Re: [Freesurfer] optseq installation
Dear Doug, Thank you for your answer. We run it from shell (a comand window of X11 because we are connected to the server by the way of a MacIntosh) but it isn't recognized. How can we make it executable ? We just upload optseq2 on the Linux server... Le 12 mars 10 à 20:30, Florence POMARES a écrit : Début du message réexpédié : De : Douglas N Greve gr...@nmr.mgh.harvard.edu Date : 12 mars 2010 20:09:57 HNEC À : Florence POMARES florence.borge...@univ-st-etienne.fr Cc : freesurfer@nmr.mgh.harvard.edu Objet : Rép : [Freesurfer] optseq installation Did you make it executable? They are run from the shell, not matlab. doug Florence POMARES wrote: Dear Optseq Developpers, Few years ago we used to design our paradigm with optseq. We would like to use it again but we can't install it. We went on the web site : http://surfer.nmr.mgh.harvard.edu/ optseq/ we download the linux version 2 we upload it to the our old linux server with matlab optseq and optseq2 aren't recognize as command. we also tried to install the cywin version on a PCwindows with cygwin and matlab. but when we execute the optseq2.exe it says that it doesn't find the input point of _isnand in the library of the dynmic links cywin1.ddl we don't know what to do. would you please help us ? thank you Isabelle Faillenot Ingénieur hospitalier service de neurologie - CM2R hôpital Nord 42055 Saint-Etienne cédex 2 ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] Pial surface- clarification
Thanks Bruce, i don't know much about ftps, do you have a ftp address (FSL they give us some ftp address which you can use to send your images) which you can send it to me and i can upload my images. I am very sorry. Thanks a lot venkat From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Sat 3/13/2010 12:35 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Pial surface- clarification Hi Venkat, the image looks ok, but it's hard to tell from a single slice or two and not being able to change the window levels. If you want to ftp a subject to us we're happy to take a look and let you know what we think. cheers, Bruce On Fri, 12 Mar 2010, Rajagopalan, Venkateswaran wrote: Hi All, I am working in ALS dementia patients where there is ventricle enlargement and more CSF filling when compared with controls. Since i am new to freesurfer and my knowledge of anatomy is limited i would like to clarify the following. Pial surface in right and left cerebral cortex looks suspicious to me, the brain extraction step left out some non brain regions, i tried to edit them but since some of the non brain regions are close to brain regions i didn't do too much editing for the fear of removing brain regions. I have attached a screen shot image in one of our subjects, kindly tell me whether the pial surface looks ok if not any suggestions to correct this problem. Thanks in advance venkat === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org http://www.clevelandclinic.org/ for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ 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. === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ 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] recon-all fails because of mri_label error
I use v4.5.0, I also downloaded the new version of mri_label and tried it, but I got another error says that mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /home/m047599/freesurfer-install/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz /home/m047599/freesurfer-install/freesurfer/bin/mri_ca_label: Permission denied. Thanks! Guang From: fis...@nmr.mgh.harvard.edu To: freesurfer...@hotmail.com Date: Sat, 13 Mar 2010 17:03:05 -0500 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all fails because of mri_label error What version are you running? On Mar 13, 2010, at 4:22 PM, Guang Zeng freesurfer...@hotmail.com wrote: Hi, there, recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions? gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.0 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010 The New Busy is not the old busy. Search, chat and e-mail from your inbox. Get started. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_3___ 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] Symmetry on four major cortex lobes on left and right hemisphere
Hello Bruce, Based on Freesurfer segmentation, we calculated the volumes of four major cortex lobes on left and right hemisphere seperately. Now I hope to find some reports illustrate the symmetry stuff using Freesurfer. Do you know where I can find it ? Thanks. Aize _ 约会说不清地方？来试试微软地图最新msn互动功能！ http://ditu.live.com/?form=TLswm=1___ 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] recon-all fails because of mri_label error
Hello, Bruce, I loaded the brainmask.mgz, it has a bad skull-stripping results with cerebellum attached. I tried to fix this problem by adjusting the watershed parameters, but the interesting thing is: this is the base template subject which is created by the command line recon-all -base base_id -tp subj1 -tp subj2 -all I am not sure what is next command line I need to use after I fix the skull-stripping problem, recon-all -base base_id -tp subj1 -tp subj2 -autorecon2 or recon-all -s base_id -autorecon2 Thanks! Guang From: fis...@nmr.mgh.harvard.edu To: freesurfer...@hotmail.com Date: Sat, 13 Mar 2010 17:03:05 -0500 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all fails because of mri_label error What version are you running? On Mar 13, 2010, at 4:22 PM, Guang Zeng freesurfer...@hotmail.com wrote: Hi, there, recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions? gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.0 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010 The New Busy is not the old busy. Search, chat and e-mail from your inbox. Get started. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/210850552/direct/01/___ 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] selxavg error
Hi Doug,
I couldn't find a -no-whiten option in the usage for either selxavg-sess or
selxavg3-sess. In any case, when I run the selxavg command, the screen output
says:
INFO: WhitenFlag = 0 (so I guess it's not whitening?).
