subject:"Re\: \[Freesurfer\] LGI problem"

Re: [Freesurfer] LGI problem

2020-05-22 Thread Angela Favaro

External Email - Use Caution

Hi Doug, 
I had the identical problem (failure at segmentation stage, as described below) 
in 4 subjects of my dataset. I have no possibility to run analyses on a linux 
machine…
Since all 4 subjects had no problem using Freesurfer 6, is it so wrong to use 
freesurfer 6 only for these 4 subjects?
Or have you any other suggestions?

Thank you for any help

Angela




> Il giorno 15 mag 2020, alle ore 23:26, Angela Favaro  
> ha scritto:
> 
> External Email - Use Caution
> 
> 
> Hi doug, 
> I tried to re-run 3 or 4 times and always failed at the segmentation stage…
> I have no linux machine, but I can try in a mac computer with a different 
> OS...
> thank you!
> 
> Angela
> 
> 
>> Il giorno 15 mag 2020, alle ore 23:08, Douglas N. Greve 
>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>> 
>> Hi Angela, I cannot replicate this error. If you re-run, does it always exit 
>> with error? You can try this quickly be running
>> 
>> setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/Aachen
>> cd /Users/angelafavaro/Desktop/Aachen/subj220/mri
>> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta 
>> /Users/angelafavaro/Desktop/Aachen/subj220/mri/transforms/cc_up.lta subj220
>> 
>> One factor may be that I'm using CentOS and not Mac. Do you have a linux 
>> machine you can try it on?
>> 
>> 
>> 
>> On 5/15/2020 10:59 AM, Angela Favaro wrote:
>>> External Email - Use Caution
>>> 
>>> I have uploaded to you the data using the Martinos Center FileDrop
>>> Hope is a good option for you
>>> 
>>> Thank you
>>> Angela
>>> 
 Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro 
 mailto:angela.fav...@unipd.it>> ha scritto:
 
 External Email - Use Caution
 
 
 Hi Doug, 
 I have some problem in uploading my subj.tar.gz using ftp. I am using a 
 MacOs Catalina and, although I am able to connect to the FTP site and open 
 the incoming window (also in binary mode), commands are not working...
 
 I am trying to overcome the problem.
 Is there any other method to transfer the data set?
 Thank you
 
 Angela
 
> Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
> 
> Hmmm, I don't know. Can you upload the data set? Follow these instructions
> 
> From the linux command line,
> Create the file you want to upload, eg, 
> cd $SUBJECTS_DIR
> tar cvfz subject.tar.gz ./subject
> Now log  into our anonymous FTP site:
> ftp surfer.nmr.mgh.harvard.edu 
> It will ask you for a user name: use "anonymous" (no quotes)
> It will ask you for a password: use "anonymous" (no quotes)
> cd transfer/incoming
> binary
> put subject.tar.gz
> Send an email that the file has been and the name of the file.
> 
> 
> On 5/14/2020 5:03 PM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> Thank you Doug!
>> It works! Great!
>> 
>> 
>> I have another problem: I am reprocessing all my database with 
>> freesurfer 7.1.0, but in one subject segmentation failed.
>> I had no problem with this subjects using freesurfer 6
>> What can be the problem?
>> 
>> I attach the log
>> 
>> Thank you for any help!
>> 
>> Angela
>> 
>> 
>> 
>>> Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> 
>>> Someone just pointed out that I posted the wrong file. Here is the 
>>> correct one. Copy it to the same folder
>>> 
>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m 
>>> 
>>> 
>>> 
>>> On 5/13/2020 11:01 PM, Douglas N. Greve wrote:
 
 Download this file
 https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
  
 
 and copy it into $FREESURFER_HOME/matlab
 and rerun. Let me know if that fixes it.
 
