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Dear Paul, On Wed, 29 Jun 2016 15:22:06 +0800, KUN HSIEN CHOU <[log in to unmask]> wrote: >Dear Dr Gaser > >Thanks for your interpretation. Now I know the issue of template selection. >However I have the other issue about how to extract the ROI value of >fractal dimension, gyrification and sqrtsulc indices. The attached file is >the setting window of the module "Extract ROI-based surface values". After >running this module , I found the corresponding XML file only contains the >regional cortical thickness value. Is the current version only support to >extract regional cortical thickness information ? You have to select the other files instead of the thickness files to extract them. However, these values have to be extracted before using the function "Extract additional surface parameters". Best, Christian > >Best > >Paul > >2016-06-26 20:07 GMT+08:00 Christian Gaser <[log in to unmask]>: > >> Dear Paul, >> >> In the default CAT12 mode only the atlases that currently work can be >> selected. You are using the expert mode where not all atlases are prepared >> for ROI analysis. >> >> Best, >> >> Christian >> >> Am 25.06.2016 um 16:36 schrieb KUN HSIEN CHOU <[log in to unmask]>: >> >> Dear Dr Gaser >> >> Sorry to bother you , I think these two issues still occurred in the CAT12 >> r961. I also obtain the error message when I use the >> lh.aparc_freesrfer.annot ROI atlas to extract regional thickness >> information in CAT12 r958. There is no error occurred with I use other >> atlases (including DKT40JT , a2005s and a2009s atlases). >> >> For the error message part >> =========================================================== >> Running 'Extract ROI-based surface values' >> Failed 'Extract ROI-based surface values' >> Invalid field name: ''. >> In file >> "/Users/PaulSmith/Research_Software/spm12/toolbox/cat12/cat_surf_surf2roi.m" >> (v959), function "cat_surf_surf2roi" at line 205. >> >> The following modules did not run: >> Failed: Extract ROI-based surface values >> =========================================================== >> >> >> In addition, I also can not obtain other regional surface indices. The >> detail description of this issue is presented as follow: >> =========================================================== >> In addition to extract the regional cortical thickness value, I also want >> to extract the regional gyrification index, cortical complexity and sulcus >> depth at once. After specify 4 "Surface Data Files" in the "Extract >> ROI-based surface values" module and select different surface measurement >> for each "Surface Data Files" option, I found the generated "catROIs_*.xml" >> file always only contain the regional cortical thickness value and lost the >> other three surface indices. I also found the "Estimate mean values inside >> ROI" module only produce the CSV file for regional cortical thickness >> information. When I try to input the other xml file of different surface >> measurements , there is no CSV file output at all. >> ======================================================= >> >> Best >> >> Paul >> >> 2016-06-23 17:24 GMT+08:00 Christian Gaser <[log in to unmask]>: >> >>> Dear Paul, >>> >>> thanks for pointing to that issue. This should be now solved with the new >>> release r959. >>> >>> Best, >>> >>> Christian >>> >>> On Thu, 23 Jun 2016 09:41:53 +0100, Paul Chou <[log in to unmask]> >>> wrote: >>> >>> >Dear Dr Gaser and all CAT12 experts >>> > >>> >I faced the error message and some potential bugs when try to extract >>> the regional value of surface measurements. >>> > >>> >For the error message part : >>> > >>> >I obtain the error message when I use the lh.aparc_freesrfer.annot ROI >>> atlas to extract regional thickness information in CAT12 r958. There is no >>> error occurred with I use other atlases (including DKT40JT , a2005s and >>> a2009s atlases) >>> > >>> >The following is the log file of the error message: >>> > >>> >************************************************** >>> >Running 'Extract ROI-based surface values' >>> >'' >>> >'' >>> >Failed 'Extract ROI-based surface values' >>> >Invalid field name: ''. >>> >In file >>> "/Users/PaulSmith/Research_Software/spm12/toolbox/cat12/cat_surf_surf2roi.m" >>> (v953), function "cat_surf_surf2roi" at line 204. >>> > >>> >The following modules did not run: >>> >Failed: Extract ROI-based surface values >>> >*************************************************** >>> > >>> >For potential bug part : >>> > >>> >In addition to extract the regional cortical thickness value, I also >>> want to extract the regional gyrification index, cortical complexity and >>> sulcus depth at once. After specify 4 "Surface Data Files" in the "Extract >>> ROI-based surface values" module and select different surface measurement >>> for each "Surface Data Files" option, I found the generated "catROIs_*.xml" >>> file always only contain the regional cortical thickness value and lost the >>> other three surface indices. I also found the "Estimate mean values inside >>> ROI" module only produce the CSV file for regional cortical thickness >>> information. When I try to input the other xml file of different surface >>> measurements , there is no CSV file output at all. Are these bugs for >>> current CAT12 (version r958) ? >>> > >>> >Sorry for my influent English and hope hear back from you. >>> > >>> >Best >>> > >>> >Paul >>> >>> >>> >> >