Re: [Freesurfer] Probably activation due to vessels
Hi Doug, the analysis is done on the cortex surface. The following commands are used for the analysis of the functional activation in the right hemisphere cortex: preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -nosmooth plot-twf-sess -s sessionID -fsd bold -mc tkregister-sess -s sessionID -fsd bold -per-run -bbr-sum mkanalysis-sess -fsd bold -surface fsaverage rh -fwhm 0 -event-related -paradigm stim.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 5 -polyfit 2 -analysis stim.sm0.rh -force mkcontrast-sess -analysis stim.sm0.rh -contrast stim-li-v-base -a 1 selxavg3-sess -s sessionID -analysis stim.sm0.rh -no-preproc tksurfer-sess -s sessionID -analysis stim.sm0.rh -c stim-li-v-base -tcl ./label_01.tcl. Left hemisphere and sub-cortical analysis are also carried out. Results are depicted on the flatted cortex surface in the primary somatosensory cortex. This label is a combination of the freesurfer areas BA1, BA2, BA3a and BA3b. The activation is masked to this label. An example of the line like pattern is uploaded on your ftp server using my email (pfannmoelj ... uni-greifswald.de, the at sign is replaced by dots) as the password. There is a snaking line in the middle of the image which is a candidate for a vessel. In other images the straight line like patterns or line like patterns with gaps are found. Is there a way to analyze the data in a volume based stream without differentiation between cortex and sub-cortical brain in which the distance of the line like pattern relative to the gray substance is visible? This could be used in order to classify between true activation and vessel activation. We have epi data with spatial resolution of 2x2x4mm^3 (used to generate attached image) and 1.5x1.5x2mm^3 which both show line like patterns. Structural data are taken using the single echo freesurfer protocol for the flash sequence, recommended for cortex. I hope those information are of help. Sincerely yours pfannmoe On Mon, 15 Oct 2012 17:52:04 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Jorg, can you tell us a little more? A picture would be good. Also, describe how you have done your analysis (eg, on the surface or in the volume, how much smoothing). doug On 10/15/2012 11:01 AM, wrote: Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them. Ideally there would be something like a volume based mode which does not sxclude the cortex. In this mode the vessels couls be identified and removed. Any help is highly apprexiated. Respectfully yours pfannmoe ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] error measuring LGI
Dear FS experts I'm trying to run the recon-all -s subjid -localGI in both terminal and matlab, and neither of them is working.I'm using currently version of FS and matlab R2009b.the following error alwais apair:INFO: FreeSurfer build stamps do not matchSubject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjectsActual FREESURFER_HOME /root/trabajo/freesurfer-rwxr-xr-x 1 root root 6867734 Oct 16 15:23 /root/trabajo/freesurfer/subjects/c_Macarena/scripts/recon-all.logLinux 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/root/trabajo/freesurfer/subjects/c_Macarena/surf##@# Local Gyrification Index lh Tue Oct 16 15:24:31 CEST 2012 mris_compute_lgi --i lh.pialERROR: Matlab is required to run mris_compute_lgi!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/Linuxrecon-all -s c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST 2012Matlab exist on the startup.m file as:% FreeSurfer -%fshome = getenv('FREESURFER_HOME');fsmatlab = sprintf('%s/root/trabajo/freesurfer/matlab',fshome);path(path,fsmatlab);clear fshome fsmatlab;%-%Can anyone help me on this?Best Regards,Gabriel
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Re: [Freesurfer] error measuring LGI
Gabriel,
If I am correct, your path (fsmatlab) is pointing to the matlab folder of
freesurfer distribution (I.e. Including the matlab scripts) whereas it should
point to the matlab installation directory.
You can check using the command getmatlab.
Let me know,
Marie
On 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla ggon...@upo.es wrote:
Dear FS experts
I'm trying to run the recon-all -s subjid -localGI in both terminal and
matlab, and neither of them is working.
I'm using currently version of FS and matlab R2009b.
the following error alwais apair:
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjects
Actual FREESURFER_HOME /root/trabajo/freesurfer
-rwxr-xr-x 1 root root 6867734 Oct 16 15:23
/root/trabajo/freesurfer/subjects/c_Macarena/scripts/recon-all.log
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
/root/trabajo/freesurfer/subjects/c_Macarena/surf
#
#@# Local Gyrification Index lh Tue Oct 16 15:24:31 CEST 2012
mris_compute_lgi --i lh.pial
ERROR: Matlab is required to run mris_compute_lgi!