 
 
 On 5/13/2020 5:57 PM, Angela Favaro wrote:
> External Email - Use Caution
> 
> Please find attached the log
> Thank you
> Angela
> 
> 
> 
>> Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>> 
>> Are you running this from recon-all? If so send the recon-all.log. 
>> If from the command line, send the command-line and all terminal 
>> output
>> 
>> On 5/13/2020 5:28 PM, Angela Favaro wrote:
>>> External Email - Use Caution
>>> 
>

Re: [Freesurfer] LGI problem

2020-05-15 Thread Angela Favaro

External Email - Use Caution

Hi doug, 
I tried to re-run 3 or 4 times and always failed at the segmentation stage…
I have no linux machine, but I can try in a mac computer with a different OS...
thank you!

Angela


> Il giorno 15 mag 2020, alle ore 23:08, Douglas N. Greve 
>  ha scritto:
> 
> Hi Angela, I cannot replicate this error. If you re-run, does it always exit 
> with error? You can try this quickly be running
> 
> setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/Aachen
> cd /Users/angelafavaro/Desktop/Aachen/subj220/mri
> mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta 
> /Users/angelafavaro/Desktop/Aachen/subj220/mri/transforms/cc_up.lta subj220
> 
> One factor may be that I'm using CentOS and not Mac. Do you have a linux 
> machine you can try it on?
> 
> 
> 
> On 5/15/2020 10:59 AM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> I have uploaded to you the data using the Martinos Center FileDrop
>> Hope is a good option for you
>> 
>> Thank you
>> Angela
>> 
>>> Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro 
>>> mailto:angela.fav...@unipd.it>> ha scritto:
>>> 
>>> External Email - Use Caution
>>> 
>>> 
>>> Hi Doug, 
>>> I have some problem in uploading my subj.tar.gz using ftp. I am using a 
>>> MacOs Catalina and, although I am able to connect to the FTP site and open 
>>> the incoming window (also in binary mode), commands are not working...
>>> 
>>> I am trying to overcome the problem.
>>> Is there any other method to transfer the data set?
>>> Thank you
>>> 
>>> Angela
>>> 
 Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve 
 mailto:dgr...@mgh.harvard.edu>> ha scritto:
 
 Hmmm, I don't know. Can you upload the data set? Follow these instructions
 
 From the linux command line,
 Create the file you want to upload, eg, 
 cd $SUBJECTS_DIR
 tar cvfz subject.tar.gz ./subject
 Now log  into our anonymous FTP site:
 ftp surfer.nmr.mgh.harvard.edu 
 It will ask you for a user name: use "anonymous" (no quotes)
 It will ask you for a password: use "anonymous" (no quotes)
 cd transfer/incoming
 binary
 put subject.tar.gz
 Send an email that the file has been and the name of the file.
 
 
 On 5/14/2020 5:03 PM, Angela Favaro wrote:
> External Email - Use Caution
> 
> Thank you Doug!
> It works! Great!
> 
> 
> I have another problem: I am reprocessing all my database with freesurfer 
> 7.1.0, but in one subject segmentation failed.
> I had no problem with this subjects using freesurfer 6
> What can be the problem?
> 
> I attach the log
> 
> Thank you for any help!
> 
> Angela
> 
> 
> 
>> Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve 
>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>> 
>> 
>> Someone just pointed out that I posted the wrong file. Here is the 
>> correct one. Copy it to the same folder
>> 
>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m 
>> 
>> 
>> 
>> On 5/13/2020 11:01 PM, Douglas N. Greve wrote:
>>> 
>>> Download this file
>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
>>>  
>>> 
>>> and copy it into $FREESURFER_HOME/matlab
>>> and rerun. Let me know if that fixes it.
>>> 
>>> 
>>> 
>>> On 5/13/2020 5:57 PM, Angela Favaro wrote:
 External Email - Use Caution
 
 Please find attached the log
 Thank you
 Angela
 
 
 
> Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
> 
> Are you running this from recon-all? If so send the recon-all.log. If 
> from the command line, send the command-line and all terminal output
> 
> On 5/13/2020 5:28 PM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> Hi Doug!
>> yes, it run under version 6!
>> Please let me know if it is something that can be solved
>> Thank you
>> Angela
>> 
>> 
>>> Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> Does it run under version 6? We are not really supporting lGI 
>>> anymore, but maybe we can get it to work
>>> 
>>> On 5/13/2020 4:24 PM, Angela Favaro wrote:
 External Email - Use Caution
 
