date:20130307


Hi Gari

we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE 
with a FLAIR inversion pulse. Andre (ccd) can give you the details


cheers
Bruce


On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:


Hi Bruce,is there any recommended protocol for T2 acquisition to be used in the 
5.2 recon-all stream?

Should we used the same voxel size as the T1? (we are using  1 mm3 right now).

If it is going to improve the skull striping and pial surface creation, we 
might acquire specific T2 images just to be
used in the recon-all stream.

many thanks,
Gari 


On Wed, Feb 27, 2013 at 2:44 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu 
wrote:
  Hi Nicola

  the T2 might in 5.2, but it is pretty thick slices so might hurt more
  than it helps. Not sure, but you can try it out

  cheers
  Bruce
  On Wed, 27 Feb 2013, Nicola
  Toschi wrote:

   Hello List,
  
   on out 3T scanner, in addition to MPRAGE images (1 mm^3), we usually
   acquire T2 and PD images - however they are at 1x1x5 mm resolution.
  
   Would you recommend passing these (T2+PD) to the recon-all stream anyway
   - would they add value/accuracy to the segmentation/parcellation (or
   would they possibly decrease accuracy)?
  
   Thanks in advance,
  
   Nicola
  
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Re: [Freesurfer] Adding low-res T2 and PD images in the recon-all stream - any advantages?

2013-03-07 Thread Nick Schmansky

see:

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFiledo=gettarget=FreeSurfer_Suggested_Morphometry_Protocols.pdf


 Hi Gari

 we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE
 with a FLAIR inversion pulse. Andre (ccd) can give you the details

 cheers
 Bruce


 On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:

 Hi Bruce,is there any recommended protocol for T2 acquisition to be used
 in the 5.2 recon-all stream?

 Should we used the same voxel size as the T1? (we are using  1 mm3 right
 now).

 If it is going to improve the skull striping and pial surface creation,
 we might acquire specific T2 images just to be
 used in the recon-all stream.

 many thanks,
 Gari 


 On Wed, Feb 27, 2013 at 2:44 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu wrote:
   Hi Nicola

   the T2 might in 5.2, but it is pretty thick slices so might hurt
 more
   than it helps. Not sure, but you can try it out

   cheers
   Bruce
   On Wed, 27 Feb 2013, Nicola
   Toschi wrote:

Hello List,
   
on out 3T scanner, in addition to MPRAGE images (1 mm^3), we
 usually
acquire T2 and PD images - however they are at 1x1x5 mm
 resolution.
   
Would you recommend passing these (T2+PD) to the recon-all
 stream anyway
- would they add value/accuracy to the segmentation/parcellation
 (or
would they possibly decrease accuracy)?
   
Thanks in advance,
   
Nicola
   
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Re: [Freesurfer] Adding low-res T2 and PD images in the recon-all stream - any advantages?


and 1mm isotropic
On Thu, 7 Mar 2013, Nick Schmansky wrote:


see:

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFiledo=gettarget=FreeSurfer_Suggested_Morphometry_Protocols.pdf



Hi Gari

we use a bandwidth and readout matched (to our multi-echo mprage) T2-SPACE
with a FLAIR inversion pulse. Andre (ccd) can give you the details

cheers
Bruce


On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:


Hi Bruce,is there any recommended protocol for T2 acquisition to be used
in the 5.2 recon-all stream?

Should we used the same voxel size as the T1? (we are using  1 mm3 right
now).

If it is going to improve the skull striping and pial surface creation,
we might acquire specific T2 images just to be
used in the recon-all stream.

many thanks,
Gari 


On Wed, Feb 27, 2013 at 2:44 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edu wrote:
  Hi Nicola

  the T2 might in 5.2, but it is pretty thick slices so might hurt
more
  than it helps. Not sure, but you can try it out

  cheers
  Bruce
  On Wed, 27 Feb 2013, Nicola
  Toschi wrote:

  Hello List,
 
  on out 3T scanner, in addition to MPRAGE images (1 mm^3), we
usually
  acquire T2 and PD images - however they are at 1x1x5 mm
resolution.
 
