Hello Freesurfer,
For the longitudinal pipeline, the website/ recon-all -help suggested that I calculate the different on the results from the longitudinal command (e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were named 1001_Baseline.long.longbase and 1001_Followup.long.longbase; is there a command i can use to preform this?
Second question, i want to extract the output of the longitudinal pipeline using asegstats2table and aparcstats2table commands. what flag/s should i include in the original command to perform this?
Thanks. Paul
Hi Paul,
for the statistical analysis take a look at the available options here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics
for asegstats2table you can use the --qdec-long flag with an appropriate text file containing the columns fsid and fsid-base . This will convince the script to look for the stats in the *.long.basename directories.
Best, Martin
Am 26.09.2017 um 17:50 schrieb miracle ozzoude:
Hello Freesurfer,
For the longitudinal pipeline, the website/ recon-all -help suggested that I calculate the different on the results from the longitudinal command (e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were named 1001_Baseline.long.longbase and 1001_Followup.long.longbase; is there a command i can use to preform this?
Second question, i want to extract the output of the longitudinal pipeline using asegstats2table and aparcstats2table commands. what flag/s should i include in the original command to perform this?
Thanks. Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you very much Martin for your response. I do understand the statistical analysis ascept, my question was more in line with the last step (i.e. step 4) of the work flow summary ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing). You suggested we calculate the difference between the timepoints. Is there a command to perform this operation?
Also, will the "-qdec-long" flag replace the "--s" flag because the qdec table will contain the names of the fsid?
Best, Paul
On Wed, Sep 27, 2017 at 11:38 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu
wrote:
Hi Paul,
for the statistical analysis take a look at the available options here:
https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics
for asegstats2table you can use the --qdec-long flag with an appropriate text file containing the columns fsid and fsid-base . This will convince the script to look for the stats in the *.long.basename directories.
Best, Martin
Am 26.09.2017 um 17:50 schrieb miracle ozzoude:
Hello Freesurfer,
For the longitudinal pipeline, the website/ recon-all -help suggested that I calculate the different on the results from the longitudinal command (e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were named 1001_Baseline.long.longbase and 1001_Followup.long.longbase; is there a command i can use to preform this?
Second question, i want to extract the output of the longitudinal pipeline using asegstats2table and aparcstats2table commands. what flag/s should i include in the original command to perform this?
Thanks. Paul
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Hi Paul,
step 4 basically means that you should take results from the *.long.baseid directories and not look at the original cross sectional directories or the base output. The page on statistic describes different tools to do that.
Yes, --s is replaced. All information on the subject ids is taken from the longitudinal qdec table file.
(Note here the naming is a little confusing, the longitudinal qdec table format follows and extends the original qdec table format, but it cannot be used in the Qdec too).
Best, Martin
Am 27.09.2017 um 18:02 schrieb miracle ozzoude:
Thank you very much Martin for your response. I do understand the statistical analysis ascept, my question was more in line with the last step (i.e. step 4) of the work flow summary (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing). You suggested we calculate the difference between the timepoints. Is there a command to perform this operation?
Also, will the "-qdec-long" flag replace the "--s" flag because the qdec table will contain the names of the fsid?
Best, Paul
On Wed, Sep 27, 2017 at 11:38 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Paul, for the statistical analysis take a look at the available options here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics <https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics> for asegstats2table you can use the --qdec-long flag with an appropriate text file containing the columns fsid and fsid-base . This will convince the script to look for the stats in the *.long.basename directories. Best, Martin Am 26.09.2017 um 17:50 schrieb miracle ozzoude:Hello Freesurfer, For the longitudinal pipeline, the website/ recon-all -help suggested that I calculate the different on the results from the longitudinal command (e.g. tp2.long.longbase - tp1.long.longbase). Let say, my timepoints were named 1001_Baseline.long.longbase and 1001_Followup.long.longbase; is there a command i can use to preform this? Second question, i want to extract the output of the longitudinal pipeline using asegstats2table and aparcstats2table commands. what flag/s should i include in the original command to perform this? Thanks. Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> 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 <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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