Dear Freesurfer experts,
I have run several subjects through the recon-all pipeline including the
hippocampal segmentation with freesurfer 6.0 on Ubuntu 16.04. However when
looking at the text file with the volumes it seems that all the numbers are
bigger than normal as all my subjects have MCI
Hi Michel Hu,
Is that a summed value of left and right hippocampus? That seems normal to me
since averaged total hippocamppal volumes for MCI have been typically reported
at around 2500-3500mm3.
Thanks,
--
Shane S
On 27 February 2017 at 09:44:27, Michel Hu (a...@live.nl) wrote:
Dear Freesurf
Dear Shane,
I apologize for not being clear. The reported value is of only one half of the
hippocampus.
I have only run 4 subjects of the 75 however they all have a reported value of
between 6000 to 1 mm^3 summed together for the hippocampus.
Sincerely,
Michel Hu
_
Hi Michel Hu,
Yes, that’s too large for MCI or even controls for that matter I think. Have
you checked the aseg.mgz? I generally find that the hippocampus is well
segmented, even in patients with a lot of atrophy.
Are you taking the measurements with the asegstats2table?
Sincerely,
--
Shane
Dear all,
I am new to FreeSurfer and I want to reproduce on 20 subjects the registration
strategy as explained in Fischl paper:
High-resolution inter-subject averaging and a coordinate system for the
cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, A.M.,
(1999). Human Brain
Dear Shane,
I have checked the aseg.mgz and in only one I would say the segmentation failed
however the others look fine and I'm taking the measurements from the text file
that is generated from the aseg.stats.
Should I redo the recon-all with a different input? I have always given
freesurfer T
Dear Michel,
Given your resolution 0.8x0.8x0.8, did you run recon-all with -hires flag? What
did you used T2 image for? As a -T2pial refinement? T2 image is not used for
hippocampal segmentation in standard recon-all stream.
But pay attention that with -hires you also have to alter default value
Dear Antonin,
I did use the T2 scan for the T2pial refinement during the recon-all however I
actually already preformed the hippocampal subfields and when i looked at the
txt file generated from that the results are quite similar.
I used the multispectral segmentation.
I didn't not use the -hire
Dear Michel,
by default in the recon-all the input images are resampled to 1x1x1mm3. To
disable this and retain your resolution, you have to add -hires flag (and adapt
the mris_inflate -n parameter).
This could improve the segmentation results, however I would not expect that it
is the reason
Dear Antonin,
Thank you for the assistance!
I really appreciate it.
My final goal is to determine the volume of the dentate gyrus however I first
wanted to establish if the volume of the whole hippocampus was within expected
boundaries before moving on to the dentate gyrus. Do you perhaps know i
Dear Michel,
not sure if I understand. Do you mean that you cropped your T2 to FOV 256 mm ?
I think that this should have no effect until you cropped parts of the brain.
Maybe, as a part of quality-check you can check whether your T2 is correctly
registered to T1 by inspection
T1_to_.v10.QC.
Dear Antonin,
I believe I figured out what I was doing wrong!
I forgot to correct the voxel volumes with the intracranial volumes.
After the correction I'm getting the expected values.
I was referring to the -cw256 flag and i will check if the T2 is correctly
registered to T1
Thanks again!
Since
Yes, it's the tail.
All subfield are segmented jointly.
Cheers
E
Sent from my phone, please excuse brevity and typos
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Jessica Sevick
Sent: Sunday, February 26, 2017 7:54:28 PM
To: Freesurfer support list
Hello Antonin and Doug,
I viewed it in tkregister2 and I think the co-registration worked. Is there
a way to extract info from both PET and anatomical to confirm the
co-registration?
Best,
Paul
On Sun, Feb 26, 2017 at 4:49 PM, Antonin Skoch wrote:
> Dear Paul,
>
> I think that the transform win
Hello!
I have gone through the TRACULA tutorial, and the tracts are pretty odd.
I'm wondering if I did something incorrectly, but as far as I can tell, I
followed the tutorial step by step. The individuals in question are
healthy, no irregularities in the brains. I have attached images of the
fmajo
I'm not sure what you mean. If the registration looks good, what do you
need to extract?
