Re: [Freesurfer] MRITOTAL

[Ali Radaideh]

Thanks Bruce,

Could you please suggest something for me t sort out this issue for future
projects. All PCs will have UBUNTU 14.04 and not of them was able to run
the 8 subjects. If I install an older version of UBUNTU then Ii dont get
and update and so can not install tcsh and csh.

Today I am running subject number 5 of those who failed to run before. It
is running fine on that PC with UBUNTU 13.1.

I want also to provide you with this info.

All the 8 subjects did not pass the talairach step. and went to the
MRITOTAL stage where they all failed to run on any PC with UBUNTU 14.01.
However, when running them on the PC with UBUNTU 13.1, they also dont pass
the talairach stage and go to MRITOTAL and then the pass this step and
carry on.

I thought this may help you figuring out the problem.

Many thanks in advance,
Ali

On Mon, Aug 31, 2015 at 10:31 AM, Bruce Fischl 
wrote:

> Hi Ali
>
> it's not that I know that the quality is fine. It might be (or not), but
> this seems to be a perl error that doesn't have to do with quality
> Bruce
> On Mon, 31 Aug 2015, Ali Radaideh wrote:
>
> Dear Bruce and ​Jürgen,
>>
>> Now I see something important which may help solving the problem.
>>
>> I have 31 PCs in my lab and all of them are installed with UBUNTU 14.04.
>> 30
>> PCs were able to process all 47 subjects successfully. But failed to
>> process
>> the remaining 8 subjects. Fortunately, one PC is installed with UBUNTU
>> 13.01. I managed to installed the tcsh and csh after update and then run
>> two
>> of the failed subjects so far successfully. I concluded it is the
>> installation version of UBUNTU. So 13.01 works fine but not 14.04.
>>
>> I tried to re-install 13.01 on another PC, and I did that successfully.
>> However, but when I come to install the tcsh, after update it fails and it
>> says it is unable to locate the package tcsh (the reason is that 13.01 has
>> not longer packages to download.
>>
>> As a summary,
>>
>> one PC with 13.01 UBUNTU is running OK (but with the tcsh installed)
>> another OC with 13.01 is not running because I was not able to install
>> tcsh
>> after update
>>
>> I am now think of copying the tcsh from one pc to the 13.01 PC to make it
>> running but still trying.
>>
>> I think as Bruce said, it is something wrong with the installation as the
>> quality is fine.
>>
>> I hope I was able to clarify the problem and hope to receive any helpful
>> answer.
>>
>> Many thanks in advance
>>
>> Ali
>>
>>
>>
>> On Sun, Aug 30, 2015 at 4:05 PM, Bruce Fischl > >
>> wrote:
>>   Hi
>> ​​Jürgen and Ali
>>
>> I don't think it has anything to do with the quality of the data, but
>> we are also happy to take a look if you upload one subject. This seems
>> more like an installation issue, and I would think it would happen on
>> every subject. Did someone upgrade perl at somepoint? Or just some
>> paths?
>>
>>
>> cheers
>> Bruce
>>
>> On Sun, 30 Aug 2015, Jürgen Hänggi wrote:
>>
>>   Dear Ali
>>
>>   instead of downgrading perl you can use the perlbrew tool
>>   that allow to
>>   install several perls in parallel and switch between perl
>>   versions.
>>   if you are able to install perl 5.12 (perlbrew install
>>   5.12, you can see the
>>   available perl versions with perlbrew available) and then
>>   use
>>   perlbrew use 5.12 before running recon-all in the
>>   terminal.
>>
>>   Does it work?
>>
>>   Cheers
>>   Jürgen
>>
>>
>>
>> ---
>>
>>   Jürgen Hänggi, Ph.D.
>>
>>   Division Neuropsychology
>>
>>   Institute of Psychology
>>
>>   University of Zurich
>>
>>   Binzmuehlestrasse 14, PO Box 25
>>
>>   8050 Zurich, Switzerland
>>
>>   0041 44 635 73 97 (phone office)
>>
>>   0041 76 445 86 84 (phone mobile)
>>
>>   0041 44 635 74 09 (fax office)
>>
>>   BIN 4.D.04 (office room number)
>>
>>   j.haenggi[at]psychologie.uzh.ch (email)
>>
>>   http://www.psychologie.uzh.ch/neuropsy/ (website)
>>
>>   http://www.juergenhaenggi.ch (private website)
>>
>>
>>   This e-mail (and any attachment/s) contains confidential
>>
>>   and/or privileged information. If you are not the intended
>>
>>   recipient (or have received this e-mail in error) please
>>   notify
>>
>>   the sender immediately and destroy this e-mail. Any
>>
>>   unauthorised copying, disclosure or distribution of the
>>
>>   material in this e-mail is strictly forbidden.
>>
>>
>> ---
>>
>>
>>
>>
>>   Von:  on behalf of
>>   Ali Radaideh
>>   
>>   Antworten an: Freesurfer Mailinglist
>>   
>>   Datum: Samstag, 29. August 2015 15:56
>>   An: Freesurfer Mailinglist
>>   
>>   Betreff: Re: [Freesurfer] MRITOTAL
>>
>> Dear Jürgen,
>>
>>   Thanks for your reply. Could you please guide me on how to
>>   downgrade

[Freesurfer] mri_compute_volume_fractions not filling some sulci properly

[Sebastien Proulx]

Hello Freesurfers,

I have been using mri_compute_volume_fractions for a while and I just noticed 
something weird. Some clearly csf pixels (sometime very large groups) are not 
filled in the *.csf.mgz image mri_compute_volume_fractions produces The first 
following figure shows a posterior coronal slice, with the csf image overlaid 
with heat colormap. Look at the curser in the left calcarine sulcus for an 
obvious example, and note that it is not due to some particular slice cut.
[cid:image002.png@01D0E413.F57966B0]

These voxels are instead wrongly assigned to gray matter by 
mri_compute_volume_fractions, as can be seen in the *.gm.mgz image below (same 
slice).
[cid:image006.png@01D0E413.F57966B0]

Seems like at least this particular spot of the volume is handled ok by other 
parts of freesurfer's pipeline since the cortical ribbon */mri/ribbon.mgz does 
not include it (does not consider it to be gray or white matter; figure below)
[cid:image008.png@01D0E413.F57966B0]

You can understand that this worries me a bit.