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 c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST 2012
Matlab exist on the startup.m file as:
% FreeSurfer -%
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/root/trabajo/freesurfer/matlab',fshome);
path(path,fsmatlab);
clear fshome fsmatlab;
%-%
Can anyone help me on this?
Best Regards,
Gabriel
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Re: [Freesurfer] error measuring LGI
Thanks Marie,You are right is pointing to the FSmatlab directory not to the installation folder, but the wiki say so:You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script. Do I need to change that in the startup.m?I did also try the getmatlab command and said that matlab does not exist, I'm guessing this is the problem.Bests,GabrielEl 16/10/12, Marie Schaer marie.sch...@unige.ch escribió:Gabriel,If I am correct, your path (fsmatlab) is pointing to the matlab folder of freesurfer distribution (I.e. Including the matlab scripts) whereas it should point to the matlab installation directory.You can check using the command getmatlab.Let me know,MarieOn 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla ggon...@upo.es wrote: Dear FS experts I'm trying to run the recon-all -s subjid -localGI in both terminal and matlab, and neither of them is working. I'm using currently version of FS and matlab R2009b. the following error alwais apair: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjects Actual FREESURFER_HOME /root/trabajo/freesurfer -rwxr-xr-x 1 root root 6867734 Oct 16 15:23 /root/trabajo/freesurfer/subjects/c_Macarena/scripts/recon-all.log 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 /root/trabajo/freesurfer/subjects/c_Macarena/surf # #@# Local Gyrification Index lh Tue Oct 16 15:24:31 CEST 2012 mris_compute_lgi --i lh.pial ERROR: Matlab is required to run mris_compute_lgi! 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 c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST 2012 Matlab exist on the startup.m file as: % FreeSurfer -% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/root/trabajo/freesurfer/matlab',fshome); path(path,fsmatlab); clear fshome fsmatlab; %-% Can anyone help me on this? Best Regards, 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.___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- --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/
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[Freesurfer] pctsurfcon question
I do not have a question on how to use the program, the wiki covered that well. My question is about the formula embedded in the program to calculate the contrast. The formula is ((wm-gm)/((wm+gm)/2))*100 This creates a dynamic range of -200 to +200. Which the last time I checked is not really a percent as the command name implies. Was there some reasoning behind this that I am missing? Phil Greer University of Pittsburgh ___ 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] error measuring LGI
Dear Marie,I've tried to set the matlab installation path, into the tcsh path (where my FS_HOME is), but It's not working. I have no idea how to change this on the startup.m, can you help me with it?Regards,GabrielEl 16/10/12, Marie Schaer marie.sch...@unige.ch escribió:Gabriel,If I am correct, your path (fsmatlab) is pointing to the matlab folder of freesurfer distribution (I.e. Including the matlab scripts) whereas it should point to the matlab installation directory.You can check using the command getmatlab.Let me know,MarieOn 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla ggon...@upo.es wrote: Dear FS experts I'm trying to run the recon-all -s subjid -localGI in both terminal and matlab, and neither of them is working. I'm using currently version of FS and matlab R2009b. the following error alwais apair: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjects Actual FREESURFER_HOME /root/trabajo/freesurfer -rwxr-xr-x 1 root root 6867734 Oct 16 15:23 /root/trabajo/freesurfer/subjects/c_Macarena/scripts/recon-all.log 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 /root/trabajo/freesurfer/subjects/c_Macarena/surf # #@# Local Gyrification Index lh Tue Oct 16 15:24:31 CEST 2012 mris_compute_lgi --i lh.pial ERROR: Matlab is required to run mris_compute_lgi! 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 c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST 2012 Matlab exist on the startup.m file as: % FreeSurfer -% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/root/trabajo/freesurfer/matlab',fshome); path(path,fsmatlab); clear fshome fsmatlab; %-% Can anyone help me on this? Best Regards, 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.___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- --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/
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Re: [Freesurfer] error measuring LGI
Gabriel,
I would start by adding the path to the matlab installation directory to $PATH.
On a Mac it looks like /Applications/Matlab_R*/bin. Then the getmatlab command
should work, and LGI as well.
Marie
On 16 oct. 2012, at 16:39, Gabriel Gonzalez Escamilla ggon...@upo.es wrote:
Thanks Marie,
You are right is pointing to the FSmatlab directory not to the installation
folder, but the wiki say so:
You will also need $FREESURFER_HOME/matlab in your matlab path set up in
your ~/matlab/starup.m script.
Do I need to change that in the startup.m?