  Would you recommend passing these (T2+PD) to the recon-all
stream anyway
  - would they add value/accuracy to the segmentation/parcellation
(or
  would they possibly decrease accuracy)?
 
  Thanks in advance,
 
  Nicola
 
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Re: [Freesurfer] Adding low-res T2 and PD images in the recon-all stream - any advantages?

2013-03-07 Thread Garikoitz Lerma-Usabiaga

Many thanks for your answers!


I have another question:
Usually we work with 1 mm3 T1-s, but we have a 0.7 mm3 sequence as well.
Lüsebrink et al (2013) say that: FreeSurfer is not designed to process
data with a spatial resolution other than 1 mm and was modified to avoid
this limitation.

When running 0.7 mm3 T1-s with the recon-all standard stream we observe the
following in recon-all.log:
Original Data has (0.35, 0.35, 0.7) mm size and (640, 640, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions

 Will FS 5.2 work with other resolutions different to 1 mm3?
 With the current limitation, can we expect any gain in cortical thickness
(or other) measurements using lower voxel size-s, if at the end everything
is conformed to 1 mm3?

many thanks again for your responses!
Gari


On Thu, Mar 7, 2013 at 4:38 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 and 1mm isotropic

 On Thu, 7 Mar 2013, Nick Schmansky wrote:

  see:

 http://surfer.nmr.mgh.harvard.**edu/fswiki/FreeSurferWiki?**
 action=AttachFiledo=get**target=FreeSurfer_Suggested_**
 Morphometry_Protocols.pdfhttp://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFiledo=gettarget=FreeSurfer_Suggested_Morphometry_Protocols.pdf


  Hi Gari

 we use a bandwidth and readout matched (to our multi-echo mprage)
 T2-SPACE
 with a FLAIR inversion pulse. Andre (ccd) can give you the details

 cheers
 Bruce


 On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:

  Hi Bruce,is there any recommended protocol for T2 acquisition to be used
 in the 5.2 recon-all stream?

 Should we used the same voxel size as the T1? (we are using  1 mm3 right
 now).

 If it is going to improve the skull striping and pial surface creation,
 we might acquire specific T2 images just to be
 used in the recon-all stream.

 many thanks,
 Gari


 On Wed, Feb 27, 2013 at 2:44 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu wrote:
   Hi Nicola

   the T2 might in 5.2, but it is pretty thick slices so might hurt
 more
   than it helps. Not sure, but you can try it out

   cheers
   Bruce
   On Wed, 27 Feb 2013, Nicola
   Toschi wrote:

   Hello List,
  
   on out 3T scanner, in addition to MPRAGE images (1 mm^3), we
 usually
   acquire T2 and PD images - however they are at 1x1x5 mm
 resolution.
  
   Would you recommend passing these (T2+PD) to the recon-all
 stream anyway
   - would they add value/accuracy to the segmentation/parcellation
 (or
   would they possibly decrease accuracy)?
  
   Thanks in advance,
  
   Nicola
  
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Re: [Freesurfer] Binary volume to surface _ mri_vol2surf


The output of mri_vol2surf is not a surface but an overlay on a surface. 
You will need to run something like:

freeview -f 
$SUBJECTS_DIR/$subject/surf/lh.inflated:overlay=lesionMask_surf.mgh

You'll need to set the threshold to 0.5 in order to see the mask.
doug

On 03/07/2013 05:53 AM, Christopher wrote:
 Dear Freesurfer community,

 I have processed a subject (name:P061_pre, 3D MPRAGE T1) with Freesurfer
 5.1. A resection area has been defiened on this volume and exists as a
 binary volume (1:voxels of interest, 0:others) lesionMask.mgz. I now
 would like to project this volume on the surface of the subject, e.g.
 lh.white.
 I have tried using mri_vol2surf :
 mri_vol2surf --src lesionMask.mgz --out lesionMask_surf.mgh --out_type
 mgh --hemi lh --regheader P061_pre

