[Freesurfer] EasyReg usage

2023-03-15 Thread fidel vila 
External Email - Use Caution

Hi,
I checked the archive for any pointers about specific use instructions for
EasyReg and read the wiki page.
I would like to register three T1w acquisitions on three planes (Axial,
Cor, Sagittal).
This was my first attempt:
*mri_easyreg --ref [myimageAXIAL.nii]  --flo [myimageCOR] --ref_seg
[filename_tobecreate_seg_not_runpreviously]  --flo_seg
/[filename_tobecreate_seg_not_runpreviously] --ref_reg
/[filename_tobecreate]*

The command run and did generate the segmentation files but froze here:

Deforming and writing to disk

  Computing backward field

  Deforming reference image

  Saving deformed reference image
I could not find a log file.
Any suggestions? My plan was to use EasyReg on this registered image and
register it to the Saggital acquisition, but maybe there is a way to do
that registration at once?
thanks for any pointers and for putting together such amazing tools,
Fidel
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[Freesurfer] ?reference(s) supporting DLPFC label

2014-06-03 Thread Fidel Vila 
Dear FS community,

I'm looking into DLPFC volume/thickness.
Following advice posted before on this forum, I'm adding G_frontal_middle.label 
+  S_frontal_inferior.label + S_frontal_middle.label from Destrieux 2009 atlas 
as a surrogate for DLPFC.

My question is whether folks could provide reference(s) from the literature 
backing up this approach?

Thanks for your time and help,

Kev
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dispose of the e-mail.

[Freesurfer] kvl binaries missing from ppc 5.1 stable release

2012-08-31 Thread Fidel Vila 
Hi Nick,

I run recon-all and worked well, but then I added the hippo-subfields  
flag and quitted with errors. The hippo-subfields.log says  
kvlSegmentHippocamlSubfields.sh: Command not found.

I went into the bin folder and all the kvl files are missing.

Advice will be appreciate it.

Thanks,

Fidel


On 20-Aug-12, at 8:48 AM, Nick Schmansky wrote:

Fidel,

I don't know why those files are missing from the Tiger ppc  
distribution,
but i confirmed that indeed they are.  Here is a tarball of the
distribution which contains everything:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz

save it to your /Applications directory, and then from the Terminal  
type:

cd /Applications
sudo tar zxvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz

you dont need to remove your existing install.

Nick



 Hi,

 I'm reposting this, hoping Nick has returned and can provide some
 guidance.

 Thanks,

 Fidel

 On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote:

 This is strange, it must be something that is specific to the PPC
 Mac distribution. Nick is going to have to deal with this, but he
 won't be back until Mon. Can you wait that long?
 doug

 On 07/31/2012 06:01 PM, Fidel Vila wrote:
 And there is nothing in /Applications/freesurfer/bin?

 There are 357 items in /Applications/freesurfer/bin

 Are there any files in the other directories?

 Indeed, from /Application/freesurfer/average (50 items in here) to /
 Applications/freesurfer/trctrain (35 items) as well as 'LICENSE'
 file, 'README' file, etc. Not to forget my user license file
 (i.e. .license)

 The executable files missing in /Applications/freesurfer/bin seem
 to be:

 talairach_avi
 ;mri_watershed
 ; ;mri_segment
 ;mri_tessellate
 ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate
 ;mris_curvature
 ;mris_sphere
 ;mris_fix_topology
 ;mris_topo_fixer
 ;mris_ca_label
 ;mris_euler_number
 ;mris_make_surfaces
 ;mris_register
 ;mris_volmask
  ;mris_anatomical_stats
 ;mrisp_paint
 ;mris_curvature_stats
 ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats

 Also, running grep -f /CommandsNotFound.txt (file listing the
 commands listed above) /Files_in_Bin.txt (list of 357 items in /
 Applications/freesurfer/bin folder) retrieves no matching pattern.

 The list of commands above matches the list of warning errors (i.e.
 command not found) when I run recon-all.

 Do you have permission to install it in that location?

 I do.

 Could this be related to compillation of files for the May 2011
 5.1. stable release for ppc?

 Appreciate your advice and support as I understand ppc machines
 might not be one of the highest priorities...