I did also try the getmatlab command and said that matlab does not exist, I'm
guessing this is the problem.
Bests,
Gabriel
El 16/10/12, Marie Schaer marie.sch...@unige.ch escribió:
Gabriel,
If I am correct, your path (fsmatlab) is pointing to the matlab folder of
freesurfer distribution (I.e. Including the matlab scripts) whereas it
should point to the matlab installation directory.
You can check using the command getmatlab.
Let me know,
Marie
On 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla ggon...@upo.es wrote:
Dear FS experts
I'm trying to run the recon-all -s subjid -localGI in both terminal and
matlab, and neither of them is working.
I'm using currently version of FS and matlab R2009b.
the following error alwais apair:
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjects
Actual FREESURFER_HOME /root/trabajo/freesurfer
-rwxr-xr-x 1 root root 6867734 Oct 16 15:23
/root/trabajo/freesurfer/subjects/c_Macarena/scripts/recon-all.log
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
/root/trabajo/freesurfer/subjects/c_Macarena/surf
#
#@# Local Gyrification Index lh Tue Oct 16 15:24:31 CEST 2012
mris_compute_lgi --i lh.pial
ERROR: Matlab is required to run mris_compute_lgi!
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 c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST 2012
Matlab exist on the startup.m file as:
% FreeSurfer -%
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/root/trabajo/freesurfer/matlab',fshome);
path(path,fsmatlab);
clear fshome fsmatlab;
%-%
Can anyone help me on this?
Best Regards,
Gabriel
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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
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--
--
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -
Email: ggon...@upo.es
http://www.upo.es/neuroaging/es/
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Re: [Freesurfer] pctsurfcon question
Yes, that was actually a mistake on my part. It does go between -200 and +200. doug On 10/16/2012 11:02 AM, Phil Greer wrote: I do not have a question on how to use the program, the wiki covered that well. My question is about the formula embedded in the program to calculate the contrast. The formula is ((wm-gm)/((wm+gm)/2))*100 This creates a dynamic range of -200 to +200. Which the last time I checked is not really a percent as the command name implies. Was there some reasoning behind this that I am missing? Phil Greer University of Pittsburgh ___ 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] error measuring LGI
Marie,I'm working on centOS 4, I'd add the path to the matlab installation folder on my PATH as:setenv MATLABPATH /root/trabajo/matlab2009
setenv PATH ${MATLABPATH}/bin:${PATH}And this is not working stillAny ideas?GabrielEl 16/10/12, Marie Schaer marie.sch...@unige.ch escribió:Gabriel,I would start by adding the path to the matlab installation directory to $PATH. On a Mac it looks like /Applications/Matlab_R*/bin. Then the getmatlab command should work, and LGI as well.MarieOn 16 oct. 2012, at 16:39, Gabriel Gonzalez Escamilla ggon...@upo.es ggon...@upo.es wrote:Thanks Marie,You are right is pointing to the FSmatlab directory not to the installation folder, but the wiki say so:You will also need $FREESURFER_HOME/matlab in your matlab path set up in your ~/matlab/starup.m script. Do I need to change that in the startup.m?I did also try the getmatlab command and said that matlab does not exist, I'm guessing this is the problem.Bests,GabrielEl 16/10/12, Marie Schaer marie.sch...@unige.ch marie.sch...@unige.ch escribió:Gabriel,If I am correct, your path (fsmatlab) is pointing to the matlab folder of freesurfer distribution (I.e. Including the matlab scripts) whereas it should point to the matlab installation directory.You can check using the command getmatlab.Let me know,MarieOn 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla ggon...@upo.es ggon...@upo.es wrote: Dear FS experts I'm trying to run the recon-all -s subjid -localGI in both terminal and matlab, and neither of them is working. I'm using currently version of FS and matlab R2009b. the following error alwais apair: INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjects Actual FREESURFER_HOME /root/trabajo/freesurfer -rwxr-xr-x 1 root root 6867734 Oct 16 15:23 /root/trabajo/freesurfer/subjects/c_Macarena/scripts/recon-all.log 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 /root/trabajo/freesurfer/subjects/c_Macarena/surf # #@# Local Gyrification Index lh Tue Oct 16 15:24:31 CEST 2012 mris_compute_lgi --i lh.pial ERROR: Matlab is required to run mris_compute_lgi! 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 c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST 2012 Matlab exist on the startup.m file as: % FreeSurfer -% fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/root/trabajo/freesurfer/matlab',fshome); path(path,fsmatlab); clear fshome fsmatlab; %-% Can anyone help me on this? Best Regards, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.eduFreesurfer@nmr.mgh.harvard.edu 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 listFreesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- --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.esggon...@upo.es ggon...@upo.eshttp://www.upo.es/neuroaging/es/
-- --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/
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Re: [Freesurfer] error measuring LGI
... Strange, then I would just quickly look at the following things (in a new
terminal, so that you are sure that everything is cleanly set):
1) whether the $PATH is indeed correctly set without typo. Either by verifying
the $PATH variable (type $PATH in your shell, you should see your full path to
matlab). Or by just prompting the command matlab in your shell, which should
open a matlab session.
