date:20130610

[Freesurfer] OptSeq first time

2013-06-10 Thread fMRI

Hello all,

This is my first question in this list and it is about OptSeq2.

I am nee to this command. 

In brief, I wish to insert the following but Some of them I could not handle it:

My experiment has three conditions although I will later specify them as one 
condition:

Moving hand at three different target level ( say 10 20 30). Then I will model 
them as a one condition and enter the parametric response as a first order 
polynomial effects. 

My design will have two columns : main effect of moving hand and the 1 order.

My contrast will be like this [1 0; 0 1]

This is what I would like to optimize using OptSeq2:

Event design
1) ISI 6 seconds + or - 1.5 seconds ( I could not do this
2) TR 3
3) volumes 150
4) 45 hand movement; 15 at each target level   ( I could not do this )
5) each movement lasts for 3 seconds

I am not sure whether I should use null events or the Period between movement 
is enough.

Also my main aim is to optimize the best design in terms of detection.

Please any guide or help

Thanks


AS

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] tksurfer overlay scale bar background color

2013-06-10 Thread Bruce Fischl


you can change it to white via:

set scalebar_bright  255

cheers,
Bruce

On Mon, 10 Jun 2013, Jörg Pfannmöller wrote:


Dear FSexperts,

the overlay scale bar consists of a colored and a gray part. 
Unfortunately, the gray in the binary colored represetation of the brain 
curvature is exactly the same as in the overlay scale bar. Is it possible 
to change the color in the scale bar background to white?


Regards Joerg



On Fri, 31 May 2013 16:20:24 -0400 (EDT)
Bruce Fischl  wrote:


mri_normalize is a binary so you can't, just recon-all.

On Fri, 31 May 2013, Caspar M. Schwiedrzik wrote:


I only find flags for mri_normalize and mri_segment in recon-all, and I have
trouble reading the contents mri_normalize with a regular text editor.
caspar


2013/5/31 Bruce Fischl 
  Hi Caspar

  it changes some parameters to the intensity normalization and
  segmentation to account for the lower SNR and increased CNR in
  the mprage. You'll need to look in the recon-all script for the
  details

  cheers
  Bruce


  On Thu, 30 May 2013, Caspar M. Schwiedrzik wrote:

Hi!
Is there more documentation on what settings the
mprage flag enables in
recon-all?
Specifically, I would be interested which individual
steps it affects and
what  the parameters are for each of the steps.
Thanks!
Caspar





The information in this e-mail is intended only for the person to whom
it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.







___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Coupling cortical and TRACULA results

2013-06-10 Thread stdp82

Hi list,
Thiebaut de Schotten et al., in an article on cortex ("Monkey to human 
comparative anatomy of the frontal lobe association tracts" reported that 
"The superior longitudinal fasciculus has three distinct branches (Petrides and 
Pandya, 1984). In humans, the first branch of the superior longitudinal 
fasciculus (SLF I) connects to the superior parietal lobule and precuneus (BA 5 
and 7), to the superior frontal (BA 8, 9, 32) and perhaps to some anterior 
cingulate areas (BA 24). The second branch (SLF II) originatesin the anterior 
intraparietal sulcus and the angular gyrus (BA 39 and 40) and terminates in the 
posterior regions of the superior and middle frontal gyrus (BA 6, 8, 9). The 
third branch (SLF III) connects the intraparietal sulcus and inferior parietal 
lobule to the inferior frontal gyrus (BA 44, 45, 47)"
By TRACULA output we have 2 output SLFp and SLFt.
Having also cortical results, I wonder if possible to know which are the seed 
and target areas of SLF p and SLFt or al least to know which is that branch 
that is described by SLFp output.
Thanks,

Stefano   ___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] volume called 001.mgz

2013-06-10 Thread Varghese Chikku

Dear All,
I am   getting this   error  message on a scan.I deleted the created
 subject folders and re-ran the command,but no luck.Any suggestions?
Thanks in advance,
CV

setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
freesurfer@freesurfer-VirtualBox:~$ recon-all -i
/home/freesurfer/Desktop/10035BL/T1pre/Image1 -autorecon-all -s
10035BLFS
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19
12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/subjects/10035BLFS

 mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image1
/usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz

mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image1
/usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz
file not found or unknown file type for file
/home/freesurfer/Desktop/10035BL/T1pre/Image1
#
#@# MotionCor Mon Jun 10 16:03:45 CEST 2013
ERROR: no run data found in /usr/local/freesurfer/subjects/10035BLFS/mri.
Make sure to
have a volume called 001.mgz in
 /usr/local/freesurfer/subjects/10035BLFS/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19
12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 10035BLFS exited with ERRORS at Mon Jun 10 16:03:45 CEST 2013

For more details, see the log file
/usr/local/freesurfer/subjects/10035BLFS/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

freesurfer@freesurfer-VirtualBox:~$
___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] volume called 001.mgz

2013-06-10 Thread Douglas Greve


Hi Varghese, is Image1 a dicom file?
doug



On 6/10/13 10:09 AM, Varghese Chikku wrote:

Dear All,
I am   getting this   error  message on a scan.I deleted the created 
 subject folders and re-ran the command,but no luck.Any suggestions?

Thanks in advance,
CV

setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
freesurfer@freesurfer-VirtualBox:~$ recon-all -i 
/home/freesurfer/Desktop/10035BL/T1pre/Image1 -autorecon-all -s 
10035BLFS

Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 
12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

/usr/local/freesurfer/subjects/10035BLFS

 mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image1 
/usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz


mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image1 
/usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz
file not found or unknown file type for file 
/home/freesurfer/Desktop/10035BL/T1pre/Image1

#
#@# MotionCor Mon Jun 10 16:03:45 CEST 2013
ERROR: no run data found in 
/usr/local/freesurfer/subjects/10035BLFS/mri. Make sure to
have a volume called 001.mgz in 
 /usr/local/freesurfer/subjects/10035BLFS/mri/orig.

If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 
12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s 10035BLFS exited with ERRORS at Mon Jun 10 16:03:45 CEST 2013

For more details, see the log file 
/usr/local/freesurfer/subjects/10035BLFS/scripts/recon-all.log
To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


freesurfer@freesurfer-VirtualBox:~$



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Coupling cortical and TRACULA results

2013-06-10 Thread Anastasia Yendiki



You can find the aparc+aseg mapped from T1 space to DWI space in the 
dlabel/diff directory. You can overlay it on the paths reconstructed from 
tracula to see which aparc+aseg labels the paths overlap with. The 
identities of the labels in the aparc+aseg are in 
$FREESURFER_HOME/FreeSurferColorLUT.txt.


On Mon, 10 Jun 2013, std...@virgilio.it wrote:


Hi list,
Thiebaut de Schotten et al., in an article on cortex ("Monkey to human
comparative anatomy of the frontal lobe association tracts" reported that 

"The superior longitudinal fasciculus has three distinct branches (Petrides
and Pandya, 1984). 
In humans, the first branch of the superior longitudinal fasciculus (SLF I)
connects to the superior parietal lobule and precuneus (BA 5 and 7), to the
superior frontal (BA 8, 9, 32) and perhaps to some anterior cingulate areas
(BA 24). The second branch (SLF II) originatesin the anterior intraparietal
sulcus and the angular gyrus (BA 39 and 40) and terminates in the posterior
regions of the superior and middle frontal gyrus (BA 6, 8, 9). The third
branch (SLF III) connects the intraparietal sulcus and inferior parietal
lobule to the inferior frontal gyrus (BA 44, 45, 47)"

By TRACULA output we have 2 output SLFp and SLFt.

Having also cortical results, I wonder if possible to know which are the
seed and target areas of SLF p and SLFt or al least to know which is that
branch that is described by SLFp output.

