Re: [Freesurfer] mris_preproc --qdec-long problem

2013-06-04 Thread Christopher McCarthy
ing on all OS), > let me know. This is the command I use: > > cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#") > printf("%s.long.%s\n", $1, $2)}' > > to generate the subjects id's from the table's first two colum

[Freesurfer] Whole Brain Volume

2012-08-23 Thread Christopher McCarthy
Hello All, We are looking into alternative measures for whole brain volume to use for covarying, and the previous topic mentioned mris_volume as a possibility but it isn't located on the top of the aseg file. Has it been moved? Chris McCarthy ___ Frees

[Freesurfer] long_qdec_table

2013-03-13 Thread Christopher McCarthy
Hey All, I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat using the following command: long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat However, when I try and load it into QDEC afterwards I get the following error: Loading data

Re: [Freesurfer] long_qdec_table

2013-03-18 Thread Christopher McCarthy
are using and what > OS version, also the version of Python) > > Thanks, Martin > > > > On 03/13/2013 08:20 AM, Christopher McCarthy wrote: > > Hey All, > > I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat > using the following command: >

[Freesurfer] FreeSurfer Questions

2011-10-19 Thread Christopher McCarthy
Dear FreeSurfer Gurus, We are looking for a way to normalize the intensity histogram for our subjects. In the past we have used Brain Image Java, using FSL-Fast inhomogeneity corrections. Unfortunately we are unable to open the output files (.img, .hdr) in FreeSurfer. When trying to import the

[Freesurfer] -notalcheck question

2011-10-26 Thread Christopher McCarthy
Freesurfer Experts, I am having lots of success, and making progress, with FreeSurfer thus far. I have been able to load DICOMS into Slicer3 to reorient, and resample them, after using FSL to extract the brain. Loading these brains into FreeSurfer is straight forward, and I've run them through th