Re: [Freesurfer] Problem with quantifyHAsubregions.sh

2023-01-26 Thread Iglesias Gonzalez, Juan E. 
Please try the command without the -4393 because now the code believes that 
-4393 is the output text file and testhippo.txt is the subjects directory…
Cheers,
/E

--
Juan Eugenio Iglesias
http://www.jeiglesias.com

From: Georgina Angelopoulou 
Date: Thursday, January 26, 2023 at 1:02 PM
To: "Iglesias Gonzalez, Juan E." , 
"freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Problem with quantifyHAsubregions.sh


External Email - Use Caution
Dear Eugenio,

Thank you for your kindly reply.
Actually, I tried both options and neither worked. When I renamed one subject 
and ran the following command, an error occurred. Please see below:

Georginas-MacBook-Pro:ALBION georginaangelopoulou$ quantifyHAsubregions.sh 
hippoSf T1 -4393 testhippo.txt
Gathering results from subjects in:
   testhippo.txt
Using the prefix name:
   hippoSf
Using the suffix name:
   T1
And writing them to:
   -4393
/Applications/freesurfer/7.3.2/bin/quantifyHAsubregions.sh: line 8: cd: 
testhippo.txt: No such file or directory
failed to do cd testhippo.txt

and then when I tried the following, another error occured:
Georginas-MacBook-Pro:ALBION georginaangelopoulou$ quantifyHAsubregions.sh 
hippoSf T1 testhippo.txt -4393
Gathering results from subjects in:
   -4393
Using the prefix name:
   hippoSf
Using the suffix name:
   T1
And writing them to:
   testhippo.txt
/Applications/freesurfer/7.3.2/bin/quantifyHAsubregions.sh: line 8: cd: -4: 
invalid option
cd: usage: cd [-L|-P] [dir]
failed to do cd -4393

The second option with the script you sent me, did not provide any error, yet 
no output appeared. Could you please help me with that?

Is there any possibility that this has to do with the version I used (7.3.2), 
using the following command: segment_subregions hippo-amygdala --cross 6608
Moreover, when compared this analysis with a previous version of Freesurfer, 
using the same subject, I noticed that all subfields’ indices are very similar 
except from three (Whole_hippocampus, Whole_hippocampal_body and 
Whole_hippocampal_head) for which all values were doubled compared to the 
previous version of FS. Could you please tell me why did this happened and 
which version should I trust?

Apologies for such a long email.
Thank you in advance.
Best,
Georgina
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Re: [Freesurfer] Problem with quantifyHAsubregions.sh

2023-01-26 Thread Georgina Angelopoulou 
External Email - Use Caution

Dear Eugenio,
 
Thank you for your kindly reply. 
Actually, I tried both options and neither worked. When I renamed one subject 
and ran the following command, an error occurred. Please see below:
 
Georginas-MacBook-Pro:ALBION georginaangelopoulou$ quantifyHAsubregions.sh 
hippoSf T1 -4393 testhippo.txt
Gathering results from subjects in: 
   testhippo.txt 
Using the prefix name: 
   hippoSf
Using the suffix name: 
   T1
And writing them to: 
   -4393 
/Applications/freesurfer/7.3.2/bin/quantifyHAsubregions.sh: line 8: cd: 
testhippo.txt: No such file or directory
failed to do cd testhippo.txt
 
and then when I tried the following, another error occured:
Georginas-MacBook-Pro:ALBION georginaangelopoulou$ quantifyHAsubregions.sh 
hippoSf T1 testhippo.txt -4393
Gathering results from subjects in: 
   -4393 
Using the prefix name: 
   hippoSf
Using the suffix name: 
   T1
And writing them to: 
   testhippo.txt 
/Applications/freesurfer/7.3.2/bin/quantifyHAsubregions.sh: line 8: cd: -4: 
invalid option
cd: usage: cd [-L|-P] [dir]
failed to do cd -4393
 
The second option with the script you sent me, did not provide any error, yet 
no output appeared. Could you please help me with that?
 
Is there any possibility that this has to do with the version I used (7.3.2), 
using the following command: segment_subregions hippo-amygdala --cross 6608
Moreover, when compared this analysis with a previous version of Freesurfer, 
using the same subject, I noticed that all subfields’ indices are very similar 
except from three (Whole_hippocampus, Whole_hippocampal_body and 
Whole_hippocampal_head) for which all values were doubled compared to the 
previous version of FS. Could you please tell me why did this happened and 
which version should I trust?
 
Apologies for such a long email. 
Thank you in advance. 
Best,
Georgina___
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 .
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Re: [Freesurfer] Problem with quantifyHAsubregions.sh

2023-01-23 Thread Iglesias Gonzalez, Juan E. 
Dear Georgina,
Can you please send me the list of files (a screenshot is also fine) inside the 
mri directory of any of your subjects, please?
Cheers,
/Eugenio


--
Juan Eugenio Iglesias
http://www.jeiglesias.com

From:  on behalf of Georgina 
Angelopoulou 
Reply-To: Freesurfer support list 
Date: Monday, January 23, 2023 at 17:28
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] Problem with quantifyHAsubregions.sh


External Email - Use Caution
Hello Freesurfer experts,

I have accomplished hippocampal subfields segmentation using Freesurfer 7.3.2. 
However, I have trouble when I try to gather all volumes of all subjects in one 
single txt file.
I type quantifyHAsubregions.sh hippoSf T1 testhippo.txt

And the output that appears is:


Gathering results from subjects in:

   /Users/…/ALBION

Using the prefix name:

   hippoSf

Using the suffix name:

   T1

And writing them to:

   testhippo.txt



However, there is no txt file in my directory. I have tried included all 
subjects’ names in the script and I am still facing the same problem. Do you 
have any ideas to resolve this?



Thank you in advance,

Best,

Georgina
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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://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.