert
>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
> mri_convert
>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
> niiWrite(): error opening file
>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from
>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz...
> TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00
>>> i_ras = (-1, 0, 0)
>>> j_ras = (-0, -0, -1)
>>> k_ras = (0, 1, 0)
>>> writing to
>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii...
> ERROR: failure writing
>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
> I tried to run the fslregister command from within the subject's
> directory
>>> (in hopes to possible correct what may be a permissions issue), but
> this
>>> produces the same final error, "ERROR: failure writing
>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii."
> Lastly, probably to no surprise, the
>>> /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any
> ideas how I may be able to correct these errors?
>>> Thank you for the help!
>>> Jacob
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> greve@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------
Message: 6
Date: Fri, 18 Jul 2014 12:18:29 +0800
From: "wang kangcheng" <kangchengwang0808@gmail.com>
Subject: Re: [Freesurfer] unit of each index (thickness, volume, sulc,
curv) after mri_glmfit-sim
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2014071812182560063617@gmail.com>
Content-Type: text/plain; charset="us-ascii"
Thank you doug
Data of thickness: 1.83629 3.01648 2.16078 corresponds to lateraloccipital, frontalpole and superiorparietal.
Why the number of volume (e.g 1.39463 1.50616 2.53250) was also so small ? was the unit cm^3?
Wang Kangcheng
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Message: 7
Date: Fri, 18 Jul 2014 00:29:50 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] unit of each index (thickness, volume, sulc,
curv) after mri_glmfit-sim
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <53C8A2BE.40205@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"
How are you computing the volume? Or is this from a volume map? It is
probably computing the average volume of each vertex in which case you
can multiple the value by the number of vertices to get the total volume
for the cluster
On 7/18/14 12:18 AM, wang kangcheng wrote:
> Thank you doug
> Data of thickness: 1.83629 3.01648
> 2.16078correspondstolateraloccipital, frontalpole and superiorparietal.
>
> Why the number of volume (e.g 1.39463 1.50616 2.53250) was also so
> small ? was the unit cm^3?
> ------------------------------------------------------------------------
>
> Wang Kangcheng
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 8
Date: Fri, 18 Jul 2014 01:12:04 -0400 (EDT)
From: "Reza Rajimehr" <reza@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Spatial smoothing in Matlab
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<64989.18.93.14.208.1405660324.squirrel@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1
Hi,
For a simulation purpose, I want to load a surface into Matlab, assign a
random value (taken from a normal distribution) to each vertex, do spatial
smoothing on the surface with a given FWHM (e.g. 5mm), then do some
computations with the smoothed values.
I am wondering if there is a Matlab code that I can use for surface
smoothing, similar to what FS-FAST preprocessing does in Freesurfer
version 5 and above.
Thanks,
Reza
*****************
Reza Rajimehr, MD
Postdoctoral Research Fellow
McGovern Institute for Brain Research
Massachusetts Institute of Technology (MIT)
NMR Martinos Center
Massachusetts General Hospital (MGH)
Harvard University
*****************
------------------------------
Message: 9
Date: Fri, 18 Jul 2014 13:37:57 +0800
From: "wang kangcheng" <kangchengwang0808@gmail.com>
Subject: Re: [Freesurfer] unit of each index (thickness, volume, sulc,
curv) after mri_glmfit-sim
To: freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2014071813373409391427@gmail.com>
Content-Type: text/plain; charset="us-ascii"
Thanks doug
I first merge the data using command of mris_preproc and then do the GLM analysis using command of mri_glmfit. After that, using the following command to look the result:
mri_surfcluster --in leg.volume.lh.10/g2v2/sig.mgh --csd /usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm15/pos/th13/mc-z.csd --mask leg.volume.lh.10/mask.mgh --cwsig leg.volume.lh.10/g2v2/cache.th13.pos.sig.cluster.mgh --vwsig leg.volume.lh.10/g2v2/cache.th13.pos.sig.voxel.mgh --sum leg.volume.lh.10/g2v2/cache.th13.pos.sig.cluster.summary --ocn leg.volume.lh.10/g2v2/cache.th13.pos.sig.ocn.mgh --oannot leg.volume.lh.10/g2v2/cache.th13.pos.sig.ocn.annot --annot aparc --csdpdf leg.volume.lh.10/g2v2/cache.th13.pos.pdf.dat --cwpvalthresh 1 --o leg.volume.lh.10/g2v2/cache.th13.pos.sig.masked.mgh --no-fixmni --bonferroni 2 --surf white
Did you mean that I multiple the value by the number of vertices (NVtxs, which in the file of cache.th13.pos.sig.cluster.summary ) to get the total volume for the cluster?
# ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot
1 4.623 7401 1647.03 -8.8 -49.3 5.4 0.00719 0.00559 0.00878 4199 isthmuscingulate
2 3.984 46872 1185.43 -7.7 -71.9 50.4 0.06375 0.05929 0.06820 2487 precuneus
3 3.960 57039 3597.23 -10.6 64.4 -5.0 0.00020 0.00000 0.00040 5545 frontalpole
Wang Kangcheng
Faculty of Psychology, Southwest University, China
Email: kangchengwang0808@gmail.com / wangkangcheng.001@163.com
Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China
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Message: 10
Date: Fri, 18 Jul 2014 09:37:46 +0200
From: Las Blawimo <lasblawimo@gmail.com>
Subject: Re: [Freesurfer] Anterior Temporal Lobe / Pial
Reconstruc?tion Troubles - part 1
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CAKBuV=Td5Z9vVab4rT1vKUyhE24-gEg1NuqSNKag45XVZ5rwoQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear dr. Fischl,
I was wondering if you've had any chance to look at our images (image 3 and
4 are attached to a second e-mail with the subject: Anterior Temporal Lobe
/ Pial Reconstruction Troubles - part 2)?
Sincerely,
Las
2014-07-11 16:06 GMT+02:00 Las Blawimo <lasblawimo@gmail.com>:
> Dear Dr. Fischl,
>
> Thanks for your quick reply.
>
> Attached you will find some images (image 1&2) showing the issues we're
> having (I'll send a second e-mail including image 3&4).
>
> The images are as follows:
>
> 1.) sagittal_1353_norm2+3T_vs_default -> the v5.3 suggested norm2 flags
> (from the release notes) and the -3T flag vs. the default v5.3 pipeline.
> Blue is the norm2/3T flag pipeline, yellow is the default.
>
> 2.) sagittal_1353_wusl_vs_default->v5.3 using the -washu_mprage flag,
> obvious improvement in temporal lobe pial surface. Blue is -washu_mprage
> flag, yellow is the default v5.3 pipeline
>
> 3.) axial_1353_norm2+3T_white -> The white surface, which appears OK
> using v5.3 with the suggested norm2 parameters and the -3T flag
>
> 4.) axial_1353_wusl_white_error -> the white surface, with an obvious
> error in the lh_postcentral area, using the -washu_mprage flag.
>
> Let me know if you have any suggestions on other parameters I should try
> to improve the temporal lobe pial surface, without compromising the white
> matter surface reconstruction.
>
> Sincerely,
>
> Las
>
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------------------------------
Message: 11
Date: Fri, 18 Jul 2014 09:38:39 +0200
From: pfannmoelj@uni-greifswald.de
Subject: Re: [Freesurfer] selxavg3-sess error in ==> fast_selxavg3 at
434
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<20140718093839.8e51a7353203ac529ee6128c@uni-greifswald.de>
Content-Type: text/plain; charset=US-ASCII
Thank you for your Help. I figured out that it was a problem with the data which caused this error.