 The command seems to work:

 srcvol = lesionMask.mgz
 srcreg unspecified
 srcregold = 0
 srcwarp unspecified
 surf = white
 hemi = lh
 reshape = 0
 interp = nearest
 float2int = round
 GetProjMax = 0
 INFO: float2int code = 0
 INFO: changing type to float
 Done loading volume
 Computing registration from header.
 Using /root/data/FS51/freesurfer/subjects/P061_pre/mri/orig.mgz as
 target reference.
 Reading surface /root/data/FS51/freesurfer/subjects/P061_pre/surf/lh.white
 Done reading source surface
 Mapping Source Volume onto Source Subject Surface
1 0 0 0
 using old
 Done mapping volume to surface
 Number of source voxels hit = 79054
 Writing to ./lesionMask_surf.mgh
 Dim: 128233 1 1

 But when trying to open the surface with freeview, it returns an error
 message :
 freeview -f lesionMask_surf.mgh
 ERROR: MRISread: cannot read surface data from file
 /home/epilepsy/sorted/P061/preMR/lesionMask_surf.mgh!

 Segmentation fault


 What did I miss ?

 Thanks for your help,


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

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[Freesurfer] optimizing output

2013-03-07 Thread Linn Mittlestein

Dear list,

I was wondering whether you have any suggestions on how to optimize
accuracy of the Freesurfer output (both cortical and subcortical) in images
aquired on lower scanning resolutions than 3 T (for examle 1 T)?

Kind Regards, Linn
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[Freesurfer] p[All] post-doc position available (fwd)

FYI

-- Forwarded message --
Date: Thu, 7 Mar 2013 11:27:02 -0500
From: Dara Manoach d...@nmr.mgh.harvard.edu
To: a...@nmr.mgh.harvard.edu
Subject: [All] post-doc position available

Postdoctoral Fellowship at the Martinos Center for Biomedical

Imaging and the Psychiatric Neuroimaging Division of the Psychiatry Department 
at Massachusetts
General Hospital, Charlestown, MA

Project: Multimodal neuroimaging studies of sleep and memory

PI: Dara S. Manoach, Ph.D.

The position will involve investigating the role of sleep in memory 
consolidation, how these
processes go awry in schizophrenia and autism, and the efficacy of 
pharmacological and other
interventions.  Our work has linked a specific cognitive deficit in 
schizophrenia (the reduction of
sleep-dependent memory consolidation) to a particular mechanism (sleep 
spindles) and we have
preliminary evidence of an effective intervention.  In collaboration with Dr. 
Robert Stickgold?s lab
at Beth Israel Deaconess Medical Center, we are extending and expanding this 
basic and clinical
research program using state-of-the art tools including high density EEG 
(polysomnography), MEG,
functional connectivity MRI, fMRI, and behavioral studies.  We are seeking 
someone to participate in
these NIMH-funded investigations who is familiar with MEG/EEG methodology and 
data analysis,
comfortable with methodological innovation, and an interested in optimizing and 
developing analysis
streams tailored to the study aims and populations.  New approaches and ideas 
are encouraged, as are
independent projects that dovetail with current studies.  The position requires 
working closely with
the PI, as well as with Dr. Stickgold, other Martinos Center investigators, 
particularly Dr. Matti
Hamalainen, Director of the MEG Core Lab, and lab mates to design studies, 
acquire data, and
develop, explore, improve and apply data analytic techniques. Training in 
clinical research and in
the acquisition, analysis, and interpretation of neuroimaging data will be 
provided.

Requirements: PhD, Experience with MEG/EEG data analysis/methodology and/or 
other signal processing.
Background in cognitive neuroscience, experimental psychology, and an interest 
in clinical
applications are a plus.

Position available immediately.  Interested applicants should email: (a) CV, 
(b) statement of
post-doctoral and career goals, (c) writing sample (e.g., a published 
manuscript), and (d) letters
and/or contact information for three references to Dara Manoach at 
d...@nmr.mgh.harvard.edu. Stipend
levels are in line with NIMH.  A two-year commitment is required.

