[Freesurfer] recon-all : command not found

2020-03-21 Thread Koustav Chatterjee 
External Email - Use Caution

Dear Sir/Madam,

Hope this mail finds you well, considering the present pandemic scenario
across globe.

I have installed FreeSurfer in my PC successfully and I have been following
tutorials and freesurfer wiki to learn the basics of it.
I have an image with .nii extension saved in usr/local/freesurfer/subjects
directory in ubuntu.
I wanted to use recon-all command for preprocessing the image.nii.

root@ubuntu:/usr/local/freesurfer/subjects# recon-all -s kctest01 -i (the
input file.nii)
the result shows, recon-all: command not found

It would be kind enough if you could please help me out.
 I am also sharing the screen shot of the terminal window I used for this
programming, if it would e of any help.

Thank you,
Best regards,
Koustav
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Re: [Freesurfer] recon-all : command not found

2020-03-24 Thread Koustav Chatterjee 
External Email - Use Caution

Thank you very much.

On Tue 24 Mar, 2020, 11:14 PM Hoopes, Andrew, 
wrote:

> Hi Koustav,
>
>
>
> My guess is you have not correctly ‘sourced’ freesurfer (made it available
> in your shell environment). Following the ‘Setup & Configuration’ steps in
> the FS download page, you should always run the following before using
> freesurfer:
>
>
>
> export FREESURFER_HOME=/usr/local/freesurfer
>
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
>
>
> Hope that helps,
>
> Andrew
>
>
>
> *From: * on behalf of Koustav
> Chatterjee 
> *Reply-To: *FS Help 
> *Date: *Saturday, March 21, 2020 at 9:35 AM
> *To: *FS Help 
> *Subject: *[Freesurfer] recon-all : command not found
>
>
>
> *External Email - Use Caution*
>
> Dear Sir/Madam,
>
>
>
> Hope this mail finds you well, considering the present pandemic scenario
> across globe.
>
>
>
> I have installed FreeSurfer in my PC successfully and I have been
> following tutorials and freesurfer wiki to learn the basics of it.
>
> I have an image with .nii extension saved in usr/local/freesurfer/subjects
> directory in ubuntu.
>
> I wanted to use recon-all command for preprocessing the image.nii.
>
>
>
> root@ubuntu:/usr/local/freesurfer/subjects# recon-all -s kctest01 -i (the
> input file.nii)
>
> the result shows, recon-all: command not found
>
>
>
> It would be kind enough if you could please help me out.
>
>  I am also sharing the screen shot of the terminal window I used for this
> programming, if it would e of any help.
>
>
>
> Thank you,
>
> Best regards,
>
> Koustav
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] libpng12.so.0

2020-03-30 Thread Koustav Chatterjee 
External Email - Use Caution

You should download lower versions. Ubuntu 16.04.1 LTS. Then only it will
work.

On Mon, Mar 30, 2020 at 8:01 AM Gonzalo Rojas Costa <
gonzalo.rojas.co...@gmail.com> wrote:

> External Email - Use Caution
>
> Hi:
>
>   I tried to use the tkregisterfv command in Ubuntu 18.04.4 LTS, but I got
> the following error:
> "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot
> open shared object file: No such file or directory". How can I solve it ?
>
>   Sincerely,
>
>
> Gonzalo Rojas Costa
>
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[Freesurfer] Queries on the Function of Freesurfer

2020-04-11 Thread Koustav Chatterjee 
External Email - Use Caution

Dear all,

I am a beginner in FreeSurfer world.
I have 4 questions. It would be kind enough if you could clarify my
confusions.

   - I have came across that 'Freesurfer can reconstruct 2D cortical
   surface from 3D T1 MRI brain image'. However, I know that T1 2D brain
   images are being fed to freesurfer for 'Recon-all...-all' to function all
   its pre-processing steps.

Whether "...reconstruct 2D cortical surface from 3D T1 MRI image"
this *statement
is true*? Is there any step where FreeSurfer make a 3D image from 2D T1
images and again reconstruct them into 2D
cortical surface through preprocessing steps?


   - Can FreeSurfer only recognize 'T1 weighted images' for processing? Why
   only T1, why not T2 or Flair etc?
   - Can we estimate the volume of substantia nigra, pedunculopontine
   nucleus and locus cereleus using FreeSurfer? If so any specific version
   of Freesurfer is required?
   - If I have Freesurfer installed in my PC; I also have T1 and diffusion
   weighted image sequence of a subject. Can I use 'Tracula' to analyse tracts
   of that subject's brain directly? How could I analyse tracts in Freesurfer?

Thank you for your time and effort.
Regards,
Koustav
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Re: [Freesurfer] Queries on the Function of Freesurfer

2020-04-12 Thread Koustav Chatterjee 
External Email - Use Caution

Thank you very much Sir for your effort and time to answer my questions.

I am afraid I have not got the answer for the following:


   - If I have Freesurfer installed in my PC; I also have T1 and diffusion
   weighted image sequence of a subject. Can I use 'Tracula' to analyse tracts
   of that subject's brain directly? How could I analyse tracts in
   Freesurfer?


It would also be kind enough *why T1 weighted or T2 can only be read by
FreeSurfer*? Is this because of the algorithm they use.

On Sun, Apr 12, 2020 at 10:46 PM Bruce Fischl 
wrote:

> Hi Koustav
>
> the current version of FS requires a T1-weighted input but could also use
> a T2 to improve accuracy and automaticity. Future versions will relax
> this constraint.
>
> As for 2D/3D, you have to distinguish the acquisition type (which almost
> always should be a 3D sequence like an MP-RAGE or a 3D FLASH/SGPR) from
> the model. When we say "2d cortical surface" we are talking about
> extracting that model ("reconstructing" it) from the 3D data
>
> As for the structures you mention, we have dev versions of labelings for
> all of them I believe, but I defer to Doug on the details
>
> cheers
> Bruce
>
>
> On Sun, 12 Apr 2020, Koustav Chatterjee wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear all,
> > I am a beginner in FreeSurfer world.
> > I have 4 questions. It would be kind enough if you could clarify my
> > confusions.
> >  *  I have came across that 'Freesurfer can reconstruct 2D cortical
> surface
> > from 3D T1 MRI brain image'. However, I know that T1 2D brain images
> are
> > being fed to freesurfer for 'Recon-all...-all' to function all its
> > pre-processing steps.
> > Whether "...reconstruct 2D cortical surface from 3D T1 MRI image"
> this
> > statement is true? Is there any step where FreeSurfer make a 3D image
> from
> > 2D T1 images and again reconstruct them into 2D
> > cortical surface through preprocessing steps?
> >
> >  *  Can FreeSurfer only recognize 'T1 weighted images' for processing?
> Why
> > only T1, why not T2 or Flair etc?
> >  *  Can we estimate the volume of substantia nigra, pedunculopontine
> nucleus
> > and locus cereleus using FreeSurfer? If so any specific version
> > of Freesurfer is required?
> >  *  If I have Freesurfer installed in my PC; I also have T1 and diffusion
> > weighted image sequence of a subject. Can I use 'Tracula' to analyse
> > tracts of that subject's brain directly? How could I analyse tracts
> in
> > Freesurfer?
> > Thank you for your time and effort.
> > Regards,
> > Koustav
> >
> >
> >___
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Re: [Freesurfer] Queries on the Function of Freesurfer

