Dear Prof Donald McLaren
I am sorry to disturb you! I have four discrete variables {factor 1(A,B),
factor 2(C,D), factor 3(G,H), and gender(M,F)} and a continuous variable (age),
I want to use the GLM to analysis the result of the interaction among factor
1(A,B), factor 2(C,D) and factor 3(E,
Hi Susie - Everything under dlabel/diff is mapped to DWI space (either
with flirt or with bbregister, whichever you use). The one in my
screenshot was dlabel/diff/aparc+aseg.flt.nii.gz.
a.y
On Wed, 27 Mar 2013, Susan Kuo wrote:
Hi Anastasia,
I see what you mean. I had previously used th
Hi,
In my case transformation to fsaverage did not work very well. What I did
was:
- from Surfrend page download Colin 27 subject and transform it to the
latest version (now 5.2)
- with bbregister obtain register.dat between this Colin 27 subject and
SPM-s single subject t1.nii, which is the 2mm v
Hi all;
I need a suface-based aal template which is compatible with FS surface
file. Is there a way i can get the surface-based aal template? I have an idea,
that is to just transform the AAL template (.nii file) in MNI space onto the
surface template (e.g. fsaverage template) in FS. Is it
Hi Anastasia,
I see what you mean. I had previously used the dtifit_FA.nii.gz image and
overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using
freeview. I didn't end up with the same images as you, however. Can you
tell me which images you used to obtain this overlay?
I am
Dear Freesurfers,
I'm interested in using FS identified labels, such as Brodman areas in the
anatomical volume, to measure a feature, say mean intensity in V1, in a second
volume registered to the first. I'm new to the use of labels, so some advice
on where to start would be appreciated. Thanks
Hi Anupa,
In addition to the Desikan and Destrieux parcellations, FreeSurfer 5.2
also include other cortical parcellations
(https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes).
In particular, the resting-state parcellation or Mindboggle atlas
might be relevant to you if you are interested in
Hi List,
with reference to my below messages, I have now determined that the
license file is considered invalid by freesurfer executables since i
have upgraded from opensuse 12.2 to 12.3.
The upgrade to freesurfer 5.2 had nothing to do with it - in fact,
setting the proper environments variabl
Does leftfrontallobe.nii.gz overlay properly in tkmedit? eg,
tkmedit subject orig.mgz -surfs -overlay leftfrontallobe.nii.gz -fminmax
.5 1
doug
On 03/26/2013 07:20 AM, Daniel Lumsden wrote:
> Bruce
>
> Many thanks - that's given me a lot more guidance. Following the help,
> i've put together th
I'm having some recon-all errors like this:
mritotal -verbose -debug -clobber -modeldir
/usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm
transforms/tmp.talairach.3505/src.mnc transforms/talairach.auto.xfm
Use of uninitialized value $path in join or string at
/usr/local/freesurfer/
i fixed the problem
- Original Message -
From: "Jon Wieser"
To: "freesurfer"
Sent: Tuesday, March 26, 2013 4:21:35 PM
Subject: [Freesurfer] trackstats2table error
I am trying to convert my dti tracts stats to a table and got the following
error
tractstats2table --inputs fmajor_PP_
Dear all,
I have a brain segmented with Freesurfer 2009 and a list with label
description looking like this:
...
11101 ctx_lh_G_and_S_frontomargin
12101 ctx_rh_G_and_S_frontomargin
11102 ctx_lh_G_and_S_occipital_inf
12102 ctx_rh_G_and_S_occipital_inf
...
What is the best way to sort labels by lob
Hi Anastasia,
It had the same issue before, but worked fine after installing the
fixed dmri patch for Snow Leopard.
Thanks.
ping
On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki
wrote:
>
> Hi Ping - Are you running this on the same system where you were running the
> 5.1 snow leopard build w
I am trying to convert my dti tracts stats to a table and got the following
error
tractstats2table --inputs fmajor_PP_avg23_mni_flt/pathstats.overall.txt
--overall --tablefile table.txt
Traceback (most recent call last):
File "/usr/local/freesurfer/bin/tractstats2table", line 9, in
Hi Ping - Are you running this on the same system where you were running
the 5.1 snow leopard build without a problem?
a.y
On Tue, 26 Mar 2013, Ping-Hong Yeh wrote:
> Hi FS users,
>
> I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into
> errors. The 5.2 recon-all of T1 was finish
Hi everyone,
My QDEC analysis ran into an error message that seems to be a "classic"
(and, so far, it seems unsolved), from mri_concat, which I've described in
a separate message, just sent.
I have, however, more theoretical questions about QDEC, which I hope some
kind soul will help me with:
Hi FS users,
I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into
errors. The 5.2 recon-all of T1 was finished ok.
Here is the final part of log file.