Thanks,


Stefano

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Installation trouble on Macbook Air (no such file or directory)

2013-06-10 Thread zkaufman

Nate,

Try typing the following from the command window:

export FREESURFER_HOME=/Applications/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

Or, you can add these lines to your .bashrc file in your home directory by
using any text editor, or by typing the following in the command line:

echo "export FREESURFER_HOME=/Applications/freesurfer" >> ~/.bashrc
echo "source $FREESURFER_HOME/SetUpFreeSurfer.sh" >> ~/.bashrc

Once these lines are in your .bashrc file, freesurfer will load everytime
you open the terminal program.

-Zeke





> I am new to Unix and FreeSurfer, and I am having some trouble installing
> FreeSurfer on my Macbook Air (10.8). I've downloaded the .dmg file just
> fine, and when I start the installation steps, I'm instructed to add some
> lines to my .cshrc or .tcshrc files in my home directory. Can anyone point
> me to this file? Also, just below on the installation dialog, it says for
> sh or bash users:
>
> export FREESURFER_HOME=/freesurfer
> source $FREESURFER_HOME/SetUpFreeSurfer.sh
>
>
> Can I use these instead of the first two lines of code? I tried to enter
> these bash lines one at a time into my terminal window. The first one
> ("export") did not give me any errors but for the "source" one, I received
> the message:
>
> bash: /freesurfer/SetUpFreeSurfer.sh: No such file or directory.
>
> Any idea as to why I am getting this error? My apologies in advance for my
> lack of experience.
>
> Many thanks,
> Nate
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] volume called 001.mgz

2013-06-10 Thread Bruce Fischl


there are 2 ways to run FS:

1. Specify the input data with -i (usually one slice from a dicom series).
2. Create the subject directory and convert the input volumes to mgz 
volumes named /mri/orig/00[1234].mgz and run recon-all without -i.



sounds like you did 2 without the conversion. Easier to just do 1 in 
general and let recon-all create what it wants


cheers
Bruce

On Mon, 10 Jun 2013, Varghese Chikku wrote:


Dear All,I am   getting this   error  message on a scan.I deleted the created  
subject folders
and re-ran the command,but no luck.Any suggestions?
Thanks in advance,
CV

setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
freesurfer@freesurfer-VirtualBox:~$ recon-all -i
/home/freesurfer/Desktop/10035BL/T1pre/Image1 -autorecon-all -s 10035BLFS
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
Actual FREESURFER_HOME /usr/local/freesurfer
Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 
UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
/usr/local/freesurfer/subjects/10035BLFS

 mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image1
/usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz 

mri_convert /home/freesurfer/Desktop/10035BL/T1pre/Image1
/usr/local/freesurfer/subjects/10035BLFS/mri/orig/001.mgz 
file not found or unknown file type for file 
/home/freesurfer/Desktop/10035BL/T1pre/Image1
#
#@# MotionCor Mon Jun 10 16:03:45 CEST 2013
ERROR: no run data found in /usr/local/freesurfer/subjects/10035BLFS/mri. Make 
sure to
have a volume called 001.mgz in  
/usr/local/freesurfer/subjects/10035BLFS/mri/orig.
If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux freesurfer-VirtualBox 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 
UTC 2013
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 10035BLFS exited with ERRORS at Mon Jun 10 16:03:45 CEST 2013

For more details, see the log file
/usr/local/freesurfer/subjects/10035BLFS/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

freesurfer@freesurfer-VirtualBox:~$ 


___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] autorecon3 error

2013-06-10 Thread Gabriel Gonzalez Escamilla

Dear Doug

Sorry for late answer.

I did open as:
tksurfer qsm1_17 lh inflated, and then File >>load surface >> lh.sphere.reg
and
tksurfer qsm1_17 lh sphere.reg

Neither of them look bad, it looks very spherical, an has nothing strange to my 
eyes...
Any other ideas???

Best Regards
Gabriel



- Mensaje original -
De: Bruce Fischl 
Fecha: Jueves, 6 de Junio de 2013, 6:16 pm
Asunto: Re: [Freesurfer] autorecon3 error
A: Gabriel Gonzalez Escamilla 
CC: freesurfer@nmr.mgh.harvard.edu

> Hi Gabriel
> 
> seems like something is wrong with that surface file. Can you 
> load the lh.sphere.reg in tksurfer and see if it looks ok?
> Bruce
> 
> 
> On Thu, 6 Jun 2013, Gabriel Gonzalez Escamilla wrote:
> 
> >Dear Freesurfers
> >
> >I am running an autorecon3 to the same subject that Rafa sent 
> you (the name
> >looks different but is exactly the same subject), with the 
> command to fix
> >the ribbon.mgz the autorecon-2 has finished, so I continued with
> >-autorecon3, but now is encountering the following error, this 
> time seems to
> >be something with the seg.mgz.
> >
> >
> >
> >#-
> >#@# Cortical Parc lh Thu Jun  6 17:01:26 CEST 2013
> >/root/trabajo/freesurfer/subjects/qsm1_17/scripts
> >
> > mris_ca_label -l ../label/lh.cortex.label -aseg 
> ../mri/aseg.mgz -seed 1234
> >qsm1_17 lh 
> ../surf/lh.sphere.reg/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_kill>iany.2010-03-25.gcs
>  ../label/lh.aparc.annot
> >
> >setting seed for random number generator to 1234
> >using ../mri/aseg.mgz aseg volume to correct midline
> >$Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $
> >  $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
> >f[113526]->v[1] = 539832625 - out of range!
> >
> >reading atlas 
> from/root/trabajo/freesurfer/average/lh.curvature.buckner40.filled.desikan_kill>iany.2010-03-25.gcs...
> >reading color table from GCSA file
> >average std = 1.0   using min determinant for regularization = 0.011
> >0 singular and 384 ill-conditioned covariance matrices regularized
> >Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 
> 06:23:23 GMT
> >2006 x86_64 x86_64 x86_64 GNU/Linux
> >
> >recon-all -s qsm1_17 exited with ERRORS at Thu Jun  6 17:01:33 
> CEST 2013
> >
> >For more details, see the log file
> >/root/trabajo/freesurfer/subjects/qsm1_17/scripts/recon-all.log
> >To report a problem, see
> >http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> >
> >
> >Any ideas how to fix this?
> >
> >Bests,
> >Gabriel>> ___
> 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 whom it is
> addressed. If you believe this e-mail was sent to you in error 
> and the e-mail
> contains patient information, please contact the Partners 
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent 
> to you in error
> but does not contain patient information, please contact the 
> sender and properly
> dispose of the e-mail.