 
 Hi all, 
 I am using the new version of Free

Re: [Freesurfer] LGI problem

2020-05-15 Thread Douglas N. Greve

Hi Angela, I cannot replicate this error. If you re-run, does it always 
exit with error? You can try this quickly be running

setenv SUBJECTS_DIR /Users/angelafavaro/Desktop/Aachen
cd /Users/angelafavaro/Desktop/Aachen/subj220/mri
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta 
/Users/angelafavaro/Desktop/Aachen/subj220/mri/transforms/cc_up.lta subj220

One factor may be that I'm using CentOS and not Mac. Do you have a linux 
machine you can try it on?

On 5/15/2020 10:59 AM, Angela Favaro wrote:

External Email - Use Caution

I have uploaded to you the data using the Martinos Center FileDrop
Hope is a good option for you

Thank you
Angela

Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro 
mailto:angela.fav...@unipd.it>> ha scritto:

External Email - Use Caution

Hi Doug,
I have some problem in uploading my subj.tar.gz using ftp. I am using 
a MacOs Catalina and, although I am able to connect to the FTP site 
and open the incoming window (also in binary mode), commands are not 
working...

I am trying to overcome the problem.
Is there any other method to transfer the data set?
Thank you

Angela

Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Hmmm, I don't know. Can you upload the data set? Follow these 
instructions

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu 
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.

On 5/14/2020 5:03 PM, Angela Favaro wrote:

External Email - Use Caution

Thank you Doug!
It works! Great!

I have another problem: I am reprocessing all my database with 
freesurfer 7.1.0, but in one subject segmentation failed.

I had no problem with this subjects using freesurfer 6
What can be the problem?

I attach the log

Thank you for any help!

Angela

Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Someone just pointed out that I posted the wrong file. Here is the 
correct one. Copy it to the same folder

https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m

On 5/13/2020 11:01 PM, Douglas N. Greve wrote:

Download this file
https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
and copy it into $FREESURFER_HOME/matlab
and rerun. Let me know if that fixes it.

On 5/13/2020 5:57 PM, Angela Favaro wrote:

External Email - Use Caution

Please find attached the log
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha 
scritto:

Are you running this from recon-all? If so send the 
recon-all.log. If from the command line, send the command-line 
and all terminal output

On 5/13/2020 5:28 PM, Angela Favaro wrote:

External Email - Use Caution

Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha 
scritto:

Does it run under version 6? We are not really supporting lGI 
anymore, but maybe we can get it to work

On 5/13/2020 4:24 PM, Angela Favaro wrote:

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image 
processing

The error is after the command 
find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
In freesurfer_read_surf (line 70)
In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = 
freesurfer_read_surf(pial);

>> 
ERROR: find_corresponding_center_FSformat did not complete 
successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu 

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list

Re: [Freesurfer] LGI problem

2020-05-15 Thread Angela Favaro

External Email - Use Caution

I have uploaded to you the data using the Martinos Center FileDrop
Hope is a good option for you

Thank you
Angela

> Il giorno 15 mag 2020, alle ore 16:40, Angela Favaro  
> ha scritto:
> 
> External Email - Use Caution
> 
> 
> Hi Doug, 
> I have some problem in uploading my subj.tar.gz using ftp. I am using a MacOs 
> Catalina and, although I am able to connect to the FTP site and open the 
> incoming window (also in binary mode), commands are not working...
> 
> I am trying to overcome the problem.
> Is there any other method to transfer the data set?
> Thank you
> 
> Angela
> 
>> Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve 
>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>> 
>> Hmmm, I don't know. Can you upload the data set? Follow these instructions
>> 
>> From the linux command line,
>> Create the file you want to upload, eg, 
>> cd $SUBJECTS_DIR
>> tar cvfz subject.tar.gz ./subject
>> Now log  into our anonymous FTP site:
>> ftp surfer.nmr.mgh.harvard.edu 
>> It will ask you for a user name: use "anonymous" (no quotes)
>> It will ask you for a password: use "anonymous" (no quotes)
>> cd transfer/incoming
>> binary
>> put subject.tar.gz
>> Send an email that the file has been and the name of the file.
>> 
>> 
>> On 5/14/2020 5:03 PM, Angela Favaro wrote:
>>> External Email - Use Caution
>>> 
>>> Thank you Doug!
>>> It works! Great!
>>> 
>>> 
>>> I have another problem: I am reprocessing all my database with freesurfer 
>>> 7.1.0, but in one subject segmentation failed.
>>> I had no problem with this subjects using freesurfer 6
>>> What can be the problem?
>>> 
>>> I attach the log
>>> 
>>> Thank you for any help!
>>> 
>>> Angela
>>> 
>>> 
>>> 
 Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve 
 mailto:dgr...@mgh.harvard.edu>> ha scritto:
 