#@# Priors Tue Mar 26 14:39:36 EDT 2013
/apps/freesurfer/bin/dmri_train --outdir
/Volumes/Access_Point_Backup/freesurfer/NCNC2348/d
Hi Josh
it might if the white matter is very dim, as it appears in your images.
You might also try 5.2, which I think is better about this kind of thing.
If you try control points, make sure that they get applied in the
mri_ca_normalize step and not just to cortical normalizaation in
mri_norml
Hi,
I was able to view retinotopic mapping results using rtview in version 5.
However, the display was on the inflated surface. Is there a way to view
the results on the flattened occipital map, similar to version 4's
surf-sess -flat?
Thanks!
-Yuhong
_
I'll bear that in mind next time!
Thank you!!
Andreia
Quoting Anastasia Yendiki :
> No problem, you can usually find the answers to most of these types
> of questions in the help text of the commands. For example if you
> run "mris_label2annot --help" you'll see:
>
> [...]
>
> --a annotname
A subcortical segmentation error sometimes get Freesurfer (v 5.1) is
cortical areas coming over into the hippocampus, ignoring the wm inferior
and lateral to the hippocmapus (coronal). See attached png.
Will adding wm control points help, or do they not inform the aseg
segmentation. What is the bes
No problem, you can usually find the answers to most of these types of
questions in the help text of the commands. For example if you run
"mris_label2annot --help" you'll see:
[...]
--a annotname
Name of the annotation to create. The actual file will be called
hemi.annotname.annot, and it wil
Hi Jon, it is not supposed to be horizontal. The anatomy in the target
is just supposed to match that in the moveable.
doug
ps. please respond to the list. thanks!
On 03/26/2013 02:35 PM, Jon Wieser wrote:
> HI doug,
> i viewed it with tkregister2. the transform looks poor, the ac-pc line is not
Unless you specifically need them for an individual, you should get them
from lh.lh-rh.thickness.mgh because that data is sampled onto the
symmetric template and so should be unbiased (ie, it will not
systematically favor lh or rh).
doug
On 03/26/2013 12:40 PM, Gabriel Gonzalez Escamilla wrote
It was automatically created in the same folder of the old one -> label
However, inside this folder there are the old rh.BAxxx.label. The new
ones (BAxxx.thresh.label) were created inside the Freesurfer folder,
could it be related to that?
Quoting Anastasia Yendiki :
> What's the location
What's the location of the new rh.BA.annot that was created by
mris_label2annot? You need to pass that same file to mris_anatomical_stats
with the -a option.
On Tue, 26 Mar 2013, _andre...@sapo.pt wrote:
After running the mri_label2label and mris_label2annot a new rh.BA.annot file
was creat
After running the mri_label2label and mris_label2annot a new
rh.BA.annot file was created (I had to remove the old one since it
doesn't overwritte) but when running
[user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f
../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white
Admin please unsubscribe this email address
Thanks,
Manish Dalwani
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to
Hi list,
I'm performing qdec. This my file.dat
1 diagnosis discrete 21 Pathology2 Controls2 Thickness_lh
continuous 03 Thickness_rh continuous 04 NPStest continuous 0
Continuous Factors: Mean: StdDev:
---
Dear Doug,I meant of a given subject, But, As I'm thinking about this, I'm wondering if
it has sense to have left and right cortical thickness of my every individual subjects, or if I should obtain the lh-rh thickness differences for the individuals?I suppose that I should read the lh.lh-rh.thickn
Thank you very much Eugenio, you are very kind!
Stefano
Messaggio originale
Da: igles...@nmr.mgh.harvard.edu
Data: 26-mar-2013 17.00
A:
Cc: ,
"freesurfer@nmr.mgh.harvard.edu"
Ogg: Re: R: Re: [Freesurfer] R: Re: R: Re: hippo subfield
I would say intracranial volume from the aseg.sta
Hi Jon, the data are not reoriented or resliced into talairach space. It
is just the transform that is computed. To inspect whether this was done
right, use
tkregister2 --s subject --fstal
doug
On 03/26/2013 12:20 PM, Jon Wieser wrote:
> Hello
> I ran recon-all auto_recon1. and the resulting
Use self for retinotopy
doug
On 03/26/2013 12:24 PM, Y.V. Jiang wrote:
> Thanks Doug, this makes sense. What about retinotopic mapping? Should
> I use fsaverage or self?
>
> -Yuhong
>
> On Tue, Mar 26, 2013 at 10:56 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> It
Thanks Doug, this makes sense. What about retinotopic mapping? Should I use
fsaverage or self?
-Yuhong
On Tue, Mar 26, 2013 at 10:56 AM, Douglas N Greve wrote:
>
> It should either be fsaverage, or self, or an average subject you have
> created. The fMRI analysis is done such that the raw data
Or mris_preproc if you want all your subjects in one file.
doug
On 03/26/2013 12:13 PM, Bruce Fischl wrote:
> Hi Rafa and Gabi
>
> yes, that's pretty much what the -qcache flag does in recon-all. Or you
> can use mri_surf2surf to do it.
