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> *From: * on behalf of Wayne Su <
> wayne...@gmail.com>
> *Reply-To: *Freesurfer support list
> *Date: *Wednesday, 2 May 2018 at 18:39
> *To: *"freesurfer@nmr.mgh.harvard.edu"
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Hello FreeSurfer Developers,
>
> I'm attempting to run longitudinal segmentation of hippocampal subfields by
> using the development version of FreeSurfer, but for some of my subjects I get
> the following error:
>
> ***
> Global ite
Dear Freesurfers,
I used Qdec to do two-group comparison on cortical thickness. Demeaned age
was used as the covariate. The question I¹m looking at is that ³Does the
thickness-age correlation differ between C1 and C3?²
When FWHM=15mm was chosen, I got confused results: When I used threshold
1.3(
om the two volumes to compute a common space
>
> On Tue, 12 Jul 2011, Wayne Su wrote:
>
>> Thank you Koen. We're investigating the VR Space volume in each hippocampal
>> subfield. Your suggestion is just what I'm looking for, very helpful.
>>
>> Yes, I ca
eft_presubiculum.mgz nu_upsampled_2_2_2.mgz 0 0 0
>>
>> will result in the files nu_upsampled_2_2_2.mgz and
>> posterior_left_presubiculum_resampled.mgz that are both in the same
>> space and contain 2^3 = 8 times more voxels than the original 1mm
>> voxels.
>>
Hi Koen,
Look like the outputs (posterior_*.mgz) are probability kind of images. How
can I transfer them back into 1x1x1 mm^3 FS space? Maybe merge them into one
image without overlapping?
Or maybe transfer my own image into this 0.5x0.5x0.5 mm^3 space. How can I
achieve this?
Thanks,
Wayne
On 0
Hello,
I am using FS 5.1 to measure lGI (local Gyrification Index). Only one
particular scan failed. Here are some messages:
³... remeasuring lGI value for vertex iV = 65101. It may take a few minutes.
WARNING -- Problem for vertex iV = 65101, lGI value is aberrantly high
(lGI=56.5472)...
...lGI
One quick question: how to convert hippocampal subfields back to FS space?
Wayne
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l take a look
> Bruce
>
>
>
> On Jun 8, 2011, at 5:22 PM, Wayne Su wrote:
>
>> Anybody can help me out? What caused the middle line (both pial and wm
>> boundary) shifted to right side even the wm mask is good? Please see the
>> attached images. Thank you v
> Hello,
> I have a subject with very big ventricle. I managed to edit wm.mask and
> aseg.mgz, and rerun the recon-all autorecon2, but the middle line separating
> left/right ventricles is still not right (attached). Is there any way to
> correct it? I¹m using FS 5.1. Thanks.
>
> Wayne
>>
>
reve wrote:
>
>> I've never heard of DTI_TK Quick Look. Does it actually read mgz files? What
>> value does it give for aparc+aseg.mgz? Try loading the file into matlab with
>> the FreeSurfer MRIread.m function and see what it gives for the max. Or just
>> run
&
his here with version 5 and cannot replicate. What version
are you
> using?
doug
Wayne Su wrote:
> Here is:
> mris_calc aparc+aseg.mgz max
>
> Max@(index)[ 2035.00 (7772808) ]
>
>
> On 05/10/10 2:20 PM, "Douglas N
> Greve" wrote:
>
>
doug
Douglas N Greve wrote:
> And what do
> you get when you run mris_calc on aparc+aseg.mgz?
>
> Wayne Su wrote:
>
>>
> Here is the output from mris_calc:
>> mris_calc aparc+aseg2.mgz max
>>
> Max@(index) [ 2145516800.00 (6400402) ]
>> W
alue does it give for aparc+aseg.mgz? Try loading the file into
> matlab with the FreeSurfer MRIread.m function and see what it gives for
> the max. Or just run
>
> mris_calc aparc+aseg2.mgz max
>
> doug
>
> Wayne Su wrote:
>> Hi Bruce,
>> I used just mri_binarize
#x27;s an FSL problem or a FreeSurfer one? If
> you don't use FSL do you still have the problem?
