Dear All,
Sorry for this email.
I think I made some mistakes. When I redone the analysis, the values were same.
Kindly ignore the email.
From: Anupa AV
To: Freesurfer ; Bruce Fischl
Sent: Thursday, October 3, 2013 11:06 AM
Subject: Difference in GMV
Dear FS experts,
I was trying to find the gray matter volume of superior temporal gyrus (STG)
for schizophrenia patients using freesurfer.
I ran recon-all and generated the rh/lh.aparc.volume.stats using qdec.
>From that, I got the volume for left hand lh_superiortemporal_volume,=11893.
Out of
Dear Koen,
It worked...
Thanks a lot
From: Koen Van Leemput
To: Anupa AV
Cc: Freesurfer Mailinglist ; Bruce Fischl
Sent: Thursday, September 19, 2013 12:48 PM
Subject: Re: [Freesurfer] recon-all-hippo-subfeilds
Hi,
I believe "recon-all -s NC -
Dear FS experts,
I've a query regarding the recon-all analysis.
I ran recon-all using the following command
eg.
recon-all -i location/nc.nii -s NC -all
I got the analysis done.
Now I'm interested to calculate the hippocampal structures.
I knw the command line for that also
recon-all -i lo
Dear All,
This worked for me...
for x in SZ1 SZ2 SZ3
do
recon-all -i $x.nii -s $x -all -hippo-subfileds
done
Thanks for your valuable inputs...
From: Bruce Fischl
To: "Watson, Christopher"
Cc: Anupa AV ; KOOL ; Freesurfer
Sent: Saturday, S
I really meant FS5.2..
Sorry for the lack of clarity of my prev. mail
From: Anupa AV
To: Freesurfer ; Bruce Fischl
Sent: Saturday, September 7, 2013 3:14 PM
Subject: version 2 FS
Dear SIr,
I made some analysis based on FS v.2.0.
Does the Deprecated
Dear Sir,
I'd like to know the command lines for running recon-all for multiple datasets.
Can you please help me on that?
I've tried using the following command lines
cd /home/john/Anu (where I kept all the .nii files)
for x in *
do
recon-all -i SZ*.nii -s $x -all
done
But this is not working
Dear SIr,
I made some analysis based on FS v.2.0.
Does the Deprecated version means that the results generated by FSv.2 can't be
published???
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Dear FS experts,
I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 for my analysis.
After recon-all with hippo-subfield, only 45 brain volumes were genreated in
aseg.stats file.
Freesurfer v.5.1 analysis were able to generate cortical structure's volumes
also.
Where v.5.2 mainly gen
Dear FS experts,
I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 for my analysis.
After recon-all with hippo-subfield, only 45 brain volumes were genreated in
aseg.stats file.
Freesurfer v.5.1 analysis were able to generate cortical structure's volumes
also.
Where v.5.2 mainly gener
Dear All,
When I tried to running qdec, I'm getting the following error.
qdec.bin: error while loading shared libraries: libjpeg.so.62: cannot open
shared object file: No such file or directory
What is the solution for this.?
Any help will be greatly appreciated.
_
Dear FS experts,
By definition bblabel means..
Applies a bounding box to a label. The bounding box is specified by
six coordinates (xmin,xmax,ymin,ymax,zmin,zmax). Only those label
points within this box are copied to the output. If a min is not
specified, then -infinity is used. If a max is not
Dear FS experts,
I'd like to know the fsaverage brain (rendered brain) generated after recon-all
analysis is same as that of individuals brain size.
I mean is rendered brain developed after recon-all = individual brain??
If not,
How much cm/mm away or towards the original brain??
__
Dear All,
I am having a total of 100 subjects for my analysis.
My aim is to seperate DLPFC by making coronal cuts.
I know the procedure to do for single subjects.
Can anyone help me with the command line for mutiple data sets..?
Any help will be greatly appreciated..