 Dara S. Manoach, Ph.D.
Psychiatric Neuroimaging
Massachusetts General Hospital
Charlestown Navy Yard
149 13th Street, Room 1.111
Charlestown, MA 02129
email: d...@nmr.mgh.harvard.edu
phone: 617-724-6148
fax: 617-726-4078

http://nmr.mgh.harvard.edu/manoachlab

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Re: [Freesurfer] Adding low-res T2 and PD images in the recon-all stream - any advantages?


Hi Gari

the post-hoc surface deformation will use whatever resolution you have, 
and works quite nicely with .7mm scans.


cheers
Bruce
On Thu, 7 Mar 2013, Garikoitz 
Lerma-Usabiaga wrote:



Many thanks for your answers! 

I have another question: 
Usually we work with 1 mm3 T1-s, but we have a 0.7 mm3 sequence as well. Lüsebrink 
et al (2013) say that: FreeSurfer is
not designed to process data with a spatial resolution other than 1 mm and was 
modified to avoid this limitation. 

When running 0.7 mm3 T1-s with the recon-all standard stream we observe the 
following in recon-all.log:
Original Data has (0.35, 0.35, 0.7) mm size and (640, 640, 256) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions

 Will FS 5.2 work with other resolutions different to 1 mm3?
 With the current limitation, can we expect any gain in cortical thickness (or 
other) measurements using lower voxel
size-s, if at the end everything is conformed to 1 mm3?

many thanks again for your responses!
Gari


On Thu, Mar 7, 2013 at 4:38 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
  and 1mm isotropic
  On Thu, 7 Mar 2013, Nick Schmansky wrote:

see:

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFiledo=gettarget=FreeSurfer_Suggested_Morphometry
_Protocols.pdf


  Hi Gari

  we use a bandwidth and readout matched (to our multi-echo 
mprage) T2-SPACE
  with a FLAIR inversion pulse. Andre (ccd) can give you the 
details

  cheers
  Bruce


  On Thu, 7 Mar 2013, Garikoitz Lerma-Usabiaga wrote:

Hi Bruce,is there any recommended protocol for T2 
acquisition to be used
in the 5.2 recon-all stream?

Should we used the same voxel size as the T1? (we are 
using  1 mm3 right
now).

If it is going to improve the skull striping and pial 
surface creation,
we might acquire specific T2 images just to be
used in the recon-all stream.

many thanks,
Gari 


On Wed, Feb 27, 2013 at 2:44 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edu wrote:
      Hi Nicola

      the T2 might in 5.2, but it is pretty thick 
slices so might hurt
more
      than it helps. Not sure, but you can try it out

      cheers
      Bruce
      On Wed, 27 Feb 2013, Nicola
      Toschi wrote:

      Hello List,
     
      on out 3T scanner, in addition to MPRAGE images 
(1 mm^3), we
usually
      acquire T2 and PD images - however they are at 
1x1x5 mm
resolution.
     
      Would you recommend passing these (T2+PD) to the 
recon-all
stream anyway
      - would they add value/accuracy to the 
segmentation/parcellation
(or
      would they possibly decrease accuracy)?
     
      Thanks in advance,
     
      Nicola
     
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[Freesurfer] Time

2013-03-07 Thread Valtina Pouegue

Hi, I have 8 folders of 26 slice odf dicom. Yesterday, I launched the 
conversion to .mgz with the command  recon-all -i
path-to-first-structural [-i path-to-second-structural] -s
subjid . All my folders are created but in the Orig folder I don't fige files 
.mgz. 
I think that the processing time is really long but I'm not sure.  Do you know 
somthing about? 
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Re: [Freesurfer] Viewing volumes and surfaces in Native Space

Hi Tim, I don't think you can use tkmedit for this. tkmedit is a bit 
rigid and expects things to be a certain way (ie, not in native space). 
Try using freeview instead.
doug

On 03/07/2013 03:19 PM, Timothy Brown wrote:
 Dear FreeSurfer users,

 I wish to view volumes and surfaces in native space.

 I used the information at:

 http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat

 to convert volumes.

