Dear all !
I know, this has been discussed a lot in the forum, however, I am still not
sure, whether my analysis pipeline is correct.
I simply want to compare volumes of FS vs. manual segmentation in the
hippocampus and calculate the dice coefficient. So these are my steps:
1. mri_convert
A) I don't think this matter, but Doug can correct me if I'm wrong.
B) You can't partial-volume correct the DICE, but you can compare the
volumes after partial-volume corrections.
C) There are references in our Neuron paper on the definition of the
hippocampus (Caviness, Makris, Kennedy papers)
I would use mri_label2vol to map your manual labels into the conformed
space (using mri_label2vol) (and assuming that your native space has
voxel sizes 1mm or greater). This is just a single step (I did not
quite follow all the steps you have below). No need to run any
registration, just
Hi Doug,
I wanted to follow up on this. Would you be able to provide a workaround
for contrasting multiple taskregs against each other? Is there something I
can try in the meantime? Thanks, Caspar
2014-11-10 13:54 GMT-05:00 Caspar M. Schwiedrzik cschwie...@rockefeller.edu
:
Hi Doug,
thanks
Actually, you can still do each contrast individually. Each will produce
ces and cesvar files. Take the difference between the ces files and the
average of the cesvar files, then feed the result into mri_glmfit FFX
doug
On 11/11/2014 11:56 AM, Caspar M. Schwiedrzik wrote:
Hi Doug,
I wanted
ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar
2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu:
Actually, you can still do each contrast individually. Each will produce
ces and cesvar files. Take the difference between the ces files and the
It will be the same as the DOF of the individual contrasts (don't sum them).
On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar
2014-11-11 12:04 GMT-05:00 Douglas N Greve gr...@nmr.mgh.harvard.edu
I'll start the process thursday.
On 11/11/2014 12:04 PM, Douglas N Greve wrote:
It will be the same as the DOF of the individual contrasts (don't sum them).
On 11/11/2014 12:58 PM, Caspar M. Schwiedrzik wrote:
ok, I will try that. How do I get the degrees of freedom? Thanks! Caspar
Sorry, Though we do have freesurfer pipelines we run in Madison, I
responded to wrong email.
Bill Taylor
Center for High Throughput Computing
Computer Sciences
University of Wisconsin, Madison
On 11/11/2014 12:09 PM, Bill Taylor wrote:
I'll start the process thursday.
On 11/11/2014 12:04 PM,
Hi Doug,
just to clarify:
If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would compute
ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6))
and
cesvar=mean(cesvar(taskreg(1,2,3,4,5,6)))
Is that correct?
Thanks, Caspar
2014-11-11 13:19 GMT-05:00 Bill Taylor b...@cs.wisc.edu:
yes
On 11/11/2014 01:28 PM, Caspar M. Schwiedrzik wrote:
Hi Doug,
just to clarify:
If I want to contrast taskreg 1 vs. mean(taskreg 2,3,4,5,6), I would
compute
ces= ces(taskreg 1) - mean(ces(taskreg 2,3,4,5,6))
and
cesvar=mean(cesvar(taskreg(1,2,3,4,5,6)))
Is that correct?
Thanks,
Dear FreeSurfer experts
I have one question regarding the labeling of cortical structures
using the Desikan-Killiany atlas and couldn't find any information in
the archives. As far as I read, this atlas has been composed by
including 40 subjects of broad age ranges (19-86 years of age),
Hi Martina
no, probably not. We use the geometry of the gray/white boundary to drive
the registration and segmentation, and it is completely invariant to gray
matter atrophy and it would take huge amounts of white matter atrophy to
cahnge it enough to mess things up.
cheers
Bruce
On Tue, 11
Hi Bruce
Thank you very much for this helpful and quick information! My
parcellations indeed look very good but I started wondering about the
DK atlas.
Best wishes
Martina
Quoting Bruce Fischl fis...@nmr.mgh.harvard.edu on Tue, 11 Nov 2014
13:58:34 -0500 (EST):
Hi Martina
no, probably
Hi Doug,
I am a little bit confused about the variance. Shouldn't the relevant
variance be the variance over the differences, not the mean variance over
all?
Of course at the level of ces and cesvar, I do not have access to the
timepoint by timepoint differences anymore.
Is there another way to do
To add to this thread, you could also use the parcellations from the DKT
atlas that we provide, produced by the -cortparc3 flag of recon-all
(which is run by default), which is based on 40 healthy subjects from
the Mindboggle-101 project, described here:
http://mindboggle.info/data.html
N.
On
Hi Doug and Bruce,
I posted this question before and I hope that you can help me to find an answer
for this issue!
I started recently using Tracula to do tractography for my DTI data. I did the
analysis exactly as mentioned in wiki and every thing ran smoothly. The problem
started when I was
Hello Sir,
I'm using FreeSurfer through Virtual Box. I tried the below command for
reslicing my volume according to a reference volume but the process gets
stuck at reading volume.
*mri_convert A.nii.gz A.resliced.nii.gz -rl B.nii.gz*
A: Volume to be resampled / resliced
B: Reference Volume
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