[Freesurfer] Tkmedit question
Dear All, I am trying to understand what should be my -fthresh and -fmax or -fmin and -fmax values while visualizing in tkmedit the significant map of uncorrected results so I can see all the clusters in this map. Further,I want to see what clusters from this map did not survived after corrections by multiple comparison for cluster voxel-wise equal 3. Thank you. Antonella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
Re: [Freesurfer] Tkmedit question
Hi Antonella it's hard for us to know without seeing your data, but certainly setting them both to 0 will show you everything Bruce On Wed, 21 Mar 2012, Antonella Kis wrote: Dear All, I am trying to understand what should be my -fthresh and -fmax or -fmin and -fmax values while visualizing in tkmedit the significant map of uncorrected results so I can see all the clusters in this map. Further,I want to see what clusters from this map did not survived after corrections by multiple comparison for cluster voxel-wise equal 3. Thank you. Antonella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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.
[Freesurfer] tkmedit question
Aloha FreeSurfers, I have a small question regarding tkmedit and the line tool. Is it possible to specify start and end point for a line on the tcl prompt? My goal is to create a line in a volume that is not parallel to one of the main axes. ATM I resort to turning the volume in question into a plane parallel to the line, but my overlays are not rotated accordingly so that is not as comfortable as I want it to be, and since it is somewhat exploratory pre-rotating volume and overlay is a bit unwieldy ;). For completeness, I am using 3.0.5 centos4-x86_64 under suse linux 10.1, but I guess that does not really matter. ahoi thanks for supplying these nice powerful tools Sebastian -- Sebastian Moeller Tel.: 04 21 - 2 18 - 78 38 oder 96 91 Fax.: 04 21 - 2 18 - 90 04 GSM: 01 62 - 3 25 45 59 [EMAIL PROTECTED] AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tkmedit question
On Tue, 2007-04-17 at 12:36 +0200, Sebastian Moeller wrote: Aloha FreeSurfers, I have a small question regarding tkmedit and the line tool. Is it possible to specify start and end point for a line on the tcl prompt? Sorry, no. My goal is to create a line in a volume that is not parallel to one of the main axes. ATM I resort to turning the volume in question into a plane parallel to the line, but my overlays are not rotated accordingly so that is not as comfortable as I want it to be, and since it is somewhat exploratory pre-rotating volume and overlay is a bit unwieldy ;). For completeness, I am using 3.0.5 centos4-x86_64 under suse linux 10.1, but I guess that does not really matter. I'm sorry but I don't understand what you're trying to do here. Why do you need to create a line parallel to the main axes? What does this have to do with specifying a line on the shell? -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] tkmedit question
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
Re: [Freesurfer] tkmedit question
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
Re: [Freesurfer] tkmedit question
At this point I have a bfloat volume, that I loaded in tkmedit, and a .label file that contains the resulting ROI. How do I obtain the volume from that? Thanks, George P. On Tue, 28 Sep 2004, 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
