Ji Jessica,
that's pretty low contrast. I would also bet that it's low bandwidth and
hence you have big temporal lobe B0 distortions that will change with
subject positioning. Are you stuck with this data going forward, or can you
change the acquisition parameters? If not, I think you will have to live
with lower reliability and sensitivity
cheers
Bruce
On Thu, 28 Jul 2011, Jessica Liu wrote:
Hi Bruce,
I was thinking it could be quality as well, since I asked about that in a
previous question where my group compared 3T and 1.5T data from the
same subject. Unfortunately we only obtained 1 scan for all of our subjects
and nearly all of our data is from a 1.5T scanner. I've attached
coronal, axial, and sagittal views with aseg+aparc, and one image without
aseg+aparc for a WM segmentation check. Thanks for your help!
Jessica
On Thu, Jul 28, 2011 at 11:39 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:
Hi Jessica
the problem may be data quality! At 1.5T with a volume coil we would
typically get 2 scans to average. A TR of 14 is pretty short
and will reduce the SNR, and a TE of 6 is quite long and will reduce
contrast. Can you send us a tif of one slice to look at?
Bruce
On Thu, 28 Jul 2011, Jessica Liu wrote:
Hi Martin,
When I did longitudinal analyses in the past, the output was very strange
even though I think I did everything correctly. If
it's not too
much trouble for you, could you please take a look at my data and tell me
what I've done wrong? Since the files are so
large, how would I
send over my data? Also, I'm using is a head coil 1.5T single-channel GE
scanner. The sequence I'm using is 3D SPGR with TR
= 14 msec, TE =
6.2 msec, TI = 450.0, FOV 24 cm, data acquisition matrix = 256x192, and
124 slices with 1.6 mm thickness. Your help is truly
appreciated!
Jessica
On Thu, Jul 28, 2011 at 7:37 AM, Martin Reuter
<mreu...@nmr.mgh.harvard.edu> wrote:
Hi Jessica,
I'd recommend to run the -base and the -long on these and see what
happens. If you then still see these differences, maybe we can take a
look at your data to figure out what causes this. It could be that
the
WM segmentation fails somewhere. Anyway, the longitudinal stream
should
help fix these things.
Are these mprages or multi echo mprages? 3T? what coil?
Best, Martin
On Wed, 2011-07-27 at 18:01 -0700, Jessica Liu wrote:
> Hi Bruce,
>
> Well for one of the subjects, the total temporal lobe volume from the
> first scan was 149937 mm3, and the second scan's total temporal lobe
> volume was 183121 mm3. These numbers were found by summing the
> volumes from the entorhinal, fusiform, parahippocampal, temporal pole,
> transverse temporal, and the inferior, middle, and superior temporal
> sections found in the lh.aparc.stats, rh.aparc.stats, and wmparc.stats
> for the respective scans. Hippocampus volumes were found by summing
> the right and left parts found in aseg.stats.
>
> Jessica
>
> On Wed, Jul 27, 2011 at 5:37 PM, Bruce Fischl
> <fis...@nmr.mgh.harvard.edu> wrote:
> how are you computing the 20% difference? We definitely don't
> see this, and Martin has done extensive testing of
> repeatability.
> Bruce
>
>
>
> On Wed, 27 Jul 2011, Jessica Liu wrote:
>
> Hi Martin,
>
> Thanks for getting back to me. Actually I have two
> young controls who have 20% differences between two
> scans a day apart. Visually, there
> are not abnormalities for the surfaces and hippocampus
> in both subjects i.e. on tkmedit, the color of the
> hippocampus area (yellow) looks
> alright to me. I don't see any motion artifacts
> either.
>
> Jessica
>
> On Wed, Jul 27, 2011 at 12:15 PM, Martin Reuter
> <mreu...@nmr.mgh.harvard.edu> wrote:
> Hi Jessica,
>
> I don't think this is normal. Is this a single
> subject? Of course in a
> single subject lots of stuff can go wrong. Are
> the surfaces correct? And
> the hippo label? Are there motion artifacts in
> the image etc.
>
> Anyway, you should process this with the
> longitudinal stream:
>
> http://freesurfer.net/fswiki/LongitudinalProcessing
> which should increase repeatability.
>
> Best, Martin
>
>
> On Wed, 2011-07-27 at 09:01 -0700, Jessica Liu wrote:
> > Hi,
> >
> > We found 20% differences in temporal lobe brain
> volume and ca. 5%
> > difference in the hippocampus volume between two
> data sets of a young
> > normal volunteer scanned 2 days apart.
> >
> > We use the one-step 19 hours recon-all -all
> procedure and directly sum
> > select values taken from the lh.aparc.stats,
> rh.aparc.stats, and
> > wmparc.stats. The values summed were based on
> information given from
> >
>
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-April/005000.html
> >
> > My question is, are these observations normal for
> Freesurfer? Any
> > comments are greatly appreciated. Thanks!
> > --
> > Pom & Jessica
> >
> >
> >
> > _______________________________________________
> > 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 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.