I found $FREESURFER_HOME/VERSION file, which tells me I am running the 
following Freesurfer version:
freesurfer-x86_64-unknown-linux-gnu-stable5-20130513
I am running Ubuntu 14.04.3 LTS on a 64-bit machine.

Thanks a lot for any help!
Sébastien Proulx
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Re: [Freesurfer] [FreeSurfer] Aseg.mgz not reflected on aparc+aseg.mgz

[fmri]

after several attempts with multiple subjects 

command -autorecon2-noaseg -subjid mysubject

followed by command recon-all -aparc2aseg

aseg.mgz edits, are Not reflected onto the aparc+aseg.mgz


On Aug 25, 2015, at 2:05 PM, Douglas N Greve wrote:

> yes
> 
> On 08/25/2015 01:11 PM, fmri wrote:
>> Should we run this after recon-all autorecon2-noaseg -subjid ?
>> 
>> On Aug 25, 2015, at 7:43 AM, Douglas Greve wrote:
>> 
>>> Run recon-all -aparc2aseg
>>> 
>>> On 8/24/15 7:00 PM, fmri wrote:
 Hello FreeSurfer,
 
 How do I get edits made on aseg.mgz to reflect onto the aparc+aseg.mgz?
 
 I have tried the *recon-all 
  
 -autorecon2-noaseg -subjid mysubject*
 *
 *
 but the aparc+aseg.mgz is not created.
 
 Afterward I ran recon-all -autorecon3 -subjid mysubject
 
 this erased my edits to aseg and gave me the same results freesurfer 
 started me with.
 
 
 Thanks so much
 
 Joseph
 
 
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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: 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/
> 
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Re: [Freesurfer] mri_volsynth

[John Anderson]

Perfect!

Thank you very much for your help.

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, August 31, 2015 at 4:30 PM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_volsynth


sorry, --res (not --volres). res is the voxel size (volume resolution). dim is the number of voxels in each dimension
 
On 8/31/15 10:16 PM, John Anderson wrote:



Thank you!

Actually when I run mri_volsynth --help

I can't find --revol. is it the same flag --res?

also what is the relationship between --dim and --volres?

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, August 31, 2015 at 4:06 PM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_volsynth


No, you will need to decide how big you want your voxels to be. If you use --volres 1 1 1 1 then that should work. It will put the center of the volume at that coordiate. If you want a single voxel, then use --dim 1 1 1 1 and --volres 6.25 6.25 7.5 1

 
On 8/31/15 7:52 PM, John Anderson wrote:



Thank you for the quick response.

I wanted to create volume has the following dimentions in mm ( 6.25 X 6.25 X 7.5) in a position where the coordinates (in mm) are X=-15 Y= -4 Z= 13

is this command line correct:

mri_volsynth --dim 6.25 6.25 7.5 1 --c_ras -15 -4.3 13 --o voxel.nii

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, August 31, 2015 at 11:30 AM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_volsynth


some of this is answered if you run the command with --help
 
On 8/31/15 3:33 PM, John Anderson wrote:




Hi Freesurfers,

I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10)

I used the following command line to create the volume but I don't know how to choose it is position in scanner space.

 

mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii

 

 

I have the following question because i didn't find enough information in FS wiki about this command:

 

1. If the flag  --dim (nc nr ns nf)  is reffering to the volume dimentions. What is the fourth number  (nf ) is standing for  ?



Number of frames (the time dimension)




2. what is the meaning of voxel resolution ( the flag --res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ?



How big the voxel is in mm




3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels?



The "center" of the volume in mm, where "center" is defined as (Nvoxels-1)/2 where Nvoxels is the number rows, cols, or slices.




 

 

Thanks in advance ,

John


 

 
 

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Re: [Freesurfer] mri_volsynth

[Douglas Greve]

sorry, --res (not --volres). res is the voxel size (volume resolution). 
dim is the number of voxels in each dimension


On 8/31/15 10:16 PM, John Anderson wrote:

Thank you!
Actually when I run mri_volsynth --help
I can't find --revol. is it the same flag --res?
also what is the relationship between --dim and --volres?
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
*Sent:* Monday, August 31, 2015 at 4:06 PM
*From:* "Douglas Greve" 
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mri_volsynth
No, you will need to decide how big you want your voxels to be. If you 
use --volres 1 1 1 1 then that should work. It will put the center of 
the volume at that coordiate. If you want a single voxel, then use 
--dim 1 1 1 1 and --volres 6.25 6.25 7.5 1


On 8/31/15 7:52 PM, John Anderson wrote:

Thank you for the quick response.
I wanted to create volume has the following dimentions in mm (
6.25 X 6.25 X 7.5) in a position where the coordinates (in mm) are
X=-15 Y= -4 Z= 13
is this command line correct:
mri_volsynth --dim 6.25 6.25 7.5 1 --c_ras -15 -4.3 13 --o voxel.nii
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
*Sent:* Monday, August 31, 2015 at 11:30 AM
*From:* "Douglas Greve" 
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mri_volsynth
some of this is answered if you run the command with --help
On 8/31/15 3:33 PM, John Anderson wrote:

Hi Freesurfers,
I want to create volume 6.25 X 6.25 X 7.5 in this position in
scanner space ( x=48, y= 48, z=10)
I used the following command line to create the volume but I
don't know how to choose it is position in scanner space.
mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii
I have the following question because i didn't find enough
information in FS wiki about this command:
1. If the flag  --dim (nc nr ns nf)  is reffering to the
volume dimentions. What is the fourth number  (nf ) is
standing for  ?

Number of frames (the time dimension)

2. what is the meaning of voxel resolution ( the flag --res
(dc dr ds df) ) and what is the meaning of the numbers dc dr
ds df ?

How big the voxel is in mm

3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume
position. If yes is it in mm or in voxels?

The "center" of the volume in mm, where "center" is defined as
(Nvoxels-1)/2 where Nvoxels is the number rows, cols, or slices.