--PhD. student Gabriel 
González-EscamillaLaboratory of Functional NeuroscienceDepartment 
of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: 
ggon...@upo.eshttp://www.upo.es/neuroaging/es/


___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] AR2 Error

2013-06-10 Thread Douglas N Greve


Copy this file to $FREESURFER_HOME/bin/mri_segstats
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.snowleopard

doug

On 06/07/2013 06:01 PM, Erin Browning wrote:
>
> The last thing I ran was
>
> recon-all -s freesurfer -autorecon2 -autorecon3
>
> Which still failed.
>
> We quality check after ar1, so we need to run ar1 separately from ar2 
> and 3.
>
> On Jun 7, 2013 4:53 PM, "Douglas N Greve"  > wrote:
>
>
> you need to include the -autorecon3 flag simultaneously with the
> -autorecon1 and -autorecon2 flags.
>
>
> On 06/07/2013 05:45 PM, Erin Browning wrote:
>
>
> It fails before ar3 runs.
>
> On Jun 7, 2013 2:54 PM, "Douglas N Greve"
> mailto:gr...@nmr.mgh.harvard.edu>
>  >> wrote:
>
>
> There is no indication in this log file that you ran
> autorecon3
> doug
>
>
> On 06/07/2013 02:51 PM, Erin Browning wrote:
>
> Here's the log. I ran mri_add_xform_to_header after it
> failed
> again last time and am currently rerunning AR2+3 on
> it, so you
> can probably ignore the latest modifications to it.
>
> http://gate.nmr.mgh.harvard.edu/filedrop2/?p=iowkgmv
>
> We're running Mac OSX 10.6.8.
>
> Thanks,
> Erin
>
>
> On Fri, Jun 7, 2013 at 12:22 PM, Douglas N Greve
>  
>  >
>  
>  
> Hmmm, I don't know. I think that something strange is
> happening.
> Can you
> send me the new recon-all.log file? Also, tell me what
> platform
> you are
> using and I'll send you a new version of mri_segstats
>
> doug
>
>
>
> On 06/07/2013 01:14 PM, Erin Browning wrote:
> > Could it be that since we skip motioncor, we
> skip the
> > mri_add_xform_to_header program as well? Should I be
> running that
> > separately?
> >
> > Thanks,
> > Erin Browning
> >
> >
> > On Fri, Jun 7, 2013 at 11:54 AM, Erin Browning
> mailto:brown...@uwm.edu>
> >
> 
> >>
> >    >
> 
>  wrote:
> >
> > Hi Doug--
> >
> > Running:
> >
> > recon-all -s freesurfer -autorecon2 -autorecon3
> >
> > produced the same error. Could you send me
> the new
> version
> of the
> > program?
> >
> > Thanks!
> > Erin Browning
> >
> >
> > On Thu, Jun 6, 2013 at 3:01 PM, Douglas N Greve
> >  
>  >
>  
>  >>
>  
>  >
>  
>   wrote:
> >
> >
> > OK, this is a known problem when running
> recon-all with
> > -autorecon1
> > -autorecon2 but

Re: [Freesurfer] surface stream steps

2013-06-10 Thread Douglas N Greve


The classification of WM probably takes the most. This includes a lot of 
things, the longest is the subcortical segmentation. See 
recon-all-status.log for a list of times of each operation.
doug

On 06/08/2013 03:05 PM, Joshua Lee wrote:
> Dear Freesurfers,
>
> From the Wiki Freesurfer surface stream follows something like:
>
>  1. Affine registration to Tal.
>  2. Bias correction and skull stripping
>  3. Classify WM
>  4. Cut hemisphere planes
>  5. Tile WM surface
>  6. Refine WM surface following GM-WM intensity gradients
>  7. Nudge (nudge?) WM surface to follow the GM-CSF gradient to
> generate pial surface
>  8. Labeling Data Set
>  9. Stats
>
> May I ask which couple of these steps tend to be the most 
> computationally taxing/longest to complete?
>
> Also, I'm not sure I understand #7. Is the WM surface scaled in some 
> sense to approximate the GM-CSF boundary, or is this just a refinement 
> step like #6 of a surface that already approximates the GM-CSF boundary?
>
> Thanks, I've spent most of my time working with the sub-cortical stream.
> -
> Joshua
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Surface area measurement method

2013-06-10 Thread Douglas N Greve


On 06/10/2013 02:18 AM, Andreas Berger wrote:
> Hi,
>
> basically, i would like to use the area measure for group analysis, but i'm
> not sure whether that's ok to do. my questions would be:
>
> is it suitable for group analysis?
yes
>
> what should i cite if i do?
We don't have a citation specifically for it. It is used by this paper, 
but it does not describe it in detail.
Greve, D. N., Van der Haegen, L., Cai, Q., Stufflebeam, S., Sabuncu, M. 
R., Fischl, B., & Brysbaert, M. (2013). A Surface-based Analysis of 
Language Lateralization and Cortical Asymmetry. /Journal of cognitive 
neuroscience/, (Early Access), 1-16.
>
> is surface area represented vertex-wise, with a vertex' adjacent face's area
> added and divided by 3?
That is how the ?h.area file is created.
>
> What happens when resampling to the standard mesh:
>> The method assures that total area (or volume) is preserved when mapping
> between subjects
> was that referring to the method described by Winkler or the default
> FreeSurfer way of doing it?
No, his way is more elaborate and probably much better but harder to 
implement and slower. The currently implemented version effectively 
preserves area over any given patch when mapping to fsaverage. I don't 
know what the size of the patch is but is probably on the order of 5mm 
(probably smaller).
doug
>
>
> andreas
>
>
> On Wednesday, June 05, 2013 23:22:46 Douglas N Greve wrote:
>> Hi Andreas, it is not the same method but somewhat related. The method
>> assures that total area (or volume) is preserved when mapping between
>> subjects. How much detail do you need?
>> doug
>>
>> On 06/04/2013 05:21 AM, Andreas Berger wrote:
>>> Hello FreeSurfers,
>>>
>>> after reading this [1] paper about measuring surface area, i realized i
>>> don't know what the default way of measuring surface area is in
>>> FreeSurfer. Is it similar to what's described in the paper? Could you
>>> point me to the right documentation or publication?
>>> Forgive me if i've overlooked it, i found something for thickness, but
>>> not for area. To clarify, i don't mean parcellation-based areas, i mean
>>> the measure that i find in /surf/hemi.area.
>>>
>>>
>>> thanks,
>>> regards,
>>> Andreas
>>>
>>>
>>> [1] Measuring and comparing brain cortical surface area and other areal
>>> quantities. Winkler AM, Sabuncu MR, Yeo BT, Fischl B, Greve DN, Kochunov
>>> P, Nichols TE, Blangero J, Glahn DC (2012). Neuroimage 61(4):1428-43
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] OptSeq first time

2013-06-10 Thread Douglas N Greve

Hi, can you at least come up with an optseq2 command line that I could 
then help you with? There are lots of examples on the web page. You 
should be able to get to a point where you have an error.
thanks
doug


On 06/10/2013 05:14 AM, fMRI wrote:
> Hello all,
>
> This is my first question in this list and it is about OptSeq2.
>
> I am nee to this command.
>
> In brief, I wish to insert the following but Some of them I could not handle 
> it:
>
> My experiment has three conditions although I will later specify them as one 
> condition:
>
> Moving hand at three different target level ( say 10 20 30). Then I will 
> model them as a one condition and enter the parametric response as a first 
> order polynomial effects.
>
> My design will have two columns : main effect of moving hand and the 1 order.
>
> My contrast will be like this [1 0; 0 1]
>
> This is what I would like to optimize using OptSeq2:
>
> Event design
> 1) ISI 6 seconds + or - 1.5 seconds ( I could not do this
> 2) TR 3
> 3) volumes 150
> 4) 45 hand movement; 15 at each target level   ( I could not do this )
> 5) each movement lasts for 3 seconds
>
> I am not sure whether I should use null events or the Period between movement 
> is enough.
>
> Also my main aim is to optimize the best design in terms of detection.
>
> Please any guide or help
>
> Thanks
>
>
> AS
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] HypoIntense Lesions

2013-06-10 Thread Fotiadis, Panagiotis

Hi FreeSurfer Community,

I was wondering whether there is an automatic tool that outlines the 
hypointense lesions in a SWI scan.