2) I would source the freesurfer environment variables again (set the
FREESURFER_HOME variable and then source SetUpFreeSurfer.csh), and check
whether getmatlab give you the location of your matlab command (something like
/root/trabajo/matlab2009/bin/matlab)
Given that I am not a centOS specialist, if this doesn't work, we should maybe
ask someone else, like e.g. Nick if he has a better idea.
Let me know,
Marie
On Oct 16, 2012, at 6:54 PM, Gabriel Gonzalez Escamilla wrote:
Marie,
I'm working on centOS 4, I'd add the path to the matlab installation folder
on my PATH as:
setenv MATLABPATH /root/trabajo/matlab2009
setenv PATH ${MATLABPATH}/bin:${PATH}
And this is not working still
Any ideas?
Gabriel
El 16/10/12, Marie Schaer marie.sch...@unige.ch escribió:
Gabriel,
I would start by adding the path to the matlab installation directory to
$PATH. On a Mac it looks like /Applications/Matlab_R*/bin. Then the
getmatlab command should work, and LGI as well.
Marie
On 16 oct. 2012, at 16:39, Gabriel Gonzalez Escamilla ggon...@upo.es
ggon...@upo.es wrote:
Thanks Marie,
You are right is pointing to the FSmatlab directory not to the installation
folder, but the wiki say so:
You will also need $FREESURFER_HOME/matlab in your matlab path set up in
your ~/matlab/starup.m script.
Do I need to change that in the startup.m?
I did also try the getmatlab command and said that matlab does not exist,
I'm guessing this is the problem.
Bests,
Gabriel
El 16/10/12, Marie Schaer marie.sch...@unige.ch marie.sch...@unige.ch
escribió:
Gabriel,
If I am correct, your path (fsmatlab) is pointing to the matlab folder of
freesurfer distribution (I.e. Including the matlab scripts) whereas it
should point to the matlab installation directory.
You can check using the command getmatlab.
Let me know,
Marie
On 16 oct. 2012, at 16:02, Gabriel Gonzalez Escamilla ggon...@upo.es
ggon...@upo.es wrote:
Dear FS experts
I'm trying to run the recon-all -s subjid -localGI in both terminal
and matlab, and neither of them is working.
I'm using currently version of FS and matlab R2009b.
the following error alwais apair:
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is /root/trabajo/freesurfer/subjects
Actual FREESURFER_HOME /root/trabajo/freesurfer
-rwxr-xr-x 1 root root 6867734 Oct 16 15:23
/root/trabajo/freesurfer/subjects/c_Macarena/scripts/recon-all.log
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
/root/trabajo/freesurfer/subjects/c_Macarena/surf
#
#@# Local Gyrification Index lh Tue Oct 16 15:24:31 CEST 2012
mris_compute_lgi --i lh.pial
ERROR: Matlab is required to run mris_compute_lgi!
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 c_Macarena exited with ERRORS at Tue Oct 16 15:24:31 CEST
2012
Matlab exist on the startup.m file as:
% FreeSurfer -%
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/root/trabajo/freesurfer/matlab',fshome);
path(path,fsmatlab);
clear fshome fsmatlab;
%-%
Can anyone help me on this?