I also looked for spikes or artifacts as you suggested and the main thing that
struck me is that for the two subjects for whom I get this error, the min value
in the 4D vol is 0 whereas for the 2 subjects that don't have this error, the
min(vol) is non-zero (negative values in one subject and non-zero, positive for
the other). Otherwise the amplitude profiles look pretty similar for all
subjects. Could this be a divide by zero error somewhere in selxavg? And is
there some way around it?
Thanks in advance,
Leila
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Leila Reddy le...@yahoo.com
Cc: freesurfer@nmr.mgh.harvard.edu
Sent: Fri, March 12, 2010 8:12:54 PM
Subject: Re: [Freesurfer] selxavg error
hmmm, something is going wrong with the whitening. Can you try it without
whitening? Also, look in the 4d volume for some artifact (eg, a spike). This
might account for it.
doug
Leila Reddy wrote:
Hi,
I'm running into an error with selxavg ('Input to SVD must not contain NaN or
Inf') that has been posted before on the mailing list but I couldn't find a
solution to it.
The command was selxavg-sess -sf sessid -df sessdir -analysis loc-sm3. The
output of the log file is:
selxavg-sess log file
$Id: selxavg-sess,v 1.15 2006/01/06 02:37:22 greve Exp $
uid=502(lreddy) gid=502(lreddy) groups=502(lreddy), 81(appserveradm),
79(appserverusr), 80(admin)
/Volumes/donnees/GR/gr_analysis/kan_gr_006
/Applications/freesurfer/fsfast/bin/selxavg-sess
-sf sessid -df sessdir -analysis loc-sm3
Darwin g5-leila.local 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10
18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386
Fri Mar 12 17:07:53 CET 2010
selxavg: Command not found.
---
/Volumes/donnees/GR/gr_data/kan_gr_006
Fri Mar 12 17:07:53 CET 2010
/Volumes/donnees/GR/gr_data/kan_gr_006/bold
selxavg2 -TR 2. -parname loc.para -o loc-sm3/h -i 018/fmc-sm3 -i
019/fmc-sm3 -i 020/fmc-sm3 -cfg
/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg -ipr 1.40625
-pomnibus loc-sm3/omnibus/fsig -fomnibus loc-sm3/omnibus/f
cat: /Applications/freesurfer/fsfast/docs/version: No such file or directory
--- Parsing Config File:
/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg
-gammafit 2.25 1.25 -timewindow 30 -prestim 6 -polyfit 1 -TER 2 -nskip 0
-fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000
Logfile is loc-sm3/h_sxa.log
matlab file is /tmp/sxa_5739.m
--- Matlab file --
% Matlab file for selxavg2 Fri Mar 12 17:07:53 CET 2010
% This file may be deleted
% /tmp/sxa_5739.m
global QuitOnError;
QuitOnError = 1;
r = fast_selxavg( '-TR', '2.', '-parname', 'loc.para', '-o', 'loc-sm3/h',
'-i', '018/fmc-sm3', '-i', '019/fmc-sm3', '-i', '020/fmc-sm3', '-cfg',
'/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg', '-ipr',
'1.40625', '-pomnibus', 'loc-sm3/omnibus/fsig', '-fomnibus',
'loc-sm3/omnibus/f');
if(r==0)
fmri_touch('/Volumes/donnees/GR/gr_data/kan_gr_006/bold/loc-sm3/selxavg.ok.5739');
end
qoe;
---
--
--- matlab output
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
M A T L A B
Copyright 1984-2007 The MathWorks, Inc.