On 2/27/17 9:03 AM, miracle ozzoude wrote:
Hello Antonin and Doug,
I viewed it in tkregister2 and I think the co-registration worked. Is
there a way to extract info from both PET and anatomical to confir
It is hard to say from those pics what is wrong as you need to look at
the ?h.orig.nofix surface on the scans. It looks like there is a lot of
skull left there, so it may be that the surface is extending out to the
skull. I don't think it is a problem with the ventricles.
On 2/26/17 6:58 AM,
I have not actually tested it on the mni152 reg. It might (probably
does) work fine.
On 2/25/17 5:33 PM, Antonin Skoch wrote:
Dear Doug,
I was wondering, why do you prefer mni152reg to mri_coreg for
gregistration to MNI? According to help, mri_coreg is also able to do
12 DOF registration.
You can do the masking with mri_mask
On 2/26/17 7:04 AM, Shane Schofield wrote:
Dear Doug,
If I want to create a new volume that is registered to the MNIspace
(using mni1525reg), can I mask out other voxels that are not part of
the mni template brain? It is a PET volume (already in individua
Hello Doug,
Thanks for replying. I meant like coordinate points on both images to
compare (i.e., any metric different from visual inspection).
Best,
Paul.
On Mon, Feb 27, 2017 at 10:50 AM, Douglas Greve
wrote:
> I'm not sure what you mean. If the registration looks good, what do you
> need to ex
It should be created by recon-all. Check that subject to see whether it
finished or had an error
On 2/24/17 3:17 PM, Limachia, Gaurang (NIH/NINDS) [F] wrote:
Hello Freesurfer Experts,
I received this error while running the make_avg_subject script. I
would greatly appreciate it if you can p
Making a new folding atlas is not an easy task. I wrote a script to help
called "make_folding_atlas". It is a very time consuming process, and
the script assumes that you have access to a cluster running PBS/Torque
through the pbsubmit command. If you don't have that, you could either
write a
But what would you compare if you had these coordinates? What would the
coordinates tell you?
On 2/27/17 11:01 AM, miracle ozzoude wrote:
Hello Doug,
Thanks for replying. I meant like coordinate points on both images to
compare (i.e., any metric different from visual inspection).
Best,
Paul.
dear FS community：
now i have many subjects may should rerun in FS6.0 so i thought could i use
gpu for accelerating, and through searching in the mailing list i got some
messages:
1. cuda was no longer supported
2. new features in cpu version were not add in gpu version
as those above, is
Hi Mel, how does the orig or orig.nofix look?
On 2/24/17 9:21 AM, Melanie Ganz wrote:
Dear list,
we are experiencing a strange wm surface error that we are not quite
sure about how to fix. The errors is at a location where the wm.mgz
look absolutely fine as well as the brainmask.mgz. Also th
Hello Doug,
Thanks for replying. It might help evaluate the accuracy of the
co-registration. Usually, We use visual inspection (placing the crosshair
on 1 image (either MRI or PET) and comparing the position of the crosshair
in 1 image to another image). However, this is subjective and based on
exp
dear FS community:
now i have more than 200 subjects which already finished recon-all with
5.3, since 6.0 released, i wonder should i re-run them with 6.0 as lots of
changes like different surf-map and registration. i ran a bit of them as test
and i found the pial problems were more than 5.3
Dear Doug,
thank you for the feedback. In this context I would like to ask you to share
your opinion on the mri_cvs_register. This tool should be far the most accurate
for the registration to MNI, than any of affine-based registration tools,
shouldn't be? Are there any pitfalls/disadvantages (a
I don't think there is a better way than visual inspection. You could
look at the final cost value, but that is relative, ie, you could get a
bunch of subjects who you know have a good registration and create a
table of the final costs, then when you get a new subject, compute the
z-score of th
Hi Antonin,
mni152reg was just meant to replicate the affine registration used by
other software and to provide users with a fast-and-easy way to do
volume-based (subcortical) analysis in FS. I would prefer to use CVS for
everything, but, as you mention, it does have a huge computational
footp
Thank you so much Dr. Doug! I just have one more question:
Now I want to compute the same information for our second modality (i.e., mean
and std intensity of different HP_subfields for our additional scan, e,g., T2
or FLAIR).