Thank you,
Panos
___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] HypoIntense Lesions

2013-06-10 Thread Bruce Fischl

Hi Panos

sorry, forgot to respond to this. We have tools for labeling 
hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It 
might work on those if you also had a good T1 and some training data. Doug 
might know

cheers
Bruce

On Mon, 10 Jun 2013, Fotiadis, Panagiotis 
wrote:

> Hi FreeSurfer Community,
>
> I was wondering whether there is an automatic tool that outlines the 
> hypointense lesions in a SWI scan.
>
> Thank you,
> Panos
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] HypoIntense Lesions

2013-06-10 Thread Douglas N Greve

Hi Panos, not in an SWI scan. The aseg.stats file created by recon-all 
will give you WM hypointensities based on the T1.
doug

On 06/10/2013 11:50 AM, Fotiadis, Panagiotis wrote:
> Hi FreeSurfer Community,
>
> I was wondering whether there is an automatic tool that outlines the 
> hypointense lesions in a SWI scan.
>
> Thank you,
> Panos
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] white matter volume per lobe...

2013-06-10 Thread Douglas N Greve

Hi Gonzalo, the segmentation that you are seeing is paired with the 
insula parcellation.
doug


On 05/30/2013 04:36 PM, Gonzalo Rojas Costa wrote:
> Hi Doug:
>
>The command is:
>
>   mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
> --volmask --o mri/lobulitos.mgz --annot lobulos --wmparc-dmax 200
>
> and the terminal output is:
>
> mri_aparc2aseg --s OAS1_0001_MR1 --labelwm --hypo-as-wm --rip-unknown
> --volmask --o mri/lobulitos_2.mgz --annot lobulos --wmparc-dmax 200
>
> SUBJECTS_DIR /usr/local/freesurfer/subjects
> subject OAS1_0001_MR1
> outvol mri/lobulitos_2.mgz
> useribbon 0
> baseoffset 0
> labeling wm
> labeling hypo-intensities as wm
> dmaxctx 200.00
> RipUnknown 1
>
> Reading lh white surface
>   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.white
>
> Reading lh pial surface
>   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/lh.pial
>
> Loading lh annotations from
> /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/lh.lobulos.annot
> reading colortable from annotation file...
> colortable with 8 entries read (originally none)
>
> Reading rh white surface
>   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.white
>
> Reading rh pial surface
>   /usr/local/freesurfer/subjects/OAS1_0001_MR1/surf/rh.pial
>
> Loading rh annotations from
> /usr/local/freesurfer/subjects/OAS1_0001_MR1/label/rh.lobulos.annot
> reading colortable from annotation file...
> colortable with 8 entries read (originally none)
> Have color table for lh white annotation
> Have color table for rh white annotation
> Loading ribbon segmentation from
> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/ribbon.mgz
> Loading filled from 
> /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/filled.mgz
> Ripping vertices labeled as unkown
> Ripped 7659 vertices from left hemi
> Ripped 7544 vertices from right hemi
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
>
> Loading aseg from /usr/local/freesurfer/subjects/OAS1_0001_MR1/mri/aseg.mgz
> ASeg Vox2RAS: ---
> -1.000   0.000   0.000   128.000;
>   0.000   0.000   1.000  -128.000;
>   0.000  -1.000   0.000   128.000;
>   0.000   0.000   0.000   1.000;
> -
>
> Labeling Slice
>0   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18  
> 19
>   20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36  37  38  
> 39
>   40  41  42  43  44  45  46  47  48  49  50  51  52  53  54  55  56  57  58  
> 59
>   60  61  62  63  64  65  66  67  68  69  70  71  72  73  74  75  76  77  78  
> 79
>   80  81  82  83  84  85  86  87  88  89  90  91  92  93  94  95  96  97  98  
> 99
> 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 
> 119
> 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 
> 139
> 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 
> 159
> 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 
> 179
> 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 
> 199
> 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 
> 219
> 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 
> 239
> 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 688931
> Used brute-force search on 139 voxels
> Fixing Parahip LH WM
>Found 0 clusters
> Fixing Parahip RH WM
>Found 0 clusters
> Writing output aseg to mri/lobulitos_2.mgz
>
>Sincerely,
>
>
> Gonzalo Rojas Costa
>
>
> On Thu, May 30, 2013 at 4:10 PM, Douglas N Greve
>  wrote:
>> can you send me your full command line as well as the terminal output?
>>
>> On 05/30/2013 02:26 PM, Gonzalo Rojas Costa wrote:
>>> Hi Doug:
>>>
>>> But, in the mri_aparc2aseg command, I test with the "--wmparc-dmax
>>> 200" option... I put that big value to test it, but I got the image
>>> that I sent you...
>>>
>>> Sincerely,
>>>
>>>
>>> Gonzalo Rojas Costa
> --
> Gonzalo Rojas Costa
> Laboratory for Advanced Medical Image Processing
> Department of Radiology
> Clínica las Condes
> Lo Fontecilla 441, Las Condes, Santiago, Chile.
> Tel: 56-2-2105170
> Cel: 56-9-97771785
> www.clc.cl
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners

Re: [Freesurfer] HypoIntense Lesions

2013-06-10 Thread Fotiadis, Panagiotis

Hi Doug and Bruce,

Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 would 
work great as well. Do you know where I could look for them?
In addition, Doug besides the WM hypointensities in the aseg.stats is there 
something that shows the number of lesions, instead of the volume (or the 
volume that corresponds to each lesion)?

Thanks for your help,
Panos

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: Monday, June 10, 2013 11:52 AM
To: Fotiadis, Panagiotis
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] HypoIntense Lesions

Hi Panos

sorry, forgot to respond to this. We have tools for labeling
hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It
might work on those if you also had a good T1 and some training data. Doug
might know

cheers
Bruce

On Mon, 10 Jun 2013, Fotiadis, Panagiotis
wrote:

> Hi FreeSurfer Community,
>
> I was wondering whether there is an automatic tool that outlines the 
> hypointense lesions in a SWI scan.
>
> Thank you,
> Panos
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] HypoIntense Lesions

2013-06-10 Thread Douglas N Greve


On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote:
> Hi Doug and Bruce,
>
> Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 
> would work great as well. Do you know where I could look for them?
This is already done in recon-all (aseg.mgz and aseg.stats)
> In addition, Doug besides the WM hypointensities in the aseg.stats is there 
> something that shows the number of lesions, instead of the volume (or the 
> volume that corresponds to each lesion)?
That is not output by default, but you can get it relatively easily in 
two steps:
mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77  -->> This 
creates a binary image
Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and 
volume of each lesion will be in the summary file
doug
>
> Thanks for your help,
> Panos
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, June 10, 2013 11:52 AM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] HypoIntense Lesions
>
> Hi Panos
>
> sorry, forgot to respond to this. We have tools for labeling
> hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It
> might work on those if you also had a good T1 and some training data. Doug
> might know
>
> cheers
> Bruce
>
>
> On Mon, 10 Jun 2013, Fotiadis, Panagiotis
> wrote:
>
>> Hi FreeSurfer Community,
>>
>> I was wondering whether there is an automatic tool that outlines the 
>> hypointense lesions in a SWI scan.
>>
>> Thank you,
>> Panos
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] OptSeq first time

2013-06-10 Thread A a

Correction

This is the lats code :

 optseq2 --ntp 140 --tr 3 --psdwin 6 15 3 --ev ev20 3 20 --ev ev40 3 20
--ev ev60 3 20 --nkeep 3 --o OptSeq_TRIALS/trial_squ --nsearch 1

So The duration is 3 seconds for each and each repeat it 20 times. What I
need is to change/add the ISI to be 7 + or - 1.5 seconds.

Any help please ?

Another point is about the psdwin, I am not sure what exactly it
represents. I saw your slides but I thought this should also change the
ISI,. Can you comment on it please ?