 I then used:

 tkregister2 --mov orig.mgz --targ rawavg.mgz --regheader --reg 
 register.dat
 cp register.dat ../surf/
 mri_surf2surf --sval-xyz pial --reg register.dat --tval pial.native 
 --tval-xyz --hemi lh --s 1158119_3_6

 When I use tkmedit to view the surfaces and volumes, the surface that 
 I thought would be in native space does not seem to correspond with 
 the native space volumes. (graphic attached)

 Can you let me know the steps/procedure to do this?

 Many thanks,

 -Tim

 Timothy Brown email: timo...@cis.jhu.edu
 Computational Anatomist   phone: 410.516.7551
 Center for Imaging Sciencefax:   410.516.4557
 Johns Hopkins University
 301 Clark Hall
 3400 N. Charles Street
 Baltimore, MD 21218


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Fax: 617-726-7422

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Re: [Freesurfer] Time

Canyou send the recon-all.log file? Is should be in the scripts folder. 
If that does not exist, send the terminal output.
doug
On 03/07/2013 03:37 PM, Valtina Pouegue wrote:
 Hi,
 I have 8 folders of 26 slice odf dicom. Yesterday, I launched the 
 conversion to .mgz with the command recon-all -i 
 path-to-first-structural [-i path-to-second-structural] -s subjid
  .
 All my folders are created but in the Orig folder I don't fige files 
 .mgz.

 I think that the processing time is really long but I'm not sure.  Do 
 you know somthing about?

 Thanks.
 VP


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gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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Re: [Freesurfer] Time

You cannot give recon-all a folder as input. It must be an image file. 
If you have multiple files, you need multiple -i flags.
doug


On 03/07/2013 03:48 PM, Valtina Pouegue wrote:
 Hi,
 Here it is
 [esther@IP132-207-67-224 ~]$ recon-all -i 
 /home/esther/Freesurfer/freesurfer/subjects/Patient13B -s 13B
 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
 INFO: SUBJECTS_DIR is /home/esther/Freesurfer/freesurfer/subjects
 Actual FREESURFER_HOME /home/esther/Freesurfer/freesurfer
 Linux IP132-207-67-224 3.4.6-2.fc17.x86_64 #1 SMP Thu Jul 19 22:54:16 
 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
 /home/esther/Freesurfer/freesurfer/subjects/13B

  mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13B 
 /home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz

 mri_convert /home/esther/Freesurfer/freesurfer/subjects/Patient13B 
 /home/esther/Freesurfer/freesurfer/subjects/13B/mri/orig/001.mgz
 corRead(): can't open file 
 /home/esther/Freesurfer/freesurfer/subjects/Patient13B/COR-.info
 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
 reading from /home/esther/Freesurfer/freesurfer/subjects/Patient13B...

 VP

-- 
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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
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Re: [Freesurfer] Freesurfer

2013-03-07 Thread Jon Wieser

Hi Nicole,
It looks like recon-all -autorecon2  had trouble segmenting the gray/white 
matter.  you can try using 3duniformize to make the gray,white matter more 
uniform, before doing the freesurfes recon-all.  you can also try  
skullstrippong in afni  with 3dskullstrip first, before freesurfer processing. 
I have attached script files for the uniformize and skullstrip. if this does 
not fix it, I can come to help you, or you can e-mail the problem to  the 
freesurfer  people at freesurfer@nmr.mgh.harvard.edu  . They are very helpful 
and will response relatively quickly.
Jon


- Original Message -
From: Nicole T Nowak-Saenz nowak...@uwm.edu
To: Jon Alan Wieser wie...@uwm.edu
Sent: Thursday, March 7, 2013 12:35:57 PM
Subject: Freesurfer

Hi Jon,
I think you mentioned working with Freesurfer. Have you ever seen anything like 
this? I'm hoping the problems with segmentation, and white/pial lines are due 
to the recon-all somehow leaving out half the brain (e.g., temporal lobes). To 
me it looks like half the brain is missing, yet some skull remains. I have a 
feeling this will require more than adjusting a watershed parameter. Any clue 
how these errors occured or what to do about them?

