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
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 georginangel@gmail.com Date: Thursday, January 26, 2023 at 1:02 PM To: "Iglesias Gonzalez, Juan E." JIGLESIASGONZALEZ@mgh.harvard.edu, "freesurfer@nmr.mgh.harvard.edu" 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
freesurfer@nmr.mgh.harvard.edu
-
Georgina Angelopoulou -
Iglesias Gonzalez, Juan E.