_
Dear All,
I was trying to create register.dat for a single subject.
Command line:
autoreg-sess -s SZ01 -d $SUBJECTS_DIR/SZ01
But it showed some error like this...
Logfile is /home/mbial/JPJ/freesurfer/SZ01/log/autoreg-sess.log
setenv SUBJECTS_DIR /home/mbial/JPJ/freesurfer/SZ01
__
load MRI volume.
Tkmedit couldn't read the functional volume you specified. This could be
because the volume wasn't found or was unreadable, or because a valid header
type couldn't be find, or a registration file couldn't be found or opened.
____
Ok...
I mean overlaying the label to T1W image
Fm: Bruce Fischl
To: Anupa AV
Cc: Freesurfer
Sent: Sunday, April 21, 2013 8:09 AM
Subject: Re: [Freesurfer] Merging the labels to T1 image
Sorry, I still don't understand. What do you mean by &
Dear Bruce,
Sorry and to be more precise...
After creating a label, say DLPFC, I want to merge it on the subject's T1
sagittal section.
I'd like to know whether that's possible with FS?
From: Bruce Fischl
To: Anupa AV
Cc: Freesurfer
Sent:
Dear FS experts,
Is it possible to merge the label obtained from tksurfer to T1 weighted image?
If yes, which method I should follow?
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corticla volume (mm3) of that created DLPFC.
Any helps'll be greatly appreciated.
From: Anupa AV
To: "Koolschijn, Cédric" ; Freesurfer
Sent: Monday, April 15, 2013 2:50 PM
Subject: Re: [Freesurfer] How to calcutate Brain volume?
Dear Cedric,
Dear All,
I want to run recon-all for multiple subjects.
I named my sbjects as SZ01.nii, SZ02.nii etc.
After setting the cd and environmanet variable, I ran using following for loop:
>for x in *
> do
>recon-all -i SZ*.nii -s $x -all
>done
I got the following error: WHAT MIGHT BE THE REASON FOR
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
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
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
Dear FreeSurfer Experts,
I'd like to know how to measure the volume of a brain region using freesurfer.
I know to obtain the volumes after runnin recon-all command. But I don't find
the brain volume of my interest which is DLPFC.
How can I get the brain volume of my interest.?
Thanks for your r
2 AM
Subject: Re: [Freesurfer] bblabel values for DLPFC
I don't know that there is such a definition of DLPFC.
doug
On 04/09/2013 04:52 AM, Anupa AV wrote:
> Dear All,
>
> I 'd like to know the xmin, ymin and zmin for creating DLPFC label
> using bblabel string.
>
Dear All,
I 'd like to know the xmin, ymin and zmin for creating DLPFC label using
bblabel string.
I want to make a coronal cut at y=26 for seperating DLPFC from premotor cortex.
I tried by giving a value of xmin=0, ymin=26 and zmin= 0.
I'd like to know whether I'm on right track.
Thanks in adv
Hello experts,
I'm in a process to make coronal cuts using tksurfer
Please help me with the following questions:
1. How to map the label(merged) to fsaverage?
2. How to use bblabels?
3. How to map back to the individuals?
What is the coomand line function used for the above questions?
Any help
Dear All,
I use Philips Achieva 3T scanner for the MRI study.
When I open the Dicom folder, (say for MPR ) the no. of items I can see is 222
images (IM_xx) for one subject and for other subject, I find it as 166 images.
Is it an error in saving the data or the no.of images vary among indiv
Dear All,
How to explore the "cut" tools in freesurfer using tksurfer?
I'd like to make a cut along the vertex on the cortical surface (say, inflated)
to divide medial and lateral components.
How to do it after loading DKatlas labels and I want to cut along the vertex to
divde medial and late
Dear All,
Can anyone tell me how to merge the parcellation labels using tksurfer.? For
eg. How can I merge, Superior frontal gyrus, middle frontal gyrus and caudal
middle frontal gyrus.
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