Freesurfer August 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
143 discussions

Re: [Freesurfer] Longitudinal vs. Cross-sectional Volumes
by Elizabeth Selgrade 31 Aug '09

31 Aug '09

Hi Bruce, I'm using v.4.4. Is there any processing that I can do to remove the bias without having to rerun everything with the newest version? Thanks, Liz -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Monday, August 31, 2009 2:17 PM To: Elizabeth Selgrade Cc: 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Longitudinal vs. Cross-sectional Volumes Hi Liz, what version are you using? Our newest longitudinal version removes this bias. cheers, Bruce On Mon, 31 Aug 2009, Elizabeth Selgrade wrote: > Hello FreeSurfer Users, > > I have been using the longitudinal stream to process four timepoints > for about 20 subjects. I've extracted 9 ROIs and gotten their volumes > for both the longitudinal segmentations and the cross-sectional > segmentations. I'm noticing that there are seemingly significant > differences in the volumes for the two processing streams. The > cross-sectional stream gives results that range from about 0.5% to 19% above the longitudinal volumes. > > Have any of you gotten similar results? > > I'm curious as to why this is happening. I'm using different tools to > register the volumes to two different spaces - tkregister2 & > mri_label2vol move my cross-sectional aseg.mgz's to native space. > Mri_convert moves the longitudinal aseg.mgz's to the base space. I > don't think the different spaces are the root of the problem, as they should have the same resolution. > Could the different tools be affecting the size of my ROIs? > > Or, could initializing the longitudinal segmentation with the base > image somehow alter the volumes? > > Thank you! > Liz Selgrade > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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FreeFurfer_volume_coordinates
by Judit Haasz 31 Aug '09

31 Aug '09

Hi, I am trying to extract Talairach coordinates belonging to white matter volumes (wmparc subregions). Although tkmedit gives the coordinates for volumes, so far I have not found a feasible way by which I could print out the Talairach coordinates for each voxel belonging to one region (volume) given by ColorLUT, eg lh-wm-parsorbitalis. Is there a way to do this? For surfaces I found out that each label file contains the list of vertices with RAS coordinates corresponding to one label. Ras coordinates can be converted to MNI, from which we can convert our region into talairach space by applying talairach.xfm. Is there a similiar approach that can be applied to volumes? I started by converting wmparc into Talairach space by mri_convert. Could you have a look at fornix segmentation? Thanks a lot, Judit Haasz

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Paradigm file stimulus onset time
by Jesse Friedman 31 Aug '09

31 Aug '09

Our group has been making paradigm files in which stimulus onset time is always a multiple of the TR (e.g. 0;2;4;8;10;12;16) even though, as a result of jitter in our stimulus presentation program, the actual stimulus onset time may be off by a couple hundred milliseconds (e.g. .08;2.13;4.21;7.82;10.02;12.30;15.86). I recently noticed this sentence in the freesurfer wiki: "The onset time does not need to be a multiple of the TR or linked in any way (e.g., the onset time could be something like 11.340)." Would it be preferable if we were to alter our stimulus onset column to reflect actual rather than intended stimulus onset time, or does the relatively low temporal resolution make it a moot point?

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Longitudinal vs. Cross-sectional Volumes
by Elizabeth Selgrade 31 Aug '09

31 Aug '09

Hello FreeSurfer Users, I have been using the longitudinal stream to process four timepoints for about 20 subjects. I've extracted 9 ROIs and gotten their volumes for both the longitudinal segmentations and the cross-sectional segmentations. I'm noticing that there are seemingly significant differences in the volumes for the two processing streams. The cross-sectional stream gives results that range from about 0.5% to 19% above the longitudinal volumes. Have any of you gotten similar results? I'm curious as to why this is happening. I'm using different tools to register the volumes to two different spaces - tkregister2 & mri_label2vol move my cross-sectional aseg.mgz's to native space. Mri_convert moves the longitudinal aseg.mgz's to the base space. I don't think the different spaces are the root of the problem, as they should have the same resolution. Could the different tools be affecting the size of my ROIs? Or, could initializing the longitudinal segmentation with the base image somehow alter the volumes? Thank you! Liz Selgrade

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question about combined volumetric and surface (CVS) registration
by bin.lv 31 Aug '09

31 Aug '09

Hi FreeSurfer experts, I'm reading a paper which published on IEEE TMI ("Combined volumetric and surface registration" G. Postelnicu, L. Zollei and B. Fischl.2009.) And I also find there is page on the wiki for it, http://surfer.nmr.mgh.harvard.edu/fswiki/CvsRegistration But it seems incomplete, the scripts for stage 2 and stage 3 can not be found in the current version of freesurfer. I am wondering if I can get them in some other places. Thanks in advance! Bin Lv 2009-08-31 bin.lv

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callosum
by laura_dg80 30 Aug '09

30 Aug '09

hi! I have some other question on corpus callosum 1) the volumes of the Corpus Callosum (i.e.CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior,CC_Anterior only) are the result of wich segmentation process? the volume based stream ? 2) You wrote me that the Callosum is segmented into five even length segments A/P, I have some difficulties on visualize it, could you help me with some immages or references? thank you in advance L.