Version 7.4.0.287 (R2007a)
January 29, 2007
Warning: Duplicate directory name: /Users/lreddy/matlab.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.comhttp://www.mathworks.com.
$Id: fast_selxavg.m,v 1.22.2.2 2006/09/29 21:54:40 greve
Exp $
Parsing Arguments
RescaleTarget = 1000
Checking Parameters
AutoStimDur: 0
StimDur: Number of Runs: 3
Input Volume List
1 018/fmc-sm3
2 019/fmc-sm3
3 020/fmc-sm3
Input Pardigm File List
1 018/loc.para
2 019/loc.para
3 020/loc.para
Output Volume loc-sm3/h
F Omnibus Volume loc-sm3/omnibus/f
Sig Omnibus Volume loc-sm3/omnibus/fsig
TR2.00
TER 2.00
Total Window 30
PreStim Window 6
Remove Baseline 1
Remove Trend0
Remove QTrend 0
Rescale Target 1000
nSkip 0
InPlane Res 1.40625
FWHM0
Hanning Radius 0
Time Offset 0
GammaFit1
1 2.25 1.25
GammaFit Alpha: 2
SPM HRF: -1
Seg Brain/Air 1
SynthSeed 0
ExtReg File mcextreg
NExtReg 3
[Freesurfer] Choroid plexus -filling
Hi All, In my filled.mgz volume choroid plexus regions are left out in both right and left hemispheres, i am wondering whether i need to fill them or it is ok to leave them unfilled. Thanks venkat === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ 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] Choroid plexus -filling
it will fill the choroid that is adjacent to ventricles, but not elsewhere cheers Bruce On Mon, 15 Mar 2010, Rajagopalan, Venkateswaran wrote: Hi All, In my filled.mgz volume choroid plexus regions are left out in both right and left hemispheres, i am wondering whether i need to fill them or it is ok to leave them unfilled. Thanks venkat === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ 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] Choroid plexus -filling
So do i need to fill it in other regions (manual editing) Thanks venkat -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Mon 3/15/2010 1:06 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Choroid plexus -filling it will fill the choroid that is adjacent to ventricles, but not elsewhere cheers Bruce On Mon, 15 Mar 2010, Rajagopalan, Venkateswaran wrote: Hi All, In my filled.mgz volume choroid plexus regions are left out in both right and left hemispheres, i am wondering whether i need to fill them or it is ok to leave them unfilled. Thanks venkat === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. 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. === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ 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] Choroid plexus -filling
you shouldn't have to. Is it causing problems? On Mon, 15 Mar 2010, Rajagopalan, Venkateswaran wrote: So do i need to fill it in other regions (manual editing) Thanks venkat -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Mon 3/15/2010 1:06 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Choroid plexus -filling it will fill the choroid that is adjacent to ventricles, but not elsewhere cheers Bruce On Mon, 15 Mar 2010, Rajagopalan, Venkateswaran wrote: Hi All, In my filled.mgz volume choroid plexus regions are left out in both right and left hemispheres, i am wondering whether i need to fill them or it is ok to leave them unfilled. Thanks venkat === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. 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. === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Choroid plexus -filling
Thanks, no it is not causing problems i just wanted to know. Thanks again venkat -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Mon 3/15/2010 1:15 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Choroid plexus -filling you shouldn't have to. Is it causing problems? On Mon, 15 Mar 2010, Rajagopalan, Venkateswaran wrote: So do i need to fill it in other regions (manual editing) Thanks venkat -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Mon 3/15/2010 1:06 PM To: Rajagopalan, Venkateswaran Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Choroid plexus -filling it will fill the choroid that is adjacent to ventricles, but not elsewhere cheers Bruce On Mon, 15 Mar 2010, Rajagopalan, Venkateswaran wrote: Hi All, In my filled.mgz volume choroid plexus regions are left out in both right and left hemispheres, i am wondering whether i need to fill them or it is ok to leave them unfilled. Thanks venkat === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. 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. === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. === P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you. ___ 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
Re: [Freesurfer] optseq installation