My question is that how could I use .FSspace.mgz (in mri folder)
and
There is usually a T2.norm.mgz file in the mri folder. If that is there,
then you should use that rather than the raw data that is not bias field
corrected
On 02/27/2017 12:30 PM, ali reza mohammadi nejad wrote:
> Thank you so much Dr. Doug! I just have one more question:
>
> Now I want to comp
I processed the T1-weighted data without T2. Therefore, we do not have
T2.norm.mgz in the mri folder of each subject.
Only for the HP-subfields segmentation, we added additional high-resolution
T2-weighted data to increase the accuracy of HP-subfields segmentation.
Thanks!
Alireza
> On Feb 27,
Is there a T2.prenorm.mgz in the mri folder? If not, you can run
bbregister --mov T2.nativespace.mgz --t2 --s subject --reg t2.reg.lta
mri_vol2vol --mov T2.nativespace.mgz --reg t2.reg.lta --targ orig.mgz
--o T2.prenorm.mgz
Then run something like
mri_normalize \
-sigma 0.5 -nonmax_su
Is there something I can do to extend the pial surface to include cortex
that it ignored? In some places there are rather large chunks of cortex
not included in the pial surface.
http://imgur.com/a/FnAgj
Link is to a screenshot, notice the top of the brain. It's fairly
pronounced, visible in 12 a
Dear Eli,
You may have to draw in voxels in the wm.mgz volume if it doesn't extend out far
enough. After rerunning, this will push out the white surface, which causes the
pial surface to be positioned further out. You can refer to our tutorial page
for more information:
https://surfer.nmr.m
Dear FreeSurfer Developers,
By using the following code, we can get volume data of different areas from
stats file.
asegstats2table --subjects N01 --meas volume --tablefile aseg_stats.txt
How can I get information of one or two areas, such as hippocampal? thanks
Best,
Gina
___
Hi weiwei
if the aseg looks good you don't have to worry about how the subcortical
structures look in the brainmask - it's irrelevant. Not sure about the pial
surfaces - we find the surfaces in 6.0 more accurate than 5.3, but maybe
not for your specific sequence? It's hard to say
cheers
Bruc
Hello,
Is there a way to use freesurfer to get coordinates and volume information from
a ct file?
Youssif
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this
you can register the CT to the T1 with bbregister
On 02/27/2017 07:17 PM, yusif Al-kheder wrote:
> Hello,
> Is there a way to use freesurfer to get coordinates and volume information
> from a ct file?
>
> Youssif
> ___
> Freesurfer mailing list
> Frees
Dear all,
I would like to use the Gordon Parcellation as segmentation atlas for my
subjects.
I have warped this atlas into individual subject space. Then I wanted to use
mris_sample_parc to apply this parcallation, but I have a few questions..
1. Is this the right command to use?
2. When
sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz returns
da39a3ee5e6b4b0d3255bfef95601890afd80709
A corrupted download three times! Do I just try downloading again?
On Thu, Feb 23, 2017 at 9:02 AM
wrote:
> Send Freesurfer mailing list submissions to
> freesurfer@nmr.mgh.
I just did a test download on my home network and I got the correct sha
1723ef916c4e74ee8fff72438e9c6c91c79bd4cb
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz
Perhaps your network times out after a certain time period, or has a cap
on the file size?
> sha1sum freesurfer-Linux-cent
Hi,
I have been trying to build the freesurfer dev version with GPU support as
per the information I had from my previous try a couple of months ago that
Richard help me to successfully complete and I have not been successful in
that.
I followed the instructions from
https://surfer.nmr.mgh.harvar
Dear Freesurfer team,
This may sound like a bit of a small question, but I could not find any exact
answer elsewhere.
Does the exact orientation of the input image have much effect on the accuracy
of the segmentation in Freesurfer?
It seems that some people apply ACPC alignment to the output of
45 matches
Mail list logo
