Dear Freesurfer Experts,
A review questioned the validity of examining volume in addition to cortical
thickness and surface area within the same study. In particular, he commented
that "The volume is the product of the thickness and area ...As the product of
two Gaussian-distributed
Dear Freesurfer experts,
I tried to do a group x gender interaction in QDEC and there is no sig
interaction, but how do I get the F or T and P values please as requested by
the reviewers?
Many thanks,
Lena
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Freesurfer mailing list
ness and area
what do you mean they do not differ in gender ratio? Just that the
relative number of M/F is the same in each group? If there is not a
significant interaction between gender and group, then you can usually
merge the genders.
On 04/05/2017 05:13 PM, Lim, Lena wrote:
>
> Dear Frees
Dear Freesurfer Experts,
1) I have 2 groups (A & B), which do not differ in terms of gender ratio. If
there were no significant regions for Group-Gender interaction in mean cortical
thickness in the QDEC analysis, can I conclude that gender does not influence
the effect of group on thickness?
Dear Freesurfer Experts,
1) I have 2 groups (A & B), which do not differ in terms of gender ratio. If
there were no significant regions for Group-Gender interaction in mean cortical
thickness in the QDEC analysis, can I conclude that gender does not influence
the effect of group on thickness?
Dear Experts,
I tried to run the following to get the segmentation volumes but encountered
the errors below... How can I get the volumes of the insula and thalamus and
also the inferior prefrontal cortex please?
[spjwker@nanlnx2 FSL]1% asegstats2table --subjects PAC01... PAC70 --segno 9 48
Dear Experts,
How do I extract the cortical thickness of a region of interest (which showed a
group difference in the Qdec between-group analysis) for all the subjects so as
to correlate with other measures in SPSS? There is no .label file in the Qdec
folder; which file shall I use or do I
Dear Doug/Experts,
I tried to compare the right area between 2 groups (A, PC) with Age, Gender and
total right surface area as covariates using Qdec but encountered the following
errors. Please kindly help?
Many thanks,
Lena
: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Lim, Lena
<lena@kcl.ac.uk>
Sent: 29 September 2015 12:42
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] qdec error
Thanks, Doug. I used the qdec table attached.
L
-Orig
error
Can you send the FSGD file?
On 09/28/2015 02:06 PM, Lim, Lena wrote:
> Sorry, please see error below:
>
>
>
> Reading
> /software/system/freesurfer/freesurfer-5.3.0/tktools/tkUtils.tcl
>
> Using
> /software/system/freesurfer/freesurfer-5.3.0//lib/tcl/fsgdfPlot
tal grey matter volume
Not for thickness. For surface area it is a good idea to do some kind of
normalization. Typically people use the estimated intracranial volume (ICV).
You can also use total brain volume or total grey volume. You just need to be
aware that each one of these tests somethi
vard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] total grey matter volume
Not for thickness. For surface area it is a good idea to do some kind of
normalization. Typically people use the estimated intracranial volume (ICV).
You can also use total brain volume
Sorry, I am re-posting below again for help...
Dear Experts,
I tried to see if the average area/thickness differ between the 2 groups (HC
and A) with IQ, Age and Gender as covariates using Qdec, but encountered the
error (pls see attached). I tried the same thing for comparison between A and
file.
doug
On 09/28/2015 12:45 PM, Lim, Lena wrote:
>
> Sorry, I am re-posting below again for help...
>
> Dear Experts,
>
> I tried to see if the average area/thickness differ between the 2
> groups (HC and A) with IQ, Age and Gender as covariates using Qdec,
> but en
Dear Experts,
Do we need to include total grey matter volume as a covariate in the freesurfer
cortical thickness and surface area analyses? I have come across papers that do
and don't; so I am not sure if I have to do that. Please kindly advice.
Many thanks,
Lena
people use the estimated intracranial volume (ICV).
You can also use total brain volume or total grey volume. You just need to be
aware that each one of these tests something different.
On 9/28/15 12:15 PM, Lim, Lena wrote:
Dear Experts,
Do we need to include total grey matter volume as a covariate
Dear Experts,
I tried to see if the average area/thickness differ between the 2 groups (HC
and A) with IQ, Age and Gender as covariates using Qdec, but encountered the
error (pls see attached). I tried the same thing for comparison between A and
PC and it works fine... please kindly help?