I should mention I had to use a flag which was provided in the failed recon-all 
log to correct an error like this one: DICOM WARNING: file 00020002.dcm has 
Rescale tags.

If this is something you know something about and have a few minutes to 
address, I would appreciate it. If not, I completely understand. 

Nicole

@skullstrip
Description: Binary data


@uniformize
Description: Binary data
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Re: [Freesurfer] FS workshop registration link

2013-03-07 Thread zkaufman

Hello Nooshin,

The email containing the registration page went out today at 11am EST. It
can be found here:

https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.7678.cgi

Unfortunately, the course was filled within the first two hours of opening
registration, but there is a waitlist and you are free to sign up for
that.

I see your name and email in our email list so you should have received
today's announcement. Maybe check your spam folder?

-Zeke


 Dear All

 I have a question about upcoming Freesurfer course registration (April 29
 _
 May 1). The registration link was supposed to be open and sent by today,
 but I still have not received it.
 I was wondering if you have any information and can help me.

 Thanks a lot
 Nooshin
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[Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

Hi all,

Did you encounter the error message talairach.m3z does not start as 'MNI
Transform File' when making average of subjects?

I checked all the recon-all.log file and did not find error, but when
running make_average_subject after recon-all, then this error shoot.

To repeat the error message, I tried the following command which is called
by make_average_subject and found all my subjects shoot this error.

mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/mni305.cor.mgz --xfm
 1173622/mri/transforms/talairach.m3z --o
/tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest

I found another same question asked before, but no answer.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024064.html

Any hint or help will be appreciated. Thank you.

-- 
Xiaowei Song
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Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

This error may come from regio_read_mincxfm function in registerio.c.
Does this mean something wrong in recon-all?

I forgot to mention that FreeSurfer version is
 freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0


On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song dawnwei.s...@gmail.com wrote:

 Hi all,

 Did you encounter the error message talairach.m3z does not start as 'MNI
 Transform File' when making average of subjects?

 I checked all the recon-all.log file and did not find error, but when
 running make_average_subject after recon-all, then this error shoot.

 To repeat the error message, I tried the following command which is called
 by make_average_subject and found all my subjects shoot this error.

 mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
 /usr/local/freesurfer/average/mni305.cor.mgz --xfm
  1173622/mri/transforms/talairach.m3z --o
 /tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest

 I found another same question asked before, but no answer.
 https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024064.html

 Any hint or help will be appreciated. Thank you.

 --
 Xiaowei Song




-- 
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

sorry, I don't understand. What was the error? I don't see one in this 
email. Can you send us the actual screen output?


cheers
Bruce
On Thu, 7 Mar 2013, Xiaowei Song wrote:


This error may come from regio_read_mincxfm function in registerio.c.Does
this mean something wrong in recon-all?

I forgot to mention that FreeSurfer version is
 freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0


On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song dawnwei.s...@gmail.com wrote:
  Hi all,

Did you encounter the error message talairach.m3z does not start as
'MNI Transform File' when making average of subjects?

I checked all the recon-all.log file and did not find error, but when
running make_average_subject after recon-all, then this error shoot.

To repeat the error message, I tried the following command which is
called by make_average_subject and found all my subjects shoot this
error.

mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/mni305.cor.mgz --xfm
 1173622/mri/transforms/talairach.m3z --o
/tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest

I found another same question asked before, but noanswer. 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024
064.html

Any hint or help will be appreciated. Thank you.

--
Xiaowei Song 




--
Xiaowei Song 

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Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

Sorry, I did not make it clear.

In make_average_volume.log, the error message is:

1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/mni305.cor.mgz --xfm
/data/lis9/fs/x/1173622/mri/transforms/talairach.m3z --o
/data/lis9/fs/x/avgGrp139/tmp/make_average_vol-tmp-55832/seg-1173622.mgh
--interp nearest
ERROR: /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z does not start
as 'MNI Transform File'/spin1/users/lis9/fs/dcm.mprage.mgz
ERROR: mri_vol2vol failed.