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which linux disto?
by Alexander Li Cohen 29 Aug '09

29 Aug '09

Hi all, quick question, I'm wanting to install freesurfer on our local linux computer, and it is running Fedora 9... but there doesn't appear to be a redhat 4.5.0 release? only the CentOS versions, so which should I use? -Alex ~)------------- ---------------------------------------------------------------------- Alexander Li Cohen alexc(a)npg.wustl.edu (WORK Email) alexcohen(a)gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine ---------------------------------------------------------------------- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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RES: which linux disto?
by Pedro Paulo de Magalhaes Oliveira Jr 29 Aug '09

29 Aug '09

You can use Ubuntu, RH, Suse, Debian, etc... I have already ran it on FreeBSD. Enviado do meu celular Nokia -----Msg original----- De: Alexander Li Cohen Enviada: 29/08/2009 18:45:45 Para: Freesurfer Mailing List Assunto: [Freesurfer] which linux disto? Hi all, quick question, I'm wanting to install freesurfer on our local linux computer, and it is running Fedora 9... but there doesn't appear to be a redhat 4.5.0 release? only the CentOS versions, so which should I use? -Alex ~)------------- ---------------------------------------------------------------------- Alexander Li Cohen alexc(a)npg.wustl.edu (WORK Email) alexcohen(a)gmail.com (Non-secure / rapid-response Email) Petersen/Schlaggar Lab Medical Scientist Training Program Washington University in St. Louis School of Medicine ---------------------------------------------------------------------- This message is intended only for the exclusive use of the intended recipient(s) named herein and may contain information that is PRIVILEGED and/or CONFIDENTIAL. If you are not the intended recipient, you are hereby notified that any use, dissemination, disclosure or copying of this communication is strictly prohibited. If you have received this communication in error, please destroy all copies of this message and its attachments and notify us immediately. The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Problem with lgi
by leemon albert 28 Aug '09

28 Aug '09

Dear all, I am trying to compute the local gyrification index but unfortunately encounter the problem below. Matlab Version ( R2007a) and also the Image Processing Toolbox are installed on my computer (Ubuntu 9.04,32-bit). I think the matlab isn't rightly called by the script. But the "make_outer_surface.m" is not a bash command. Here, how does it invoke the Matlab? Any help is greatly appreciated! Best wishes, /mnt/freesurfer/subjects$ recon-all -s dinghai_4 -localGI Subject Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0 INFO: SUBJECTS_DIR is /mnt/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 huiguang huiguang 803627 Aug 25 09:44 /mnt/freesurfer/subjects/dinghai_4/scripts/recon-all.log Linux hhg-linux 2.6.24-19-generic #1 SMP Wed Aug 20 22:56:21 UTC 2008 i686 GNU/Linux /mnt/freesurfer/subjects/dinghai_4/surf #-------------------------------------------- #@# Local Gyrification Index lh Tue Aug 25 09:54:08 CST 2009 mris_compute_lgi --i lh.pial ================= rm -Rf /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= if: Expression Syntax. ERROR: make_outer_surface did not create output file '/mnt/freesurfer/subjects/dinghai_4/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux hhg-linux 2.6.24-19-generic #1 SMP Wed Aug 20 22:56:21 UTC 2008 i686 GNU/Linux recon-all exited with ERRORS at Tue Aug 25 09:54:18 CST 2009 Then I open the matlab ,there is a warning: "Executing startup failed in matlabrc.',... 'This indicates a potentially serious problem in your MATLAB setup,',... 'which should be resolved as soon as possible. " -- Albert Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA

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installation help
by Matthew Alexander Hevey 28 Aug '09

28 Aug '09

Hi, My name is Matthew Hevey from Vanderbilt University. We are having a little trouble installing FreeSurfer on our Linux computer (Ubuntu 9.04). I have followed the steps in the Wiki about installing through the part on setenv FREESURFER_HOME <freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh and i get Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni After this I'm a little stumped. When I try tkmedit or tksurfer all it says is tkmedit.bin command not found. I have my FREESURFER_HOME at /home/administrator/Desktop/freesurfer and I can see the tkmedit.bin file in the bin folder. I just haven't been able to find anywhere in the forums how to actually open freesurfer. When I type freesurfer it says what version it is but I've never gotten a window to open or anything. Any help would be appreciated. Thanks -Matthew Hevey

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Freesurfer August 2009