 
 Someone just pointed out that I posted the wrong file. Here is the correct 
 one. Copy it to the same folder
 
 https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m 
 
 
 
 On 5/13/2020 11:01 PM, Douglas N. Greve wrote:
> 
> Download this file
> https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
>  
> 
> and copy it into $FREESURFER_HOME/matlab
> and rerun. Let me know if that fixes it.
> 
> 
> 
> On 5/13/2020 5:57 PM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> Please find attached the log
>> Thank you
>> Angela
>> 
>> 
>> 
>>> Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> Are you running this from recon-all? If so send the recon-all.log. If 
>>> from the command line, send the command-line and all terminal output
>>> 
>>> On 5/13/2020 5:28 PM, Angela Favaro wrote:
 External Email - Use Caution
 
 Hi Doug!
 yes, it run under version 6!
 Please let me know if it is something that can be solved
 Thank you
 Angela
 
 
> Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
> mailto:dgr...@mgh.harvard.edu>> ha scritto:
> 
> Does it run under version 6? We are not really supporting lGI 
> anymore, but maybe we can get it to work
> 
> On 5/13/2020 4:24 PM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> 
>> Hi all, 
>> I am using the new version of Freesurfer 7.1.0
>> And I am finding problems in running gyrification analysis.
>> I have Matlab 2016a (and 2019b) with the toolbox image processing
>> 
>> The error is after the command find_corresponding_center_FSformat
>> 
>> Matlab seems to start, but then the following message appears:
>> 
>> >> Warning: Input argument must be a string. 
>> > In ver (line 41)
>>   In freesurfer_read_surf (line 70)
>>   In find_corresponding_center_FSformat (line 26) 
>> Error using fprintf
>> Function is not defined for 'struct' inputs.
>> 
>> Error in freesurfer_read_surf (line 70)
>> fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
>> 
>> Error in find_corresponding_center_FSformat (line 26)
>> [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
>>  
>> >> 
>> ERROR: find_corresponding_center_FSformat did not complete 
>> successfully!
>> 
>> I tried with both the Matlab version, but the error is the same
>> An

Re: [Freesurfer] LGI problem

2020-05-15 Thread Angela Favaro

External Email - Use Caution

Hi Doug, 
I have some problem in uploading my subj.tar.gz using ftp. I am using a MacOs 
Catalina and, although I am able to connect to the FTP site and open the 
incoming window (also in binary mode), commands are not working...

I am trying to overcome the problem.
Is there any other method to transfer the data set?
Thank you