2020-04-13 Thread Koustav Chatterjee 
External Email - Use Caution

Thank you so much, Sir

On Mon, Apr 13, 2020 at 1:45 AM Bruce Fischl 
wrote:

> yes, if you run your T1 through FreeSurfer's recon-all you should be able
> to use tracula afterwards to reconstruct tract models from your dwi data.
>
> We use T1 because it is by far the most common anatomical sequence and
> historically has had better cnr/unit-time
>
> cheers
> Bruce
>
> On
> Mon, 13 Apr 2020, Koustav Chatterjee wrote:
>
> >
> > External Email - Use Caution
> >
> > Thank you very much Sir for your effort and time to answer my questions.
> > I am afraid I have not got the answer for the following:
> >
> >  *  If I have Freesurfer installed in my PC; I also have T1 and diffusion
> > weighted image sequence of a subject. Can I use 'Tracula' to analyse
> > tracts of that subject's brain directly? How could I analyse tracts
> in
> > Freesurfer?
> >
> > It would also be kind enough why T1 weighted or T2 can only be read by
> > FreeSurfer? Is this because of the algorithm they use.
> >
> > On Sun, Apr 12, 2020 at 10:46 PM Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > wrote:
> >   Hi Koustav
> >
> >   the current version of FS requires a T1-weighted input but could
> >   also use
> >   a T2 to improve accuracy and automaticity. Future versions will
> >   relax
> >   this constraint.
> >
> >   As for 2D/3D, you have to distinguish the acquisition type
> >   (which almost
> >   always should be a 3D sequence like an MP-RAGE or a 3D
> >   FLASH/SGPR) from
> >   the model. When we say "2d cortical surface" we are talking
> >   about
> >   extracting that model ("reconstructing" it) from the 3D data
> >
> >   As for the structures you mention, we have dev versions of
> >   labelings for
> >   all of them I believe, but I defer to Doug on the details
> >
> >   cheers
> >   Bruce
> >
> >
> >   On Sun, 12 Apr 2020, Koustav Chatterjee wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Dear all,
> >   > I am a beginner in FreeSurfer world.
> >   > I have 4 questions. It would be kind enough if you could
> >   clarify my
> >   > confusions.
> >   >  *  I have came across that 'Freesurfer can reconstruct 2D
> >   cortical surface
> >   > from 3D T1 MRI brain image'. However, I know that T1 2D
> >   brain images are
> >   > being fed to freesurfer for 'Recon-all...-all' to function
> >   all its
> >   > pre-processing steps.
> >   > Whether "...reconstruct 2D cortical surface from 3D T1 MRI
> >   image" this
> >   > statement is true? Is there any step where FreeSurfer make a
> >   3D image from
> >   > 2D T1 images and again reconstruct them into 2D
> >   > cortical surface through preprocessing steps?
> >   >
> >   >  *  Can FreeSurfer only recognize 'T1 weighted images' for
> >   processing? Why
> >   > only T1, why not T2 or Flair etc?
> >   >  *  Can we estimate the volume of substantia nigra,
> >   pedunculopontine nucleus
> >   > and locus cereleus using FreeSurfer? If so any specific
> >   version
> >   > of Freesurfer is required?
> >   >  *  If I have Freesurfer installed in my PC; I also have T1
> >   and diffusion
> >   > weighted image sequence of a subject. Can I use 'Tracula'
> >   to analyse
> >   > tracts of that subject's brain directly? How could I
> >   analyse tracts in
> >   > Freesurfer?
> >   > Thank you for your time and effort.
> >   > Regards,
> >   > Koustav
> >   >
> >   >
> >   >___
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> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
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Re: [Freesurfer] Queries on the Function of Freesurfer

2020-04-13 Thread Koustav Chatterjee 
External Email - Use Caution

Dear Sir,
I am afraid I am yet to find *pedunculopontine nucleus *and *locus
coeruleus *in particular through FS dev versions of labelings volume.
Could you please help me out?
Best Regards,
KC


On Sun, Apr 12, 2020 at 10:46 PM Bruce Fischl 
wrote:

> Hi Koustav
>
> the current version of FS requires a T1-weighted input but could also use
> a T2 to improve accuracy and automaticity. Future versions will relax
> this constraint.
>
> As for 2D/3D, you have to distinguish the acquisition type (which almost
> always should be a 3D sequence like an MP-RAGE or a 3D FLASH/SGPR) from
> the model. When we say "2d cortical surface" we are talking about
> extracting that model ("reconstructing" it) from the 3D data
>
> As for the structures you mention, we have dev versions of labelings for
> all of them I believe, but I defer to Doug on the details
>
> cheers
> Bruce
>
>
> On Sun, 12 Apr 2020, Koustav Chatterjee wrote:
>
> >
> > External Email - Use Caution
> >
> > Dear all,
> > I am a beginner in FreeSurfer world.
> > I have 4 questions. It would be kind enough if you could clarify my
> > confusions.
> >  *  I have came across that 'Freesurfer can reconstruct 2D cortical
> surface
> > from 3D T1 MRI brain image'. However, I know that T1 2D brain images
> are
> > being fed to freesurfer for 'Recon-all...-all' to function all its
> > pre-processing steps.
> > Whether "...reconstruct 2D cortical surface from 3D T1 MRI image"
> this
> > statement is true? Is there any step where FreeSurfer make a 3D image
> from
> > 2D T1 images and again reconstruct them into 2D
> > cortical surface through preprocessing steps?
> >
> >  *  Can FreeSurfer only recognize 'T1 weighted images' for processing?
> Why
> > only T1, why not T2 or Flair etc?
> >  *  Can we estimate the volume of substantia nigra, pedunculopontine
> nucleus
> > and locus cereleus using FreeSurfer? If so any specific version
> > of Freesurfer is required?
> >  *  If I have Freesurfer installed in my PC; I also have T1 and diffusion
> > weighted image sequence of a subject. Can I use 'Tracula' to analyse
> > tracts of that subject's brain directly? How could I analyse tracts
> in
> > Freesurfer?
> > Thank you for your time and effort.
> > Regards,
> > Koustav
> >
> >
> >___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Re: [Freesurfer] Queries on the Function of Freesurfer

2020-04-13 Thread Koustav Chatterjee 
External Email - Use Caution

*Thank you Sir for your reply.*


On Tue, Apr 14, 2020 at 12:20 AM Douglas N. Greve 
wrote:

