Hi,
I have been able to do the longitudinal processing steps for a number of subjects with 3 time points each, and then extract the generated statistics using aparcstats2table and asegstats2table. Is it possible to perform longitudinal analysis of the hippocampal subfields? If so, could someone point me to how to perform this analysis, as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the output files I've generated.
Thank you.
Salil Soman, MD, MS
Hi Salil,
just run the hippo-subfields on the longitudinal results like this:
recon-all -long <tpNi> <templateid> -hippo-subfields
to generate the subfield data. I am not familiar with the kvlQuantify... script and think it works on all subjects in the Subjects dir. Not sure what the best way is to solve this as your subject dir contains also the cross and base results. Probably you can run the script and it will simply skip the cross and base directories (as no -hippo-subfields was run on them).
Best, Martin
On 01/05/2014 01:40 AM, Salil Soman wrote:
Hi,
I have been able to do the longitudinal processing steps for a number of subjects with 3 time points each, and then extract the generated statistics using aparcstats2table and asegstats2table. Is it possible to perform longitudinal analysis of the hippocampal subfields? If so, could someone point me to how to perform this analysis, as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the output files I've generated.
Thank you.
Salil Soman, MD, MS
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you Martin.
I will try this approach. I was able to temporarily move the longitudinal subject data to its own folder to run aparc2table and aseg2table. Hopefully this will also work for the hippocampal subfield script.
Best wishes,
Sal
Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System On Jan 7, 2014 8:07 AM, "Martin Reuter" mreuter@nmr.mgh.harvard.edu wrote:
Hi Salil,
just run the hippo-subfields on the longitudinal results like this:
recon-all -long <tpNi> <templateid> -hippo-subfields
to generate the subfield data. I am not familiar with the kvlQuantify... script and think it works on all subjects in the Subjects dir. Not sure what the best way is to solve this as your subject dir contains also the cross and base results. Probably you can run the script and it will simply skip the cross and base directories (as no -hippo-subfields was run on them).
Best, Martin
On 01/05/2014 01:40 AM, Salil Soman wrote:
Hi,
I have been able to do the longitudinal processing steps for a number of subjects with 3 time points each, and then extract the generated statistics using aparcstats2table and asegstats2table. Is it possible to perform longitudinal analysis of the hippocampal subfields? If so, could someone point me to how to perform this analysis, as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the output files I've generated.
Thank you.
Salil Soman, MD, MS
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129
Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Sal,
asegstats2table (and aparc..) will take the longitudinal qdec file and then automatically select the *.long.* directories to create the table. So there is no need to move them to a separate folder.
The longitudinal qdec file is simply a table with at least 2 columns (for stacking results, 2 is enough): fsid fsid-base
where fsid is the id of the time point and fsid-base is the name of the base :
fsid fsid-base me1 me me2 me you1 you you2 you you3 you
etc.. It will then take the data from me1.long.me ... You can have other columns, e.g. time_from_baseline, age, gender, disease_group, drug_status, ...
Best, Martin
On 01/08/2014 01:27 PM, Salil Soman wrote:
Thank you Martin.
I will try this approach. I was able to temporarily move the longitudinal subject data to its own folder to run aparc2table and aseg2table. Hopefully this will also work for the hippocampal subfield script.
Best wishes,
Sal
Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
On Jan 7, 2014 8:07 AM, "Martin Reuter" <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Salil, just run the hippo-subfields on the longitudinal results like this: recon-all -long <tpNi> <templateid> -hippo-subfields to generate the subfield data. I am not familiar with the kvlQuantify... script and think it works on all subjects in the Subjects dir. Not sure what the best way is to solve this as your subject dir contains also the cross and base results. Probably you can run the script and it will simply skip the cross and base directories (as no -hippo-subfields was run on them). Best, Martin On 01/05/2014 01:40 AM, Salil Soman wrote:Hi, I have been able to do the longitudinal processing steps for a number of subjects with 3 time points each, and then extract the generated statistics using aparcstats2table and asegstats2table. Is it possible to perform longitudinal analysis of the hippocampal subfields? If so, could someone point me to how to perform this analysis, as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the output files I've generated. Thank you. Salil Soman, MD, MS _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> Email: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web :http://reuter.mit.edu 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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