Hi, I took a look at this and saw that the error comes from the "getmatlab"
script ($FREESURFER_HOME/fsfast/bin/getmatlab). It is a CSH script, which I
thought might be the issue.
Specifically, the script checks for the existence of matlab by
(unsurprisingly)
set MATLAB = `which matlab`;
On Dr.
Hi Jennifer -
Ostensibly your pathways and environment variables look correct. I ran into
this problem once before, so I changed from BASH to the enhanced C shell
and it worked. You may want to try that. All you need to do is to exit out
of bash and set the environment in tcsh and it could work.
Agreed, especially so with MD. Keep in mind that you¹re upsampling MD from
a lower-res (diffusion) space to a higher-res (T1) space, so it should be
smooth already, relatively to measure derived from the T1. And MD varies
pretty smoothly (it¹s a mean of 3 things, after all).
On 8/11/17, 1:11 PM, "
that is experimental to look at the "weight" of the cluster (ie,
size*intensity)
On 08/11/2017 11:50 AM, Van Der Deijl, Rosanne wrote:
> Thanks for the link, I hadn't seen that one indeed!
> However, the variable WghtVtx is not explained on this page. What is
> this variable?
>
> Thank you!
>
>
Hi Shane
not really - it totally depends on the size of the effect you are looking
for. I would be *very* careful about partial volume effects though
cheers
Bruce
On Fri,
11 Aug 2017, Shane Schofield wrote:
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am
Appreciate it Dr Bruce. Do you have guidelines for smoothing MD?
Dr Yendiki, I am trying to investigate whether cortical MD can be a marker of
neurodegeneration. The idea is that during the early stages of a disease,
cellular microstructure may breakdown before cortical thinning occurs. This
re
Hi Shane
you probably don't need cvs as it is more to extend the surface-based
registration to the entire volume. Here you just need the surface-based
registration I believe. Use mri_vol2surf to sample the FA onto the surface.
After that it is identical to a thickness study
cheers
Bruce
O
Hi Rose
do you mean cross-sectional or longitudinal analysis?
cheers
Bruce
On Fri, 11 Aug 2017,
Van Der Deijl, Rosanne wrote:
> Dear Freesurfer team,
>
> I was wondering what the test-retest reliability is of comparing small
> regions in the subcortical volume, e.g. the amygdala. Has this imp
Dear Freesurfer team,
I was wondering what the test-retest reliability is of comparing small regions
in the subcortical volume, e.g. the amygdala. Has this improved with the 6.0
version?
Thank you!
Kind regards,
Rose
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Free
Thanks for the link, I hadn't seen that one indeed!
However, the variable WghtVtx is not explained on this page. What is this
variable?
Thank you!
Message: 8
Date: Mon, 7 Aug 2017 15:01:46 -0400
From: Douglas N Greve
Subject: Re: [Freesurfer] mri_glmfit-sim output
To: freesurfer@nmr.mgh.harvard
Hello Dr. Fischl,
Thanks for the feedback. Can the flattened patches be "re-inflated" into
surface files again after being flattened?
I am also continuing to run into the issue with the label2vol function
where I end up with a volume that is completely filled. The steps I have
been following to r
Hi Dr Greve,
Thanks again for the great explanation and for clarifying how smoothing may
exacerbate the partial volume effects.
I have additional question and I appreciate your answer:
In the literature of the voxel-wise analysis using FSL/randomise to study the
difference between two groups
Sorry, my question wasn't very clear. I meant to ask what sort of biological
effect you're hoping to measure using MD.
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Shane Schofield
[shane.schofi...@yahoo.com]
Hi Mateus,
Please attach the recon-all.log file for your subject and I will take a look.
Best,
Emma
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of MATEUS ROZALEM ARANHA
Sent: Friday, August 11, 2017 9:56 AM
To: freesurfer@nmr.mgh.harvard.edu
Su
Hi,
I had problems with skullstriping. I ran recon-all and part of the skull is
being considered as cortex in the segmentation. I tried to fix this using:
*recon-all -skullstrip -wsthresh 50 -clean-bm -subjid *
and than
*recon-all -autorecon-pial -subjid *
But nothing changed.
Do I need to ru
Hi Dr Yendiki, I am studying a group of people with APOE4 and I want to see
whether cortical MD increases can be detected relative to non-carriers, and if
so, is the effect size bigger than changes in cortical thickness.
On Friday, August 11, 2017, 11:19:32 AM GMT+1, Yendiki, Anastasia
wrote:
What effect are you trying to measure with MD on the cortex?
From: Shane Schofield [shane.schofi...@yahoo.com]
Sent: Friday, August 11, 2017 3:12 AM
To: Freesurfer Support List; Yendiki, Anastasia
Subject: Re: Mean diffusivity on cortex?
Thanks Dr Yendiki.
I am m
Dear Freesurfer,
I would like to test if the percentage change (two time points) of cortical
thickness is different between two groups.
What i have done:
FIRST: long_stats_slopes --qdec ./qdec/long.qdec.table.dat --stats
lh.aparc.stats --meas thickness --sd $SUBJECTS_DIR --do-spc --generic-ti
Thanks Dr Yendiki.
I am more interested to compare MD in grey matter regions by putting the MD on
the surface, and then do a glmfit type of comparisons. Is that OK? Would you
recommend me to smooth the data after spatial normalisation? I have also used
the mri_cvs_register as described on the t
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