Thanks in advance ,
John

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Re: [Freesurfer] mri_volsynth

[John Anderson]

Thank you!

Actually when I run mri_volsynth --help

I can't find --revol. is it the same flag --res?

also what is the relationship between --dim and --volres?

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, August 31, 2015 at 4:06 PM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_volsynth


No, you will need to decide how big you want your voxels to be. If you use --volres 1 1 1 1 then that should work. It will put the center of the volume at that coordiate. If you want a single voxel, then use --dim 1 1 1 1 and --volres 6.25 6.25 7.5 1

 
On 8/31/15 7:52 PM, John Anderson wrote:



Thank you for the quick response.

I wanted to create volume has the following dimentions in mm ( 6.25 X 6.25 X 7.5) in a position where the coordinates (in mm) are X=-15 Y= -4 Z= 13

is this command line correct:

mri_volsynth --dim 6.25 6.25 7.5 1 --c_ras -15 -4.3 13 --o voxel.nii

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, August 31, 2015 at 11:30 AM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_volsynth


some of this is answered if you run the command with --help
 
On 8/31/15 3:33 PM, John Anderson wrote:




Hi Freesurfers,

I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10)

I used the following command line to create the volume but I don't know how to choose it is position in scanner space.

 

mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii

 

 

I have the following question because i didn't find enough information in FS wiki about this command:

 

1. If the flag  --dim (nc nr ns nf)  is reffering to the volume dimentions. What is the fourth number  (nf ) is standing for  ?



Number of frames (the time dimension)




2. what is the meaning of voxel resolution ( the flag --res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ?



How big the voxel is in mm




3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels?



The "center" of the volume in mm, where "center" is defined as (Nvoxels-1)/2 where Nvoxels is the number rows, cols, or slices.




 

 

Thanks in advance ,

John


 

 
 

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Re: [Freesurfer] mri_volsynth

[Douglas Greve]

No, you will need to decide how big you want your voxels to be. If you 
use --volres 1 1 1 1 then that should work. It will put the center of 
the volume at that coordiate. If you want a single voxel, then use --dim 
1 1 1 1 and --volres 6.25 6.25 7.5 1



On 8/31/15 7:52 PM, John Anderson wrote:

Thank you for the quick response.
I wanted to create volume has the following dimentions in mm ( 6.25 X 
6.25 X 7.5) in a position where the coordinates (in mm) are X=-15 Y= 
-4 Z= 13

is this command line correct:
mri_volsynth --dim 6.25 6.25 7.5 1 --c_ras -15 -4.3 13 --o voxel.nii
Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419
*Sent:* Monday, August 31, 2015 at 11:30 AM
*From:* "Douglas Greve" 
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] mri_volsynth
some of this is answered if you run the command with --help
On 8/31/15 3:33 PM, John Anderson wrote:

Hi Freesurfers,
I want to create volume 6.25 X 6.25 X 7.5 in this position in
scanner space ( x=48, y= 48, z=10)
I used the following command line to create the volume but I don't
know how to choose it is position in scanner space.
mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii
I have the following question because i didn't find enough
information in FS wiki about this command:
1. If the flag  --dim (nc nr ns nf)  is reffering to the volume
dimentions. What is the fourth number  (nf ) is standing for  ?

Number of frames (the time dimension)

2. what is the meaning of voxel resolution ( the flag --res (dc dr
ds df) ) and what is the meaning of the numbers dc dr ds df ?

How big the voxel is in mm

3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume
position. If yes is it in mm or in voxels?

The "center" of the volume in mm, where "center" is defined as 
(Nvoxels-1)/2 where Nvoxels is the number rows, cols, or slices.


Thanks in advance ,
John

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Re: [Freesurfer] Did not find any volume geometry information in the surface

[dgw]

Eric,

It will be easier to help, if you provide a much more detailed
description of what you did: the full command line, the version of
freesurfer, and all terminal output
(http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting this may help).

hth
D

On Mon, Aug 31, 2015 at 3:27 PM, Erik Lindberg
 wrote:
> Hi,
> I am running mri_glmfit followed by mri_glmfit-sim
>
> running the left hemisphere everything works perfect all the way to the
> visualization in freeview  - then I just chift the command to rh instead -
> running exactly the same command and when I am opening my results in
> freeview everything gets yellow and I get the following error message: Did
> not find any volume geometry information in the surface.
>
> could you please inform me how this can happen?
>
> THANKS
> ERIC
>
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>
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> addressed. If you believe this e-mail was sent to you in error and the
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> 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] Did not find any volume geometry information in the surface

[Erik Lindberg]

Hi,
I am running mri_glmfit followed by mri_glmfit-sim

running the left hemisphere everything works perfect all the way to the
visualization in freeview  - then I just chift the command to rh instead -
running exactly the same command and when I am opening my results in
freeview everything gets yellow and I get the following error message: Did
not find any volume geometry information in the surface.

could you please inform me how this can happen?

THANKS
ERIC
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Re: [Freesurfer] mri_volsynth

[John Anderson]

Thank you for the quick response.

I wanted to create volume has the following dimentions in mm ( 6.25 X 6.25 X 7.5) in a position where the coordinates (in mm) are X=-15 Y= -4 Z= 13

is this command line correct:

mri_volsynth --dim 6.25 6.25 7.5 1 --c_ras -15 -4.3 13 --o voxel.nii

 

Bests,
John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Monday, August 31, 2015 at 11:30 AM
From: "Douglas Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_volsynth


some of this is answered if you run the command with --help
 
On 8/31/15 3:33 PM, John Anderson wrote:




Hi Freesurfers,

I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10)

I used the following command line to create the volume but I don't know how to choose it is position in scanner space.

 

mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii

 

 

I have the following question because i didn't find enough information in FS wiki about this command:

 

1. If the flag  --dim (nc nr ns nf)  is reffering to the volume dimentions. What is the fourth number  (nf ) is standing for  ?



Number of frames (the time dimension)




2. what is the meaning of voxel resolution ( the flag --res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ?



How big the voxel is in mm




3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels?