Angela

> Il giorno 15 mag 2020, alle ore 00:15, Douglas N. Greve 
>  ha scritto:
> 
> Hmmm, I don't know. Can you upload the data set? Follow these instructions
> 
> From the linux command line,
> Create the file you want to upload, eg, 
> cd $SUBJECTS_DIR
> tar cvfz subject.tar.gz ./subject
> Now log  into our anonymous FTP site:
> ftp surfer.nmr.mgh.harvard.edu
> It will ask you for a user name: use "anonymous" (no quotes)
> It will ask you for a password: use "anonymous" (no quotes)
> cd transfer/incoming
> binary
> put subject.tar.gz
> Send an email that the file has been and the name of the file.
> 
> 
> On 5/14/2020 5:03 PM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> Thank you Doug!
>> It works! Great!
>> 
>> 
>> I have another problem: I am reprocessing all my database with freesurfer 
>> 7.1.0, but in one subject segmentation failed.
>> I had no problem with this subjects using freesurfer 6
>> What can be the problem?
>> 
>> I attach the log
>> 
>> Thank you for any help!
>> 
>> Angela
>> 
>> 
>> 
>>> Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve 
>>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>>> 
>>> 
>>> Someone just pointed out that I posted the wrong file. Here is the correct 
>>> one. Copy it to the same folder
>>> 
>>> https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m 
>>> 
>>> 
>>> 
>>> On 5/13/2020 11:01 PM, Douglas N. Greve wrote:
 
 Download this file
 https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
  
 
 and copy it into $FREESURFER_HOME/matlab
 and rerun. Let me know if that fixes it.
 
 
 
 On 5/13/2020 5:57 PM, Angela Favaro wrote:
> External Email - Use Caution
> 
> Please find attached the log
> Thank you
> Angela
> 
> 
> 
>> Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
>> mailto:dgr...@mgh.harvard.edu>> ha scritto:
>> 
>> Are you running this from recon-all? If so send the recon-all.log. If 
>> from the command line, send the command-line and all terminal output
>> 
>> On 5/13/2020 5:28 PM, Angela Favaro wrote:
>>> External Email - Use Caution
>>> 
>>> Hi Doug!
>>> yes, it run under version 6!
>>> Please let me know if it is something that can be solved
>>> Thank you
>>> Angela
>>> 
>>> 
 Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
 mailto:dgr...@mgh.harvard.edu>> ha scritto:
 
 Does it run under version 6? We are not really supporting lGI anymore, 
 but maybe we can get it to work
 
 On 5/13/2020 4:24 PM, Angela Favaro wrote:
> External Email - Use Caution
> 
> 
> Hi all, 
> I am using the new version of Freesurfer 7.1.0
> And I am finding problems in running gyrification analysis.
> I have Matlab 2016a (and 2019b) with the toolbox image processing
> 
> The error is after the command find_corresponding_center_FSformat
> 
> Matlab seems to start, but then the following message appears:
> 
> >> Warning: Input argument must be a string. 
> > In ver (line 41)
>   In freesurfer_read_surf (line 70)
>   In find_corresponding_center_FSformat (line 26) 
> Error using fprintf
> Function is not defined for 'struct' inputs.
> 
> Error in freesurfer_read_surf (line 70)
> fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
> 
> Error in find_corresponding_center_FSformat (line 26)
> [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
>  
> >> 
> ERROR: find_corresponding_center_FSformat did not complete 
> successfully!
> 
> I tried with both the Matlab version, but the error is the same
> Any help is appreciated. Thank you so much
> 
> Angela
> 
> 
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu 
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> 
> 
> 
>

Re: [Freesurfer] LGI problem

2020-05-14 Thread Douglas N. Greve

Hmmm, I don't know. Can you upload the data set? Follow these instructions

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.

On 5/14/2020 5:03 PM, Angela Favaro wrote:

External Email - Use Caution

Thank you Doug!
It works! Great!

I have another problem: I am reprocessing all my database with 
freesurfer 7.1.0, but in one subject segmentation failed.

I had no problem with this subjects using freesurfer 6
What can be the problem?

I attach the log

Thank you for any help!

Angela

Il giorno 14 mag 2020, alle ore 17:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Someone just pointed out that I posted the wrong file. Here is the 
correct one. Copy it to the same folder

https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m

On 5/13/2020 11:01 PM, Douglas N. Greve wrote:

Download this file
https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
and copy it into $FREESURFER_HOME/matlab
and rerun. Let me know if that fixes it.