Best Regards,
Gabriel
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contains patient information, please contact the Partners Compliance
HelpLine at
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--
--
PhD. student Gabriel González-Escamilla
Laboratory of Functional
Re: [Freesurfer] Mixed-effects models for longitudinal data analysis in Freesurfer
If you want to do a repeated measures ANOVA with more than two time points, I've put a page together here: http://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova doug On 10/15/2012 08:24 PM, Harry Hallock [hhal5...@uni.sydney.edu.au] wrote: Hi Martin, If you could make available that lme toolbox link, that would be great! Thanks for the help. Cheers, Harry *From:* jorge luis [jbernal0...@yahoo.es] *Sent:* Tuesday, 16 October 2012 8:16 AM *To:* Martin Reuter; Harry Hallock [hhal5...@uni.sydney.edu.au] *Cc:* freesurfer@nmr.mgh.harvard.edu *Subject:* Mixed-effects models for longitudinal data analysis in Freesurfer Hi Harry As Martin said, longitudinal linear mixed-effects models (lme) are the recommended tool for analyzing longitudinal data obtained from the Freesurfer longitudinal image processing pipeline. The increase in power can be dramatic. Coming up there is a paper about this subject. We are working on making our lme tools available and easy to use but in the mean time, if you are interested, I can make available a link for you to download our Matlab-based lme toolbox. Best -Jorge *De:* Martin Reuter mreu...@nmr.mgh.harvard.edu *Para:* Harry Hallock hhal5...@uni.sydney.edu.au; Douglas N Greve gr...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Enviado:* Domingo 14 de octubre de 2012 21:06 *Asunto:* Re: [Freesurfer] 3 Factor glm group analysis Hi Harry. I have some scripts to compute a slope into the time thickness or volume (linear fits) and then run a standard glm on that . However, we recommend to run a linear mixed effects model (external software). We are working on making that available. Best Martin Harry Hallock hhal5...@uni.sydney.edu.au wrote: Thanks Doug! If i wanted to add a third time-point, what would u suggest would be a good method to use for time x group interaction? Harry 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: Wednesday, 10 October 2012 1:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] 3 Factor glm group analysis Hi Harry, I would do a time1-time2 subtraction (fscalc) and then do a 2 group analysis (search for paired on our wiki). doug On 10/09/2012 12:45 AM, hhal5...@uni.sydney.edu.au wrote: Hello, We are currently doing a longitudinal Group Analysis using FreeSurfer, and were wondering if there is a way to run a 3 factor design (time is 2 levels, group is 2 levels, subject is 10 levels) using the mri_glmfit model, as i want to test the time by group interaction? Is there a way of writing this model in an FSDG file? If we can't do this using mri_glmfit, is it possible to do this using QDEC? Regards, Harry 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 http://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 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 -- Sent from my phone, please excuse brevity.
[Freesurfer] DODS and group age interaction
Dear Experts, I have 2 groups - controls (22 subjects) and patients (19 subjects) with mean ages that are not significantly different, though ranges/median are. I want to compare cortical thickness between groups while allowing for age (age as nuisance factor) but also want to see if there is an interaction between age and group (age as continuous variable). I have demeaned the age across both controls and patients and then used qdec. 1) Using DODS and demeaned ages I find that there is an age-gp interaction such that patients have quicker thickness decline with age than controls. This survives FDR 0.05 and monte carlo VWP 0.005 CWP 0.05. Is this finding valid given that I used demeaned ages (rather than absolute ages) to look for interaction or does it make no difference ? 2) When I come to look to see whether there is a gp difference in thickness I enter age as a nuisance variable in qdec (as opposed to continuous variable above) and use DODS with demeaned age variable across gp. Am I safe to interpret my findings normally given age-gp interaction or is is not safe - if it is not safe how can I look for gp differences or it ok to interpret results provided gp differences are not in regions where I see an interaction ? Thanks. Mahinda ___ 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] Installation difficulties (Mac)