The "center" of the volume in mm, where "center" is defined as (Nvoxels-1)/2 where Nvoxels is the number rows, cols, or slices.




 

 

Thanks in advance ,

John


 

 
 

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Re: [Freesurfer] Error running recon-all -localGI

[Philip Deming]

Marie,


Yes, I'm getting this error for all subjects. Unfortunately, I'm unable to send 
you any of our subjects to look at.

You've helped in identifying that our ROIs are not getting saved, though. Do 
you have a guess as to why that might be? Otherwise, we'll have to figure out 
why they're not saving on our own.

Thanks for your help!


Phil



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Marie Schaer 

Sent: Wednesday, August 26, 2015 2:19 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Error running recon-all -localGI


Hi Philip,

It seems that for a strange reason your ROIs are not getting saved. I never saw 
this one. I suppose that you are getting this error for all subjects? Do you 
have a way to transfer me one of your subject so that I can have a closer look?

Thanks,

Marie


On Aug 26, 2015, at 11:37 AM, Philip Deming 
mailto:pdem...@wisc.edu>>
 wrote:

Thanks for the quick response, Marie. Here's the full recon-all.log for this 
subject:

FREESURFER_HOME /Volumes/apps/rhel6/freesurfer/freesurfer-latest
Actual FREESURFER_HOME /Volumes/apps/rhel6/freesurfer/freesurfer_5.10_x86_64
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux MRI-APP1.heri.psychiatry.wisc.edu 
2.6.32-431.11.2.el6.x86_64 #1 SMP Mon Mar 3 13:32:45 EST 2014 x86_64 x86_64 
x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize10240 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024
memorylocked 64 kbytes
maxproc  1024

 total   used   free sharedbuffers cached
Mem:  99032816   98557552 475264600 106540   92215824
-/+ buffers/cache:6235188   92797628
Swap:  419429611543883039908


program versions used
$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2015/07/23-15:03:11-GMT  BuildTimeStamp: May 22 2011 
08:23:31  CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $  
User: pdeming  Machine: 
MRI-APP1.heri.psychiatry.wisc.edu  Platform: 
Linux  PlatformVersion: 2.6.32-431.11.2.el6.x86_64  CompilerName: GCC  
CompilerVersion: 30400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl  ProgramArguments: --all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2015/07/23-15:03:11-GMT  BuildTimeStamp: May 22 
2011 08:23:31  CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve 
Exp $  User: pdeming  Machine: 
MRI-APP1.heri.psychiatry.wisc.edu  Platform: 
Linux  PlatformVersion: 2.6.32-431.11.2.el6.x86_64  CompilerName: GCC  
CompilerVersion: 30400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva 
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable5 $  TimeStamp: 2015/07/23-15:03:11-GMT  BuildTimeStamp: May 22 
2011 08:23:31  CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ 
 User: pdeming  Machine: 
MRI-APP1.heri.psychiatry.wisc.edu  Platform: 
Linux  PlatformVersion: 2.6.32-431.11.2.el6.x86_64  CompilerName: GCC  
CompilerVersion: 30400
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2015/07/23-15:03:11-GMT  BuildTimeStamp: May 22 2011 
08:23:31  CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $  
User: pdeming  Machine: 
MRI-APP1.heri.psychiatry.wisc.edu  Platform: 
Linux  PlatformVersion: 2.6.32-431.11.2.el6.x86_64  CompilerName: GCC  
CompilerVersion: 30400
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2015/07/23-15:03:11-GMT  BuildTimeStamp: May 22 2011 
08:23:31  CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $  
User: pdeming  Machine: 
MRI-APP1.heri.psychiatry.wisc.edu  Platform: 
Linux  PlatformVersion: 2.6.32-431.11.2.el6.x86_64  CompilerName: GCC  
CompilerVersion: 30400
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable5 $  TimeStamp: 2015/07/23-15:03:11-GMT  BuildTimeStamp: May 22 2011 
08:23:31  CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $  User: 
pdeming  Machine: 
MRI-APP1.heri.psychiatry.wisc.edu  Platform: 
Linux  PlatformVersion: 2.6.32-431.11.2.el6.x86_64  CompilerName: GCC  
CompilerVersion: 30400
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name: 
st

Re: [Freesurfer] converting ROI .label to MNI space for SPM8

[Douglas Greve]

I'm not sure what is going wrong, but I would use mri_label2vol directly 
instead of using the combination of mri_convert and tkregister. Instead 
of passing it a registration file, use --regheader brainmask.mgz


On 8/31/15 5:26 PM, Emma Thompson wrote:

Forgive me, but I'm re-posting my query below hoping someone will respond this 
time around.
Thanks in advance!

Dear Freesurfers,
I'm hoping you can help me resolve an issue I'm having with regard to
converting my ROI labels from freesurfer space (Taliarach) to MNI space in
prep for using these as seeds for a functional connectivity analysis.
I created several ROIs labels (.label files), which I hand drew onto my
study average brain (inflated surface) in qdec. I then used the following
script to produce labels specific for each subject's brain in my analysis

thePath='/pathtomydirectory/FS/subjects'

subjects=(
'PAT01'\
'PAT02'\
)

nsubjects=${#subjects[*]}
lastsubj=`expr $nsubjects - 1`

for m in `seq 0 ${lastsubj}`
do

mri_label2label \
  --srcsubject MyAverageBrain \
  --srclabel ${thePath}/MyAverageBrain/label/lh.dACC.label \
  --trgsubject ${subjects[m]} \
  --trglabel ${thePath}/${subjects[m]}/label/lh.dACCi.label\
  --hemi lh \
  --regmethod surface

done


I then converted the .label files from .mgz format to nii using the
following:

mri_convert --in_type mgz --out_type nii --out_orientation RAS
/pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz
/pathtomydirectory/FS/subjects/PAT01/mri/brainmask.nii.gz

Next, I used the following scripts to get the registration matrix and to
try and convert the label to a ROI that I can use in SPM:

tkregister2 --mov /pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz
--noedit --s PAT01 --regheader --reg
/pathtomydirectory/FS/subjects/PAT01/mri/register.dat

mri_label2vol --label
/pathtomydirectory/FS/subjects/PAT01/label/lh.dACC.label --temp
/pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz --subject PAT01
--hemi lh --o /pathtomydirectory/FS/subjects/PAT01_lhdACC.nii.gz --proj
frac 0 1 .1 --fillthresh .3 --reg
/pathtomydirectory/FS/subjects/PAT01/mri/register.dat

the resulting ROI (PAT01_lhdACC.nii.gz) is close to the original surface
ROI, but not exactly right, for example the ROI is a little more ventral
than it should be when I overlay it onto mni152T1 average brain template.

