External Email - Use Caution
Dear Freesurfer experts,
I used the freesurfer dev version to estimate hippocampal subfields using mode B (additional scan).
All have worked fine although when I tried to export the results I can not find the txt file created
This is the output
rmnlab1:~ neucoga$ quantifyHippocampalSubfields.sh HIPOAMYG HipoAmyg_results.txt /Applications/freesurfer/subjects/4001T1
Gathering results from subjects in:
/Applications/freesurfer/subjects/4001T1
Using the suffix name:
HIPOAMYG
And writing them to:
HipoAmyg_results.txt
Where is saved the HipoAmyg_results.txt file?? I have searched it and I can't find it...
Excuse me for this basic question.
Thanks in advance.
Best regards,
Dear Steve, Can you please send us: - The segmentation command you used for a sample subject - A list of the files under the mri directory for that subject. Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Steve Petersen marfneuro@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 11 December 2019 at 03:54 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal subfields: exporting results
External Email - Use Caution Dear Freesurfer experts,
I used the freesurfer dev version to estimate hippocampal subfields using mode B (additional scan).
All have worked fine although when I tried to export the results I can not find the txt file created
This is the output
rmnlab1:~ neucoga$ quantifyHippocampalSubfields.sh HIPOAMYG HipoAmyg_results.txt /Applications/freesurfer/subjects/4001T1
Gathering results from subjects in:
/Applications/freesurfer/subjects/4001T1
Using the suffix name:
HIPOAMYG
And writing them to:
HipoAmyg_results.txt
Where is saved the HipoAmyg_results.txt file?? I have searched it and I can't find it...
Excuse me for this basic question.
Thanks in advance.
Best regards,
External Email - Use Caution
Dear Eugenio,
I noticed what was the problem. I used freesurfer dev version with the following command:
segmentHA_T2.sh
I tried to export the hippocampal and amygdala results of several subjects with these commands and now everything works fine.
quantifyHAsubregions.sh hippoSf HIPO-AMY hippocampal_results.txt
quantifyHAsubregions.sh amygNuc HIPO-AMY amygdala_results.txt
Is there some difference between the *segmentHA_T2.sh* that I used and the command of the website? In that case I would like to use the most appropriated.
recon-all -s <subject_name> *-hippocampal-subfields-T2* <file name of additional scan> <analysisID>
Thanks in advance.
Best regards,
Yes, you should be following the instructions here: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmy... rather than the wiki page for 6.0 here: https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Steve Petersen marfneuro@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Wednesday, 11 December 2019 at 10:28 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal subfields: exporting results
External Email - Use Caution Dear Eugenio,
I noticed what was the problem. I used freesurfer dev version with the following command:
segmentHA_T2.sh
I tried to export the hippocampal and amygdala results of several subjects with these commands and now everything works fine.
quantifyHAsubregions.sh hippoSf HIPO-AMY hippocampal_results.txt
quantifyHAsubregions.sh amygNuc HIPO-AMY amygdala_results.txt
Is there some difference between the segmentHA_T2.sh that I used and the command of the website? In that case I would like to use the most appropriated.
recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of additional scan> <analysisID>
Thanks in advance.
Best regards,
freesurfer@nmr.mgh.harvard.edu
-
Iglesias Gonzalez, Juan E. -
Steve Petersen