Re: [Freesurfer] tkmedit question
Hello Brian, I found this email fascinating because I didn't know FS had the ability to measure hippocampal volumes. Naively, I tried your suggestion, but found that the mri/aseg directory doesn't exist. How is that normally created? At this point I am using a somewhat archaic (year old ... but stable) version of FS so that might be the problem. Any hints you can give would be greatly appreciated. Best regards, Ray Fix On Sep 28, 2004, at 3:57 PM, Brian T. Quinn wrote: mri_label_volume -s subject_name -l logfile segdir labelvalue(s) will output to the logfile the volumes for each of the labelvalue(s) you list. example: mri_label_volume -s s126 -l s126hipps.log $SUBJECTS_DIR/s126/mri/aseg 17 53 will output the hippocampal volumes for subject s126. -- brian t. quinn On Tue, 28 Sep 2004, George Papadimitriou wrote: Hi all, How can I compute the volume of a label created using tkmedit? Is there a program to do this, or is it sufficient to count the number of points listed in the label file and multiply by the volume per voxel? (And if so, is the volume per voxel the voxel size for my original 40 slice axial volume, or the voxel size for the 256 slice resampled volume that tkmedit displays?) Thanks, George P. ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit question
Hi Ray, we do indeed have full subcortical labeling (see Neuron, 2002 paper), but aren't able to distribute it yet. We will do so when able to, hopefully sometime in the next year. cheers, Bruce On Wed, 29 Sep 2004, Ray Fix wrote: Hello Brian, I found this email fascinating because I didn't know FS had the ability to measure hippocampal volumes. Naively, I tried your suggestion, but found that the mri/aseg directory doesn't exist. How is that normally created? At this point I am using a somewhat archaic (year old ... but stable) version of FS so that might be the problem. Any hints you can give would be greatly appreciated. Best regards, Ray Fix On Sep 28, 2004, at 3:57 PM, Brian T. Quinn wrote: mri_label_volume -s subject_name -l logfile segdir labelvalue(s) will output to the logfile the volumes for each of the labelvalue(s) you list. example: mri_label_volume -s s126 -l s126hipps.log $SUBJECTS_DIR/s126/mri/aseg 17 53 will output the hippocampal volumes for subject s126. -- brian t. quinn On Tue, 28 Sep 2004, George Papadimitriou wrote: Hi all, How can I compute the volume of a label created using tkmedit? Is there a program to do this, or is it sufficient to count the number of points listed in the label file and multiply by the volume per voxel? (And if so, is the volume per voxel the voxel size for my original 40 slice axial volume, or the voxel size for the 256 slice resampled volume that tkmedit displays?) Thanks, George P. ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] problem to source FreeSurfer.cshrc
Hello, I'm trying to install FreeSurfer0.8 on linux. Since the linux computer doesn't have an internet connection, I write off what from the shell: [EMAIL PROTECTED] sepirat]$ ls etc/ FreeSurfer.cshrc [EMAIL PROTECTED] sepirat]$tcsh : Command not found. : Command not found. : label not found. [EMAIL PROTECTED] ~]$ source etc/FreeSurfer.cshrc : Command not found. : Command not found. : label not found. [EMAIL PROTECTED] ~]$ newdefs newdefs: Command not found. I don't have a solid unix background. Is this a problem with tcsh? Sep -- +++ GMX DSL Premiumtarife 3 Monate gratis* + WLAN-Router 0,- EUR* +++ Clevere DSL-Nutzer wechseln jetzt zu GMX: http://www.gmx.net/de/go/dsl ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem to source FreeSurfer.cshrc
Where did you get the version you are trying to install, and what instructions are you using to install it? On Wed, 29 Sep 2004, Sepideh Sadaghiani wrote: Hello, I'm trying to install FreeSurfer0.8 on linux. Since the linux computer doesn't have an internet connection, I write off what from the shell: [EMAIL PROTECTED] sepirat]$ ls etc/ FreeSurfer.cshrc [EMAIL PROTECTED] sepirat]$tcsh : Command not found. : Command not found. : label not found. [EMAIL PROTECTED] ~]$ source etc/FreeSurfer.cshrc : Command not found. : Command not found. : label not found. [EMAIL PROTECTED] ~]$ newdefs newdefs: Command not found. I don't have a solid unix background. Is this a problem with tcsh? Sep -- +++ GMX DSL Premiumtarife 3 Monate gratis* + WLAN-Router 0,- EUR* +++ Clevere DSL-Nutzer wechseln jetzt zu GMX: http://www.gmx.net/de/go/dsl ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