I'm not sure how to proceed or where I might have gone wrong, any ideas on
how to go about this?

Thanks!!!

p.s. I love Freesurfer!!!


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Re: [Freesurfer] mri_volsynth

[Douglas Greve]

some of this is answered if you run the command with --help

On 8/31/15 3:33 PM, John Anderson wrote:

Hi Freesurfers,
I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner 
space ( x=48, y= 48, z=10)
I used the following command line to create the volume but I don't 
know how to choose it is position in scanner space.

mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii
I have the following question because i didn't find enough information 
in FS wiki about this command:
1. If the flag  --dim (nc nr ns nf)  is reffering to the volume 
dimentions. What is the fourth number  (nf ) is standing for  ?

Number of frames (the time dimension)
2. what is the meaning of voxel resolution ( the flag --res (dc dr ds 
df) ) and what is the meaning of the numbers dc dr ds df ?

How big the voxel is in mm
3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. 
If yes is it in mm or in voxels?
The "center" of the volume in mm, where "center" is defined as 
(Nvoxels-1)/2 where Nvoxels is the number rows, cols, or slices.

Thanks in advance ,
John


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[Freesurfer] converting ROI .label to MNI space for SPM8

[Emma Thompson]

Forgive me, but I'm re-posting my query below hoping someone will
respond this time around.

Thanks in advance!



Dear Freesurfers,
I'm hoping you can help me resolve an issue I'm having with regard to
converting my ROI labels from freesurfer space (Taliarach) to MNI space in
prep for using these as seeds for a functional connectivity analysis.

I created several ROIs labels (.label files), which I hand drew onto my
study average brain (inflated surface) in qdec. I then used the following
script to produce labels specific for each subject's brain in my analysis

thePath='/pathtomydirectory/FS/subjects'

subjects=(
'PAT01'\
'PAT02'\
)

nsubjects=${#subjects[*]}
lastsubj=`expr $nsubjects - 1`

for m in `seq 0 ${lastsubj}`
do

mri_label2label \
 --srcsubject MyAverageBrain \
 --srclabel ${thePath}/MyAverageBrain/label/lh.dACC.label \
 --trgsubject ${subjects[m]} \
 --trglabel ${thePath}/${subjects[m]}/label/lh.dACCi.label\
 --hemi lh \
 --regmethod surface

done


I then converted the .label files from .mgz format to nii using the
following:

mri_convert --in_type mgz --out_type nii --out_orientation RAS
/pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz
/pathtomydirectory/FS/subjects/PAT01/mri/brainmask.nii.gz

Next, I used the following scripts to get the registration matrix and to
try and convert the label to a ROI that I can use in SPM:

tkregister2 --mov /pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz
--noedit --s PAT01 --regheader --reg
/pathtomydirectory/FS/subjects/PAT01/mri/register.dat

mri_label2vol --label
/pathtomydirectory/FS/subjects/PAT01/label/lh.dACC.label --temp
/pathtomydirectory/FS/subjects/PAT01/mri/brainmask.mgz --subject PAT01
--hemi lh --o /pathtomydirectory/FS/subjects/PAT01_lhdACC.nii.gz --proj
frac 0 1 .1 --fillthresh .3 --reg
/pathtomydirectory/FS/subjects/PAT01/mri/register.dat

the resulting ROI (PAT01_lhdACC.nii.gz) is close to the original surface
ROI, but not exactly right, for example the ROI is a little more ventral
than it should be when I overlay it onto mni152T1 average brain template.

I'm not sure how to proceed or where I might have gone wrong, any ideas on
how to go about this?

Thanks!!!

p.s. I love Freesurfer!!!
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Re: [Freesurfer] Thalamic sub-nuclei

[Bruce Fischl]

Hi Cristina

sorry, while thalamic nuclei are of interest to us we haven't developed 
anything for labeling them yet.


cheers
Bruce


On Mon, 31 Aug 2015, Lois Gomez, Cristina wrote:



Dear all,

 

I am interested in analyzing thalamic sub-nuclei separately, instead of the
whole thalamus. I've noticed that in the FreeSurferColorLUT.txt file there
are some labels that correspond to thalamic sub-nuclei (Labels #No.
8001-8014). However, I do not find those labels in my aparc+aseg file, where
the highest number is 2035.

 

Is the thalamic sub-nuclei segmentation implemented in the current version
of FreeSurfer? If so, where can I find those labels?

 

Many thanks in advance!

 

Best regards,

Cristina


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[Freesurfer] Thalamic sub-nuclei

[Lois Gomez, Cristina]

Dear all,



I am interested in analyzing thalamic sub-nuclei separately, instead of the 
whole thalamus. I've noticed that in the FreeSurferColorLUT.txt file there are 
some labels that correspond to thalamic sub-nuclei (Labels #No. 8001-8014). 
However, I do not find those labels in my aparc+aseg file, where the highest 
number is 2035.



Is the thalamic sub-nuclei segmentation implemented in the current version of 
FreeSurfer? If so, where can I find those labels?



Many thanks in advance!



Best regards,

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

Re: [Freesurfer] MRITOTAL

[Bruce Fischl]

Hi Ali

it's not that I know that the quality is fine. It might be (or not), but 
this seems to be a perl error that doesn't have to do with quality

Bruce
On Mon, 
31 Aug 2015, Ali Radaideh wrote:



Dear Bruce and ​Jürgen,

Now I see something important which may help solving the problem.