 Regards,

 Fidel


 On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:

 And there is nothing in /Applications/freesurfer/bin? Are there
 any files in the other directories? Do you have permission to
 install it in that location? If nothing is in the bin dir, then
 there is no need to try recon-all, it will always fail.
 doug



 On 07/31/2012 04:05 PM, Fidel Vila wrote:
 Hi Doug,

 I re-installed freesurfer, and I still get the same error message
 (terminal output attached); bin files are still missing from bin
 folder.

 Shall I report this as a bug?

 Regards,

 Fidel




 On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:

 did you set up your environment so that your path environment
 variable has all the proper paths in it? Look at the wiki for
 instructions.
 doug

 On 7/25/12 7:57 PM, Fidel Vila wrote:
 Hi Freesurfer experts,

 I recently installed FS (PowerPC architecture version available
 on FS website) on a Mac OS X 10.4.11 and I get the attached
 output error when running recon-all.

 Advice on how to troubleshoot this would be appreciate.

 Thanks,

 Fidel



 ___
 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.



 --
 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




 --
 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


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 Freesurfer mailing list
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Re: [Freesurfer] tcsh: tailarach_avi: Command not found

2012-08-28 Thread Fidel Vila 

Thanks a lot Nick.

It worked like a charm:

recon-all -s struct_FS finished without error at Thu Aug 23 03:52:39  
PDT 2012

done

For other users whose OS automatically unzips the .gz,

the command to type is:

sudo tar xvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar

Thanks!

Fidel


On 20-Aug-12, at 8:48 AM, Nick Schmansky wrote:

Fidel,

I don't know why those files are missing from the Tiger ppc  
distribution,

but i confirmed that indeed they are.  Here is a tarball of the
distribution which contains everything:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz

save it to your /Applications directory, and then from the Terminal  
type:


cd /Applications
sudo tar zxvf freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0.tar.gz

you dont need to remove your existing install.

Nick




Hi,

I'm reposting this, hoping Nick has returned and can provide some
guidance.

Thanks,

Fidel

On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote:


This is strange, it must be something that is specific to the PPC
Mac distribution. Nick is going to have to deal with this, but he
won't be back until Mon. Can you wait that long?
doug

On 07/31/2012 06:01 PM, Fidel Vila wrote:

And there is nothing in /Applications/freesurfer/bin?


There are 357 items in /Applications/freesurfer/bin


Are there any files in the other directories?


Indeed, from /Application/freesurfer/average (50 items in here) to /
Applications/freesurfer/trctrain (35 items) as well as 'LICENSE'
file, 'README' file, etc. Not to forget my user license file
(i.e. .license)

The executable files missing in /Applications/freesurfer/bin seem
to be:

talairach_avi
;mri_watershed
; ;mri_segment
;mri_tessellate
;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate
;mris_curvature
;mris_sphere
;mris_fix_topology
;mris_topo_fixer
;mris_ca_label
;mris_euler_number
;mris_make_surfaces
;mris_register
;mris_volmask
 ;mris_anatomical_stats
;mrisp_paint
;mris_curvature_stats
;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats

Also, running grep -f /CommandsNotFound.txt (file listing the
commands listed above) /Files_in_Bin.txt (list of 357 items in /
Applications/freesurfer/bin folder) retrieves no matching pattern.

The list of commands above matches the list of warning errors (i.e.
command not found) when I run recon-all.


Do you have permission to install it in that location?


I do.

Could this be related to compillation of files for the May 2011
5.1. stable release for ppc?

Appreciate your advice and support as I understand ppc machines
might not be one of the highest priorities...

Regards,

Fidel


On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:


And there is nothing in /Applications/freesurfer/bin? Are there
any files in the other directories? Do you have permission to
install it in that location? If nothing is in the bin dir, then
there is no need to try recon-all, it will always fail.
doug



On 07/31/2012 04:05 PM, Fidel Vila wrote:

Hi Doug,

I re-installed freesurfer, and I still get the same error message
(terminal output attached); bin files are still missing from bin
folder.

Shall I report this as a bug?

