Thanks Doug,
I used the first link and works perfectly now!
Best regards,
Amirhossein Manzouri
On Tue, May 20, 2014 at 5:03 PM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
I just ran it, and it works fine. It may be that I need to give you more
libraries.
Start with this one
im get it
-- Forwarded message --
From: freesurfer-requ...@nmr.mgh.harvard.edu
Date: Wed, 21 May 2014 09:51:02 -0400
Subject: Welcome to the Freesurfer mailing list
To: bara9...@gmail.com
Welcome to the Freesurfer@nmr.mgh.harvard.edu mailing list!
To post to this list, send your
Dear all,
I want to get the measurements of meancurvature, thickness, white matter
volume and gray matter volume based on Desikan-Killiay Atlas.
I would like to learn whether the commands I used to get them are the
correct ones (in terms of content) for Desikan Killiany atlas?
*For meancurv: *
Freesurfer folks,
I'm trying to compile an annotation using mris_label2annot after
transferring fsaverage5 labels to a single subject. I'm getting a strange
error. Essentially it looks like it can't find most of my transferred
labels, which doesn't make sense as they are definitely in the
Hi Rujing,
If you load the surface up in freeview you can change the background
color.
-Louis
On Wed, 14 May 2014, charujing123 wrote:
Hi Bruce and Doug,
Ok, I see. That's all right.
All the best.
Rujing Zha
2014-05-14
Hi Anastasia,
I have a large set of freesurfer recons (T1) already processed through FS
version 5.2 longitudinal stream while ago. However, I see now that there is an
advantage of using Tracula 5.3 longitudinal stream for DTI longitudinal
analysis. Do you know if I run the DWI data using 5.3
On 05/21/2014 08:30 AM, Paola Valsasina wrote:
Dear Doug,
thank you so much for your help, it worked! now I pre-processed the flipped
images and estimated my GLM model.
I had a look at my results with tksurfer, as explained in the xhemi tool
page (e.g., tksurfer fsaverage_sym lh inflated
Your color table appears to have been created in windows (or maybe mac).
Convert it to a unix text file.
doug
On 05/21/2014 10:40 AM, Paul Beach wrote:
Freesurfer folks,
I'm trying to compile an annotation using mris_label2annot after
transferring fsaverage5 labels to a single subject. I'm
Oy.
Thanks - that worked.
On Wed, May 21, 2014 at 11:21 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Your color table appears to have been created in windows (or maybe mac).
Convert it to a unix text file.
doug
On 05/21/2014 10:40 AM, Paul Beach wrote:
Freesurfer folks,
Thank you so much! Can I also learn what is the difference between the gray
matter values in lh.aparc.stats file and the gray matter values from the
command below;
aparcstats2table --subjects S1 S2 S3 --hemi lh --meas
volume--parc=aparc --tablefile aparc_lh_volume_table.txt
Thanks,
--
21
aparc.stats has all of the values (eg, thickness, area, volume, curv)
for each ROI for a single subject. When you run aparcstats2table, you
extract one of those for each subject for all ROIs and put them into a
single table file
On 05/21/2014 01:21 PM, Buse Merve Urgen wrote:
Thank you so
Hello all,
My site has recently upgraded to the newest version of Freesurfer, and I've
run a set of subjects on recon-all using the hippocampal subfield
segmentation flag. Everything went well. Then in running
kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages
indicating
Hi Freesurfer experts,
I was running recon-all on a cluster and encountered the following error:
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz
Linux compute-g20-12.deepthought.umd.edu 2.6.18-371.3.1.el5 #1 SMP Mon Nov
11 03:23:58 EST 2013
Dear All,
As suggested, I am reposting a previous question.
I am trying to run a single subject in TRACULA (trac-all -corr -c config), 148,
for who there is a folder ‘1482’ with all DWI DICOMs and a folder ‘ESNA148’
with the recon-all processing (Freesurfer 5.3). Also in $SUBJECTS_DIR there is
Follow-up: I then run into indexing problems when calling freeview with
subfield volumes (similar to http://bit.ly/1pdEWRZ), which leads me to
believe kvlQuantify is the only script that relies on the old convention.
Changing the names back to CA2_3.mgz, etc., fixes THAT problem.
Rather than
Hi all,
If I understand correctly, the surface-based morphometry (SBM) done by
Freesurfer offers superior registration as compared to voxel-based methods
such as VBM, in that:
1. SBM smoothing respects anatomical boundaries better than the 3D VBM
smoothing.
2. SBM group analysis employs
Hi Tudor
1. The smoothing we do is along the surface, so no matter how huge the
kernel gets it only ever includes cortical gray matter. In contrast, volume
smoothing kernels will happily smooth in white matter, skull, csf, the bore
of the scanner, etc as the kernels get big.
2. Yes, we
Thanks very much for explaining this Bruce.
Tudor
On 21 May 2014 22:01, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Tudor
1. The smoothing we do is along the surface, so no matter how huge the
kernel gets it only ever includes cortical gray matter. In contrast, volume
smoothing
Hello all,
I am doing pre-processing for resting-state fMRI volumes, but I have
encountered an error and am unsure of how to correct it:
I have previously determined the nonlinear warping transformations from my
subjects' anatomical (T1) space to the 2mm MNI template using ANTs. At the
end of my
Hi,
Wanted to check in about Mac OS X and any effects on recon-all that I may not
be aware of. A while back the Mac was updated to 10.9.2 from some other version
of 10.x.x. I ran half of my recon-all on 10.x.x, and am running my 2nd half on
10.9.2. The update was due to some IT person thinking
Hi Yoonho - Tracula did not change at all between the 5.2 and 5.3
releases. It was recon-all that changed, and in fact 5.3 was released to
correct a bug in 5.2, so it is not recommended to use 5.2 recon-all.
For info about tracula versions, see:
Thank you very much! We'll certainly fix this in the next release
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
- Original Message -
From: C.P. Frost
mri_vol2vol when used in this way does not manage memory very well. It
resamples the time series into a 256^3 volume of floats. Even for a
small number of time points, this becomes unmanagebly huge
On 05/21/2014 06:06 PM, Ben Mooneyham wrote:
Hello all,
I am doing pre-processing for
Dear Freesurfer experts,
Last week I asked a question about altering annotation and color tables so
that I could plot groups of vertices that covaried together. I have
figured out the solution to this, if anyone else is trying to do this too. You
can read in an annotation file with the
Hi Maria
I think we didn't realize there was any standard. As I remember, we do:
r 16 + g 8 + b
and stuff them into a 32 bit quantity
cheers
Bruce
On
Wed, 21 May 2014, Maria Jalbrzikowski wrote:
Dear Freesurfer experts,
Last week I asked a question about altering annotation and
Hi Eileen
Does adding control points to both temporal lobes fix it?
Cheers
Bruce
On May 20, 2014, at 9:34 AM, Daly, Eileen eileen.d...@kcl.ac.uk wrote:
Hello all,
We are having trouble with the output after running recon-all -all -subjid
subjectx on our scans.
Registrations and skull
Hi there,
I tried to put more CP, so all the temporal lobe tissue is in the mask. This
will end up in overestimation of white matter. So in a second step you will
have to manually adjust WM mask.
In my dataset, after adjusting WM mask, WM ist still little bit oversetimated,
but at least i am
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