I have 31 PCs in my lab and all of them are installed with UBUNTU 14.04. 30
PCs were able to process all 47 subjects successfully. But failed to process
the remaining 8 subjects. Fortunately, one PC is installed with UBUNTU
13.01. I managed to installed the tcsh and csh after update and then run two
of the failed subjects so far successfully. I concluded it is the
installation version of UBUNTU. So 13.01 works fine but not 14.04.

I tried to re-install 13.01 on another PC, and I did that successfully.
However, but when I come to install the tcsh, after update it fails and it
says it is unable to locate the package tcsh (the reason is that 13.01 has
not longer packages to download.

As a summary,

one PC with 13.01 UBUNTU is running OK (but with the tcsh installed)
another OC with 13.01 is not running because I was not able to install tcsh
after update

I am now think of copying the tcsh from one pc to the 13.01 PC to make it
running but still trying.

I think as Bruce said, it is something wrong with the installation as the
quality is fine.

I hope I was able to clarify the problem and hope to receive any helpful
answer.

Many thanks in advance

Ali



On Sun, Aug 30, 2015 at 4:05 PM, Bruce Fischl 
wrote:
  Hi
​​Jürgen and Ali

I don't think it has anything to do with the quality of the data, but
we are also happy to take a look if you upload one subject. This seems
more like an installation issue, and I would think it would happen on
every subject. Did someone upgrade perl at somepoint? Or just some
paths?


cheers
Bruce

On Sun, 30 Aug 2015, Jürgen Hänggi wrote:

  Dear Ali

  instead of downgrading perl you can use the perlbrew tool
  that allow to
  install several perls in parallel and switch between perl
  versions.
  if you are able to install perl 5.12 (perlbrew install
  5.12, you can see the
  available perl versions with perlbrew available) and then
  use 
  perlbrew use 5.12 before running recon-all in the
  terminal.

  Does it work?

  Cheers
  Jürgen


---

  Jürgen Hänggi, Ph.D.

  Division Neuropsychology

  Institute of Psychology

  University of Zurich

  Binzmuehlestrasse 14, PO Box 25

  8050 Zurich, Switzerland

  0041 44 635 73 97 (phone office)

  0041 76 445 86 84 (phone mobile)

  0041 44 635 74 09 (fax office)

  BIN 4.D.04 (office room number)

  j.haenggi[at]psychologie.uzh.ch (email)

  http://www.psychologie.uzh.ch/neuropsy/ (website) 

  http://www.juergenhaenggi.ch (private website)


  This e-mail (and any attachment/s) contains confidential 

  and/or privileged information. If you are not the intended

  recipient (or have received this e-mail in error) please
  notify 

  the sender immediately and destroy this e-mail. Any

  unauthorised copying, disclosure or distribution of the 

  material in this e-mail is strictly forbidden.

---




  Von:  on behalf of
  Ali Radaideh
  
  Antworten an: Freesurfer Mailinglist
  
  Datum: Samstag, 29. August 2015 15:56
  An: Freesurfer Mailinglist
  
  Betreff: Re: [Freesurfer] MRITOTAL

        Dear Jürgen,

  Thanks for your reply. Could you please guide me on how to
  downgrade
  it? I need to try everything with these 8 subjects to
  finish the whole
  cohort of subjects.

  Your help is so appreciated.

  Thanks,
  Ali

  On Sat, Aug 29, 2015 at 4:16 PM, Jürgen Hänggi
   wrote:
        Dear Ali


  if Talairach alignment is not of good quality, then
  mritotal is
  used and the shellwords.pl problem is related to the fact
  that
  you have a newer version of perl that no longer contain
  shellwords.pl.

  you can downgrade perl to 5.12 or so, which however, is
  not a
  good idea.


  I have no other solution


  Cheers

  Jürgen



  Von:  on behalf of
  Ali
  Radaideh 
  Antworten an: Freesurfer Mailinglist
  
  Datum: Samstag, 29. August 2015 13:41
  An: Freesurfer Mailinglist
  
  Betreff: [Freesurfer] MRITOTAL

        Dear FreeSurfer experts,

  I have sent email 10 days ago asking for a help with
  processing 8 out of 55 subjects who failed to pass the
  Talairach phase and gave me the following error:

  tmpdir is transforms/tmp.talairach.5272
/media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/ANALYZE_FILES/

  MS_patients/freesurfer_test/Images_test/S

Re: [Freesurfer] MRITOTAL

[Ali Radaideh]

Dear Bruce and ​Jürgen,

Now I see something important which may help solving the problem.

I have 31 PCs in my lab and all of them are installed with UBUNTU 14.04. 30
PCs were able to process all 47 subjects successfully. But failed to
process the remaining 8 subjects. Fortunately, one PC is installed with
UBUNTU 13.01. I managed to installed the tcsh and csh after update and then
run two of the failed subjects so far successfully. I concluded it is the
installation version of UBUNTU. So 13.01 works fine but not 14.04.

I tried to re-install 13.01 on another PC, and I did that successfully.
However, but when I come to install the tcsh, after update it fails and it
says it is unable to locate the package tcsh (the reason is that 13.01 has
not longer packages to download.

As a summary,

one PC with 13.01 UBUNTU is running OK (but with the tcsh installed)
another OC with 13.01 is not running because I was not able to install tcsh
after update

I am now think of copying the tcsh from one pc to the 13.01 PC to make it
running but still trying.

I think as Bruce said, it is something wrong with the installation as the
quality is fine.

I hope I was able to clarify the problem and hope to receive any helpful
answer.