Regards,

Fidel




On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:


did you set up your environment so that your path environment
variable has all the proper paths in it? Look at the wiki for
instructions.
doug

On 7/25/12 7:57 PM, Fidel Vila wrote:

Hi Freesurfer experts,

I recently installed FS (PowerPC architecture version available
on FS website) on a Mac OS X 10.4.11 and I get the attached
output error when running recon-all.

Advice on how to troubleshoot this would be appreciate.

Thanks,

Fidel



___
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.





--
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






--
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



___
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Re: [Freesurfer] tcsh: tailarach_avi: Command not found

2012-08-07 Thread Fidel Vila 
Hi,

I'm reposting this, hoping Nick has returned and can provide some  
guidance.

Thanks,

Fidel

On 1-Aug-12, at 8:16 AM, Douglas N Greve wrote:

 This is strange, it must be something that is specific to the PPC  
 Mac distribution. Nick is going to have to deal with this, but he  
 won't be back until Mon. Can you wait that long?
 doug

 On 07/31/2012 06:01 PM, Fidel Vila wrote:
 And there is nothing in /Applications/freesurfer/bin?

 There are 357 items in /Applications/freesurfer/bin

 Are there any files in the other directories?

 Indeed, from /Application/freesurfer/average (50 items in here) to / 
 Applications/freesurfer/trctrain (35 items) as well as 'LICENSE'  
 file, 'README' file, etc. Not to forget my user license file  
 (i.e. .license)

 The executable files missing in /Applications/freesurfer/bin seem  
 to be:

 talairach_avi 
  ;mri_watershed 
  ; ;mri_segment 
  ;mri_tessellate 
  ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate
 ;mris_curvature 
  ;mris_sphere 
  ;mris_fix_topology 
  ;mris_topo_fixer 
  ;mris_ca_label 
  ;mris_euler_number 
  ;mris_make_surfaces 
  ;mris_register 
  ;mris_volmask 
   ;mris_anatomical_stats 
  ;mrisp_paint 
  ;mris_curvature_stats 
  ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats

 Also, running grep -f /CommandsNotFound.txt (file listing the  
 commands listed above) /Files_in_Bin.txt (list of 357 items in / 
 Applications/freesurfer/bin folder) retrieves no matching pattern.

 The list of commands above matches the list of warning errors (i.e.  
 command not found) when I run recon-all.

 Do you have permission to install it in that location?

 I do.

 Could this be related to compillation of files for the May 2011  
 5.1. stable release for ppc?

 Appreciate your advice and support as I understand ppc machines  
 might not be one of the highest priorities...

 Regards,

 Fidel


 On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:

 And there is nothing in /Applications/freesurfer/bin? Are there  
 any files in the other directories? Do you have permission to  
 install it in that location? If nothing is in the bin dir, then  
 there is no need to try recon-all, it will always fail.
 doug



 On 07/31/2012 04:05 PM, Fidel Vila wrote:
 Hi Doug,

 I re-installed freesurfer, and I still get the same error message  
 (terminal output attached); bin files are still missing from bin  
 folder.

 Shall I report this as a bug?

 Regards,

 Fidel




 On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:

 did you set up your environment so that your path environment  
 variable has all the proper paths in it? Look at the wiki for  
 instructions.
 doug

 On 7/25/12 7:57 PM, Fidel Vila wrote:
 Hi Freesurfer experts,

 I recently installed FS (PowerPC architecture version available  
 on FS website) on a Mac OS X 10.4.11 and I get the attached  
 output error when running recon-all.

 Advice on how to troubleshoot this would be appreciate.

