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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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