> We do not label those (yet!)
>
> On 4/13/2020 2:42 PM, Koustav Chatterjee wrote:
>
> External Email - Use Caution
> Dear Sir,
> I am afraid I am yet to find *pedunculopontine nucleus *and *locus
> coeruleus *in particular through FS dev versions of labelings volume.
> Could you please help me out?
> Best Regards,
> KC
>
>
> On Sun, Apr 12, 2020 at 10:46 PM Bruce Fischl 
> wrote:
>
>> Hi Koustav
>>
>> the current version of FS requires a T1-weighted input but could also use
>> a T2 to improve accuracy and automaticity. Future versions will relax
>> this constraint.
>>
>> As for 2D/3D, you have to distinguish the acquisition type (which almost
>> always should be a 3D sequence like an MP-RAGE or a 3D FLASH/SGPR) from
>> the model. When we say "2d cortical surface" we are talking about
>> extracting that model ("reconstructing" it) from the 3D data
>>
>> As for the structures you mention, we have dev versions of labelings for
>> all of them I believe, but I defer to Doug on the details
>>
>> cheers
>> Bruce
>>
>>
>> On Sun, 12 Apr 2020, Koustav Chatterjee wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > Dear all,
>> > I am a beginner in FreeSurfer world.
>> > I have 4 questions. It would be kind enough if you could clarify my
>> > confusions.
>> >  *  I have came across that 'Freesurfer can reconstruct 2D cortical
>> surface
>> > from 3D T1 MRI brain image'. However, I know that T1 2D brain
>> images are
>> > being fed to freesurfer for 'Recon-all...-all' to function all its
>> > pre-processing steps.
>> > Whether "...reconstruct 2D cortical surface from 3D T1 MRI image"
>> this
>> > statement is true? Is there any step where FreeSurfer make a 3D image
>> from
>> > 2D T1 images and again reconstruct them into 2D
>> > cortical surface through preprocessing steps?
>> >
>> >  *  Can FreeSurfer only recognize 'T1 weighted images' for processing?
>> Why
>> > only T1, why not T2 or Flair etc?
>> >  *  Can we estimate the volume of substantia nigra, pedunculopontine
>> nucleus
>> > and locus cereleus using FreeSurfer? If so any specific version
>> > of Freesurfer is required?
>> >  *  If I have Freesurfer installed in my PC; I also have T1 and
>> diffusion
>> > weighted image sequence of a subject. Can I use 'Tracula' to analyse
>> > tracts of that subject's brain directly? How could I analyse tracts
>> in
>> > Freesurfer?
>> > Thank you for your time and effort.
>> > Regards,
>> > Koustav
>> >
>> >
>> >___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
>
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[Freesurfer] Queries on Freeview and opening files of 'stat' and 'surf' folders

2020-10-01 Thread Koustav Chatterjee 
External Email - Use Caution

Dear Sir,

I have stuck with two basic steps while installing FreesUrfer in my new
system. May I request you to help me resolving the problem.

1. After successful completion of  'recon-all' command , a folder named as
'samplept1' has been formed under /usr/local/freesurfer/subjects.
Subjectpt1 consists of different folders including 'label', 'mri', 'stat',
'surf' etc. Now, I was trying to acquire data from 'surf' and 'stat'
folders. However, I am unable to open them. It seems to me a specific
application is required. Please advise.

2. Could you please explain what is the purpose of having 'freeview'. Is it
only only to check manually whether all the preprocessing steps such as
skull stripping has been done correctly by recon-all or not?

3. I am unable to surf images  one by one using  "P age up and down keys in
keyboard". How should I surf the images one by one?

Your help is appreciated.

Thank you very much.
KC
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Re: [Freesurfer] Queries on Freeview and opening files of 'stat' and 'surf' folders

2020-10-02 Thread Koustav Chatterjee 
External Email - Use Caution

Thanks Ruopeng.
Can you please answer *why I won't be able to open files in 'stat','surf'
folder.* It seems an application is required to open it. Can you tell
please?
Thank you,
KC

On Fri, Oct 2, 2020 at 8:25 PM Wang, Ruopeng  wrote:

> Hi KC,
>
> Freeview is a comprehensive volume and surface viewer and editor. You can
> load mri, surf and label files in it. Regarding your last question, if you
> meant going through slices, you can use up/down arrow keys. If you meant
> going through different volume images, you can use Alt+C key to cycle
> through them.
>
> Best,
> Ruopeng
>
> On Oct 2, 2020, at 2:44 AM, Koustav Chatterjee <
> chatterjeekous...@gmail.com> wrote:
>
> External Email - Use Caution
>
>
> Dear Sir,
>
> I have stuck with two basic steps while installing FreesUrfer in my new
> system. May I request you to help me resolving the problem.
>
> 1. After successful completion of  'recon-all' command , a folder named as
> 'samplept1' has been formed under /usr/local/freesurfer/subjects.
> Subjectpt1 consists of different folders including 'label', 'mri', 'stat',
> 'surf' etc. Now, I was trying to acquire data from 'surf' and 'stat'
> folders. However, I am unable to open them. It seems to me a specific
> application is required. Please advise.
>
> 2. Could you please explain what is the purpose of having 'freeview'. Is
> it only only to check manually whether all the preprocessing steps such as
> skull stripping has been done correctly by recon-all or not?
>
> 3. I am unable to surf images  one by one using  "P age up and down keys
> in keyboard". How should I surf the images one by one?
>
> Your help is appreciated.
>
> Thank you very much.
> KC
>
>
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>
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[Freesurfer] Error in QDEC

2020-10-16 Thread Koustav Chatterjee 
External Email - Use Caution

Hello,
I have found the following error while click on 'Generate Stats Data
Tables' to import the aseg and aparc data from the FreeSurfer-processed
group data, Could you please suggest how to overcome the issue?

[image: image.png]
Thank you,
KC
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[Freesurfer] a query on gray volume from parcellating data

2021-06-11 Thread Koustav Chatterjee 
External Email - Use Caution

Dear Sir/Madam,

Could you please tell what does it mean by 'Gray volume' and  'avg
thickness' of various structures while we are parcellating cortical
surfaces through FreeSurfer and getting 'aparcstats2table'.
Thank you for your help.

Regards,
KC


[image: image.png]
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[Freesurfer] Requesting to clarify doubts on data analysis

2021-11-21 Thread Koustav Chatterjee 
External Email - Use Caution

Dear FreeSurfer team,

I have a few questions to clarify the confusion regarding data analysis.

   1. For each subject, is it recommended to normalize the raw volumetric
   data by total intracranial volume? If so, is it true only for volumes of
   subcortical structures or, both subcortical and cortical structures?
   2.  In the same way, do I suppose to normalize


   - Different cortical thickness with mean cortical thickness
   - Cortical surface area with total surface area
   - Different cortical curvature with mean cortical curvature

Thank you for your time and help.