 Thanks,

 Fidel



 ___
 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.



 -- 
 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




 -- 
 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


___
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Re: [Freesurfer] tcsh: tailarach_avi: Command not found

2012-07-31 Thread Fidel Vila 
Hi Doug,I re-installed freesurfer, and I still get the same error message (terminal output attached); bin files are still missing from bin folder.Shall I report this as a bug?Regards,Fidel
Last login: Tue Jul 31 12:51:32 on ttyp2
Welcome to Darwin!
a3128u:~ FVila$ export FREESURFER_HOME=/Applications/freesurfer
a3128u:~ FVila$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /Applications//fsl
a3128u:~ FVila$ recon-all -i 
/Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz -subjid 
struct_FS
Subject Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0
Current Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
Darwin a3128u.bcricwh.lan 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 
18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc
tcsh: talairach_avi: Command not found.
tcsh: mri_watershed: Command not found.
tcsh: mri_segment: Command not found.
tcsh: mri_tessellate: Command not found.
tcsh: mri_concatenate_lta: Command not found.
tcsh: mri_normalize_tp2: Command not found.
tcsh: mris_smooth: Command not found.
tcsh: mris_inflate: Command not found.
tcsh: mris_curvature: Command not found.
tcsh: mris_sphere: Command not found.
tcsh: mris_fix_topology: Command not found.
tcsh: mris_topo_fixer: Command not found.
tcsh: mris_ca_label: Command not found.
tcsh: mris_euler_number: Command not found.
tcsh: mris_make_surfaces: Command not found.
tcsh: mris_register: Command not found.
tcsh: mris_volmask: Command not found.
tcsh: mris_anatomical_stats: Command not found.
tcsh: mrisp_paint: Command not found.
tcsh: mris_curvature_stats: Command not found.
tcsh: mris_calc: Command not found.
tcsh: mri_robust_register: Command not found.
tcsh: mri_robust_template: Command not found.
tcsh: mri_segstats: Command not found.
/Applications/freesurfer/subjects/struct_FS
\n mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz 
/Applications/freesurfer/subjects/struct_FS/mri/orig/001.mgz \n
mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz 
/Applications/freesurfer/subjects/struct_FS/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to /Applications/freesurfer/subjects/struct_FS/mri/orig/001.mgz...

#--

recon-all -s struct_FS finished without error at Tue Jul 31 12:54:59 PDT 2012
done
a3128u:~ FVila$ 
 On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:  did you set up your environment so that your path environmentvariable has all the proper paths in it? Look at the wiki forinstructions.dougOn 7/25/12 7:57 PM, Fidel Vila wrote:Hi Freesurfer experts,  I recently installed FS (PowerPC architecture version available on  FS website) on a Mac OS X 10.4.11 and I get the attached output  error when running recon-all.  Advice on how to troubleshoot this would be appreciate.  Thanks,  Fidel___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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


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] tcsh: tailarach_avi: Command not found

2012-07-31 Thread Fidel Vila 
 And there is nothing in /Applications/freesurfer/bin?

There are 357 items in /Applications/freesurfer/bin

 Are there any files in the other directories?

Indeed, from /Application/freesurfer/average (50 items in here) to / 
Applications/freesurfer/trctrain (35 items) as well as 'LICENSE' file,  
'README' file, etc. Not to forget my user license file (i.e. .license)

The executable files missing in /Applications/freesurfer/bin seem to be:

talairach_avi 
  ;mri_watershed 
  ; ;mri_segment 
  ;mri_tessellate 
  ;mri_concatenate_lta ;mri_normalize_tp2 ;mris_smooth ;mris_inflate
;mris_curvature 
  ;mris_sphere 
  ;mris_fix_topology 
  ;mris_topo_fixer 
  ;mris_ca_label 
  ;mris_euler_number 
  ;mris_make_surfaces 
  ;mris_register 
  ;mris_volmask 
   ;mris_anatomical_stats 
  ;mrisp_paint 
  ;mris_curvature_stats 
  ;mris_calc ;mri_robust_register ;mri_robust_template ;mri_segstats

Also, running grep -f /CommandsNotFound.txt (file listing the commands  
listed above) /Files_in_Bin.txt (list of 357 items in /Applications/ 
freesurfer/bin folder) retrieves no matching pattern.

The list of commands above matches the list of warning errors (i.e.  
command not found) when I run recon-all.

 Do you have permission to install it in that location?

I do.

Could this be related to compillation of files for the May 2011 5.1.  
stable release for ppc?

Appreciate your advice and support as I understand ppc machines might  
not be one of the highest priorities...