On 5/13/2020 5:57 PM, Angela Favaro wrote:

External Email - Use Caution

Please find attached the log
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Are you running this from recon-all? If so send the recon-all.log. 
If from the command line, send the command-line and all terminal 
output

On 5/13/2020 5:28 PM, Angela Favaro wrote:

External Email - Use Caution

Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Does it run under version 6? We are not really supporting lGI 
anymore, but maybe we can get it to work

On 5/13/2020 4:24 PM, Angela Favaro wrote:

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing

The error is after the command find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
In freesurfer_read_surf (line 70)
In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>> 
ERROR: find_corresponding_center_FSformat did not complete 
successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela

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Re: [Freesurfer] LGI problem

2020-05-14 Thread Douglas N. Greve

Someone just pointed out that I posted the wrong file. Here is the 
correct one. Copy it to the same folder

https://gate.nmr.mgh.harvard.edu/safelinks/greve/freesurfer_read_surf.m

On 5/13/2020 11:01 PM, Douglas N. Greve wrote:

Download this file
https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
and copy it into $FREESURFER_HOME/matlab
and rerun. Let me know if that fixes it.

On 5/13/2020 5:57 PM, Angela Favaro wrote:

External Email - Use Caution

Please find attached the log
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Are you running this from recon-all? If so send the recon-all.log. 
If from the command line, send the command-line and all terminal output

On 5/13/2020 5:28 PM, Angela Favaro wrote:

External Email - Use Caution

Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Does it run under version 6? We are not really supporting lGI 
anymore, but maybe we can get it to work

On 5/13/2020 4:24 PM, Angela Favaro wrote:

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing

The error is after the command find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
In freesurfer_read_surf (line 70)
In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>> 
ERROR: find_corresponding_center_FSformat did not complete 
successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela

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Re: [Freesurfer] LGI problem

2020-05-13 Thread Douglas N. Greve

Download this file
https://gate.nmr.mgh.harvard.edu/safelinks/greve/find_corresponding_center_FSformat.m
and copy it into $FREESURFER_HOME/matlab
and rerun. Let me know if that fixes it.

On 5/13/2020 5:57 PM, Angela Favaro wrote:

External Email - Use Caution

Please find attached the log
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:35, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Are you running this from recon-all? If so send the recon-all.log. If 
from the command line, send the command-line and all terminal output

On 5/13/2020 5:28 PM, Angela Favaro wrote:

External Email - Use Caution

Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Does it run under version 6? We are not really supporting lGI 
anymore, but maybe we can get it to work

On 5/13/2020 4:24 PM, Angela Favaro wrote:

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing

The error is after the command find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
In freesurfer_read_surf (line 70)
In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>> 
ERROR: find_corresponding_center_FSformat did not complete 
successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela

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Re: [Freesurfer] LGI problem

2020-05-13 Thread Douglas N. Greve

Are you running this from recon-all? If so send the recon-all.log. If 
from the command line, send the command-line and all terminal output

On 5/13/2020 5:28 PM, Angela Favaro wrote:

External Email - Use Caution

Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela

Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> ha scritto:

Does it run under version 6? We are not really supporting lGI 
anymore, but maybe we can get it to work

On 5/13/2020 4:24 PM, Angela Favaro wrote:

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing

The error is after the command find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
  In freesurfer_read_surf (line 70)
  In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>> 
ERROR: find_corresponding_center_FSformat did not complete successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela

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Re: [Freesurfer] LGI problem

2020-05-13 Thread Angela Favaro

External Email - Use Caution

Hi Doug!
yes, it run under version 6!
Please let me know if it is something that can be solved
Thank you
Angela