Regards,
KC
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[Freesurfer] Queries on DK Atlas and No of regions

2021-11-30 Thread Koustav Chatterjee 
External Email - Use Caution

Dear all,

I had an understanding that Desikan-Killiiany atlas can parcellate total of
68 regions from both hemispheres. However, after running recon-all -all,  I
can see total of 62 regions. I am afraid if you could help me understanding
these discrepancies..

Thank you for your help.

Regards,
KC
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Re: [Freesurfer] Queries on DK Atlas and No of regions

2021-12-01 Thread Koustav Chatterjee 
External Email - Use Caution

Thank you, Bruce.

Just a follow-up question for my clarification, recon -all - all provides
different files including

1. aparc. a2009s. stats
2. aparc. DKTatlas. stats
3. aparc. stats

Now, which one of these files should I use if I would like to consider
Desikan-Killiany atlas?

Thanks you for your help.
Regards


On Wed, 1 Dec, 2021, 8:29 pm Fischl, Bruce,  wrote:

> Hi KC
>
>
>
> I think that not all regions occur in all subjects. I know that is true of
> Christophe’s parcellation and think it is also true of Ron and Rahul’s, but
> I’ll cc Ron who can comment
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Koustav Chatterjee
> *Sent:* Wednesday, December 1, 2021 2:11 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Queries on DK Atlas and No of regions
>
>
>
> *External Email - Use Caution*
>
> Dear all,
>
>
>
> I had an understanding that Desikan-Killiiany atlas can parcellate total
> of 68 regions from both hemispheres. However, after running recon-all
> -all,  I can see total of 62 regions. I am afraid if you could help me
> understanding these discrepancies..
>
>
>
> Thank you for your help.
>
>
>
> Regards,
>
> KC
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Queries on DK Atlas and No of regions

2021-12-01 Thread Koustav Chatterjee 
External Email - Use Caution

Thank you so much for your time and help.
Regards,
Koustav

On Wed, 1 Dec, 2021, 9:43 pm Fischl, Bruce,  wrote:

> aparc.stats is the DK atlas. Aparc.DKTatlas.stats is the DKT one
>
>
>
> cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Koustav Chatterjee
> *Sent:* Wednesday, December 1, 2021 10:48 AM
> *To:* Freesurfer support list 
> *Cc:* ron_killiany Ron KILLIANY (rkilli...@cajal-1.bu.edu) <
> rkilli...@cajal-1.bu.edu>
> *Subject:* Re: [Freesurfer] Queries on DK Atlas and No of regions
>
>
>
> *External Email - Use Caution*
>
> Thank you, Bruce.
>
>
>
> Just a follow-up question for my clarification, recon -all - all provides
> different files including
>
>
>
> 1. aparc. a2009s. stats
>
> 2. aparc. DKTatlas. stats
>
> 3. aparc. stats
>
>
>
> Now, which one of these files should I use if I would like to consider
> Desikan-Killiany atlas?
>
>
>
> Thanks you for your help.
>
> Regards
>
>
>
>
>
> On Wed, 1 Dec, 2021, 8:29 pm Fischl, Bruce, 
> wrote:
>
> Hi KC
>
>
>
> I think that not all regions occur in all subjects. I know that is true of
> Christophe’s parcellation and think it is also true of Ron and Rahul’s, but
> I’ll cc Ron who can comment
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Koustav Chatterjee
> *Sent:* Wednesday, December 1, 2021 2:11 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Queries on DK Atlas and No of regions
>
>
>
> *External Email - Use Caution*
>
> Dear all,
>
>
>
> I had an understanding that Desikan-Killiiany atlas can parcellate total
> of 68 regions from both hemispheres. However, after running recon-all
> -all,  I can see total of 62 regions. I am afraid if you could help me
> understanding these discrepancies..
>
>
>
> Thank you for your help.
>
>
>
> Regards,
>
> KC
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> *MailScanner has detected a possible fraud attempt from
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[Freesurfer] How to measure correlation using FreeSurfer

2022-02-13 Thread Koustav Chatterjee 
External Email - Use Caution

Dear FreeSurfer experts,

I am trying to find the correlation between the regional cortical thickness
and volume with different clinical measures of a neurodegenerative
condition. I am using DK atlas to get the cortical measures and establish
the correlation using SPSS, a statistical software.

But, I would like to get FreeSurfer developed images. I would like to
learn how to get the areas through images (the FreeSurfer pipeline
generated images showing brain regions associated with clinical measures I
am interested in).

Looking for your kind help.

Regards,
KC
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Re: [Freesurfer] How to measure correlation using FreeSurfer

2022-02-14 Thread Koustav Chatterjee 
External Email - Use Caution

Thanks.
I am afraid since I am working on a single group ( only patient group), can
I run the same?

On Mon, 14 Feb, 2022, 9:51 pm Douglas N. Greve, 
wrote:

> You can run a group analysis
> https://secure-web.cisco.com/1Ff-dG17xkRm3OY5bDYlwFveyhE5l-WyDkWe_cFQyvOPXWqZtusTfsRPvlPr3yJR_a7H0wxgFYw-HsZJFFWr-500I3mRgVJO3GhgT_MzGifPJZXW4OVwN0rpx8Mi51yAC41a-Uihdgf0OE_F8EJ1o4oInwE8B6GJjH_Y6fFTZ0QBGnKj2UFByxPmtaXUAu-5-whHQd7ix5RLtWdRXuhRwZAHKyITK2bG_iOoUR7UBm5dK0M2bP4LV6x92HJGYCw_oJGhpL8tvMhl8UeAmtCU9deV3FLuLoTBkSvHw0-5NJAAQuiJYK1gyeuU3norr7mIYPeZ6qkyiBP0topWayXXHTg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis
> One of the outputs will be the correlation (along with the sig of the
> correlation)
>
>
> On 2/13/2022 6:35 PM, Koustav Chatterjee wrote:
>
> External Email - Use Caution
> Dear FreeSurfer experts,
>
> I am trying to find the correlation between the regional cortical
> thickness and volume with different clinical measures of a
> neurodegenerative condition. I am using DK atlas to get the cortical
> measures and establish the correlation using SPSS, a statistical software.
>
> But, I would like to get FreeSurfer developed images. I would like to
> learn how to get the areas through images (the FreeSurfer pipeline
> generated images showing brain regions associated with clinical measures I
> am interested in).
>
> Looking for your kind help.
>
> Regards,
> KC
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] How to measure correlation using FreeSurfer

2022-02-14 Thread Koustav Chatterjee 
External Email - Use Caution

Thanks a lot.




