External Email - Use Caution
Hi Fatih,
Instead of mri_label2vol and mri_concat, you can simply call
mri_aparc2aseg --s yoursubject --annot
Schaefer2018_400Parcels_7Networks_order_native --o
$SUBJECTS_DIR/yoursubject/mri/outputfile.mgz
One thing to note: "mri_aparc2aseg" will aut
Hi Kody
there definitely are flags like this in the dev version. e.g.:
case "-no-cerebellum":
case "-nocerebellum":
case "-NO-CEREBELLUM":
case "-NOCEREBELLUM":
set nocerebellum=( -nocerebellum)
breaksw ;
Maybe you should just grab the dev version?
And sorry, we
Hi Matthieu
Doug or Andrew can correct me if I'm wrong, but I believe you only need
-FLAIR once (to import and normalize the flair volume), but you need to
specify FLAIRpial each time if you want it to be rerun
cheers
Bruce
On Thu, 14 Mar 2019, Matthieu VANHOUTTE wrote:
>External Ema
Hi Arsenije,
the file name should be (with a starting “.” and no file extension):
$SUBJECTS_DIR/qdec/.Qdecrc
Best, Martin
> On 22. Feb 2019, at 00:22, Arsenije Subotic
> wrote:
>
> Dear Freesurfer experts,
>
> I am having issues choosing the spc option for my QDEC two stage longitudinal
also note the file name starts with a “.”
.Qdecrc
> On 18. Mar 2019, at 21:16, Martin Reuter wrote:
>
> Hi Theo,
>
> the file should be :
> $SUBJECTS_DIR/qdec/.Qdecrc
>
> it is important that it is at that location and should not have an extension
> (not .txt !)
>
> Best, Martin
>
>> On 1
Hi Theo,
the file should be :
$SUBJECTS_DIR/qdec/.Qdecrc
it is important that it is at that location and should not have an extension
(not .txt !)
Best, Martin
> On 18. Mar 2019, at 16:16, AKUDJEDU, THEOPHILUS
> wrote:
>
> External Email - Use Caution
> Dear All,
>
> I am r
I changed my SUBJECTS_DIR folder, but I did not delete the old one at that time.
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Monday, March 18, 2019 12:34:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesu
External Email - Use Caution
Hello Freesurfer experts,
I would like to extract time series of pre-processed data from each vortex
of ROIs in a annotation file, may I ask how could I achieve this? I tried
'mri_segstats' which only generated the mean time series of each ROI. I
also
Did you delete the bad registration file and re-run the registration
(preproc-sess)?
On 3/18/19 11:53 AM, Nasiriavanaki, Zahra wrote:
Dear Freesurfers
Hi
I was checking the functional on structural data registration quality by using
the below command.
tkregister-sess -s $subj -fsd bold -pe
Dear Freesurfers
Hi
I was checking the functional on structural data registration quality by using
the below command.
tkregister-sess -s $subj -fsd bold -per-run -bbr-sum
I observed high values (around 0.9) for one of my subjects, and I figured out,
that subject was registered to another su
External Email - Use Caution
Hello,
I have a subset of subjects that were processed with an older version of
FreeSurfer and would like to run FreeSurfer in the subjects directory such
that it skips all the subjects already processed by my version of
freesurfer and only reruns recon
External Email - Use Caution
THank you so much for your help!
Le lun. 18 mars 2019 à 16:32, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> a écrit :
> The vertices chosen for the cluster depend only on the cluster forming
> threshold (CFT). Once that is chosen, the vertices in
The vertices chosen for the cluster depend only on the cluster forming
threshold (CFT). Once that is chosen, the vertices in the cluster are fixed.
The permutation judges how likely the cluster as a whole would be seen by
chance. There are other ways to do permutation, but this is the way we do
External Email - Use Caution
Ok, well then I do not understand the purpose of the permutation testing if
the number of permutation would not change the size of the clusters. What
is it doing if not refining what vertices are significant? Perhaps I am
just missing a key idea.
Best,
Hi Theo, sorry, QDEC is not really being supported anymore. Try using the
command line stream.
On 3/18/19 11:16 AM, AKUDJEDU, THEOPHILUS wrote:
External Email - Use Caution
Dear All,
I am running a longitudinal (2-time points) group cortical analysis in
Freesurfer 5.3 with Qdec. After
can you send the terminal output? I realize it might be quite big. You can ftp
it to here: /autofs/space/nihilus_001/CICS/ACRsoftware/ACRcurrent
On 3/18/19 11:12 AM, Sims, Sara A (Campus) wrote:
External Email - Use Caution
Hello!
I have 786 subjects that I am trying to do a paired di
External Email - Use Caution
Dear All,
I am running a longitudinal (2-time points) group cortical analysis in
Freesurfer 5.3 with Qdec. After shrinking the longitudinal QDEC table into a
cross-sectional form, I added a text file containing the lines
MEASURE1 = long.thickness-av
External Email - Use Caution
Hello!
I have 786 subjects that I am trying to do a paired difference analysis using
mri_glm. I am getting stuck at the mris_preproc stage. I have tried running it
on a handful of subjects and it works wonderfully. However, when I run it on
all the s
They do not have any normalization applied. BTW, you should not scale the
thickness by the ICV
On 3/18/19 10:24 AM, Bunting, Emma wrote:
External Email - Use Caution
Hi Freesurfer experts,
I used a script created by ENIGMA to extract the cortical thickness values for
129 subjects that
See slide 30 here. does that work? If so, you have my permission to use it in
your publication or presentation or whatever
http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.pptx
On 3/18/19 8:33 AM, Mageshwar Selvakumar wrote:
External Email - Use Caution
Dear Freesurfer Community,
We
External Email - Use Caution
Hi Freesurfer experts,
I used a script created by ENIGMA to extract the cortical thickness values for
129 subjects that had undergone reconall processing.
We are using these values in VBM analysis. From reading other papers, we notice
that all regi
External Email - Use Caution
Dear Freesurfer Community,
We are working on a publication on chronic pain and for explanation purposes,
we would like to show how the brain inflates from the anatomy. For this
purpose, we thought a video on how inflation takes place could be interes
22 matches
Mail list logo