Thanks

AS



On Mon, Jun 10, 2013 at 5:49 PM, fMRI  wrote:

> Dear Prof Douglas,
>
> Thanks for your response.
>
> I managed to do the following:
>
> optseq2  --ntp 140 --tr 3 --padwin 0 12 3 --ev ev15 --ev ev30 --ev ev45
> --nkeep 3 --o trial --nsearch 1
>
> Now what I really want to do is to make the ISI 7 seconds + or - 1.5
> seconds. I am not sure how I should use the percentage option if this is
> what I should change plus the ISI time?
>
> I hope this clarifies it more
>
> Regards,
>
> AS
>
> On 10 Jun 2013, at 16:21, Douglas N Greve 
> wrote:
>
> > Hi, can you at least come up with an optseq2 command line that I could
> > then help you with? There are lots of examples on the web page. You
> > should be able to get to a point where you have an error.
> > thanks
> > doug
> >
> >
> > On 06/10/2013 05:14 AM, fMRI wrote:
> >> Hello all,
> >>
> >> This is my first question in this list and it is about OptSeq2.
> >>
> >> I am nee to this command.
> >>
> >> In brief, I wish to insert the following but Some of them I could not
> handle it:
> >>
> >> My experiment has three conditions although I will later specify them
> as one condition:
> >>
> >> Moving hand at three different target level ( say 10 20 30). Then I
> will model them as a one condition and enter the parametric response as a
> first order polynomial effects.
> >>
> >> My design will have two columns : main effect of moving hand and the 1
> order.
> >>
> >> My contrast will be like this [1 0; 0 1]
> >>
> >> This is what I would like to optimize using OptSeq2:
> >>
> >> Event design
> >> 1) ISI 6 seconds + or - 1.5 seconds ( I could not do this
> >> 2) TR 3
> >> 3) volumes 150
> >> 4) 45 hand movement; 15 at each target level   ( I could not do this )
> >> 5) each movement lasts for 3 seconds
> >>
> >> I am not sure whether I should use null events or the Period between
> movement is enough.
> >>
> >> Also my main aim is to optimize the best design in terms of detection.
> >>
> >> Please any guide or help
> >>
> >> Thanks
> >>
> >>
> >> AS
> >>
> >> ___
> >> Freesurfer mailing list
> >> Freesurfer@nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > gr...@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> >
> > ___
> > 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 whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> > contains patient information, please contact the Partners Compliance
> HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in error
> > but does not contain patient information, please contact the sender and
> properly
> > dispose of the e-mail.
> >
>
___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Hippocampal subfields intensity

2013-06-10 Thread Marcos Martins da Silva

Hi, Freesurfer Experts

After usual processing with recon-all -all we get the aseg.stats file
with several data including intensity values like:
normMean normStdDev
normMin normMax normRange
Left-Hippocampus  77.8939 7.574846.
105.59.

How could I get similar results for each hippocampal subfield, assuming
I also generated all posterior*.mgz files corresponding to each
subfield?
I guess I should first binarize each of the subfields file with a
threshold=127 to map all the pertinent voxels, and then use these files
as masks over nu.mgz and calculate the intensities values. But I do not
know the best way to accomplish this after the binarize step.

Thank you in advance for any help.

Marcos
___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Hippocampal subfields intensity

2013-06-10 Thread Juan Eugenio Iglesias

Hi Marcos,
the right way of doing this is using the soft posteriors to compute the
mean and variance, rather than thresholding at p=0.5. For instance, if
you wanted to compute the mean and variance of the intensitites of the
subiculum, you would do something like this:
mean=sum(Ps.*NU)/sum(Ps);
variance=sum(Ps.*(NU-mean).^2)/sum(Ps);
(where Ps is the posterior of the subiculum)
Cheers,
/Eugenio

On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote:
> Hi, Freesurfer Experts
> 
> After usual processing with recon-all -all we get the aseg.stats file
> with several data including intensity values like:
> normMean normStdDev
> normMin normMax normRange
> Left-Hippocampus  77.8939 7.574846.
> 105.59.
> 
> How could I get similar results for each hippocampal subfield,
> assuming I also generated all posterior*.mgz files corresponding to
> each subfield?
> I guess I should first binarize each of the subfields file with a
> threshold=127 to map all the pertinent voxels, and then use these
> files as masks over nu.mgz and calculate the intensities values. But I
> do not know the best way to accomplish this after the binarize step.
> 
> Thank you in advance for any help.
> 
> Marcos 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

2013-06-10 Thread Glen Lee

Dear freesurfer users

I'm wondering if there is any way of figuring out the surface size within a
mask image (mask.mgh)
which is generated after running a group-level GLM analysis (2nd RFX) using
mri_glmfit.

As I'm thinking, this may be:
  number of vertex by dimension of one vertex (1mm).

But I could be wrong and let me know if anyone knows the solution.

-Glen

fyi) the group analysis was performed in freesurfer sym space.
___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] HypoIntense Lesions

2013-06-10 Thread Fotiadis, Panagiotis

Hi Doug,

Thanks for your response, it was really helpful. In addition to the previous 
comments, I have some subjects that have a hematoma that is not shown in the 
aseg.mgz file, and hence is not shown as a hypointense cluster after doing the 
analysis provided below. Do you know if there is any other way to extract 
information (such as outlining it and/or acquiring its volume) about something 
like?

Thanks again,
Panos

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, June 10, 2013 12:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] HypoIntense Lesions

On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote:
> Hi Doug and Bruce,
>
> Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 
> would work great as well. Do you know where I could look for them?
This is already done in recon-all (aseg.mgz and aseg.stats)
> In addition, Doug besides the WM hypointensities in the aseg.stats is there 
> something that shows the number of lesions, instead of the volume (or the 
> volume that corresponds to each lesion)?
That is not output by default, but you can get it relatively easily in
two steps:
mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77  -->> This
creates a binary image
Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and
volume of each lesion will be in the summary file
doug
>
> Thanks for your help,
> Panos
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: Monday, June 10, 2013 11:52 AM
> To: Fotiadis, Panagiotis
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] HypoIntense Lesions
>
> Hi Panos
>
> sorry, forgot to respond to this. We have tools for labeling
> hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It
> might work on those if you also had a good T1 and some training data. Doug
> might know
>
> cheers
> Bruce
>
>
> On Mon, 10 Jun 2013, Fotiadis, Panagiotis
> wrote:
>
>> Hi FreeSurfer Community,
>>
>> I was wondering whether there is an automatic tool that outlines the 
>> hypointense lesions in a SWI scan.
>>
>> Thank you,
>> Panos
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Set Up question

2013-06-10 Thread David Dalton

Hello FreeSurfer experts,

I recently downloaded and installed FreeSurfer on my Mac computer, but I
have a few questions about the startup.

1. When I run FreeSurfer, I get the following.  I know the Wiki says to
ignore the warning, and FreeSurfer does run normally after this, but I
wanted to be sure it really was not a problem.

[SiriasBook:/] csirias% setenv FREESURFER_HOME Applications/freesurfer/
[SiriasBook:/] csirias% source Applications/freesurfer/SetUpFreeSurfer.csh
 freesurfer-Darwin-lion-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   Applications/freesurfer/
FSFAST_HOME   Applications/freesurfer//fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  Applications/freesurfer//subjects

WARNING: The /Users/csirias/matlab/startup.m file does not appear to be
 configured correctly. You may not be able
 to run the FS-FAST programs
Try adding the following lines to /Users/csirias/matlab/startup.m
-cut-
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
path(path,fsmatlab);
end
clear fshome fsmatlab;
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
if (exist(fsfasttoolbox) == 7)
path(path,fsfasttoolbox);
end
clear fsfasthome fsfasttoolbox;
-cut-

MNI_DIR   Applications/freesurfer//mni
[SiriasBook:/] csirias%


2. When I type in 'freeview' to the command line, I get several other
messages as the program opens.  I am not sure if they are a problem, but
here they are. I seem to be able to run freeview despite these messages,
but some others have told me that these messages do not appear on their
computers, so I am wondering why they appear.