On Mon, Feb 14, 2022 at 10:48 PM Douglas N. Greve 
wrote:

> Yes, single group just means a single class in the FSGD file. Then just
> include your clinical measure as a variable in the FSGD
>
> On 2/14/2022 11:39 AM, Koustav Chatterjee wrote:
>
> External Email - Use Caution
> Thanks.
> I am afraid since I am working on a single group ( only patient group),
> can I run the same?
>
> On Mon, 14 Feb, 2022, 9:51 pm Douglas N. Greve, 
> wrote:
>
>> You can run a group analysis
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1pu85rMIoVS6omz09hQIjJs-MYDKG4N-68rPVzWyxtNPcxBifaCZhtc-dBlbH0aciA_EymTNKJ-VRxI7OatAUvM-aOLvNcEjD904Kb4i-6qD8QMie99uRrsz9L04lHGAxq430VxB1DoPFfCezL_yB64qXntUQhMdFghos64Xcdo4_-AobzYKlMFA6ZSZ0cXCyYSqnTvEHxxGRc99DDqfPV_rAFhkruKx7YT7YL1OI1Vm8f0Mif0jF_ONafiUcP4OixgiGJV5x8FCkvvVpGEe3kxVrXdwOnA9TLSBDO307NBEgzivNZkEwFUz8tzqM6JKdpDJhDyEYK9KMOmCzqzusfw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis
>> <https://secure-web.cisco.com/1Ff-dG17xkRm3OY5bDYlwFveyhE5l-WyDkWe_cFQyvOPXWqZtusTfsRPvlPr3yJR_a7H0wxgFYw-HsZJFFWr-500I3mRgVJO3GhgT_MzGifPJZXW4OVwN0rpx8Mi51yAC41a-Uihdgf0OE_F8EJ1o4oInwE8B6GJjH_Y6fFTZ0QBGnKj2UFByxPmtaXUAu-5-whHQd7ix5RLtWdRXuhRwZAHKyITK2bG_iOoUR7UBm5dK0M2bP4LV6x92HJGYCw_oJGhpL8tvMhl8UeAmtCU9deV3FLuLoTBkSvHw0-5NJAAQuiJYK1gyeuU3norr7mIYPeZ6qkyiBP0topWayXXHTg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis>
>> One of the outputs will be the correlation (along with the sig of the
>> correlation)
>>
>>
>> On 2/13/2022 6:35 PM, Koustav Chatterjee wrote:
>>
>> External Email - Use Caution
>> Dear FreeSurfer experts,
>>
>> I am trying to find the correlation between the regional cortical
>> thickness and volume with different clinical measures of a
>> neurodegenerative condition. I am using DK atlas to get the cortical
>> measures and establish the correlation using SPSS, a statistical software.
>>
>> But, I would like to get FreeSurfer developed images. I would like to
>> learn how to get the areas through images (the FreeSurfer pipeline
>> generated images showing brain regions associated with clinical measures I
>> am interested in).
>>
>> Looking for your kind help.
>>
>> Regards,
>> KC
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1ikk1uPuujAL2Sdfx5d3Znrn3UL_leQCnqPByI0OjDLIGdIsPavnP4WRbbUI2pSkhSBEM37mUSzI0S0lXX1SH1AJfThPMbHzGnVacWQXNRQgjyvuL5bQszp5ZdsNl1f4qkNz5yIgEHolncKpqO00qkZX6zTcU4hGY8P9OGBvWuNlyUVdTubO_qBb5oTOUs20MFA8s_R3NZL4zs5axHtTynZd93vF8G20ifLQqUrBDjQ5rabWuZ55zkR4xV-xPkIuAC7-_6NKWw48NXiWBUPWOUt-KihNPhF2yPUY_gf8nP9FAA8EqOEELCtHiN6Jzryb-EOM3QyvEkzNgQJ8nN0qGqA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>  
>> <https://secure-web.cisco.com/1vmI2rQNZhXFW1eSQ50tThABmAXKnIkegT3FEjChe5oy0YfRN9qSvq1heX8tLBV6_YgS70TxxUk2qDYJEDjZAWbzc44AinVPSYX-IUWAYWzqaCGzgqcfC0yDy5htaDCtbvRqom9zOtJl41o9DNRgBZopDt-twGierCA-LmhditLTvENqU2PjBo6FUnPj8XTc-bPQtcP5wUtiYLLRAAzNcF4JDHhBc8tDmDcQxTDzA3aSiaImM3vs5mdExCyarv21uPkcw-cHN1En21nkax_b2Dxu_lk7mYQWBJE5667jUSJdYWO3NGOTceCuOjDVUJQ63bQ6x1MK99DKRj7BZhK5tog/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1ikk1uPuujAL2Sdfx5d3Znrn3UL_leQCnqPByI0OjDLIGdIsPavnP4WRbbUI2pSkhSBEM37mUSzI0S0lXX1SH1AJfThPMbHzGnVacWQXNRQgjyvuL5bQszp5ZdsNl1f4qkNz5yIgEHolncKpqO00qkZX6zTcU4hGY8P9OGBvWuNlyUVdTubO_qBb5oTOUs20MFA8s_R3NZL4zs5axHtTynZd93vF8G20ifLQqUrBDjQ5rabWuZ55zkR4xV-xPkIuAC7-_6NKWw48NXiWBUPWOUt-KihNPhF2yPUY_gf8nP9FAA8EqOEELCtHiN6Jzryb-EOM3QyvEkzNgQJ8nN0qGqA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>> <https://secure-web.cisco.com/1vmI2rQNZhXFW1eSQ50tThABmAXKnIkegT3FEjChe5oy0YfRN9qSvq1heX8tLBV6_YgS70TxxUk2qDYJEDjZAWbzc44AinVPSYX-IUWAYWzqaCGzgqcfC0yDy5htaDCtbvRqom9zOtJl41o9DNRgBZopDt-twGierCA-LmhditLTvENqU2PjBo6FUnPj8XTc-bPQtcP5wUtiYLLRAAzNcF4JDHhBc8tDmDcQxTDzA3aSiaImM3vs5mdExCyarv21uPkcw-cHN1En21nkax_b2Dxu_lk7mYQWBJE5667jUSJdYWO3NGOTceCuOjDVUJQ63bQ6x1MK99DKRj7BZhK5tog/https%3A%2F%2Fmail.nmr.mgh.harvard.e

Re: [Freesurfer] How to measure correlation using FreeSurfer

2022-02-16 Thread Koustav Chatterjee 
External Email - Use Caution

Hello Douglas,

I am afraid I am getting error while running "mris_preproc --fsgd
steplengthSD_vol.fsgd"

ERROR: no subjects specified

I believe I am missing very basic and doing wrong while exporting specific
paths and subject names. Could you please help to resolve the issue?

I am working on bash shell. So, I first ran . like the
following

export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

 freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl

All my 'recon-all -all -qcache' data are kept in
/usr/local/freesurfer/subjects. I have created a folder 'glm' here and
transferred all the data. I have also created.fsgd and .mtx file and saved
them inside the 'glm' folder.