I have downloaded the FreeSurfer software onto a Mac computer. I did the setenv/source steps and got this output: 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 MNI_DIR /Applications/freesurfer//mni Next, I obtained a license and finally got the text to go into a pico .license file after doing this: [Lisa-Koskis-iMac:~] rsussex% sudo -s Password: [Lisa-Koskis-iMac:~] root# cd /Applications/freesurfer/ [Lisa-Koskis-iMac:/Applications/freesurfer] root# pico $FREESURFER_HOME .license FREESURFER_HOME: Undefined variable. [Lisa-Koskis-iMac:/Applications/freesurfer] root# pico .license [Lisa-Koskis-iMac:/Applications/freesurfer] root# ls ASegStatsLUT.txtSetUpFreeSurfer.sh fsfast AUTHORS Simple_surface_labels2009.txt lib DefectLUT.txt VERSION matlab FreeSurferColorLUT.txt WMParcStatsLUT.txt mni FreeSurferEnv.csh average sessions FreeSurferEnv.shbin subjects LICENSE build-stamp.txt tkmeditParcColorsCMA NOTICE datatktools README diffusion trctrain SegmentNoLUT.txtdocs SetUpFreeSurfer.csh fsafd [Lisa-Koskis-iMac:/Applications/freesurfer] root# cd ../.. [Lisa-Koskis-iMac:/] root# cd /Applications/freesurfer//subjects/ [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# ls README bertfsaverage fsaverage4 fsaverage6 rh.EC_average sample-002.mgz V1_average cvs_avg35 fsaverage3 fsaverage5 lh.EC_average sample-001.mgz [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# tkmedit bert orig.mgz tkmedit: Command not found. [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# qdec qdec: Command not found. Since the 'Testing your FreeSurfer installation commands from the wiki page are not working, I may not have installed this properly. Any insights as to how this could be resolved would be much appreciated. Thank you, Julia ___ 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 difficulties (Mac)
Hi Julia, I'm not certain, but I think you just need to define FREESURFER_HOME source FS again before trying to run tkmedit or qdec. The pico $FREESURFER_HOME .license command resulted in FREESURFER_HOME: Undefined variable., so that environment variable needs to be set. I think after the sudo command you were then logged in as root and so the previous environment variables were not carried over. -Louis On Tue, 16 Oct 2012, Julia Nantes wrote: I have downloaded the FreeSurfer software onto a Mac computer. I did the setenv/source steps and got this output: 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 MNI_DIR /Applications/freesurfer//mni Next, I obtained a license and finally got the text to go into a pico .license file after doing this: [Lisa-Koskis-iMac:~] rsussex% sudo -s Password: [Lisa-Koskis-iMac:~] root# cd /Applications/freesurfer/ [Lisa-Koskis-iMac:/Applications/freesurfer] root# pico $FREESURFER_HOME .license FREESURFER_HOME: Undefined variable. [Lisa-Koskis-iMac:/Applications/freesurfer] root# pico .license [Lisa-Koskis-iMac:/Applications/freesurfer] root# ls ASegStatsLUT.txtSetUpFreeSurfer.sh fsfast AUTHORS Simple_surface_labels2009.txt lib DefectLUT.txt VERSION matlab FreeSurferColorLUT.txt WMParcStatsLUT.txt mni FreeSurferEnv.csh average sessions FreeSurferEnv.shbin subjects LICENSE build-stamp.txt tkmeditParcColorsCMA NOTICE datatktools README diffusion trctrain SegmentNoLUT.txtdocs SetUpFreeSurfer.csh fsafd [Lisa-Koskis-iMac:/Applications/freesurfer] root# cd ../.. [Lisa-Koskis-iMac:/] root# cd /Applications/freesurfer//subjects/ [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# ls README bertfsaverage fsaverage4 fsaverage6 rh.EC_average sample-002.mgz V1_average cvs_avg35 fsaverage3 fsaverage5 lh.EC_average sample-001.mgz [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# tkmedit bert orig.mgz tkmedit: Command not found. [Lisa-Koskis-iMac:/Applications/freesurfer/subjects] root# qdec qdec: Command not found. Since the 'Testing your FreeSurfer installation commands from the wiki page are not working, I may not have installed this properly. Any insights as to how this could be resolved would be much appreciated. Thank you, Julia ___ 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] Freesurfer 1mm Isotropic standard and the Future
Hi Everyone, Back in May I was very excited to learn that there was some movement toward allowing Freesurfer to utilize the higher than 1mm iso. resolutions of some of our structural images, which could be fantastic help in subcortical segmentations. Is this something that is still in the works for the next release? gratefully, Joshua - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 On Thu, May 31, 2012 at 5:49 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Joshua sorry, I haven't found the time to really work on it. I spent a couple of hours and found some problems, but haven't found the time to fix them Bruce On Thu, 31 May 2012, Joshua Lee wrote: Hi Bruce, I'm just checking in to see how it turned out with the subcortical segmentation using the high resolution images I sent. Best, Joshua - Joshua Lee Graduate Student Center for Mind and Brain Department of Psychology University of California, Davis 530.747.3805 On Tue, May 15, 2012 at 5:29 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: you need to call mris_make_surfaces directly. It's a bit complicated as you need to intensity normalize and register the hires volume to the surfaces first. I have an example script if anyone is interested, but no one has used it yet but me I don't think (unless Matt Glasser has gotten his version working, which on second thought he probably has) On Mon, 14 May 2012, Michael Waskom wrote: Hi Bruce, Is there a flag for this on recon-all? áOr do you need to use mri_make_surfaces directly? Best, Michael On Mon, May 14, 2012 at 2:09 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: á á áHi Joshua á á áyes, we already have upgraded mris_make_surfaces to take higher á á áres data á á áand refine the surfaces with it. Haven't tried it on the aseg á á áyet, but if á á áyou upload a sample dataset I could see how hard it is. á á ácheers á á áBruce