On Wed, 04 Jun 2014 12:00:08 -0400
Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
>
> This is a strange error that I cannot figure out from the terminal
> output. What version of FS are you using? Here's something you can try:
>
> Run selxavg3-sess with --monly sxa3.m This will return right away having
> created sxa3.m
>
> Start matlab and run sxa3. It will stop at the error below. Then type
>
> flac0.inorm
>
> gmean
>
> Each of these will print something out to the terminal. Send the results
> to the list
>
> doug
>
>
> On 06/02/2014 06:27 AM, pfannmoelj@uni-greifswald.de wrote:
> > Dear Experts,
> >
> > during an fsfast analysis an error occured after selxavg3-sess was executed. The corresponding commands were:
> >
> > mkanalysis-sess -fsd bold -surface self lh -fwhm 0 -event-related -paradigm sensory.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 8 -polyfit 2 -analysis analysis.lh -delay 0 -per-run -force -mcextreg
> > mkcontrast-sess -analysis analysis.lh -contrast stim-v-base -a 1
> >
> > selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force
> >
> >
> >
> > The output of selxavg3-sess was:
> >
> >
> > sxa3pwd =
> >
> > /.../evaluation
> >
> > sxa3cmd =
> >
> > /usr/local/freesurfer/fsfast/bin/selxavg3-sess -s ./sessdir -analysis analysis.lh -no-preproc -force
> >
> >>> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> > #@# sessdir ###############################
> > /.../evaluation/sessdir
> > -------------------------
> > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $
> > /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m
> > /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m
> > /usr/local/freesurfer/matlab/MRIread.m
> > -------------------------
> > outtop = /.../evaluation
> > Extension format = nii.gz
> > 1 stim-v-base.mat
> > Excluding 8 points
> > nruns = 1
> > autostimdur =
> >
> >
> > outanadir = /.../evaluation/sessdir/bold/analysis.lh
> > Excluding 8 points
> > Found 145573/155188 (93.8) voxels in mask
> > Creating Design Matrix
> > ... creation time = 0.008 sec
> > DoMCFit = 1
> > ntptot = 108, nX = 15, DOF = 93
> > Saving X matrix to /.../evaluation/sessdir/bold/analysis.lh/Xtmp.mat
> > XCond = 64.7067 (normalized)
> > Computing compensation for resdual AR1 bias
> > 1 -0.5 -0.468819 (t=0.005249)
> > 2 -0.25 -0.252194 (t=0.007053)
> > 3 0 -0.0449419 (t=0.008126)
> > 4 0.25 0.149516 (t=0.00935)
> > 5 0.5 0.319324 (t=0.010795)
> > AR1 Correction M: 0.0749452 1.26122
> > Computing contrast matrices
> > OLS Beta Pass
> > run 1 t= 0.0
> > Global Mean
> > Global In-Mask Mean = (0.664951)
> > ??? Error using ==> mrdivide
> > Matrix dimensions must agree.
> >
> > Error in ==> fast_selxavg3 at 434
> > RescaleFactor = flac0.inorm/gmean;
> >
> >>> ------------------------------------------
> > ERROR: fast_selxavg3() failed\n
> >
> >
> > Do you have an idea what went wrong?
> >
> > Sincerely yours pfannmoe
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> 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.
>
--
Joerg Pfannmoeller <pfannmoelj@uni-greifswald.de>
------------------------------
Message: 12
Date: Fri, 18 Jul 2014 09:58:52 +0200
From: pfannmoelj@uni-greifswald.de
Subject: [Freesurfer] Errors in Mapping of Brodmann Areas
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<20140718095852.02c2fb37113fc851d9188a53@uni-greifswald.de>
Content-Type: text/plain; charset="us-ascii"
Dear Experts,
I am working with freesurfer 5.3 on Mac OSX. I applied recon-all to a data set. This has been done with the same data on a Linux system with Freesurfer 5.3 without any problems. Everything works fine on the Mac except of the labelling of Brodmann Areas. On the Mac the regions are not created as a single areal with a border at the outline. Instead they consist of an outside border and several small regions inside the label.
I already tried to create the Brodmann Areas by myself using the command:
mri_label2label --srclabel /.../subjects/fsaverage/label/lh.BA3b.label --srcsubject fsaverage --trglabel lh.BA3b.test.label --trgsubject subjid --regmethod surface --hemi lh
This does not change the result. I attached a screen shot of the label in fsaverage and one of my subjects. Any help is highly appreciated.