On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

sorry, I don't understand. What was the error? I don't see one in this
email. Can you send us the actual screen output?

cheers
Bruce

On Thu, 7 Mar 2013, Xiaowei Song wrote:

This error may come from regio_read_mincxfm function in registerio.c.Does
this mean something wrong in recon-all?

I forgot to mention that FreeSurfer version is
freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0

On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song dawnwei.s...@gmail.com
wrote:
Hi all,

Did you encounter the error message talairach.m3z does not start as
'MNI Transform File' when making average of subjects?

I checked all the recon-all.log file and did not find error, but when
running make_average_subject after recon-all, then this error shoot.

To repeat the error message, I tried the following command which is
called by make_average_subject and found all my subjects shoot this
error.

mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/**mni305.cor.mgz --xfm
1173622/mri/transforms/**talairach.m3z --o
/tmp/make_average_vol-tmp-**164320_seg-1173622.mgh --interp nearest

I found another same question asked before, but noanswer.
https://mail.nmr.**mgh.harvard.edu/pipermail//**freesurfer/2012-May/024https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024
064.html

Any hint or help will be appreciated. Thank you.

--
Xiaowei Song

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/**compliancelinehttp://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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Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'


what was your command line?
On Thu, 7 Mar 2013, Xiaowei Song wrote:


Sorry, I did not make it clear.
In make_average_volume.log, the error message is:

1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/mni305.cor.mgz --xfm
/data/lis9/fs/x/1173622/mri/transforms/talairach.m3z --o
/data/lis9/fs/x/avgGrp139/tmp/make_average_vol-tmp-55832/seg-1173622.mgh
--interp nearest
ERROR: /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z does not start
as 'MNI Transform File'/spin1/users/lis9/fs/dcm.mprage.mgz
ERROR: mri_vol2vol failed.


On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
  sorry, I don't understand. What was the error? I don't see one
  in this email. Can you send us the actual screen output?

  cheers
  Bruce
  On Thu, 7 Mar 2013, Xiaowei Song wrote:

This error may come from regio_read_mincxfm function
in registerio.c.Does
this mean something wrong in recon-all?

I forgot to mention that FreeSurfer version is
 freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0


On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song
dawnwei.s...@gmail.com wrote:
      Hi all,

Did you encounter the error message talairach.m3z
does not start as
'MNI Transform File' when making average of
subjects?

I checked all the recon-all.log file and did not
find error, but when
running make_average_subject after recon-all, then
this error shoot.

To repeat the error message, I tried the following
command which is
called by make_average_subject and found all my
subjects shoot this
error.

mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
/usr/local/freesurfer/average/mni305.cor.mgz --xfm
 1173622/mri/transforms/talairach.m3z --o
/tmp/make_average_vol-tmp-164320_seg-1173622.mgh
--interp nearest

I found another same question asked before, butnoanswer. 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/0
24
064.html

Any hint or help will be appreciated. Thank you.

--
Xiaowei Song 




--
Xiaowei Song 




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.




--
Xiaowei Song 

___
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

Thanks for your help.

My command line is
make_average_subject --out avgGrp139  --subjects `cat
script/subjects.id`  --xform
talairach.m3z


On Thu, Mar 7, 2013 at 6:15 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:

 what was your command line?

 On Thu, 7 Mar 2013, Xiaowei Song wrote:

  Sorry, I did not make it clear.
 In make_average_volume.log, the error message is:

 1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
 mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/**aseg.mgz --targ
 /usr/local/freesurfer/average/**mni305.cor.mgz --xfm
 /data/lis9/fs/x/1173622/mri/**transforms/talairach.m3z --o
 /data/lis9/fs/x/avgGrp139/tmp/**make_average_vol-tmp-55832/**
 seg-1173622.mgh
 --interp nearest
 ERROR: /data/lis9/fs/x/1173622/mri/**transforms/talairach.m3z does not
 start
 as 'MNI Transform File'/spin1/users/lis9/fs/dcm.**mprage.mgz
 ERROR: mri_vol2vol failed.