á á áOn Mon, 14 May 2012, á á áJoshua Lee wrote: á á á Dear Freesurfers, á á á á á á Over the last years, MR imaging technology hasimproved such á á áthat sub 1-mm á á á isotropic scans can be obtained with good signal to noise á á ácharacteristics. á á á For example, our lab uses 0.7mm isotropic structural MR á á áimages. I understand á á á that the Freesurfer pipeline will up-sample these to 1mm á á áisotropic, but it á á á seems a shame that so much information is left unused which á á ácould be used to á á á improve the accuracy of sub-cortical and cortical á á ásegmentation. My question á á á is whether there are any plans at Freesurfer to change the á á áreference á á á standard resolution from 1mm isotropic, or provide another á á ásolution that can á á á help researchers make the most of your technology. á á á á á á Sincerely, á á á á á á á á á Joshua á á á - á á á Joshua á á á á á á á á á __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** freesurfer 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/**compliancelinehttp://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/**freesurferhttps://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
Re: [Freesurfer] DODS and group age interaction
On 10/16/2012 02:08 PM, Mahinda Yogarajah wrote: Dear Experts, I have 2 groups - controls (22 subjects) and patients (19 subjects) with mean ages that are not significantly different, though ranges/median are. I want to compare cortical thickness between groups while allowing for age (age as nuisance factor) but also want to see if there is an interaction between age and group (age as continuous variable). I have demeaned the age across both controls and patients and then used qdec. 1) Using DODS and demeaned ages I find that there is an age-gp interaction such that patients have quicker thickness decline with age than controls. This survives FDR 0.05 and monte carlo VWP 0.005 CWP 0.05. Is this finding valid given that I used demeaned ages (rather than absolute ages) to look for interaction or does it make no difference ? For this contrast (group-slope interaction), it makes no difference. 2) When I come to look to see whether there is a gp difference in thickness I enter age as a nuisance variable in qdec (as opposed to continuous variable above) and use DODS with demeaned age variable across gp. Am I safe to interpret my findings normally given age-gp interaction or is is not safe - if it is not safe how can I look for gp differences or it ok to interpret results provided gp differences are not in regions where I see an interaction ? It is not safe. If there is an interaction, then the difference between groups changes with age. You can think of it as two thickness vs age lines, one for each group. If there is no interaction, then these lines will be parallel, meaning that the difference between the groups will be the same no matter what age. If there is an interaction, these lines will not be parallel, meaning that the group difference changes with age, and so whether you see a difference between them or not depends on what age you test them at. Without demeaning, this test age will be age=0. If you demean, then the age will be age=mean(age). doug Thanks. Mahinda ___ 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] Probably activation due to vessels
can you send a pic? On 10/16/2012 05:44 AM, Jörg Pfannmöller wrote: Hi Doug, the analysis is done on the cortex surface. The following commands are used for the analysis of the functional activation in the right hemisphere cortex: preproc-sess -s sessionID -fsd bold -nostc -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -nosmooth plot-twf-sess -s sessionID -fsd bold -mc tkregister-sess -s sessionID -fsd bold -per-run -bbr-sum mkanalysis-sess -fsd bold -surface fsaverage rh -fwhm 0 -event-related -paradigm stim.par -nconditions 1 -spmhrf 0 -TR 2 -refeventdur 10 -nskip 5 -polyfit 2 -analysis stim.sm0.rh -force mkcontrast-sess -analysis stim.sm0.rh -contrast stim-li-v-base -a 1 selxavg3-sess -s sessionID -analysis stim.sm0.rh -no-preproc tksurfer-sess -s sessionID -analysis stim.sm0.rh -c stim-li-v-base -tcl ./label_01.tcl. Left hemisphere and sub-cortical analysis are also carried out. Results are depicted on the flatted cortex surface in the primary somatosensory cortex. This label is a combination of the freesurfer areas BA1, BA2, BA3a and BA3b. The activation is masked to this label. An example of the line like pattern is uploaded on your ftp server using my email (pfannmoelj ... uni-greifswald.de, the at sign is replaced by dots) as the password. There is a snaking line in the middle of the image which is a candidate for a vessel. In other images the straight line like patterns or line like patterns with gaps are found. Is there a way to analyze the data in a volume based stream without differentiation between cortex and sub-cortical brain in which the distance of the line like pattern relative to the gray substance is visible? This could be used in order to classify between true activation and vessel activation. We have epi data with spatial resolution of 2x2x4mm^3 (used to generate attached image) and 1.5x1.5x2mm^3 which both show line like patterns. Structural data are taken using the single echo freesurfer protocol for the flash sequence, recommended for cortex. I hope those information are of help. Sincerely yours pfannmoe On Mon, 15 Oct 2012 17:52:04 -0400 Douglas N Grevegr...