Regards pfannmoe
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------------------------------
Message: 13
Date: Fri, 18 Jul 2014 08:34:09 -0400 (EDT)
From: "JacobML@nmr.mgh.harvard.edu" <jacobml@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mni152reg error
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Cc: ablood@nmr.mgh.harvard.edu
Message-ID:
<45924.172.20.147.36.1405686849.squirrel@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1
Hello Doug,
Ideally, I am trying to take subject tstat maps from FsFast (stable3
environment) and register these native structural space maps to the
MNI152_2mm standard brain.
The t_000.bfloat file is what was generated relative to my contrast that
was set up in FsFast stable3. There are a series of these files ranging
from t_000.bfloat to t_029.bfloat and there are also these same named
files with a .hdr extension. t_000.bfloat is the file I designate when I
select an overlay within tkmedit.
Your help sorting out this registration is very appreciated.
Thank you,
Jacob
>
> I'm not sure what you are trying to do, but that command line looks like
> things are not set up properly. What is t_000.bfloat? (And why are you
> using bfloats?)
> doug
>
>
> On 7/17/14 1:14 PM, JacobML@nmr.mgh.harvard.edu wrote:
>> Hello again Doug,
>>
>> Thank you for sending the updated version of mri152reg. It ran without
>> error and generated the reg.mni152.2mm.dat registration matrix.
>>
>> Unfortunately though, when I tried to apply the transformation to the
>> same
>> subject's t_000.bfloat, the registration is not correct (command below).
>>
>> mri_vol2vol --inv --targ /.../t_000.bfloat --mov
>> $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --o
>> CD_cerv_pat4_sess1_tstat1_MNI152.nii.gz --interp nearest --reg
>> /.../CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
>>
>> On a positive note, I was able to load the output image and
>> MNI152_T1_2mm.nii.gz within fslview, but the functional data seemed to
>> be
>> shifted too far anterior.
>>
>> With my next attempt, I used mri_convert to make the t_000.bfloat into a
>> .mgz and than ran mri_vol2vol, but the same misalignment occurred (see
>> attached photo).
>>
>> Using tkmedit, I have confirmed that this file aligns properly on this
>> subject's native structural image, so I am not quite sure why the
>> registration matrix may be off. Given that the reg.mni152.2mm.dat file
>> reflects the transformation of the native struc to MNI, I wonder if I
>> need
>> to account for the reg file between the func data and the native struc?
>>
>> Can you please let me know what I may be doing incorrectly?
>>
>> As always, your help is very appreciated.
>>
>> Jacob
>>
>>
>>
>>> Yea, i fixed this problem. I've attached a new version with the fix.
>>> doug
>>>
>>> On 07/17/2014 10:35 AM, JacobML@nmr.mgh.harvard.edu wrote:
>>>> Hello Freesurfer Experts,
>>>> I am trying to view stats generated with FsFast in fslview/MNIspace,
>> and
>>>> in doing so I have run mni152reg to generate the registration matrix.
>> That said, mni152reg did not complete correctly and below I have pasted
>> the terminal output:
>>>> Thu Jul 17 09:58:10 EDT 2014
>>>> setenv SUBJECTS_DIR
>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
>>>> cd /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
>> /usr/local/freesurfer/stable5_3_0/bin/mni152reg --s
>>>> CD_cerv_pat4_sess1_recon
>>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
>> UTC
>>>> 2014 x86_64 x86_64 x86_64 GNU/Linux
>>>> fslregister --mov
>>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
>> --s CD_cerv_pat4_sess1_recon --reg
>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
>> --dof 12
>>>> mkdir: cannot create directory
>>>> `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833':
>> Permission denied
>>>> Log file is
>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat.fslregister.log
>> Thu Jul 17 09:58:11 EDT 2014
>>>> --mov
>>>> /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz
>> --s CD_cerv_pat4_sess1_recon --reg
>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/transforms/reg.mni152.2mm.dat
>> --dof 12
>>>> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
>>>> purkinje
>>>> Linux purkinje 2.6.32-431.20.3.el6.x86_64 #1 SMP Thu Jun 19 21:14:45
>> UTC
>>>> 2014 x86_64 x86_64 x86_64 GNU/Linux
>>>> nIters 1
>>>> --------------------------------------
>>>> /autofs/cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons
>>>> mri_convert
>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
>> mri_convert
>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz
>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
>> niiWrite(): error opening file
>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from
>>>> /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_cerv_pat4_sess1_recon/mri/brainmask.mgz...