So, next two steps I did-

export SUBJECTS_DIR=/usr/local/freesurfer/subjects
cd $SUBJECTS_DIR/glm

Thank you for your time and help.
Regards,
KC


On Mon, Feb 14, 2022 at 10:48 PM Douglas N. Greve 
wrote:

> Yes, single group just means a single class in the FSGD file. Then just
> include your clinical measure as a variable in the FSGD
>
> On 2/14/2022 11:39 AM, Koustav Chatterjee wrote:
>
> External Email - Use Caution
> Thanks.
> I am afraid since I am working on a single group ( only patient group),
> can I run the same?
>
> On Mon, 14 Feb, 2022, 9:51 pm Douglas N. Greve, 
> wrote:
>
>> You can run a group analysis
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1rRbPK8Ag291KHeTtdIMQM42oPAVg-pl1Ee4UYnkQ4czZh0Cqw9ym6yDwJfF4g3p7Me3WHtD4PADqZU0V1YnNUeVpNsv0ViKUUd2ihQZ6RBTurqLhEKQ5GjsY5MDqxE5zbGeCc0TrP2d_NGG5KnJUI3i4YrpXBAqc0ACrZzksh6FNWPDTJnVXz2GSbxO8lcyM2uyuWgqPdtn4tAinZmQQY_nz8KMcbYrvZPLPUeaS9NLmQoi1of9ubw1WGSzuRwHYh0pZOsSpNsd-qSH7r-oxJ4KDHvGE6l104y1vSthS0XG32tiKPFDP9kjx8YlwCH86OnU5d-iGg5gJsXjtJEAlGg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis
>> <https://secure-web.cisco.com/1Ff-dG17xkRm3OY5bDYlwFveyhE5l-WyDkWe_cFQyvOPXWqZtusTfsRPvlPr3yJR_a7H0wxgFYw-HsZJFFWr-500I3mRgVJO3GhgT_MzGifPJZXW4OVwN0rpx8Mi51yAC41a-Uihdgf0OE_F8EJ1o4oInwE8B6GJjH_Y6fFTZ0QBGnKj2UFByxPmtaXUAu-5-whHQd7ix5RLtWdRXuhRwZAHKyITK2bG_iOoUR7UBm5dK0M2bP4LV6x92HJGYCw_oJGhpL8tvMhl8UeAmtCU9deV3FLuLoTBkSvHw0-5NJAAQuiJYK1gyeuU3norr7mIYPeZ6qkyiBP0topWayXXHTg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysis>
>> One of the outputs will be the correlation (along with the sig of the
>> correlation)
>>
>>
>> On 2/13/2022 6:35 PM, Koustav Chatterjee wrote:
>>
>> External Email - Use Caution
>> Dear FreeSurfer experts,
>>
>> I am trying to find the correlation between the regional cortical
>> thickness and volume with different clinical measures of a
>> neurodegenerative condition. I am using DK atlas to get the cortical
>> measures and establish the correlation using SPSS, a statistical software.
>>
>> But, I would like to get FreeSurfer developed images. I would like to
>> learn how to get the areas through images (the FreeSurfer pipeline
>> generated images showing brain regions associated with clinical measures I
>> am interested in).
>>
>> Looking for your kind help.
>>
>> Regards,
>> KC
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1vQwXqNPiE3wE9rcRkdbs_n20_x6bWGvTn0zOvNjaVmHJnNnGtvv0HcFEAyc3rbkZ_qgQYhzG9exaAuwV4UnAZP1cncAOExBANDKUpUEmgeCqh1fpZfqFvm2PZHbRLkk7sQwGU7OONtwAxLVGax9dLkB79Um1E15ZguEJ4wsljruAdw54hMKhM6vBhPsbi6UdAfr0qdwwzc1mRmfpeviONV32Xc3AQ_J46LDTvCU9YANl6dC9339srgQkDSlgbQ-0MO7HUzvTOELXYyy9GhEO5Y8YB-wSyDXrnm_AwgID1WXF-WIWlJPTKp240VuFl80lFKGwuQGRimEfL5J4HJSqJA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>  
>> <https://secure-web.cisco.com/1vmI2rQNZhXFW1eSQ50tThABmAXKnIkegT3FEjChe5oy0YfRN9qSvq1heX8tLBV6_YgS70TxxUk2qDYJEDjZAWbzc44AinVPSYX-IUWAYWzqaCGzgqcfC0yDy5htaDCtbvRqom9zOtJl41o9DNRgBZopDt-twGierCA-LmhditLTvENqU2PjBo6FUnPj8XTc-bPQtcP5wUtiYLLRAAzNcF4JDHhBc8tDmDcQxTDzA3aSiaImM3vs5mdExCyarv21uPkcw-cHN1En21nkax_b2Dxu_lk7mYQWBJE5667jUSJdYWO3NGOTceCuOjDVUJQ63bQ6x1MK99DKRj7BZhK5tog/

[Freesurfer] mris_preproc error: no source hemi specified

2022-02-17 Thread Koustav Chatterjee 
External Email - Use Caution

Dear FreeSurfer experts,

I need your help.
I am trying to run mris_preproc --fsgd in order to see the effect of
cortical volume on velocity, accounting for the effects of eTIV in the
analysis.
My .fsgd file looks like

GroupDescriptorFile 1
Title Vel_vol.glmdir
MeasurementName volume
Class Main
Variables Velocity Totalintracranialvolume
Input pt001 Main 57 1233150.571288
Input pt002 Main 44 1441659.580634
Input pt003 Main 60 1534770.256493
Input pt004 Main 55 1374671.330735
Input pt005 Main 29 1252775.397585
Input pt007 Main 42 1466033.251447
Input pt011 Main 82 1565625.985727
Input pt015 Main 30 1255088.0327
Input pt016.nii Main 79 1604469.84187
Input pt018.nii Main 45 1410265.173839
Input pt023 Main 70 1376261.088728
Input pt025 Main 49 1317185.172994
Input pt026 Main 45 1484779.378359
Input pt031 Main 53 1269043.642534

and .mtx file looks like
1 0

I am getting* e**rror: no source hemi specified.*

Thanks,
KC
___
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[Freesurfer] FreeSurfer license key error

2022-03-26 Thread Koustav Chatterjee 
External Email - Use Caution

Dear FreeSurfer experts,

I have reinstalled FreeSurfer 6 in my new system following the FreeSurfer
wiki.
I have saved the 'licence.txt' in /usr/local/freesurfer.
However, I am getting following error-

ERROR: Invalid FreeSurfer license key found in license file
/usr/local/freesurfer/license.txt
  If you are outside the NMR-Martinos Center,
  go to 
http://secure-web.cisco.com/16tgEh0sPXTbDRDMUvw9zB7Em9ZdUbHl0MZ9k7-9-sJxU6uO61aZatlIAPDci4XOpRmE5DXCLKENfhBVjm9fbFbjlbse-aP4MNQGlmQqy2vwXtBksJhbpPuyiX5rqx1zv_gK1VZmYSG41bdvz2to3TypA98frJku23Gtn7a87XYimVbVMAMHLugYUWqk538AIwXdauP0VkW58t6iMsTOMPrt_A9ePE3MKxf8EIuMzNw0MSRbqZdz7IiI4Z-mQsJFbP7t_PEvEvjU2ak72IXnWRgFDnY3xBmC1s1F1E9I9D4DVUBlqghHRo1oaS7KIXSpkuq2do2MbXGXmhBYb6qa6Tg/http%3A%2F%2Fsurfer.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.