Dear Experts,
I tried to extract freesurfer cortical values for a ROI defined in a spm-vbm
analysis following the instructions
(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) and got
stuck at step 2. Please could you kindly assist?
[spjwker@nanlnx2 FSL]0% cd
Dear Experts,
I need some help regarding saving the brain images in Freesurfer/Qdec please:
1) Can I save the brain regions shown in Qdec group analysis as other files and
view them in MRIcroN etc or does it only allow us to save the images as tiff
files (inflated medial, inflated lateral,
Dear Experts,
I am re-posting this again as i am still stuck, please kindly help?
I tried to extract freesurfer cortical values for a ROI defined in a spm-vbm
analysis using the commands below but it didn't work.. please could you kindly
assist (log attached)?
[spjwker@nanlnx2 FSL]0%
Dear Experts,
I tried to extract freesurfer cortical values for a ROI defined in a spm-vbm
analysis using the commands below but it didn't work.. please could you kindly
assist (log attached)?
[spjwker@nanlnx2 FSL]0% cd $SUBJECTS_DIR/fsaverage/surf
[spjwker@nanlnx2 surf]0% fslregister --s
Dear Experts,
I need some help regarding saving the brain images in Freesurfer/Qdec please:
1) Can I save the brain regions shown in Qdec group analysis as other files and
view them in MRIcroN etc or does it only allow us to save the images as tiff
files (inflated medial, inflated lateral,
Sorry, I haven't heard any replies so am re-posting this again for help please:
Dear Experts,
I have 3 groups: A, PC, HC
I did a VBM analysis in SPM and found group differences in grey matter volume
in 2 clusters:
1) Bilateral pre-/SMA, left middle/superior frontal gryi
2) left
fsaverage.
Cheers
Bruce
On Sep 4, 2015, at 9:27 AM, Lim, Lena
<lena@kcl.ac.uk<mailto:lena@kcl.ac.uk>> wrote:
Sorry, I haven’t heard any replies so am re-posting this again for help please:
Dear Experts,
I have 3 groups: A, PC, HC
I did a VBM analysis in SPM and found group
Dear Experts,
I have 3 groups: A, PC, HC
I did a VBM analysis in SPM and found group differences in grey matter volume
in 2 clusters:
1) Bilateral pre-/SMA, left middle/superior frontal gryi
2) left inferior/middle temporal/fusiform/inferior/middle occipital
gyri/superior/inferior posterior
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] F test results
You need to use
1 -1 0 0
1 0 -1 0
On 8/19/15 11:38 AM, Lim, Lena wrote:
Dear experts,
I have 3 groups (A, PC, HC) and IQ as cov and I tried to do a F test on the
cortical thickness but the output doesn't make sense as it covered the whole
...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: 04 August 2015 19:52
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] contrasts
The F would be
1 -1 0 0
0 0 -1 0
Your t-contrasts are correct (you don't need to do both directions)
On 08/03/2015 03:40 PM, Lim, Lena wrote:
Hi
list
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
no! Don't delete those files - we need them. Just don't include them in your
for loop
cheers
Bruce
On Mon, 3 Aug 2015,
Lim, Lena wrote:
Thanks, Bruce. So do I delete that files and run recon-all -qcache -subjid $i
for all
Subject: Re: [Freesurfer] Help with Freesurfer preprocessing pls
I think you should be all set. I meant don't delete fsaverage and all
On
Mon, 3 Aug 2015, Lim, Lena wrote:
Sorry, I don’t understand. Those files are now in the directory. What exactly
should I run next?
-Original Message
with Freesurfer preprocessing pls
Hi Lena
you need to run the hippocampal subfield code. Depending on what version you
are running it could mean adding something like:
-hippocampal-subfields-T1/T1T2/T2
and removing the -autorecon-all
cheers
Bruce
On Thu, 30 Jul 2015, Lim, Lena wrote
are running -qcache on
cheers
Bruce
On Mon, 3 Aug 2015, Lim, Lena wrote:
Thanks Bruce.
I managed to get the hippo files for the 3 new subjects.
However, when I ran
#! /bin/bash
for i in $ ( ls ) ; do
recon-all -qcache -subjid $i
done
Hi experts,
I have 3 groups: (A, PC and HC) and 1 covariate: IQ. For a DOSS file, how
should I define the F contrast? Would it still be: I -1 0 ?
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