> Il giorno 13 mag 2020, alle ore 23:06, Douglas N. Greve 
>  ha scritto:
> 
> Does it run under version 6? We are not really supporting lGI anymore, but 
> maybe we can get it to work
> 
> On 5/13/2020 4:24 PM, Angela Favaro wrote:
>> External Email - Use Caution
>> 
>> 
>> Hi all, 
>> I am using the new version of Freesurfer 7.1.0
>> And I am finding problems in running gyrification analysis.
>> I have Matlab 2016a (and 2019b) with the toolbox image processing
>> 
>> The error is after the command find_corresponding_center_FSformat
>> 
>> Matlab seems to start, but then the following message appears:
>> 
>> >> Warning: Input argument must be a string. 
>> > In ver (line 41)
>>   In freesurfer_read_surf (line 70)
>>   In find_corresponding_center_FSformat (line 26) 
>> Error using fprintf
>> Function is not defined for 'struct' inputs.
>> 
>> Error in freesurfer_read_surf (line 70)
>> fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
>> 
>> Error in find_corresponding_center_FSformat (line 26)
>> [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
>>  
>> >> 
>> ERROR: find_corresponding_center_FSformat did not complete successfully!
>> 
>> I tried with both the Matlab version, but the error is the same
>> Any help is appreciated. Thank you so much
>> 
>> Angela
>> 
>> 
>>> ___
>>> 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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Re: [Freesurfer] LGI problem

2020-05-13 Thread Douglas N. Greve

Does it run under version 6? We are not really supporting lGI anymore, 
but maybe we can get it to work

On 5/13/2020 4:24 PM, Angela Favaro wrote:

External Email - Use Caution

Hi all,
I am using the new version of Freesurfer 7.1.0
And I am finding problems in running gyrification analysis.
I have Matlab 2016a (and 2019b) with the toolbox image processing

The error is after the command find_corresponding_center_FSformat

Matlab seems to start, but then the following message appears:

>> Warning: Input argument must be a string.
> In ver (line 41)
  In freesurfer_read_surf (line 70)
  In find_corresponding_center_FSformat (line 26)
Error using fprintf
Function is not defined for 'struct' inputs.

Error in freesurfer_read_surf (line 70)
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));

Error in find_corresponding_center_FSformat (line 26)
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);

>> 
ERROR: find_corresponding_center_FSformat did not complete successfully!

I tried with both the Matlab version, but the error is the same
Any help is appreciated. Thank you so much

Angela

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Re: [Freesurfer] LGI problem

2015-05-05 Thread Alan Francis

Hi Marie:

I just had another problem with the LGI processing. Here is the log:

thanks,

Alan

[alanf@micc FreeSurfer_5.3]$ recon-all -s Asperger1 -localGI

INFO: FreeSurfer build stamps do not match

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /data/alanf/FreeSurfer_5.3

Actual FREESURFER_HOME /cm/shared/freesurfer

-rwxr-xr-x 1 alanf fiarl 1231328 May  5 10:27
/data/alanf/FreeSurfer_5.3/Asperger1/scripts/recon-all.log

Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64
x86_64 x86_64 GNU/Linux

INFO: current FREESURFER_HOME does not match that of previous processing.

Current: /cm/shared/freesurfer

Previous: /usr/local/freesurfer/stable5_3_0/

/data/alanf/FreeSurfer_5.3/Asperger1/surf

#

#@# Local Gyrification Index lh Tue May  5 11:19:06 EDT 2015


 mris_compute_lgi --i lh.pial


=

rm -Rf
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial

=

=

mkdir -p
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial

=

=

mris_fill -c -r 1 lh.pial
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz

=

reading surface from lh.pial...

writing filled volume to
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...

conforming output volume

setting resolution for intermediate calculations to 1.

=

make_outer_surface('/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
exit

=


< M A T L A B (R) >

  Copyright 1984-2015 The MathWorks, Inc.

   R2015a (8.5.0.197613) 64-bit (glnxa64)

 February 12, 2015


For online documentation, see http://www.mathworks.com/support

For product information, visit www.mathworks.com.



Academic License

>> reading filled volume...

closing volume...

morphological closing done.

writing outer surface...


=

mris_extract_main_component
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main

=


counting number of connected components...

   64236 voxel in cpt #1: X=2 [v=64236,e=192702,f=128468] located at
(-23.607313, -17.955009, 25.682032)

For the whole surface: X=2 [v=64236,e=192702,f=128468]

One single component has been found

nothing to do

done


=

mris_smooth -nw -n 30
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main
./lh.pial-outer-smoothed

=

smoothing for 30 iterations

smoothing surface tessellation for 30 iterations...

smoothing complete - recomputing first and second fundamental forms...