Please help me resolving the issue.

Thank you.
KC
___
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Re: [Freesurfer] FreeSurfer license key error

2022-03-26 Thread Koustav Chatterjee 
External Email - Use Caution

Yes, I named the file correctly as “license.txt” and saved it in
/usr/local/freesurfer. ERROR: Invalid FreeSurfer license key found in
license file /usr/local/freesurfer/license.txt

Besides the error I mentioned already, I am also getting another error
while trying to run 'Freeview'.

*freeview.bin: error while loading shared libraries: libpng12.so.0: cannot
open shared object file: No such file or directory.*

Please advise.
Regards,
KC


On Sat, Mar 26, 2022 at 8:10 PM Fischl, Bruce 
wrote:

> Hi KC
>
>
>
> Are you naming the file “license.txt” or “licence.txt”. We look for the
> former, not the latter. And is there a .license.txt in that directory? And
> if so, where did it come from?
>
> Cheers
>
> Bruce
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Koustav Chatterjee
> *Sent:* Saturday, March 26, 2022 5:40 AM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] FreeSurfer license key error
>
>
>
> *External Email - Use Caution*
>
> Dear FreeSurfer experts,
>
>
>
> I have reinstalled FreeSurfer 6 in my new system following the FreeSurfer
> wiki.
>
> I have saved the 'licence.txt' in /usr/local/freesurfer.
>
> However, I am getting following error-
>
>
>
> ERROR: Invalid FreeSurfer license key found in license file
> /usr/local/freesurfer/license.txt
>   If you are outside the NMR-Martinos Center,
>   go to *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be* 
> http://secure-web.cisco.com/1DlM2rg5k-q8mqyUGAueUQ4TQ5sMGi0l8mQOhZNnYQIRZNgMpgHolOTsCbO6KKXFSjq4fHe7sll0j-b3GBvGV9rF2vAS9JHGccTvMjWObTtg-HNBlijng3TVFr0lJzB26HFDeUkG7wxMn5arkH6pBPLq2oyxDZ5gJEqlMaN_TZ6DuTQqxh-0Fw2G05c-_NOuBYmhzEaLokgrBNRuGVIm2mSltagmTL8GusGGy5z6Xl79oNDRnfw5vsgo9Kug2Leu18qYLCYDNS8Arg8v4y_dVPQzF0d_QnAiyCqI38KEKOOWvimE-UqQSgfKVesAPQOxYX_an0AvFY0JsBneuyC33kg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu
> <http://secure-web.cisco.com/16tgEh0sPXTbDRDMUvw9zB7Em9ZdUbHl0MZ9k7-9-sJxU6uO61aZatlIAPDci4XOpRmE5DXCLKENfhBVjm9fbFbjlbse-aP4MNQGlmQqy2vwXtBksJhbpPuyiX5rqx1zv_gK1VZmYSG41bdvz2to3TypA98frJku23Gtn7a87XYimVbVMAMHLugYUWqk538AIwXdauP0VkW58t6iMsTOMPrt_A9ePE3MKxf8EIuMzNw0MSRbqZdz7IiI4Z-mQsJFbP7t_PEvEvjU2ak72IXnWRgFDnY3xBmC1s1F1E9I9D4DVUBlqghHRo1oaS7KIXSpkuq2do2MbXGXmhBYb6qa6Tg/http%3A%2F%2Fsurfer.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.
>
> 
>
> Please help me resolving the issue.
>
>
>
> Thank you.
>
> KC
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1Bs1fbuRqymoj3tLjRsVfYeOvMX3HQzE3Mok1pQRc4Dfu2UkT8twy5dGMq4SZ9-7bvniEawLwvIfoa7wADkxSe4hJDBtpKv_mRBn43CWvlADFTazXZSNx_Z_DN_Jjj39Wx_BmTYnB7q1ciIIpP0dgLDtUoIVarpTgumq5QDR12p5ImU3iOf_DjrwqT9AEsdk23C7RfkvtlVlKivE4W2FOHaq2GSe7uSKhsbk2-isBn0sxWtaJ-Hrjpt9_wiMSYILVRXaRuF3A6c8nulGumoQUkqHZAKv3Hd88_2DHDUf1x9RHoM1n-sJLtFeX4G4eb7fQXEkEPSstJa6ui0SW_0ncGg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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 Mass General
> Brigham Compliance HelpLine at
> https://secure-web.cisco.com/1fewSZNZlTKZT1T5dz8gsDR6urGouaV00tWxLguJRneFuI_PFEOiz6pkgOcK14ntJwX8rm8S3r2LLBA2Ael1CGp5e60t_SPj6s8lbpsZ4tLCnxFCLP3Zokw1HIVf3WNsaziEeIH90KT1G0wtJG5zj9HoSKwSV5F9NN3W8lwbmxaz-GloZXAY_b0Ygk-U5raUBWSr75dH5EEOLRH8LS7fXzdJnSY2_AmPG2a9N97uFpz3o8K-Spbzk7VMZTPnTFJLa2hafryWovVo2UJs52NwWI2rfcqLZBCIWoTFv4CGygNv1wLrdyQsg1jgErrUEZY3u__4WwKEN9NoojP9Hsp8VDg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1fewSZNZlTKZT1T5dz8gsDR6urGouaV00tWxLguJRneFuI_PFEOiz6pkgOcK14ntJwX8rm8S3r2LLBA2Ael1CGp5e60t_SPj6s8lbpsZ4tLCnxFCLP3Zokw1HIVf3WNsaziEeIH90KT1G0wtJG5zj9HoSKwSV5F9NN3W8lwbmxaz-GloZXAY_b0Ygk-U5raUBWSr75dH5EEOLRH8LS7fXzdJnSY2_AmPG2a9N97uFpz3o8K-Spbzk7VMZTPnTFJLa2hafryWovVo2UJs52NwWI2rfcqLZBCIWoTFv4CGygNv1wLrdyQsg1jgErrUEZY3u__4WwKEN9NoojP9Hsp8VDg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
> Please note that this e-mail is not secure (encrypted).  If you do not
> wish to continue communication over unencrypted e-mail, please notify the
> sender of this message immediately.  Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e

[Freesurfer] Seeking help:error in FreeSurfer license key and Freeview

2022-03-28 Thread Koustav Chatterjee 
External Email - Use Caution

Dear FreeSurfer experts,


I have reinstalled FreeSurfer 6 in my new system following the
FreeSurferes. I saved  “license.txt” in /usr/local/freesurfer. I am getting
the following error.