>
> cheers
> Bruce
> On Tue, 26 Mar 2013, Rafa X wrote:
>
>> H
Hi Rafa and Gabi
yes, that's pretty much what the -qcache flag does in recon-all. Or you
can use mri_surf2surf to do it.
cheers
Bruce
On Tue, 26 Mar 2013, Rafa X wrote:
> Hi Freesurfers,
> We would need to obtain the cortical thickness of each subject in the
> space of the average subject (buil
I would say intracranial volume from the aseg.stat table
Cheers,
/Eugenio
On Tue, 2013-03-26 at 16:49 +0100, std...@virgilio.it wrote:
> Thank you very much Eugenio.
>
>
> I have a last question: Who is the best way to normalize
> the HippocampalSubfieldSegmentation volume results?
>
>
> Ste
It should either be fsaverage, or self, or an average subject you have
created. The fMRI analysis is done such that the raw data are resampled
into the fsaverage space (unless you use self) and processed there in
anticipation of doing group analysis.
doug
On 03/26/2013 10:37 AM, Y.V. Jiang wr
Thank you very much Eugenio.
I have a last question: Who is the best way to normalize the
HippocampalSubfieldSegmentation volume results?
Stefano
Messaggio originale
Da: igles...@nmr.mgh.harvard.edu
Data: 26-mar-2013 14.37
A:
Cc: ,
"freesurfer@nmr.mgh.harvard.edu"
Ogg: Re: [Freesurf
Hi Anastasia,
I did as you recommended and checked the diffusion-to-anatomical
registration, and the overlay of aparc+aseg_mask on FA, and these views
seem to be good. Upon closer inspection, what I find is that there are
incipient 'bits' of all the tracts, but they seem to not have 'grown',
thou
In the "BA label" section there are:
- Several mri_label2label commands that map each label from fsaverage
space to your indidvidual's space
- One mris_label2annot command that combines the mapped label into an
annotation file.
- One mris_anatomical_stats command that gets stats for that annot
Hi Freesurfers,
We would need to obtain the cortical thickness of each subject in the
space of the average subject (built from our subject population), Does
it exists?
If so, Can I use the label files produced by mri_surfcluster to
directly extract the mean cortical thickness of each ROI in each
su
Hi,
I wonder if you could help with a basic question for preproc-sess in
Version 5.2.0.
The flag "-surface subject hemi": what should be the entry to "subject?"
The tutorial says fsaverage, but for first-level analysis, should it match
subjectname? Or should it always be fsaverage?
If it needs t
Nevermind the last email... If I change the output (wich is the second
place where BAxx.label appears, right?) file name and give the subjs
id this won't be a problem... Anyway, what are these files for? Will I
need to use them somehow?
Thanks
Andreia
Quoting _andre...@sapo.pt:
> Addicion
Hi,
I run the command for each BA labels of the right hemisphere and then run:
[user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f
../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT
rh white
Which resulted in:
INFO: assuming MGZ format for volumes.
computing statistics
Ciao, Stefano
to compute subfield volumes, you need to use the script
kvlQuantifyHippocampalSubfieldSegmentations.sh. The instructions are here:
http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation
In the wiki page you'll also find instructions to visualize the output.
Cheer
Hi,
I'm performing qdec. This my file.dat
1 diagnosis discrete 21 Pathology2 Controls2 Thickness_lh
continuous 03 Thickness_rh continuous 04 NPStest continuous 0
Continuous Factors: Mean: StdDev:
--- -
Hi Linn
what was your mris_anatomical_stats commandline?
Bruce
On Tue, 26 Mar 2013, Linn
Mittlestein wrote:
Dear Bruce,
I first used the example command line from the wiki: mri_annotation2label
--subject LW \ --hemi rh --outdir ./labels(on
my own subject) and then used
mri_mergelabels -i
Bruce
Many thanks - that's given me a lot more guidance. Following the help, i've put
together the command below:
mri_surf2vol --hemi lh --template /orig.mgz --outvol /leftfrontallobe.nii.gz --surfval /left_frontal_lobe.gii
--fillribbon --volregidentity mov07
Where mov07 is my subjid a
Hi Zeke and other users,
I have finished the Hippocampal Subfields parcellation. New files .mgz are
located in $SUBJECTS_DIR/mri.
Now, I do not understand as I can calculate for each region the thickness and
volume.
Can you help me, please?
Stefano
Messaggio originale
Da: zkauf...@nm
Dear Bruce,
I first used the example command line from the wiki: mri_annotation2label
--subject LW \ --hemi rh --outdir ./labels(on my own subject) and then used
mri_mergelabels -i lh.entorhinal.label -i lh.cuneus.label -o test.label
I use Freesurfer 5.1 on Linux system. Are commands incorrect
51 matches
Mail list logo
