Hi list. I'm looking mailing list to find responce to this question. "Estimated Total Intra Cranial Vol" obtained by asegstats2table also included ventricles volume? I'd like to assess the volumetric changes of a subcortical structures. Do you advise me to consider "Estimated Total Intra Cranial Vol" (with or without ventricles?) or, alternatively, subcortical brain volume?
Thank you very much,
Stefano
Hi Stefano, the ICV is not computed by counting voxels. See this page:
http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV
doug
On 08/20/2013 02:34 PM, stdp82@virgilio.it wrote:
Hi list.
I'm looking mailing list to find responce to this question.
"Estimated Total Intra Cranial Vol" obtained by asegstats2table also included ventricles volume?
I'd like to assess the volumetric changes of a subcortical structures. Do you advise me to consider "Estimated Total Intra Cranial Vol" (with or without ventricles?) or, alternatively, subcortical brain volume?
Thank you very much,
Stefano
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Freesurfers, I am re-running an older analysis in stable3. I know that this version is out of date, but I'm trying to line up new data with old data. I have previously run a script that uses the func2roi-sess command with no problems. Now, when I run the same script, I'm getting a new error -
command line: func2roi-sess -roidef M6_LH_t6_0_sm5_0thresh -analysis tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5 -maskcontrast tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5_contrast -labelfile /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_ctrl1_sess1_recon/label/M6_LH_CD_R01BTX_ctrl1_sess1.label -maskthresh 6.0 -masktail pos -maskmap t -s CD_R01BTX_ctrl1_sess1 -df sessdirfile
returns: ---------------------------------------------------------- func2roi-sess logfile is /autofs/cluster/ablood/1/AdjustedParadigmFiles/log/func2roi-sess.log ---------------------------------------------------------- ERROR: cannot find tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5/analysis.info
The analysis.info file (and all other files called upon in the script) are in place and seem to be correctly constructed. The log file (/cluster/ablood/1/AdjustedParadigmFiles/log/func2roi-sess.log) doesn't give me any new info.
Did something change in the last ~6 months with the func2roi command? Any insights on why it can't find the analysis.info file?
Thank you! Jeff
Hello Freesurfers, I am re-running an older analysis in stable3. I know that this version is out of date, but I'm trying to line up new data with old data. I have previously run a script that uses the func2roi-sess command with no problems. Now, when I run the same script, I'm getting a new error -
command line: func2roi-sess -roidef M6_LH_t6_0_sm5_0thresh -analysis tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5 -maskcontrast tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5_contrast -labelfile /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_ctrl1_sess1_recon/label/M6_LH_CD_R01BTX_ctrl1_sess1.label -maskthresh 6.0 -masktail pos -maskmap t -s CD_R01BTX_ctrl1_sess1 -df sessdirfile
returns: ---------------------------------------------------------- func2roi-sess logfile is /autofs/cluster/ablood/1/AdjustedParadigmFiles/log/func2roi-sess.log ---------------------------------------------------------- ERROR: cannot find tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5/analysis.info
The analysis.info file (and all other files called upon in the script) are in place and seem to be correctly constructed. The log file (/cluster/ablood/1/AdjustedParadigmFiles/log/func2roi-sess.log) doesn't give me any new info.
Did something change in the last ~6 months with the func2roi command? Any insights on why it can't find the analysis.info file?
Thank you! Jeff
Hi Jeff, func2roi-sess is obsolete (should not have included it in 5.3). You need to use a combination of funcroi-config and funcroi-sess. See the help with funcroi-config doug
On 09/05/2013 03:45 PM, jwaugh@nmr.mgh.harvard.edu wrote:
Hello Freesurfers, I am re-running an older analysis in stable3. I know that this version is out of date, but I'm trying to line up new data with old data. I have previously run a script that uses the func2roi-sess command with no problems. Now, when I run the same script, I'm getting a new error
command line: func2roi-sess -roidef M6_LH_t6_0_sm5_0thresh -analysis tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5 -maskcontrast tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5_contrast -labelfile /cluster/ablood/1/AdjustedParadigmFiles/Adjusted_recons/CD_R01BTX_ctrl1_sess1_recon/label/M6_LH_CD_R01BTX_ctrl1_sess1.label -maskthresh 6.0 -masktail pos -maskmap t -s CD_R01BTX_ctrl1_sess1 -df sessdirfile
returns: ---------------------------------------------------------- func2roi-sess logfile is /autofs/cluster/ablood/1/AdjustedParadigmFiles/log/func2roi-sess.log
ERROR: cannot find tap_lh_long_CD_R01BTX_ctrl1_sess1_sm5/analysis.info
The analysis.info file (and all other files called upon in the script) are in place and seem to be correctly constructed. The log file (/cluster/ablood/1/AdjustedParadigmFiles/log/func2roi-sess.log) doesn't give me any new info.
Did something change in the last ~6 months with the func2roi command? Any insights on why it can't find the analysis.info file?
Thank you! Jeff
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
jwaugh＠nmr.mgh.harvard.edu -
stdp82＠virgilio.it