[SiriasBook:/] csirias% freeview
2013-06-10 12:22:57.739 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.740 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.754 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.755 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.768 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.769 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.781 Freeview[1200:303] invalid drawable
2013-06-10 12:22:57.782 Freeview[1200:303] invalid drawable

3. And my last question. How do I run FreeSurfer automatically when I open
the terminal window? I would like to just type 'freeview' into the command
line to have the program run, but I currently have to type

setenv FREESURFER_HOME Applications/freesurfer/

followed by

source Applications/freesurfer/SetUpFreeSurfer.csh

in order for the program to run.

Thank you so much for any help you can give!  Like I said, the program
appears to run normally despite the messages, but I just want to know why
they are appearing. The last question is more of a convenience issue.

Thanks,
David
___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

2013-06-10 Thread Douglas N Greve


Hi Glen, you can use

mri_segstats --seg mask.mgh --id 1 --i 
$SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat

doug


On 06/10/2013 03:17 PM, Glen Lee wrote:
> Dear freesurfer users
>
> I'm wondering if there is any way of figuring out the surface size 
> within a mask image (mask.mgh)
> which is generated after running a group-level GLM analysis (2nd RFX) 
> using mri_glmfit.
>
> As I'm thinking, this may be:
>   number of vertex by dimension of one vertex (1mm).
>
> But I could be wrong and let me know if anyone knows the solution.
>
> -Glen
>
> fyi) the group analysis was performed in freesurfer sym space.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] HypoIntense Lesions

2013-06-10 Thread Douglas N Greve

Hi Panos, I don't know an automatic way to do it. You could label it by 
hand on tkmedit or freeview.
doug


On 06/10/2013 03:31 PM, Fotiadis, Panagiotis wrote:
> Hi Doug,
>
> Thanks for your response, it was really helpful. In addition to the previous 
> comments, I have some subjects that have a hematoma that is not shown in the 
> aseg.mgz file, and hence is not shown as a hypointense cluster after doing 
> the analysis provided below. Do you know if there is any other way to extract 
> information (such as outlining it and/or acquiring its volume) about 
> something like?
>
> Thanks again,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, June 10, 2013 12:18 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] HypoIntense Lesions
>
> On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote:
>> Hi Doug and Bruce,
>>
>> Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 
>> would work great as well. Do you know where I could look for them?
> This is already done in recon-all (aseg.mgz and aseg.stats)
>> In addition, Doug besides the WM hypointensities in the aseg.stats is there 
>> something that shows the number of lesions, instead of the volume (or the 
>> volume that corresponds to each lesion)?
> That is not output by default, but you can get it relatively easily in
> two steps:
> mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77  -->> This
> creates a binary image
> Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and
> volume of each lesion will be in the summary file
> doug
>> Thanks for your help,
>> Panos
>> 
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, June 10, 2013 11:52 AM
>> To: Fotiadis, Panagiotis
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] HypoIntense Lesions
>>
>> Hi Panos
>>
>> sorry, forgot to respond to this. We have tools for labeling
>> hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It
>> might work on those if you also had a good T1 and some training data. Doug
>> might know
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 10 Jun 2013, Fotiadis, Panagiotis
>> wrote:
>>
>>> Hi FreeSurfer Community,
>>>
>>> I was wondering whether there is an automatic tool that outlines the 
>>> hypointense lesions in a SWI scan.
>>>
>>> Thank you,
>>> Panos
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Set Up question

2013-06-10 Thread Douglas N Greve

Hi David, it is not a problem if you're not going to run FS-FAST. If it 
bugs you, you can
setenv NO_FSFAST 1
in your cshrc file prior to sourcing the FS env

doug




On 06/10/2013 03:35 PM, David Dalton wrote:
> Hello FreeSurfer experts,
>
> I recently downloaded and installed FreeSurfer on my Mac computer, but 
> I have a few questions about the startup.
>
> 1. When I run FreeSurfer, I get the following.  I know the Wiki says 
> to ignore the warning, and FreeSurfer does run normally after this, 
> but I wanted to be sure it really was not a problem.
>
> [SiriasBook:/] csirias% setenv FREESURFER_HOME Applications/freesurfer/
> [SiriasBook:/] csirias% source Applications/freesurfer/SetUpFreeSurfer.csh
>  freesurfer-Darwin-lion-stable-pub-v5.3.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   Applications/freesurfer/
> FSFAST_HOME   Applications/freesurfer//fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  Applications/freesurfer//subjects
>
> WARNING: The /Users/csirias/matlab/startup.m file does not appear to be
>  configured correctly. You may not be able
>  to run the FS-FAST programs
> Try adding the following lines to /Users/csirias/matlab/startup.m
> -cut-
> fshome = getenv('FREESURFER_HOME');
> fsmatlab = sprintf('%s/matlab',fshome);
> if (exist(fsmatlab) == 7)
> path(path,fsmatlab);
> end
> clear fshome fsmatlab;
> fsfasthome = getenv('FSFAST_HOME');
> fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
> if (exist(fsfasttoolbox) == 7)
> path(path,fsfasttoolbox);
> end
> clear fsfasthome fsfasttoolbox;
> -cut-
>
> MNI_DIR   Applications/freesurfer//mni
> [SiriasBook:/] csirias%
>
>
> 2. When I type in 'freeview' to the command line, I get several other 
> messages as the program opens.  I am not sure if they are a problem, 
> but here they are. I seem to be able to run freeview despite these 
> messages, but some others have told me that these messages do not 
> appear on their computers, so I am wondering why they appear.
>
> [SiriasBook:/] csirias% freeview
> 2013-06-10 12:22:57.739 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.740 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.754 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.755 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.768 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.769 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.781 Freeview[1200:303] invalid drawable
> 2013-06-10 12:22:57.782 Freeview[1200:303] invalid drawable
>
> 3. And my last question. How do I run FreeSurfer automatically when I 
> open the terminal window? I would like to just type 'freeview' into 
> the command line to have the program run, but I currently have to type
>
> setenv FREESURFER_HOME Applications/freesurfer/
>
> followed by
>
> source Applications/freesurfer/SetUpFreeSurfer.csh
>
> in order for the program to run.
>
> Thank you so much for any help you can give!  Like I said, the program 
> appears to run normally despite the messages, but I just want to know 
> why they are appearing. The last question is more of a convenience issue.
>
> Thanks,
> David
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Neuroinformatics Database (NIDB) 4.2.0 released

2013-06-10 Thread Greg Book

This is an announcement that Neuroinformatics Database version 4.2.0 has
been released. This version includes many performance enhancements and new
features. There is also a demo server available with some sample MR data
and the ABIDE dataset hosted for users who want to test the database
without needing to install it locally.

General features:
* store any binary or text data, including MR (any dicom modality), EEG,
SNP, video, audio, images, etc.
* store assessment/clinical measure values (DSM code, etc, only values, not
full assessments)
* real-time QC for MR data, with values stored in the database
* automatic pipeline processing of any image data, with results stored in
the database
* query and retrieve any of the above data and dump to local/remote FTP,
NFS share, or export in NiDB format
* additionally: DICOM receiver, store family pedigree information, store MR
behavioral data, download stats, reports

New features:
* sharing of imaging data between NiDB instances, while maintaining
anonymity and eliminating subject duplication
* improved pipelines: testing mechanism for new pipelines, creating/editing
scripts, and second level pipelines
* query performance improved on pipeline results: 4.4 million result values
retrieved in 107 seconds.
* methods for creating new back-end NiDB modules

Download version 4.2.0 in .tar.gz format or VirtualBox VM:
http://nidb.sourceforge.net. We'll be presenting at HBM in Seattle next
week, so stop by! NiDB is developed by and with support from the Olin
Neuropsychiatry Research Center at Hartford Hospital/Institute of Living.
___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] HypoIntense Lesions

2013-06-10 Thread Fotiadis, Panagiotis

Great, thank you!