=

mris_euler_number ./lh.pial-outer-smoothed

=

euler # = v-e+f = 2g-2: 64236 - 192702 + 128468 = 2 --> 0 holes

  F =2V-4:  128468 = 128472-4 (0)

  2E=3F:385404 = 385404 (0)


total defect index = 0

=

mris_convert -n lh.pial-outer-smoothed
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc

=

=

find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_2521_.m');
exit

=


< M A T L A B (R) >

  Copyright 1984-2015 The MathWorks, Inc.

   R2015a (8.5.0.197613) 64-bit (glnxa64)

 February 12, 2015




For online documentation, see http://www.mathworks.com/support

For product information, visit www.mathworks.com.




 Academic License


>> FREESURFER_READ_SURF [v  1.2 ]

...reading surface file: lh.pial

...reading triangle file

...adding 1 to face indices for matlab compatibility.

...done (  0.05 sec)


FREESURFER_READ_SURF [v  1.2 ]

...reading surface file: lh.pial-outer-smoothed

...reading triangle file

...adding 1 to face indices for matlab compatibility.

...done (  0.01 sec)



deltaT =


   12.1200



=

make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_2521_.m');
exit

=


< M A T L A B (R) >

  Copyright 1984-2015 The MathWorks, Inc.

   R2015a (8.5.0.197613) 64-bit (glnxa64)

 February 12, 2015




For online documentation,

Re: [Freesurfer] LGI problem

2015-04-30 Thread Marie Schaer

Hi Alan,

Do you have the image processing toolbox installed in matlab? If not, I guess 
this is the source of the error.

Best,

Marie

On Apr 30, 2015, at 7:51 AM, Alan Francis 
mailto:alandarkene...@gmail.com>> wrote:

Hi Marie:

I am trying to run the LGI post processing step on 60 ASD subjects. I am using 
FreeSurfer 5.3. The recons went well and the processed brains look great. 
However when I run the LGI step, I am getting the following error which is as 
follows: Could you please help me?

[alanf@micc FreeSurfer_5.3]$ recon-all -s Asperger1 -localGI

INFO: FreeSurfer build stamps do not match

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514

Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /data/alanf/FreeSurfer_5.3

Actual FREESURFER_HOME /cm/shared/freesurfer

-rwxr-xr-x 1 alanf fiarl 963340 Apr 30 10:30 
/data/alanf/FreeSurfer_5.3/Asperger1/scripts/recon-all.log

Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 
x86_64 x86_64 GNU/Linux

INFO: current FREESURFER_HOME does not match that of previous processing.

Current: /cm/shared/freesurfer

Previous: /usr/local/freesurfer/stable5_3_0/

/data/alanf/FreeSurfer_5.3/Asperger1/surf

#

#@# Local Gyrification Index lh Thu Apr 30 10:35:41 EDT 2015

 mris_compute_lgi --i lh.pial

=

rm -Rf /data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial

=

=

mkdir -p /data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial

=

=

mris_fill -c -r 1 lh.pial 
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz

=

reading surface from lh.pial...

writing filled volume to 
/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...

conforming output volume

setting resolution for intermediate calculations to 1.

=

make_outer_surface('/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit

=

< M A T L A B (R) >

  Copyright 1984-2014 The MathWorks, Inc.

R2014a (8.3.0.532) 64-bit (glnxa64)

 February 11, 2014

To get started, type one of these: helpwin, helpdesk, or demo.

For product information, visit www.mathworks.com.

>> reading filled volume...

closing volume...

Undefined function 'fspecial' for input arguments of type 'char'.

Error in make_outer_surface (line 31)

Gaussian = fspecial('gaussian',[2 2],1);

>>

ERROR: make_outer_surface did not create output file 
'/data/alanf/FreeSurfer_5.3/Asperger1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!

Linux micc 2.6.32-358.el6.x86_64 #1 SMP Tue Jan 29 11:47:41 EST 2013 x86_64 
x86_64 x86_64 GNU/Linux

recon-all -s Asperger1 exited with ERRORS at Thu Apr 30 10:35:55 EDT 2015

--
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Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.edu

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