Many thanks in advance

Ali



On Sun, Aug 30, 2015 at 4:05 PM, Bruce Fischl 
wrote:

> Hi
> ​​
> Jürgen and Ali
>
> I don't think it has anything to do with the quality of the data, but we
> are also happy to take a look if you upload one subject. This seems more
> like an installation issue, and I would think it would happen on every
> subject. Did someone upgrade perl at somepoint? Or just some paths?
>
>
> cheers
> Bruce
>
> On Sun, 30 Aug 2015, Jürgen Hänggi wrote:
>
> Dear Ali
>>
>> instead of downgrading perl you can use the perlbrew tool that allow to
>> install several perls in parallel and switch between perl versions.
>> if you are able to install perl 5.12 (perlbrew install 5.12, you can see
>> the
>> available perl versions with perlbrew available) and then use
>> perlbrew use 5.12 before running recon-all in the terminal.
>>
>> Does it work?
>>
>> Cheers
>> Jürgen
>>
>>
>>
>> ---
>> Jürgen Hänggi, Ph.D.
>>
>> Division Neuropsychology
>>
>> Institute of Psychology
>>
>> University of Zurich
>>
>> Binzmuehlestrasse 14, PO Box 25
>>
>> 8050 Zurich, Switzerland
>>
>> 0041 44 635 73 97 (phone office)
>>
>> 0041 76 445 86 84 (phone mobile)
>>
>> 0041 44 635 74 09 (fax office)
>>
>> BIN 4.D.04 (office room number)
>>
>> j.haenggi[at]psychologie.uzh.ch (email)
>>
>> http://www.psychologie.uzh.ch/neuropsy/ (website)
>>
>> http://www.juergenhaenggi.ch (private website)
>>
>>
>> This e-mail (and any attachment/s) contains confidential
>>
>> and/or privileged information. If you are not the intended
>>
>> recipient (or have received this e-mail in error) please notify
>>
>> the sender immediately and destroy this e-mail. Any
>>
>> unauthorised copying, disclosure or distribution of the
>>
>> material in this e-mail is strictly forbidden.
>>
>>
>> ---
>>
>>
>>
>> Von:  on behalf of Ali Radaideh
>> 
>> Antworten an: Freesurfer Mailinglist 
>> Datum: Samstag, 29. August 2015 15:56
>> An: Freesurfer Mailinglist 
>> Betreff: Re: [Freesurfer] MRITOTAL
>>
>>   Dear Jürgen,
>>
>> Thanks for your reply. Could you please guide me on how to downgrade
>> it? I need to try everything with these 8 subjects to finish the whole
>> cohort of subjects.
>>
>> Your help is so appreciated.
>>
>> Thanks,
>> Ali
>>
>> On Sat, Aug 29, 2015 at 4:16 PM, Jürgen Hänggi
>>  wrote:
>>   Dear Ali
>>
>>
>> if Talairach alignment is not of good quality, then mritotal is
>> used and the shellwords.pl problem is related to the fact that
>> you have a newer version of perl that no longer contain
>> shellwords.pl.
>>
>> you can downgrade perl to 5.12 or so, which however, is not a
>> good idea.
>>
>>
>> I have no other solution
>>
>>
>> Cheers
>>
>> Jürgen
>>
>>
>>
>> Von:  on behalf of Ali
>> Radaideh 
>> Antworten an: Freesurfer Mailinglist
>> 
>> Datum: Samstag, 29. August 2015 13:41
>> An: Freesurfer Mailinglist 
>> Betreff: [Freesurfer] MRITOTAL
>>
>>   Dear FreeSurfer experts,
>>
>> I have sent email 10 days ago asking for a help with
>> processing 8 out of 55 subjects who failed to pass the
>> Talairach phase and gave me the following error:
>>
>> tmpdir is transforms/tmp.talairach.5272
>>
>> /media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/ANALYZE_FILES/
>> MS_patients/freesurfer_test/Images_test/Samer/mri
>> mri_convert orig_nu.mgz
>> transforms/tmp.talairach.5272/src.mnc
>> mri_convert orig_nu.mgz
>> transforms/tmp.talairach.5272/src.mnc
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter
>> Exp $
>> reading from orig_nu.mgz...
>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-1, 0, 0)
>> j_ras = (0, 0, -1)
>> k_ras = (0, 1, 0)
>> writing 

Re: [Freesurfer] license file not found

[Amlung, Michael]

Yep, that did the trick. I found an archived post where someone had a similar 
issue.

Thanks.




Michael Amlung, Ph.D.
Assistant Professor

Department of Psychiatry and Behavioural Neurosciences
DeGroote School of Medicine
McMaster University

Peter Boris Centre for Addictions Research
100 West 5th Street
Hamilton, Ontario L8N 3K7 
Canada

Telephone: (+1) 905-522-1155, ext. 39014
Email: amlu...@mcmaster.ca


-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Monday, August 31, 2015 9:58 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] license file not found

Hi Michael

does  /Applications/freesurfer/.license exist? Do you have permission to read 
it? Don't name the file license.txt - rename it to .license

cheers
Bruce

On Mon, 31 Aug 2015, Amlung, Michael wrote:

> Hi All,
> 
> This is my first time using the software. I have installed FreeSurfer 
> on a Mac machine and everything installed fine. I obtained a license 
> using the form and saved the four lines to a license.txt file in my 
> FREESURFER_HOME directory (/Applications/freesurfer on my computer). 
> Yet when I try to load tkmedit I get the following error:
> 
> 
> ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
> 
>   If you are outside the NMR-Martinos Center,
> 
>   go to http://surfer.nmr.mgh.harvard.edu to
> 
>   get a valid license file (it's free).
> 
>   If you are inside the NMR-Martinos Center,
> 
>   make sure to source the standard environment.
> 
> 
> 
> Thanks for any solutions.
> 
> 
> Michael Amlung
> 
> McMaster University
> 
> 
>

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Re: [Freesurfer] license file not found

[Bruce Fischl]

Hi Michael

does  /Applications/freesurfer/.license exist? Do you have permission to 
read it? Don't name the file license.txt - rename it to .license


cheers
Bruce

On Mon, 31 Aug 2015, Amlung, Michael wrote:


Hi All,

This is my first time using the software. I have installed FreeSurfer on a
Mac machine and everything installed fine. I obtained a license using the
form and saved the four lines to a license.txt file in my FREESURFER_HOME
directory (/Applications/freesurfer on my computer). Yet when I try to load
tkmedit I get the following error: 


ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.

  If you are outside the NMR-Martinos Center,

  go to http://surfer.nmr.mgh.harvard.edu to 

  get a valid license file (it's free).

  If you are inside the NMR-Martinos Center,

  make sure to source the standard environment.



Thanks for any solutions.


