Dear experts,
Recently I run freesurfer longitudinal analysis
(freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0), during the creation of
the BASE, I get the following error "Volumes differ in geometry row=1 col=4
diff=4.745766(4.74577)". We did not change the protocol during the study
period. I ch
t; On Jan 28, 2015, at 4:33 PM, Liu Y wrote:
>
> Dear experts,
> Recently I run freesurfer longitudinal analysis
> (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0), during the creation of
> the BASE, I get the following error "Volumes differ in geometry row=1 col=4
> diff=
> send us the command and the full screen output?
>
> thanks
> Bruce
>
> On Thu, 29 Jan 2015, Liu Y wrote:
>
> Hi Bruce,
>>
>> I have uploaded the baseline K_EL03_1.nii.gz and followup K_EL03_2.nii.gz
>>
malized out by the
> longitudinal stream.
>
> cheers
> Bruce
>
>
> On Fri, 30 Jan 2015, Liu Y wrote:
>
> Hi Bruce,I run the command recon-all -base K_EL03_base -tp K_EL03_1 -tp
>>
>> K_EL03_2 -all.I am to upload the recon_all.log to you.
>> Thanks,
idea to change the resolution (voxel size)
> of your inputs across time. Can you send the output of
>
> mri_info /usr/local/src/freesurfer/subjects/K_EL03_1/mri/rawavg.mgz
>
> and
>
> mri_info /usr/local/src/freesurfer/subjects/K_EL03_2/mri/rawavg.mgz
>
> Thanks,
Dear Experts,
When I run recon-all -cw256 -s problemcase -all, the program seems not able
accurately to recognize the voxel size in this problematic case, in other
cases there is no problem. The program gave a warning like this:
WARNING
=====
an mri_convert your input volume nifti or mgz and
> override what is in the header (e.g. mri_convert -iks 1 ...)
>
> cheers
> Bruce
> On Fri, 6 Feb
> 2015, Liu Y wrote:
>
> > Dear Experts,
> > When I run recon-all -cw256 -s problemcase -all, the program seems not
>
eing converted incorrectly, or you can try the mri_convert
> command line I gave below (check out mri_convert --help) to override the
> voxel size info we read out of the header
>
> On Fri, 6 Feb 2015, Liu Y wrote:
>
> Hi Bruce,The full recon-all command line is "recon-all -cw256
Dear Freesurfers,
I tried to generate annotations by using the command mris_label2annot --s
K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits nhits.mgh. But Could
not succeed. Any helps would be appreciated.
--- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Setting up environm
no ./rh.unknown.label was created.
Yawu
On Mon, May 25, 2015 at 7:22 PM, Douglas Greve
wrote:
> Is there a file called ./rh.unknown.label ?
>
>
>
> On 5/25/15 5:37 AM, Liu Y wrote:
>
> Dear Freesurfers,
> I tried to generate annotations by using the command mris_
Dear Freesurfer experts
In the command "long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas
thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack
--do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR", Do-avg
will compute
the temporal average. I do not quite understand
1 a year later,
> it would look like a .5 years time point. This is used to compute
> symmetrized percent change, representing the change with respect to the
> temporal average to make it more symmetric.
>
> Cheers, Martin
>
>
> On 07/03/2015 08:43 AM, Liu Y wrote:
>
>
Dear Expert,
How to run the correlation analysis between cortical thickness and
cognitive function with Qdec?
Best regards,
Yawu
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The
Dear Freesurfer Developers,
After updating my op to Ubunto from 14 to 16.04, and re-installing the
Freesurfer, when I run recon-all, it ended with an error message:
/media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mg
Hi Freesurfers,
I am using the degree of cortical atrophy between two groups. The atrophy
rate had no significant difference between two groups, but the average
thickness of the baseline and followup showed significant clusters in two
regions between the two groups. My question is how to create th
mfit, then you can use mri_glmfit-sim to create
> > significant clusters. It will create an annotation of the significant
> > clusters, and you can pass that to mri_segstats along with the stack of
> > thickness images to extract the mean thickness in each cluster.
> >
>
Hi Freesurfers,
I calculated the thicknesses of a cluster for some subjects, and each of
the measure was saved under each subject' s folder. How to create a table
containing all the measures? What is the command?
Thanks,
Yawu
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F
ith mris_anatomical_stats, then use
> can use aparcstats2table
>
> On 05/19/2016 03:06 AM, Liu Y wrote:
> > Hi Freesurfers,
> > I calculated the thicknesses of a cluster for some subjects, and each
> > of the measure was saved under each subject' s folder. How to create a
> >
Dear Experts,
Is there any instruction to analyze correlation between cortical thickness
and cognitive measure?
Thanks,
Yawu
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The inf
ther variables you
> want to the design matrix.
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Liu Y [
> liuy8...@gmail.com]
> *Sent:* Wednesday, March 29, 2017 9:03 AM
> *To:*
Dear Experts,
When I run qdec, it showed me error message, any suggestins?
qdec
X Error of failed request: BadValue (integer parameter out of range for
operation)
Major opcode of failed request: 154 (GLX)
Minor opcode of failed request: 3 (X_GLXCreateContext)
Value in failed request: 0x0
using?
>
> Andrew
>
>
> > On Oct 24, 2017, at 3:36 AM, Liu Y wrote:
> >
> > Dear Experts,
> > When I run qdec, it showed me error message, any suggestins?
> > qdec
> > X Error of failed request: BadValue (integer parameter out of range for
> opera
Dear Experts,
Is there an acurate way to anayze the longitudianl changes in regional gray
matter volumes and corticl thicknesses in children (several months to 8
years). How accurate are freesurfer of fsl-FIRST?
Best regards,
Yawu
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Hi Freesurfers,
The contrast between GM/WM may vary regions by regions. Some regions have
high contrast, some regions have low contrast, is there a method can map
the reliability of separating gray and subcortical white matter?
Thanks in advance,
Yawu
it for you
>
> cheers
> Bruce
>
> On
> Thu, 19 Dec 2019, Liu Y wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Freesurfers,
> > The contrast between GM/WM may vary regions by regions. Some regions have
> > high contrast, some
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