>
> cheers
> Bruce
> On Tue, 5 Oct 2010, Wayne
> Su wrote:
>
>> Well, I tried to avoid FSL, and used only Freesurfer tool to do the same
>> thing. I found there wa
AM, "Wayne Su" wrote:
> Hello Freesurfer Users,
>
> I am feeling very bad when I am using mri_convert. There are two problems:
> 1. When I converted a file in mgz format to nii.gz format, and did some
> volume calculation (mask and addition) by using fslmaths from FSL,
Hello Freesurfer Users,
I am feeling very bad when I am using mri_convert. There are two problems:
1. When I converted a file in mgz format to nii.gz format, and did some
volume calculation (mask and addition) by using fslmaths from FSL, then
converted back to mgz. If the image type is uchar, it
, "Wayne Su" wrote:
> I re-ran over 400 scans by using Freesurfer 4.3.0 on Mac OS 10.5.6. Well, I¹m
> very happy on the results. Anyway there are two issues I encountered:
> 1) I have 3 scans hanging on the last second step when creating the
> aparc+aseg.mgz by using mri_apar
volume, which replaced it.
>
> cheers
> Bruce
> On Wed,
> 29 Apr 2009, Wayne Su wrote:
>
>> The Freesurfer 4.3 segments the cc into 5 parts. But the wmparc.mgz has both
>> 5 parts along with ctx-?h-corpuscallosum/ wm-?h-corpuscallosum. I think th
The Freesurfer 4.3 segments the cc into 5 parts. But the wmparc.mgz has both
5 parts along with ctx-?h-corpuscallosum/ wm-?h-corpuscallosum. I think they
should not co-exist. Maybe I¹m wrong.
Wayne
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Bruce Fischl" wrote:
> Hi Wayne,
>
> why are you trying to convert the label to an annotation? Not sure why
> it's not working, but I don't know that I've ever used the tksurfer export
> feature.
>
> Bruce
>
> On Tue, 28 Apr 2009, Wayne Su wrote:
I have the trouble to convert the BA label to annotation file. The
Freesurfer 4.3.0 is on Mac OS 10.5.6.
First, I got the BA label:
mri_label2label --srcsubject fsaverage --srclabel
fsaverage/label/lh.BA1.label --trgsubject 001 --trglabel
001/label/lh.BA1.label --hemi lh --regmethod surface
This wo
Sorry, I found the error in my script. The ctxseg option cannot be used
here, and we should use a2005s option for mri_aparc2aseg command.
Wayne
On 27/04/09 10:25 AM, "Wayne Su" wrote:
> Hello,
>
> Is there a way to get white matter volumes of gyrus and sulcus in Destrie
Hello,
Is there a way to get white matter volumes of gyrus and sulcus in Destrieux
atlas? I tried to use the same method used by white matter parcellation for
Desikan-Killiany atlas, but no wm volumes were reported. Or we get the total
volume of the label (how?), then subtract the gray volume to
I looked into the ctx volumes reported in ?h.aparc.stats (such as
frontalpole) and the same one in wmparc.stats (labelled as
ctx-?h-frontalpole). The volumes are slightly different. I am wondering why
this happened and which one is better.
Thanks.
Wayne
I'm trying to use Flirt from FSL to get talairach.xfm. Here are the steps I
took:
1) recon-all -autorecon1 -notalairach -subjid $subject
2) mri_convert $SUBJECTS_DIR/$subject/mri/nu.mgz
$SUBJECTS_DIR/$subject/mri/nu.img
3) bet $SUBJECTS_DIR/$subject/mri/nu $SUBJECTS_DIR/$subject/mri/nu_brain
4) fsl
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