Panos 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Monday, June 10, 2013 3:40 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] HypoIntense Lesions

Hi Panos, I don't know an automatic way to do it. You could label it by
hand on tkmedit or freeview.
doug


On 06/10/2013 03:31 PM, Fotiadis, Panagiotis wrote:
> Hi Doug,
>
> Thanks for your response, it was really helpful. In addition to the previous 
> comments, I have some subjects that have a hematoma that is not shown in the 
> aseg.mgz file, and hence is not shown as a hypointense cluster after doing 
> the analysis provided below. Do you know if there is any other way to extract 
> information (such as outlining it and/or acquiring its volume) about 
> something like?
>
> Thanks again,
> Panos
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Monday, June 10, 2013 12:18 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] HypoIntense Lesions
>
> On 06/10/2013 12:12 PM, Fotiadis, Panagiotis wrote:
>> Hi Doug and Bruce,
>>
>> Don't worry about it! Actually, Bruce, tools for labeling hypo-intense T1 
>> would work great as well. Do you know where I could look for them?
> This is already done in recon-all (aseg.mgz and aseg.stats)
>> In addition, Doug besides the WM hypointensities in the aseg.stats is there 
>> something that shows the number of lesions, instead of the volume (or the 
>> volume that corresponds to each lesion)?
> That is not output by default, but you can get it relatively easily in
> two steps:
> mri_binarize --i aseg.mgz --o wmhypo.mgz --match 77  -->> This
> creates a binary image
> Then run mri_volcluster with --in wmhypo.mgz --thmin .5. The number and
> volume of each lesion will be in the summary file
> doug
>> Thanks for your help,
>> Panos
>> 
>> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, June 10, 2013 11:52 AM
>> To: Fotiadis, Panagiotis
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] HypoIntense Lesions
>>
>> Hi Panos
>>
>> sorry, forgot to respond to this. We have tools for labeling
>> hyper-intense T2/hypo-intense T1. Not sure about the hypointense SWI. It
>> might work on those if you also had a good T1 and some training data. Doug
>> might know
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 10 Jun 2013, Fotiadis, Panagiotis
>> wrote:
>>
>>> Hi FreeSurfer Community,
>>>
>>> I was wondering whether there is an automatic tool that outlines the 
>>> hypointense lesions in a SWI scan.
>>>
>>> Thank you,
>>> Panos
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please conta

Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

2013-06-10 Thread Glen Lee

Thanks Doug!

I just tried, but I got an error:
mri_segstats --seg mask.mgh --id 1 --i
/fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat
ERROR: Option --o unknown

I don't see --o option when I looked up mri_segstats --help either. FYI,
I'm using v5.1.
Any idea?



On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve
wrote:

>
> Hi Glen, you can use
>
> mri_segstats --seg mask.mgh --id 1 --i
> $SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat
>
> doug
>
>
> On 06/10/2013 03:17 PM, Glen Lee wrote:
> > Dear freesurfer users
> >
> > I'm wondering if there is any way of figuring out the surface size
> > within a mask image (mask.mgh)
> > which is generated after running a group-level GLM analysis (2nd RFX)
> > using mri_glmfit.
> >
> > As I'm thinking, this may be:
> >   number of vertex by dimension of one vertex (1mm).
> >
> > But I could be wrong and let me know if anyone knows the solution.
> >
> > -Glen
> >
> > fyi) the group analysis was performed in freesurfer sym space.
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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 whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Hippocampal subfields intensity

2013-06-10 Thread Juan Eugenio Iglesias

Hi Marcos,
1. your fix of MRIread.m is great. I forgot of this bug; we should
totally take care of it.
2. a problem is that nu.mgz (or norm.mgz) and the posteriors are in
difference voxel space. So, you need to resample norm.mgz to the space
of the subfields. To do so, you can use mri_convert with the option -rl
("reslice like"):
mri_convert norm.mgz norm_resampled.mgz -rl posterior_subiculum.mgz 
3. Now you can do:
A=MRIread('norm.mgz');
data=A.vol(:);
B=MRIread('posterior_subiculum.mgz');
post=double(B.vol(:));
mean=sum(data.*post)/sum(post);
variance=sum((data-mean).^2.*post)/sum(post);
Cheers,
/Eugenio

On Mon, 2013-06-10 at 17:17 -0300, Marcos Martins da Silva wrote:
> Hi, Eugenio
> TY for your fast help. I understood you were suggesting to compute
> that on MatLab and I tried this:
> 
> NU=MRIread('nu.mgz')### that runs ok
> Ps=MRIread('posterior_left_subiculum.mgz')  ### it fails with the
> following message 
> WARNING: error reading MR params
> Attempted to access mr_parms(1); index out of bounds because
> numel(mr_parms)=0.
> 
> Error in MRIread (line 100)
>   tr = mr_parms(1);
> 
> I solved creating a little customized nMRIread.m with the following
> changes:
> 
> if numel(mr_parms) > 0
> tr = mr_parms(1);
> flip_angle = mr_parms(2);
> te = mr_parms(3);
> ti = mr_parms(4);
>   else
> mr_parms(1) = 0;
> mr_parms(2) = 0;
> mr_parms(3) = 0;
> mr_parms(4) = 0;
> tr = mr_parms(1);
> flip_angle = mr_parms(2);
> te = mr_parms(3);
> ti = mr_parms(4);
>   end
>   
> With those changes I assigned 0 to mr-parms elements so it runs
> without errors
> But whe I tried the following line I copy and pasted from your
> message:
>mean=sum(Ps.*NU)/sum(Ps);  ### I got the following error
> Undefined function 'times' for input arguments of type 'struct'.
> 
> Any help?
> Cheers, Marcos
> 
> PS: I promised I will post the final solution to list. But I guess it
> is more didactic if these little problems are solved before.
> TY, again.
> Em Seg, 2013-06-10 às 14:19 -0400, Juan Eugenio Iglesias escreveu: 
> > Hi Marcos,
> > the right way of doing this is using the soft posteriors to compute the
> > mean and variance, rather than thresholding at p=0.5. For instance, if
> > you wanted to compute the mean and variance of the intensitites of the
> > subiculum, you would do something like this:
> > mean=sum(Ps.*NU)/sum(Ps);
> > variance=sum(Ps.*(NU-mean).^2)/sum(Ps);
> > (where Ps is the posterior of the subiculum)
> > Cheers,
> > /Eugenio
> > 
> > 
> > 
> > On Mon, 2013-06-10 at 15:12 -0300, Marcos Martins da Silva wrote:
> > > Hi, Freesurfer Experts
> > > 
> > > After usual processing with recon-all -all we get the aseg.stats file
> > > with several data including intensity values like:
> > > normMean normStdDev
> > > normMin normMax normRange
> > > Left-Hippocampus  77.8939 7.574846.
> > > 105.59.
> > > 
> > > How could I get similar results for each hippocampal subfield,
> > > assuming I also generated all posterior*.mgz files corresponding to
> > > each subfield?
> > > I guess I should first binarize each of the subfields file with a
> > > threshold=127 to map all the pertinent voxels, and then use these
> > > files as masks over nu.mgz and calculate the intensities values. But I
> > > do not know the best way to accomplish this after the binarize step.
> > > 
> > > Thank you in advance for any help.
> > > 
> > > Marcos 
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> 

-- 
Juan Eugenio Iglesias, PhD
http://www.jeiglesias.com
igles...@nmr.mgh.harvard.edu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.



___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Fwd: problem about file format

2013-06-10 Thread huang bs

Thanks.