>> TR=2530.00, TE=3.25, TI=1100.00, flip angle=7.00
>>>> i_ras = (-1, 0, 0)
>>>> j_ras = (-0, -0, -1)
>>>> k_ras = (0, 1, 0)
>>>> writing to
>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii...
>> ERROR: failure writing
>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.20833/refvol.fslregister.nii
>> I tried to run the fslregister command from within the subject's
>> directory
>>>> (in hopes to possible correct what may be a permissions issue), but
>> this
>>>> produces the same final error, "ERROR: failure writing
>>>> /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.24919/refvol.fslregister.nii."
>> Lastly, probably to no surprise, the
>>>> /.../mri/transforms/reg.mni152.2mm.dat file was never generated. Any
>> ideas how I may be able to correct these errors?
>>>> Thank you for the help!
>>>> Jacob
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> greve@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 14
Date: Fri, 18 Jul 2014 09:18:15 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Errors in Mapping of Brodmann Areas
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: Zeke Kaufman <zkaufman@nmr.mgh.harvard.edu>
Message-ID: <alpine.LRH.2.03.1407180917340.32116@nmr.mgh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Hi pfannmoe
this is a bug in mri_label2label that we fixed a while ago. Zeke: can
post a new version and let people on the list know where it is?
thanks
Bruce
On Fri, 18 Jul 2014,
pfannmoelj@uni-greifswald.de wrote:
> Dear Experts,
>
> I am working with freesurfer 5.3 on Mac OSX. I applied recon-all to a data set. This has been done with the same data on a Linux system with Freesurfer 5.3 without any problems. Everything works fine on the Mac except of the labelling of Brodmann Areas. On the Mac the regions are not created as a single areal with a border at the outline. Instead they consist of an outside border and several small regions inside the label.
>
> I already tried to create the Brodmann Areas by myself using the command:
>
> mri_label2label --srclabel /.../subjects/fsaverage/label/lh.BA3b.label --srcsubject fsaverage --trglabel lh.BA3b.test.label --trgsubject subjid --regmethod surface --hemi lh
>
>
> This does not change the result. I attached a screen shot of the label in fsaverage and one of my subjects. Any help is highly appreciated.
>
> Regards pfannmoe
>
>
>
------------------------------
Message: 15
Date: Fri, 18 Jul 2014 15:37:39 +0200
From: pfannmoelj@uni-greifswald.de
Subject: Re: [Freesurfer] Errors in Mapping of Brodmann Areas
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<20140718153739.4cf68ead20e0e95074a7a045@uni-greifswald.de>
Content-Type: text/plain; charset=US-ASCII
It would be very helpful for me.
On Fri, 18 Jul 2014 09:18:15 -0400 (EDT)
Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
> Hi pfannmoe
>
> this is a bug in mri_label2label that we fixed a while ago. Zeke: can
> post a new version and let people on the list know where it is?
>
> thanks
> Bruce
>
> On Fri, 18 Jul 2014,
> pfannmoelj@uni-greifswald.de wrote:
>
> > Dear Experts,
> >
> > I am working with freesurfer 5.3 on Mac OSX. I applied recon-all to a data set. This has been done with the same data on a Linux system with Freesurfer 5.3 without any problems. Everything works fine on the Mac except of the labelling of Brodmann Areas. On the Mac the regions are not created as a single areal with a border at the outline. Instead they consist of an outside border and several small regions inside the label.
