Hi, Christopher!
Best of luck to you all in these difficult times!
Thank you very much for your advice. I'll try this as well.
Best wishes,
Veronica
-Original Message-
From: Watson, Christopher [mailto:christopher.wat...@childrens.harvard.edu]
Sent: Tuesday, 16 April, 2013 07:15
To: Bruc
Hello,
In our lab, we create a txt file with all the subject names (as they appear
on their respective folders). Name that txt file whatever you want (like "*
subs.txt*") and save it somewhere in one of the paths (we use /Users/*
Home_User*).
Then in terminal, after setting the environments for
Hi Veronica,
Did you try initially doing "recon-all -i $FLAIR -s $SUBJECT"?
And then, when you do the remaining recon-all steps:
recon-all -autorecon3 -s $SUBJECT -FLAIRpial
It has worked for me. (And worked very well! No edits necessary for the pial
surface!)
___
Dear FS experts,
I'd like to know about the for loop command for running recon-all for multiple
subjects.
I went thru this link,
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2006-November/004083.html
But didn't get much info.
Can anyone please tell me how to run recon-all for multiple
Marcos,
Can you give this version of tkmedit a try on your Fedora 18 system?
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
you will need to copy tkmedit.bin to your freesurfer/tktools directory
(not the freesurfer/bin directory). you may need to type this to ma
Marcos,
Thanks for looking into this. We dont have a Fedora 18 system to
replicate the problem on, but we're looking at the section of code
described in bugzilla report. We may need your help to test any fixes
we devise.
Nick
On Mon, 2013-04-15 at 17:59 -0300, Marcos Martins da Silva wrote:
>
Tudor,
In the recon-all.log, it has this line:
ERROR: writing lh.jacobian_white.fwhm15.fsaverage.mgh
but earlier in the log it saved lh.jacobian_white.fwhm10.fsaverage.mgh
correctly, so this indicates to me that it might have run out of disk
space. is that the case?
to answer the others:
2. not
I had several problems testing freesurfer 5.2 installation, as
previously posted. Now it is all OK and I would like to share what I
could learn:
1- It does not work on Fedora 18 (segfaults with all tests with tkmedit,
tksurfer and recon-all) that is due to a restriction imposed by glibc
(only ne
Hi Anastasia,
We were viewing the arcuate fasiculus tract created by TRACULA, and
noticed that the tract did not reach Broca's area. While there exists
literature that now challenges this neuroanatomical convention, I would
like to investigate the possibility of creating and inputting on our ow
Thanks Nick -- that fixed it.
-MH
--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6
Veronica,
Hi, can you copy me on the subject data upload? You can upload data
here:
https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Nick
On Mon, 2013-04-15 at 12:30 -0400, Bruce Fischl wrote:
> Hi Veronica,
>
> we haven't seen that before. Can you upload your subject including th
Hi Marie,
But division by 5 would give the average area of the 5 mid slices. Maybe
that is even more meaningful (reliable) than just a single slice.
Best, Martin
On 04/14/2013 09:05 AM, Bruce Fischl wrote:
> Hi Marie,
>
> no, that won't account for variability across slices in the l/r
> directi
Hey
I wrote out to .w since I couldn't write to curv. (And I'm old fashioned!)
But actually it's because I am really behind the times and forgot that .mgh was
also used for surface data. And yup, this worked fine.
So in answer to my question 'Bug or stupidity' - the latter!
Thanks Doug,
Fred
Hi Fred, why do you want to save it as a wfile? We're trying to phase
wfiles out. Can you use mgh format?
doug
On 4/15/13 12:56 PM, Fred Dick wrote:
Hey again
sorry, I seem not to be able to accomplish this very simple thing!
First wrote out mask as .w file using vol2surf, but mri_cor2label
Hey again
sorry, I seem not to be able to accomplish this very simple thing!
First wrote out mask as .w file using vol2surf, but mri_cor2label couldn't read
('mri_read(): couldn't determine type of file ./rh.R2MaskBrain.w').
Then tried writing out as curv using the following command:
mri_vol2
Hi Veronica,
we haven't seen that before. Can you upload your subject including the
FLAIR and we'll take a look?
thanks
Bruce
On Mon, 15 Apr 2013, Popescu, Veronica wrote:
Dear all,
I have already run the FreeSurfer 5.2 -all, and I would like to improve the
pial surface recongition using
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Dear all,
I have already run the FreeSurfer 5.2 -all, and I would like to improve the
pial surface recongition using the FLAIR. From the $SUBJECTS_DIR (where I have
also placed the FLAIR file) I use the following syntax:
recon-all -autorecon3 -subjid ${SUBJ_ID} -FLAIR $FLAIRFILE -FLAIRpial
It sta
Hey, thanks Bruce. I will let you know what happens with -n 0. Area not a big
deal for this.
cheers,
Fred
On 15 Apr 2013, at 14:32, Bruce Fischl wrote:
> Hi Fred
>
> mris_thickness will make thickness. Not sure we have anything to make area. I
> guess you could try setting -n 0 in mris_make_
Daniel,
Unfortunately, since I run all the individuals again with FreeSurfer 5.2, I
just saved from the 5.1 the info I was using for comparison between version
- the aseg stats.
I don't have cortical thickness information for 5.1 unless we run all the
cases again in 5.1
---
Hi Fred
mris_thickness will make thickness. Not sure we have anything to make
area. I guess you could try setting -n 0 in mris_make_surfaces to it runs
for 0 iterations. Or we can put something together to create area - it
should be trivial
cheers
Bruce
On Mon, 15 Apr 2013, Fred Dick wrote:
>
Hi all,
I want to convert a mask I made in MNI152 space using the Harvard-Oxford Atlas
into a (subcortical) label file so that I can run an ROI analysis using
func2roi-sess. Does anyone know what commands I would need to do so?
Thanks!
Emily___
Free
Hi there
[Doug/Bruce, sorry for storm of enquiries!]
V quick question: I've fixed up some small defects in white and pial surfs
(using reposition), and need to regenerate area/thickness/curv etc without
changing them. Is there a straightforward way to do this with
mris_make_surfaces, or shoul
The 5.2 image has been smoothed, by a small degree, relative to 5.1.
Either prior to FS processing or by FS, it would seem.
On Mon, Apr 15, 2013 at 3:29 AM, Christopher Bell <
christopherbell2...@gmail.com> wrote:
> Looking at the image posted previously.
>
> https://yalesurvey.qualtrics.com
Dear All,
I'm working with a system, where 32 bit ubuntu is loaded on to a 64 bit
computer.
Previously there were graphics problem (Screen gets stuck-- So I restarts it
and 'll log in again).
Now I'm facing a problem where I cannot enter into ubuntu.
Any solutions for this problem will be greatl
Looking at the image posted previously.
https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
I think it is pretty clear the 5.1 picture has better gray/white contrast.
It is a very subtle difference, but you can see it if you look at some
pieces of
wm that were "missed" by 5.2 in this
Dear Cedric,
Thanks a bunch.
I'll try with mri_label2label.
From: "Koolschijn, Cédric"
To: Anupa AV
Sent: Monday, April 15, 2013 1:07 PM
Subject: Re: [Freesurfer] How to calcutate Brain volume?
Dear Anupa,
The DLPFC is not a standard label in FS. So yo
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