 On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu
 wrote:
   sorry, I don't understand. What was the error? I don't see one
   in this email. Can you send us the actual screen output?

   cheers
   Bruce
   On Thu, 7 Mar 2013, Xiaowei Song wrote:

 This error may come from regio_read_mincxfm function
 in registerio.c.Does
 this mean something wrong in recon-all?

 I forgot to mention that FreeSurfer version is
  freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0


 On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song
 dawnwei.s...@gmail.com wrote:
   Hi all,

 Did you encounter the error message talairach.m3z
 does not start as
 'MNI Transform File' when making average of
 subjects?

 I checked all the recon-all.log file and did not
 find error, but when
 running make_average_subject after recon-all, then
 this error shoot.

 To repeat the error message, I tried the following
 command which is
 called by make_average_subject and found all my
 subjects shoot this
 error.

 mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
 /usr/local/freesurfer/average/**mni305.cor.mgz --xfm
  1173622/mri/transforms/**talairach.m3z --o
 /tmp/make_average_vol-tmp-**164320_seg-1173622.mgh
 --interp nearest

 I found another same question asked before, butnoanswer.
 https://mail.nmr.**mgh.harvard.edu/pipermail//**freesurfer/2012-May/0https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/0
 24
 064.html

 Any hint or help will be appreciated. Thank you.

 --
 Xiaowei Song




 --
 Xiaowei Song




 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/**compliancelinehttp://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.




 --
 Xiaowei Song




-- 
Xiaowei Song
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Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

The xform has to be linear in the xfm format. The m3z cannot be used.
doug

On 03/07/2013 06:44 PM, Xiaowei Song wrote:
 Thanks for your help.

 My command line is
 make_average_subject --out avgGrp139 --subjects `cat 
 script/subjects.id http://subjects.id` --xform talairach.m3z


 On Thu, Mar 7, 2013 at 6:15 PM, Bruce Fischl 
 fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote:

 what was your command line?

 On Thu, 7 Mar 2013, Xiaowei Song wrote:

 Sorry, I did not make it clear.
 In make_average_volume.log, the error message is:

 1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013
 mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ
 /usr/local/freesurfer/average/mni305.cor.mgz --xfm
 /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z --o
 
 /data/lis9/fs/x/avgGrp139/tmp/make_average_vol-tmp-55832/seg-1173622.mgh
 --interp nearest
 ERROR: /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z
 does not start
 as 'MNI Transform File'/spin1/users/lis9/fs/dcm.mprage.mgz
 ERROR: mri_vol2vol failed.


 On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl
 fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu
 wrote:
   sorry, I don't understand. What was the error? I don't
 see one
   in this email. Can you send us the actual screen output?

   cheers
   Bruce
   On Thu, 7 Mar 2013, Xiaowei Song wrote:

 This error may come from regio_read_mincxfm function
 in registerio.c.Does
 this mean something wrong in recon-all?

 I forgot to mention that FreeSurfer version is
  freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0


 On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song
 dawnwei.s...@gmail.com
 mailto:dawnwei.s...@gmail.com wrote:
   Hi all,

 Did you encounter the error message talairach.m3z
 does not start as
 'MNI Transform File' when making average of
 subjects?

 I checked all the recon-all.log file and did not
 find error, but when
 running make_average_subject after recon-all, then
 this error shoot.

 To repeat the error message, I tried the following
 command which is
 called by make_average_subject and found all my
 subjects shoot this
 error.

 mri_vol2vol --mov 1173622/mri/aseg.mgz --targ
 /usr/local/freesurfer/average/mni305.cor.mgz --xfm
  1173622/mri/transforms/talairach.m3z --o
 /tmp/make_average_vol-tmp-164320_seg-1173622.mgh
 --interp nearest

 I found another same question asked before,
 butnoanswer.
 https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/0
 24
 064.html

 Any hint or help will be appreciated. Thank you.

 --
 Xiaowei Song




 --
 Xiaowei Song




 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.




 --
 Xiaowei Song




 -- 
 Xiaowei Song


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Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'