Michael Amlung

McMaster University


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Re: [Freesurfer] niiRead error

[Bruce Fischl]

Hi Katarina

it looks like that file might be corrupted. Where did you get it from? 
Can you view it in freeview? Maybe that partition was full when you copied 
it there or something similar?


cheers
Bruce

On Mon, 31 Aug 2015, Katarina Trojacanec wrote:



Dear experts,


After running recon-all I got this output: 

---


Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /home/local/katarina.trojachanec/freesurfer/subjects

Actual FREESURFER_HOME /home/local/katarina.trojachanec/freesurfer

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64
x86_64 x86_64 GNU/Linux

/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD


 
mri_convert/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_
5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S2
9339_I89671.nii/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD/mri/orig/001.mgz


mri_convert/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_
5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S2
9339_I89671.nii/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD/mri/orig/001.mgz

INFO: using NIfTI-1 qform

niiRead(): error reading 
from/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_
5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S2
9339_I89671.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading 
from/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_
5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S2
9339_I89671.nii...

ERROR: Read 70, expected 256

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64
x86_64 x86_64 GNU/Linux


recon-all -s ADNI_137_S_0796_S29339_I89671_1.5T_AD exited with ERRORS at Mon
Aug 31 13:10:05 CEST 2015


For more details, see the log 
file/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /home/local/katarina.trojachanec/freesurfer/subjects

Actual FREESURFER_HOME /home/local/katarina.trojachanec/freesurfer

-rw-rw-r-- 1 katarina.trojachanec margi 17946 Aug 31 
13:10/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD/scripts/recon-all.log

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64
x86_64 x86_64 GNU/Linux

#

#@# MotionCor Mon Aug 31 13:10:10 CEST 2015

ERROR: no run data found 
in/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD/mri. Make sure to

have a volume called 001.mgz in 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S2933
9_I89671_1.5T_AD/mri/orig.

If you have a second run of data call it 002.mgz, etc.

See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64
x86_64 x86_64 GNU/Linux


recon-all -s ADNI_137_S_0796_S29339_I89671_1.5T_AD exited with ERRORS at Mon
Aug 31 13:10:10 CEST 2015


For more details, see the log 
file/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339
_I89671_1.5T_AD/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

---
---
-

This is happening only for one file (from multiple that I have tried with). 
Would you please be able to answer me what might be the problem?

Thank you in advance.
Katarina


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia  

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[Freesurfer] mri_volsynth

[John Anderson]

Hi Freesurfers,

I want to create volume 6.25 X 6.25 X 7.5 in this position in scanner space ( x=48, y= 48, z=10)

I used the following command line to create the volume but I don't know how to choose it is position in scanner space.

 

mri_volsynth --dim 6.25 6.25 7.5 0 --o voxel.nii

 

 

I have the following question because i didn't find enough information in FS wiki about this command:

 

1. If the flag  --dim (nc nr ns nf)  is reffering to the volume dimentions. What is the fourth number  (nf ) is standing for  ?

2. what is the meaning of voxel resolution ( the flag --res (dc dr ds df) ) and what is the meaning of the numbers dc dr ds df ?

3. Is the flag c_ras ( c_r c_a c_s) reffering to the volume position. If yes is it in mm or in voxels?

 

 

Thanks in advance ,

John

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[Freesurfer] license file not found

[Amlung, Michael]

Hi All, 


This is my first time using the software. I have installed FreeSurfer on a Mac machine and everything installed fine. I obtained a license using the form and saved the four lines to a license.txt file in my FREESURFER_HOME
 directory (/Applications/freesurfer on my computer). Yet when I try to load tkmedit I get the following error: 





ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.




Thanks for any solutions.


Michael Amlung
McMaster University






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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] niiRead error

[Katarina Trojacanec]

Dear experts,


After running recon-all I got this output:

---

Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /home/local/katarina.trojachanec/freesurfer/subjects

Actual FREESURFER_HOME /home/local/katarina.trojachanec/freesurfer

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64 x86_64 
x86_64 GNU/Linux

/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD


 mri_convert 
/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S29339_I89671.nii
 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/mri/orig/001.mgz


mri_convert 
/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S29339_I89671.nii
 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/mri/orig/001.mgz

INFO: using NIfTI-1 qform

niiRead(): error reading from 
/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S29339_I89671.nii

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from 
/home/local/katarina.trojachanec/freesurfer/subjects/nii/ADNI1Complete2Yr1_5TAD/ADNI_137_S_0796_MR_MPR-R__GradWarp__N3__Scaled_Br_20080206164645389_S29339_I89671.nii...

ERROR: Read 70, expected 256

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64 x86_64 
x86_64 GNU/Linux


recon-all -s ADNI_137_S_0796_S29339_I89671_1.5T_AD exited with ERRORS at Mon 
Aug 31 13:10:05 CEST 2015


For more details, see the log file 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /home/local/katarina.trojachanec/freesurfer/subjects

Actual FREESURFER_HOME /home/local/katarina.trojachanec/freesurfer

-rw-rw-r-- 1 katarina.trojachanec margi 17946 Aug 31 13:10 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/scripts/recon-all.log

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64 x86_64 
x86_64 GNU/Linux

#

#@# MotionCor Mon Aug 31 13:10:10 CEST 2015

ERROR: no run data found in 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/mri.
 Make sure to

have a volume called 001.mgz in  
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/mri/orig.

If you have a second run of data call it 002.mgz, etc.

See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion

Linux cn15 2.6.18-400.1.1.el5 #1 SMP Wed Dec 17 14:22:42 CST 2014 x86_64 x86_64 
x86_64 GNU/Linux


recon-all -s ADNI_137_S_0796_S29339_I89671_1.5T_AD exited with ERRORS at Mon 
Aug 31 13:10:10 CEST 2015


For more details, see the log file 
/home/local/katarina.trojachanec/freesurfer/subjects/ADNI_137_S_0796_S29339_I89671_1.5T_AD/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

---

This is happening only for one file (from multiple that I have tried with).
Would you please be able to answer me what might be the problem?

Thank you in advance.
Katarina


Katarina Trojacanec, M.Sc.
Teaching and research assistant

Faculty of Computer Science and Engineering
Ss. Cyril and Methodius University - Skopje, Republic of Macedonia

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