Regards,

Fidel


On 31-Jul-12, at 1:12 PM, Douglas N Greve wrote:

 And there is nothing in /Applications/freesurfer/bin? Are there any  
 files in the other directories? Do you have permission to install it  
 in that location? If nothing is in the bin dir, then there is no  
 need to try recon-all, it will always fail.
 doug



 On 07/31/2012 04:05 PM, Fidel Vila wrote:
 Hi Doug,

 I re-installed freesurfer, and I still get the same error message  
 (terminal output attached); bin files are still missing from bin  
 folder.

 Shall I report this as a bug?

 Regards,

 Fidel




 On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:

 did you set up your environment so that your path environment  
 variable has all the proper paths in it? Look at the wiki for  
 instructions.
 doug

 On 7/25/12 7:57 PM, Fidel Vila wrote:
 Hi Freesurfer experts,

 I recently installed FS (PowerPC architecture version available  
 on FS website) on a Mac OS X 10.4.11 and I get the attached  
 output error when running recon-all.

 Advice on how to troubleshoot this would be appreciate.

 Thanks,

 Fidel



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 -- 
 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


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Re: [Freesurfer] tcsh: tailarach_avi: Command not found

2012-07-29 Thread Fidel Vila 

Hi Doug.
The missing files are NOT in $FREESURFER_HOME/bin; So, I guess that's  
why they are not found even though the path is set up in the system  
PATH variable.

Suggestions?
Fidel

Are the missing files in $FREESURFER_HOME/bin and is that path in your
system PATH variable?

On 07/26/2012 01:29 PM, Fidel Vila wrote:
 Thanks for your prompt reply, Doug.

 I've been checking and following the wiki instructions with regards  
to

 setting up proper paths, and I could not find an obvious (to me)
 problem there.

 I attach a file with things I have tried and issues I have found.

 Further advice will be greatly appreciate it.

 Many thanks,

 Fidel





 On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:

 did you set up your environment so that your path environment
 variable has all the proper paths in it? Look at the wiki for
 instructions.
 doug

 On 7/25/12 7:57 PM, Fidel Vila wrote:
 Hi Freesurfer experts,

 I recently installed FS (PowerPC architecture version available on
 FS website) on a Mac OS X 10.4.11 and I get the attached output
 error when running recon-all.

 Advice on how to troubleshoot this would be appreciate.

 Thanks,

 Fidel



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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.




 ___
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 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

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Fidel Vila-Rodriguez, MD, FRCPC
Clinical Assistant Professor, Faculty of Medicine, Dpt. of Psychiatry,  
University of British Columbia

UBC Clinician Investigator Fellow
UBC Graduate Program in Neuroscience Ph.D Candidate

BC Mental Health and Addiction Research Institute
A3-128-4, 938 West 28th Ave
Vancouver, BC
V5Z 4H4
Tel: 604-875-2000 Ext. 4732
Fax: 604-875-3871

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Re: [Freesurfer] tcsh: tailarach_avi: Command not found

2012-07-26 Thread Fidel Vila 
 not executable.\
tcsh: /Applications/freesurfer/bin/mri_segstats: Exec format error. Binary file not executable.\
/Applications/freesurfer/subjects/FS_struct.nii.gz\
\\n mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz /Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz \\n\
tcsh: /Applications/freesurfer/bin/mri_convert: Exec format error. Binary file not executable.\
Darwin a3128u.bcricwh.lan 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc\
\
recon-all -s FS_struct.nii.gz exited with ERRORS at Thu Jul 26 09:16:57 PDT 2012\
\
For more details, see the log file /Applications/freesurfer/subjects/FS_struct.nii.gz/scripts/recon-all.log\
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting\
\

\b # I chmod +x to the list of files reported as not executable, but made no difference. Same error as above is given. \
#At this point I'm not sure what to do next. \
#I wonder why the bin files are missing in the first place, because I'm under the impression that I installed the package the right way.\
# ?Advice, ?comments, ?suggestions
\b0 \
\
\
}On 25-Jul-12, at 8:22 PM, Douglas Greve wrote:  did you set up your environment so that your path environmentvariable has all the proper paths in it? Look at the wiki forinstructions.dougOn 7/25/12 7:57 PM, Fidel Vila wrote:Hi Freesurfer experts,  I recently installed FS (PowerPC architecture version available on  FS website) on a Mac OS X 10.4.11 and I get the attached output  error when running recon-all.  Advice on how to troubleshoot this would be appreciate.  Thanks,  Fidel___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___
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[Freesurfer] tcsh: tailarach_avi: Command not found

2012-07-25 Thread Fidel Vila 

Hi Freesurfer experts,

I recently installed FS (PowerPC architecture version available on FS  
website) on a Mac OS X 10.4.11 and I get the attached output error  
when running recon-all.