ERROR: Invalid FreeSurfer license key found in license file
/usr/local/freesurfer/license.txt
  If you are outside the NMR-Martinos Center,
  go to *MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be* 
http://secure-web.cisco.com/1Mmk36ObciQH40e9fApFJZJ-8R9hBltfDgy2k6XwbkAfyNdwATHCDhilggtSvCl-jOcVQC9u6d4Vz8XwXuGqKxB00u2qK_KH_P0TQZo0mwfl2tCii7bxmIP2ztZzk_d2rBbxWgSM_-WpCHElRgQi16N0nd1cKS7POy-MSzzJrzsoGEs9ko8BXQBuA5vgsaWTOFLN7oKGrygT92sCNjapOkq-qoQMyrpzTrmg-0Wllh_XwmII1ma2rBJUN_Eg50WvwS4JchHvxwtTtvXorBUpfKXMBw4Z5N-GNUhT65doDYqNmrGR_4D_IQ0fkcEDxBj_hxvH-iygihQVWPVP-q-sELQ/http%3A%2F%2Fsurfer.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.


 I am also getting another error while trying to run 'Freeview'.

*freeview.bin: error while loading shared libraries: libpng12.so.0: cannot
open shared object file: No such file or directory.*

Please advise.
Regards,
KC
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Seeking help:error in FreeSurfer license key and Freeview

2022-03-29 Thread Koustav Chatterjee 
External Email - Use Caution

Thank you so much for your reply, Bruce and Ruopeng.
I will do what you have advised. However, when I reinstalled FreeSurfer
(Version 6) in my system (ubuntu 16.04 LTS), I downloaded the new
license.txt. I did not use the existing one. Also, I used a separate email
ID for getting a new license file in my new system in the notion that I
already had a license file in my other email ID.

I will do as you advised.
Regards,
KC


On Tue, Mar 29, 2022 at 7:23 PM Fischl, Bruce 
wrote:

> Hi KC
>
>
>
> Where did you get the license.txt file originally? Can you try requesting
> another? I’ll leave the freeview question for Ruopeng.
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Koustav Chatterjee
> *Sent:* Monday, March 28, 2022 11:04 PM
> *To:* Freesurfer support list 
> *Subject:* [Freesurfer] Seeking help:error in FreeSurfer license key and
> Freeview
>
>
>
> *External Email - Use Caution*
>
> Dear FreeSurfer experts,
>
>
>
> I have reinstalled FreeSurfer 6 in my new system following the
> FreeSurferes. I saved  “license.txt” in /usr/local/freesurfer. I am getting
> the following error.
>
>
>
> ERROR: Invalid FreeSurfer license key found in license file
> /usr/local/freesurfer/license.txt
>   If you are outside the NMR-Martinos Center,
>   go to *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be* 
> http://secure-web.cisco.com/1GGegjGUlnBWkBKlQPbwRkD8_0LQPb2yb4ZYIMo32IzHTGHU61HAKRbwKXnxdSu7Q7vBqpeHttE69H6rKVRIA3iOuVvBiqAz8gn_rZVGjr3v2eFRsrUR4qpy7EIGxXrvO-nPNkSVaPLUCTbfarIDYjo19m8s6tNA-nhVfkfgGVqEhrtFz8Kwl7LGEDv6ulZNP-qQSXXdudDrlKx9EmvVEB97keRQg_3eBhSgF1o5Wpi1-VvJn5eL53jdqc5YaO_qqO6p7mDa6JCn9QiDdaPZgNA_K8ACsEau13Bh3OmLFC7tPi0tQWJwv1WJYKQuA5z3J/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu
> <http://secure-web.cisco.com/16tgEh0sPXTbDRDMUvw9zB7Em9ZdUbHl0MZ9k7-9-sJxU6uO61aZatlIAPDci4XOpRmE5DXCLKENfhBVjm9fbFbjlbse-aP4MNQGlmQqy2vwXtBksJhbpPuyiX5rqx1zv_gK1VZmYSG41bdvz2to3TypA98frJku23Gtn7a87XYimVbVMAMHLugYUWqk538AIwXdauP0VkW58t6iMsTOMPrt_A9ePE3MKxf8EIuMzNw0MSRbqZdz7IiI4Z-mQsJFbP7t_PEvEvjU2ak72IXnWRgFDnY3xBmC1s1F1E9I9D4DVUBlqghHRo1oaS7KIXSpkuq2do2MbXGXmhBYb6qa6Tg/http%3A%2F%2Fsurfer.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.
>
>
>
>
>
>  I am also getting another error while trying to run 'Freeview'.
>
>
>
> *freeview.bin: error while loading shared libraries: libpng12.so.0: cannot
> open shared object file: No such file or directory.*
>
>
>
> Please advise.
>
> Regards,
>
> KC
> ___
> Freesurfer mailing list
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> 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 Mass General
> Brigham Compliance HelpLine at
> https://secure-web.cisco.com/1PpmwimElwq8_yoZz7G8900eC9PM0DjBlcnpznXcWqRCtZU0b1OOtDUCgKkQZGMN5C6tIDtR1k8UtZ3CAWkZix9LOH3Q-Cp3SlBmGX0lNZB7okBS24h8NGHmkztlZE5JdNInI2eE0bsprzQ2Tvklou7JX_ifpdD745Ea6-UTEF09qpsxsELpH8yJkpx8fuEI_2z_CavJiPE9CPTPRidYlR7jgc5Vy2NF2tBzqmwp9rgHGXjNBw_1dXY5Ur8xLiH8tEsLZ1puikDQBtmC0bcwgd2qT4-VzoLLVVc8FriDmO5OBgqy7ocf6LJKC8nbLJt8x/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  <
> https://secure-web.cisco.com/1PpmwimElwq8_yoZz7G8900eC9PM0DjBlcnpznXcWqRCtZU0b1OOtDUCgKkQZGMN5C6tIDtR1k8UtZ3CAWkZix9LOH3Q-Cp3SlBmGX0lNZB7okBS24h8NGHmkztlZE5JdNInI2eE0bsprzQ2Tvklou7JX_ifpdD745Ea6-UTEF09qpsxsELpH8yJkpx8fuEI_2z_CavJiPE9CPTPRidYlR7jgc5Vy2NF2tBzqmwp9rgHGXjNBw_1dXY5Ur8xLiH8tEsLZ1puikDQBtmC0bcwgd2qT4-VzoLLVVc8FriDmO5OBgqy7ocf6LJKC8nbLJt8x/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
>  .
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