@nmr.mgh.harvard.edu wrote: Hi Jorg, can you tell us a little more? A picture would be good. Also, describe how you have done your analysis (eg, on the surface or in the volume, how much smoothing). doug On 10/15/2012 11:01 AM, wrote: Dear Freesurfers, I computed the functional activation in a sensory task using freesurfer's fsfast stream. In the cortex surface line like activated regions are present. Their extension is much larger than the extension of the expected regions. Therefore, I suppose that those regions are due to vessels. Is there a possibility in freesurfer to remove them. Ideally there would be something like a volume based mode which does not sxclude the cortex. In this mode the vessels couls be identified and removed. Any help is highly apprexiated. Respectfully yours pfannmoe ___ 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. ___ 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
Re: [Freesurfer] Control point edits adversely affect cortical surfaces using FS 5.1
Thank-you Bruce! On 16/10/12 12:25 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Vanessa I'm running some tests now Bruce On Oct 15, 2012, at 9:10 PM, Vanessa Louise Cropley vcrop...@unimelb.edu.au wrote: Dear Bruce/freesurfer community, Thank-you for offering to take a look at our data. I have uploaded two files to the ftp. They are called Subject_Before_CP.zip and Subject_After_Cpedit.zip. Please let me know if you haven't received them. I uploaded these last Friday but haven't as yet had a reply. I did this as a test as I assumed that a single ctrl point in WM would have no effect on the surfaces. The 1 ctrl point was added to the LH WM in temporal cortex (slice 120). Thank-you for your help, it would be great if we could find a solution to this problem. - Vanessa On 12/10/12 1:24 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Vanessa if you can upload an example (the entire subject dir) before adding the single control point you refer to, and after adding it we'll track it down. thanks Bruce On Thu, 11 Oct 2012, Vanessa Louise Cropley wrote: Hi all, I have seen others post a similar problem on the freesurfer mailing list but I could not find a solution. When I edit a volume using control points, I am noticing that the use of CP edits adversely effects the wm/gm surfaces in the resulting re-processed image. Like others have reported, the surfaces are adversely affected in locations distant from the CP edits. The temporal lobes are particularly affected. We are using freesurfer 5.1. I have noticed the following things: 1. The problem occurs irrespective of the number of control points added, i.e. whether 100 or 10 control points added 2. The problem occurred when only one CP was added in a voxel that was clearly wm 3. The problem did not occur after reprocessing with FS 4.5 4. I have tried the flag to disable mri_ca_normalize when reprocessing with ?autorecon2. This did not seem to help. I used the command: recon-all ?nocanorm ?autorecon2-cp ?subjid $SUBJ I have screenshots available that illustrate the changes in the surfaces after reprocessing. Could anyone help with this problem? Thank-you, Vanessa ___ 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. -- End of Forwarded Message ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] DODS and group age interaction
Dear Doug, Many thanks for reply. Given the age-group interaction, and the fact that even when age is demeaned it simply means a difference in thickness will be tested for at age=mean age (as opposed to age=0) can I at least interpret the findings when using DODS model with age as a nuisance factor by saying that the difference in thickness between groups represents the difference between groups at the mean age across both groups. Beyond that limited interpretation, is there any other way to analyse the data ? Is there a another model I could use ? My age-group interactions are in a different location to the group differences - does this make any interpretation of group differences more robust ? Thanks. Mahinda ___ 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] DODS and group age interaction
On 10/16/12 8:27 PM, MAHINDA YOGARAJAH wrote: Dear Doug, Many thanks for reply. Given the age-group interaction, and the fact that even when age is demeaned it simply means a difference in thickness will be tested for at age=mean age (as opposed to age=0) can I at least interpret the findings when using DODS model with age as a nuisance factor by saying that the difference in thickness between groups represents the difference between groups at the mean age across both groups. Yes. Beyond that limited interpretation, is there any other way to analyse the data ? Is there a another model I could use ? My age-group interactions are in a different location to the group differences - does this make any interpretation of group differences more robust ? You can reanalyze using DOSS and look for group differences. If those differences are in a different location than the interaction, then you are good to go. doug Thanks. Mahinda ___ 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.