I now find that, when I copy (or cut) the re-con folder from SUBJECTS_DIR
to the shared folder (with XP), it seems that no changes happen - the file
format remains the same.

But if I restart the Xubuntu, and copy (or cut) this re-con folder from
shared folder back to SUBJECTS_DIR, then the file format automatically
changes and the re-con results can not be recognized. This is quite odd...

I have to move the re-con results to the shared folder because in the
Xubuntu FSV5.1.0 virtual hard disk the space is only 10G. So to me now, if
I can expand the disk to, say for example, 50G, then at least I don't need
to move the re-con results but just save them in SUBJECTS_DIR, and so the
file formats will not change.

On 7 June 2013 20:38, Bruce Fischl  wrote:

> I meant for you to cat them and put them in the text of the email.
> Something is badly wrong with them. They should be simple text files with a
> 4x3 matrix and a couple of header lines. Not sure what happened but you
> will need to delete them and regenerat them
>
> cheers
> Bruce
>
> On Fri, 7 Jun 2013, huang bs wrote:
>
>  Seems that I can not post the attachements...
>>
>> -- Forwarded message --
>> From: huang bs 
>> Date: 5 June 2013 22:51
>> Subject: Re: [Freesurfer] problem about file format
>> To: Bruce Fischl 
>> Cc: freesurfer@nmr.mgh.harvard.edu
>>
>>
>> Dear Bruce,
>>
>> Yes, sure. I printed the screens and showed you two cases. One can be
>> recognized, the other one can not. Please find attached for the six
>> figures. I also attached the files talairach.xfm and
>> talairach.auto.xfm for the subject linziyi.
>>
>> One more question: how to extend the hard disk space in Xubuntu,
>> especially in the folder /home/virtualuser/freesurfer/**subjects ? If
>> possible, I don't want to move the data to the shared folder and then
>> face such problem.
>>
>> Sorry I am quite new to Linux so some questions may be quite stupid.
>>
>> Thank you very much!
>>
>> On 05/06/2013, Bruce Fischl  wrote:
>> > no, I haven't seen that before. Can you cat
>> > /home/virtualuser/freesurfer/**subjects/linziyi/mri/**
>> transforms/talairach.xfm
>> >
>> > and send us the contents?
>> >
>> > Bruce
>> > On
>> > Wed, 5 Jun 2013, huang bs wrote:
>> >
>> >> Hi All,
>> >>
>> >> Sorry to take up your time.
>> >>
>> >> My freesurfer now can not recognize the re-con files (such as the .mgz
>> >> files, or .xfm files, etc).
>> >> For example, I run this command to check the talairach transform:
>> >> tkregister2 --mgz --s linziyi --fstal --surf orig
>> >> The terminal then reports:
>> >> ERROR:
>> >>
>> /home/virtualuser/freesurfer/**subjects/linziyi/mri/**
>> transforms/talairach.xfm
>> >> does not start as 'MNI Transform File
>> >> This file talairach.xfm does exist. But under Xubuntu, this
>> >> talairach.auto.xfm file has a different icon and appears as "executable
>> >> file". That's quite strange because I did not make such change to it.
>> >>
>> >> These files did work when I just finished the re-con. But afer the
>> re-con,
>> >> I
>> >> moved them from the freesurfer subjects folder to the shared folder
>> >> (shard
>> >> with XP), because the freesurfer subjects folder has a limited space.
>> >> After
>> >> a few days, I moved them back to the subjects folder for doing the
>> >> statistical analysis, and then I have such problem. Even under the
>> shared
>> >> folder, the files can not be read either.
>> >>
>> >> For the cases I just re-con, since they are not moved to elsewhere,
>> >> everything seems OK.
>> >>
>> >> Have you guys had such problem before and how to fix it? Thanks!
>> >>
>> >> --
>> >> Best Regards,
>> >>
>> >> B Huang
>> >>
>> >>
>> >>
>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> it
>> > is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
>> > http://www.partners.org/**complianceline.
>> >  If the e-mail was sent to you in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
>>
>>
>> --
>> Best Regards,
>>
>> Bingsheng Huang
>> Postdoctoral Research Fellow
>> Diagnostic Radiology, The University of Hong Kong
>>
>>
>>
>> --
>> Best Regards,
>>
>> Bingsheng Huang
>> Postdoctoral Research Fellow
>> Diagnostic Radiology, The University of Hong Kong
>>
>>


-- 
Best Regards,

Bingsheng Huang
Postdoctoral Research Fellow
Diagnostic Radiology, The University of Hong Kong
___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners

Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

2013-06-10 Thread Douglas Greve

It's --sum for this, not --o
doug

On 6/10/13 4:44 PM, Glen Lee wrote:

Thanks Doug!

I just tried, but I got an error:
mri_segstats --seg mask.mgh --id 1 --i 
/fMRI/2D/freesurfer/fsaverage_sym/surf/lh.area --o sum.dat

ERROR: Option --o unknown

I don't see --o option when I looked up mri_segstats --help either. 
FYI, I'm using v5.1.

Any idea?

On Mon, Jun 10, 2013 at 3:39 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:

Hi Glen, you can use

mri_segstats --seg mask.mgh --id 1 --i
$SUBJECTS_DIR/fsaverage_sym/surf/lh.area --o sum.dat

doug

On 06/10/2013 03:17 PM, Glen Lee wrote:
> Dear freesurfer users
>
> I'm wondering if there is any way of figuring out the surface size
> within a mask image (mask.mgh)
> which is generated after running a group-level GLM analysis (2nd
RFX)
> using mri_glmfit.
>
> As I'm thinking, this may be:
>   number of vertex by dimension of one vertex (1mm).
>
> But I could be wrong and let me know if anyone knows the solution.
>
> -Glen
>
> fyi) the group analysis was performed in freesurfer sym space.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.

___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Dimension of brain

2013-06-10 Thread Anupa AV

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??
___
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 whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] OptSeq first time

Re: [Freesurfer] tksurfer overlay scale bar background color

[Freesurfer] Coupling cortical and TRACULA results

[Freesurfer] volume called 001.mgz

Re: [Freesurfer] volume called 001.mgz

Re: [Freesurfer] Coupling cortical and TRACULA results

Re: [Freesurfer] Installation trouble on Macbook Air (no such file or directory)

Re: [Freesurfer] volume called 001.mgz

Re: [Freesurfer] autorecon3 error

Re: [Freesurfer] AR2 Error

Re: [Freesurfer] surface stream steps

Re: [Freesurfer] Surface area measurement method

Re: [Freesurfer] OptSeq first time

[Freesurfer] HypoIntense Lesions

Re: [Freesurfer] HypoIntense Lesions

Re: [Freesurfer] HypoIntense Lesions

Re: [Freesurfer] white matter volume per lobe...

Re: [Freesurfer] HypoIntense Lesions

Re: [Freesurfer] HypoIntense Lesions

Re: [Freesurfer] OptSeq first time

[Freesurfer] Hippocampal subfields intensity

Re: [Freesurfer] Hippocampal subfields intensity

[Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

Re: [Freesurfer] HypoIntense Lesions

[Freesurfer] Set Up question

Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

Re: [Freesurfer] HypoIntense Lesions

Re: [Freesurfer] Set Up question

[Freesurfer] Neuroinformatics Database (NIDB) 4.2.0 released

Re: [Freesurfer] HypoIntense Lesions

Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

Re: [Freesurfer] Hippocampal subfields intensity

Re: [Freesurfer] Fwd: problem about file format

Re: [Freesurfer] How to measure the surface dimension in a mask image after mri_glmfit?

[Freesurfer] Dimension of brain

35 matches

Site Navigation

Mail list logo

Footer information