Advice on how to troubleshoot this would be appreciate.

Thanks,

Fidel

a3128u:/Applications FVila$ export FREESURFER_HOME=/Applications/freesurfer
a3128u:/Applications FVila$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer
FSFAST_HOME   /Applications/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/subjects
MNI_DIR   /Applications/freesurfer/mni
FSL_DIR   /users/FVila/fsl
a3128u:/Applications FVila$ recon-all -i 
/Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz -subjid 
FS_struct.nii.gz ERROR: You are trying to re-run an existing subject with 
(possibly)
 new input data (-i). If this is truly new input data, you should delete
 the subject folder and re-run, or specify a different subject name.
 If you are just continuing an analysis of an existing subject, then 
 omit all -i flags.
a3128u:/Applications FVila$ recon-all -i 
/Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz -subjid 
FS_struct.nii.gz 
Subject Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0
Current Stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
Darwin a3128u.bcricwh.lan 8.11.0 Darwin Kernel Version 8.11.0: Wed Oct 10 
18:26:00 PDT 2007; root:xnu-792.24.17~1/RELEASE_PPC Power Macintosh powerpc
tcsh: talairach_avi: Command not found.
tcsh: mri_watershed: Command not found.
tcsh: mri_segment: Command not found.
tcsh: mri_tessellate: Command not found.
tcsh: mri_concatenate_lta: Command not found.
tcsh: mri_normalize_tp2: Command not found.
tcsh: mris_smooth: Command not found.
tcsh: mris_inflate: Command not found.
tcsh: mris_curvature: Command not found.
tcsh: mris_sphere: Command not found.
tcsh: mris_fix_topology: Command not found.
tcsh: mris_topo_fixer: Command not found.
tcsh: mris_ca_label: Command not found.
tcsh: mris_euler_number: Command not found.
tcsh: mris_make_surfaces: Command not found.
tcsh: mris_register: Command not found.
tcsh: mris_volmask: Command not found.
tcsh: mris_anatomical_stats: Command not found.
tcsh: mrisp_paint: Command not found.
tcsh: mris_curvature_stats: Command not found.
tcsh: mris_calc: Command not found.
tcsh: mri_robust_register: Command not found.
tcsh: mri_robust_template: Command not found.
tcsh: mri_segstats: Command not found.
/Applications/freesurfer/subjects/FS_struct.nii.gz
\n mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz 
/Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz \n
mri_convert /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz 
/Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /Users/FVila/CCD_imagingreliability/ERP/ERP1000M0/struct.nii.gz...
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 1, 0)
k_ras = (0, 0, 1)
writing to 
/Applications/freesurfer/subjects/FS_struct.nii.gz/mri/orig/001.mgz...

#--

recon-all -s FS_struct.nii.gz finished without error at Wed Jul 25 16:46:00 PDT 
2012
done
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[Freesurfer] qdec.table.dat file

2012-05-15 Thread Fidel Vila 

Hi Freesurfer experts,

A newbie question regarding working with QDEC. When I try to upload  
the qdec.table.dat file (attached) an error messages pops up Error  
loading the data table.
To the best of my knowledge I've followed the guidelines on the  
tutorial in terms of formatting. What would be your suggestions to  
troubleshoot this?


Thanks!

Fidel




qdec.table.dat
Description: Binary data
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[Freesurfer] bash freesurferstats2table script

2012-02-16 Thread Fidel Vila 

Hi there,

I was wondering if it would be possible to obtain a copy of the  
freesurferstats2table script that is posted on the Wiki. When I try to  
access it it requests a user name and password (I tried my mailing  
list username and psswd, but didn't work).


Greatly appreciate it,

Fidel

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