what do you mean it is not recognized? To make it executable, you need to run chmod a+x optseq2 to run it, either put it into your PATH, or cd to where it is located and run ./optseq2 the ./ is necessary if it is not in the PATH doug Florence POMARES wrote: Dear Doug, Thank you for your answer. We run it from shell (a comand window of X11 because we are connected to the server by the way of a MacIntosh) but it isn't recognized. How can we make it executable ? We just upload optseq2 on the Linux server... Le 12 mars 10 à 20:30, Florence POMARES a écrit : Début du message réexpédié : *De : *Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu *Date : *12 mars 2010 20:09:57 HNEC *À : *Florence POMARES florence.borge...@univ-st-etienne.fr mailto:florence.borge...@univ-st-etienne.fr *Cc : *freesur...@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Objet : **Rép : [Freesurfer] optseq installation* Did you make it executable? They are run from the shell, not matlab. doug Florence POMARES wrote: Dear Optseq Developpers, Few years ago we used to design our paradigm with optseq. We would like to use it again but we can't install it. We went on the web site : http://surfer.nmr.mgh.harvard.edu/optseq/ we download the linux version 2 we upload it to the our old linux server with matlab optseq and optseq2 aren't recognize as command. we also tried to install the cywin version on a PCwindows with cygwin and matlab. but when we execute the optseq2.exe it says that it doesn't find the input point of _isnand in the library of the dynmic links cywin1.ddl we don't know what to do. would you please help us ? thank you Isabelle Faillenot Ingénieur hospitalier service de neurologie - CM2R hôpital Nord 42055 Saint-Etienne cédex 2 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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 transform brain.mgz back to native space
Liang, You can find instructions on how to do this here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat Sometimes using mri_convert will cause the orientation to be off so you may want to follow those instructions instead. Allison -- On Sat, 13 Mar 2010, Bruce Fischl wrote: Hi Liang, you should just be able to use the -rl (reslice like) option in mri_convert and give the orig/001.mgz as the target. cheers Bruce On Fri, 12 Mar 2010, liang wang wrote: Hi FS experts, I find that FS does make a great skullstrip and extract a perfect brain (ie. brain.mgz). I am thinking to register this brain to MNI152 standard space using FSL. Does anyone know how to transfer the brain (256.^3, 1mm ) to subject-specific native space (224*256*176, 1mm). Thanks in advance. Liang ___ 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] How to compare conditions scanned within different runs?
Were these all in the same session or different sessions? doug Shahin wrote: I want to compare 2 different experimental conditions that were scanned within different runs. For example assume that, in ten runs I have had conditions 1 and 2 and in another ten runs I have had condition 3 and 4. Now I want to compare condition 1 and 3. Is it possible? Regards Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard University ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] recon-all fails because of mri_label error
Hi Guang, yes, this should work: recon-all -base base_id -tp subj1 -tp subj2 -autorecon2 -autorecon3 Let us know how it goes, -Martin On Mon, 2010-03-15 at 10:31 -0500, Guang Zeng wrote: Hello, Bruce, I loaded the brainmask.mgz, it has a bad skull-stripping results with cerebellum attached. I tried to fix this problem by adjusting the watershed parameters, but the interesting thing is: this is the base template subject which is created by the command line recon-all -base base_id -tp subj1 -tp subj2 -all I am not sure what is next command line I need to use after I fix the skull-stripping problem, recon-all -base base_id -tp subj1 -tp subj2 -autorecon2 or recon-all -s base_id -autorecon2 Thanks! Guang __ From: fis...@nmr.mgh.harvard.edu To: freesurfer...@hotmail.com Date: Sat, 13 Mar 2010 17:03:05 -0500 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all fails because of mri_label error What version are you running? On Mar 13, 2010, at 4:22 PM, Guang Zeng freesurfer...@hotmail.com wrote: Hi, there, recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions? gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.0 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010 __ The New Busy is not the old busy. Search, chat and e-mail from your inbox. Get started. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer __ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. Sign up now. ___ 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.