> >
> > I already tried to create the Brodmann Areas by myself using the command:
> >
> > mri_label2label --srclabel /.../subjects/fsaverage/label/lh.BA3b.label --srcsubject fsaverage --trglabel lh.BA3b.test.label --trgsubject subjid --regmethod surface --hemi lh
> >
> >
> > This does not change the result. I attached a screen shot of the label in fsaverage and one of my subjects. Any help is highly appreciated.
> >
> > Regards pfannmoe
> >
> >
> >
> _______________________________________________
> 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.
>
--
Joerg Pfannmoeller <pfannmoelj@uni-greifswald.de>
------------------------------
Message: 16
Date: Fri, 18 Jul 2014 09:58:22 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Anterior Temporal Lobe / Pial
Reconstruc?tion Troubles - part 1
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <alpine.LRH.2.03.1407180958020.32116@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
Hi Las
it's tough to tell from just those images. Can you upload the entire
subject directory?
cheers
Bruce
On Fri, 18 Jul 2014, Las Blawimo wrote:
> Dear dr. Fischl,
> ?
> I was wondering if you've had any chance to look at our images (image 3 and
> 4 are attached to a second e-mail with the subject: Anterior Temporal Lobe /
> Pial Reconstruction Troubles - part 2)?
> ?
> Sincerely,
> Las
>
>
> 2014-07-11 16:06 GMT+02:00 Las Blawimo <lasblawimo@gmail.com>:
>
> Dear Dr. Fischl,
>
> Thanks for your quick reply.
>
> Attached you will find some images (image 1&2) showing the
> issues we're having (I'll send a second e-mail including image
> 3&4).
>
> The images are as follows:
>
> 1.) sagittal_1353_norm2+3T_vs_default -> the v5.3 suggested
> norm2 flags (from the release notes) and the -3T flag vs. the
> default v5.3 pipeline. Blue is the norm2/3T flag pipeline,
> yellow is the default.
>
> 2.) sagittal_1353_wusl_vs_default->v5.3 using the -washu_mprage
> flag, obvious improvement in temporal lobe pial surface. Blue is
> -washu_mprage flag, yellow is the default v5.3 pipeline
>
> 3.) axial_1353_norm2+3T_white -> The white surface, which
> appears OK using v5.3 with the suggested norm2 parameters and
> the -3T flag
>
> 4.) axial_1353_wusl_white_error -> the white surface, with an
> obvious error in the lh_postcentral area, using the
> -washu_mprage flag.
>
> Let me know if you have any suggestions on other parameters I
> should try to improve the temporal lobe pial surface, without
> compromising the white matter surface reconstruction.
>
> Sincerely,
>
> Las
>
>
>
>
------------------------------
Message: 17
Date: Fri, 18 Jul 2014 16:45:52 +0200
From: Bastian Cheng <bastiancheng@gmail.com>
Subject: [Freesurfer] Thickness measurements on longitudinal data set
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CA+oKOp=7Tc1_-96p_0h5_oQEYBtWVmwk-9MfdvP8t_sW0UHSsg@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear Freesurfer-Experts,
I am currently trying to measure Cortical Thickness of a
Volume-defined ROI in a patient measured at 4 timepoints.
Basically, I am interested in a ROI resulting from fMRI activation
measured on Timepoint 1.
I would then like to get thickness values in the same ROI for all
Timepoints 1-4.
I have read the instructions here:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness
this works.
now, my idea is:
ROI from TP1 >> register to base image of longit. recon. ("base")
ROI from base >> TP1.long (from long recon)
ROI from base >> TP2.long (from long recon)
ROI from base >> TP3 long (from long recon)
ROI from base >> TP4.long (from long recon)
OR should I simpy map my ROI to fsaverage and project it back all
individual timepoints?
ROI from TP1 >> register to fsaverage
ROI from fsaverage >> TP1 (not from long recon)
ROI from fsaverage >> TP2 (not from long recon)
etc.
I understand that registration using the long. recon is more robust...
Best regards,
Bastian
------------------------------
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End of Freesurfer Digest, Vol 125, Issue 30
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