[Freesurfer] Tracula prep help
*Dear Freesurfer experts, **I have encountered the following error while running the tracula **pre-processing command and was hoping you could help me understand how **to correct this.* *from the log file * *INFO: input image orientation is LPS INFO: input image determinant is 3.51562 fslswapdim /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig.nii.gz x -y z /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig_flip.nii.gz INFO: found /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig_flip.mghdti.bvecs /mnt/hgfs/linux_share/subjects/TB_400/dmri/bvecs mv -f /mnt/hgfs/linux_share/subjects/TB_400/dmri/dwi_orig_flip.mghdti.bvals /mnt/hgfs/linux_share/subjects/TB_400/dmri/bvals mri_convert / /mnt/hgfs/linux_share/subjects/TB_400/dmri/b0mag.nii.gz mri_convert / /mnt/hgfs/linux_share/subjects/TB_400/dmri/b0mag.nii.gz corRead(): can't open file /COR-.info $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /...* Thanks Efrat ___ 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] CNR in the hippocampus
Dear Freesurfer expert, I received a comment from the reviewer regarding CNR in the hippocampus. "CNR is known to decrease with age (see papers by Fischl’s group). How does the automated routine for hippocampal volumetry take this into considerations?" Any suggestions how to respond? Thank you Efrat ___ 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] Fwd: CNR in the hippocampus
Dear Freesurfer expert, I'm reposting this mail. any suggestions? Thank you efrat -- Forwarded message -- From: Efrat Kliper Date: Tue, Jun 9, 2015 at 8:11 AM Subject: CNR in the hippocampus To: freesurfer@nmr.mgh.harvard.edu Dear Freesurfer expert, I received a comment from the reviewer regarding CNR in the hippocampus. "CNR is known to decrease with age (see papers by Fischl’s group). How does the automated routine for hippocampal volumetry take this into considerations?" Any suggestions how to respond? Thank you Efrat ___ 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] Tracula problems (creating symbolic link)
Dear Freesurfer experts, I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the preprocessing has already been completed in Freesurfer 5.1) in order to run some new functions of Tracula (I have also installed the latest Tracula update (tracula.update.centos4_x86_64.5.3.2014_05_26). I am using: FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 RedHat release: CentOS release 5.3 (Final) Kernel info: Linux 2.6.18-128.1.6.el5 x86_64 I encountered two problems: 1. When I run the initial code of Tracula: trac-all –prep code: /home/fsl/ usr/local/freesurfer/bin/trac-all -prep -c /mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt Subject TB_480 SUBJECTS_DIR /mnt/hgfs/linux_share/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 fsl localhost.localdomain Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux *I am getting the following message:* ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz ln: creating symbolic link `/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to `/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation not supported 2. If I run the trac-all –bedp command of Tracula (on already trac-all data which was preproc on Freesurfer version 5.1. /home/fsl /usr/local/freesurfer/bin/trac-all -bedp -c /home/fsl/Desktop/xxx.txt Subject TB_201 SUBJECTS_DIR /mnt/hgfs/linux_share/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 fsl localhost.localdomain Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux *I am getting the following message:* Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_paths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_pathstats ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_mergepaths ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_group ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /mnt/hgfs/linux_share/subjects/TB_201/dmri subjectdir is /mnt/hgfs/linux_share/subjects/TB_201/dmri /mnt/hgfs/linux_share/subjects/TB_201/dmri/data not found I am guessing those problems are from the same source. Do you have any suggestions on how can I resolve these issues? Is there a way to overcome the "ln" command and to create this data file without it? (I have also tried to run it from local OS linux and
Re: [Freesurfer] Tracula problems (creating symbolic link)
Dear Anastasia, Thank you for the fast replay. I have tried both suggestions, however it still reports: Operation not supported Also, I have used the links that you have sent me but non work. This time (after changing according to the links), I got the message: operation denied I don’t know how to resolve the issue of virtual machine, as not much is written about that and the links are not helping with that issue. Do you have other suggestions regarding how to change the script, so it will create the data.nii without the symbolic link (there are plenty "ln" commands uses in the script)? Many thanks, Efrat On Wed, Mar 30, 2016 at 12:39 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Efrat - This appears to be a virtual machine problem: > > https://communities.vmware.com/thread/312591?tstart=0 > > There are some solutions suggested in that thread. I'm wondering if using > a relative instead of an absolute path for the symlink works, i.e., > > ln -sf dwi.nii.gz /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz > > instead of: > > ln -sf /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz > /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz > > Can you please try it both ways and let me know if the former works on a > computer where the latter doesn't? > > And yes, if you fix error #1 it'll fix error #2 as well. > > Thanks, > a.y > > > > On Tue, 29 Mar 2016, Efrat Kliper wrote: > > >> Dear Freesurfer experts, >> >> >> I upgraded to Freesurfer 5.3 from Freesurfer 5.1 (all of the >> preprocessing has already been completed in Freesurfer 5.1) in order to run >> some new functions >> of Tracula (I have also installed the latest Tracula update >> (tracula.update.centos4_x86_64.5.3.2014_05_26). >> >> >> I am using: >> >> FREESURFER_HOME: /usr/local/freesurfer >> >> Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 >> >> RedHat release: CentOS release 5.3 (Final) >> >> Kernel info: Linux 2.6.18-128.1.6.el5 x86_64 >> >> >> >> I encountered two problems: >> >> >> 1. When I run the initial code of Tracula: trac-all –prep code: >> >> /home/fsl/ >> >> usr/local/freesurfer/bin/trac-all -prep -c >> /mnt/hgfs/linux_share/Scripts/FreeSurfersScript/config_2.txt >> >> Subject TB_480 >> >> SUBJECTS_DIR /mnt/hgfs/linux_share/subjects >> >> FREESURFER_HOME /usr/local/freesurfer >> >> Actual FREESURFER_HOME /usr/local/freesurfer >> >> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 >> >> fsl >> >> localhost.localdomain >> >> Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 >> EDT 2009 x86_64 x86_64 x86_64 GNU/Linux >> >> >> >> I am getting the following message: ln -sf >> /mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz >> /mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz >> >> >> >> ln: creating symbolic link >> `/mnt/hgfs/linux_share/subjects/TB_480/dmri/data.nii.gz' to >> `/mnt/hgfs/linux_share/subjects/TB_480/dmri/dwi.nii.gz': Operation not >> supported >> >> >> >> 2. If I run the trac-all –bedp command of Tracula (on already >> trac-all data which was preproc on Freesurfer version 5.1. /home/fsl >> >> /usr/local/freesurfer/bin/trac-all >> >> -bedp -c /home/fsl/Desktop/xxx.txt >> >> Subject TB_201 >> >> SUBJECTS_DIR /mnt/hgfs/linux_share/subjects >> >> FREESURFER_HOME /usr/local/freesurfer >> >> Actual FREESURFER_HOME /usr/local/freesurfer >> >> build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 >> >> fsl >> >> localhost.localdomain >> >> Linux localhost.localdomain 2.6.18-128.1.6.el5 #1 SMP Wed Apr 1 09:10:25 >> EDT 2009 x86_64 x86_64 x86_64 GNU/Linux >> >> >> >> I am getting the following message: >> >> Program versions: >> >> $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ >> >> mri_convert --all-info >> >> ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: >> $Name: $ TimeStamp: 2016/03/29-13:00:54-GMT BuildTimeStamp: Aug 16 2014 >> 05:13:24 >> CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: >> fsl Machine: localhost.localdomain Platform: Linux PlatformVersion: >> 2.6.18-128.1.6.el5 CompilerName: GCC CompilerVersion: 30400 >> >> FLIRT version 6.0 >> >>
[Freesurfer] Resting state analysis
Dear freeSurfer expert, I am trying to perform whole brain functional connectivity analysis Is there a wiki for resting state analysis? I have only found this wiki page https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc So far I have run the following commands: preproc-sess -s TB_482 -fsd Rest -stc odd -surface fsaverage lhrh -mni305 -fwhm 5 -per-run What is the next step? Should I use the mkanalysis-sess command? (mkanalysis-sess -TR 3 -fsd Rest -stc odd -surface fsaverage lh -mni305 2 -fwhm 5 -analysis TB_482_lh -notask)? Running this command it seems to create only an output file with a list of information and nothing more, what am i doing wrong? In addition for resting state analysis, band filter of 0.01-0.08Hz needs to be done. How do i do that and to which of the output files? I don’t find any record about that either. Thanks in advance, Efrat ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] How to report aseg.state values
Dear FreeSurfer expert, If I want to report on hippocampal volume in an article, should I report the value as stated in the aseg.state table or should I normalize the value to the eTICV ( i.e aseg value/eTICV )? Thanks in advance Efrat ___ 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] Triangulated surfaces
Dear FreeSurfer Users, I have created a binary mask for the hippocampi and now i want to create the triangulated surfaces of the hippocampi? An one know how to do it? Thanks, Efrat ___ 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] ADC map negative values
Dear FreeSurfers Users, When i am using the dt_recon function to create adc map i get quite a lot negative values, dose anyone encounter this problem? Thanks, Efrat ___ 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] recon-all
Dear Freesurfer expert, I am using Freesurfer version 5.1.0. After I ran the freesurfer recon-all -autorecon-all and checked the data I saw that the skull wasn't removed as a whole (yet it is not part of the pial or white matter margin). I was wondering if it just doesn't look good or that part of the skull that was not removed was calculated as part of the ICV or somthing else. Thanks in advance, efrat ___ 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] QA TOOL
Dear Freesurfer expert, I am using Freesurfer version 5.1.0. I am dealing with some problems with recon_checker command. I cannot open the html file to see the figures. The command generates the images but they are not saved. It is written that: *converting snapshots to tiff and making html page...* *Convert: command not found* Any suggestions? Thanks in advance, efrat ___ 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] QA Tool Help - Outliers
Dear FreeSurfer expert, I am using Freesurfer version 5.1.0. After I run the QA Tool and check my data, I am getting 39 outliers or more for each subject. When I look at the AsegMeans and DefaultAsegMeans files in the QATool library, i see that the mean values in these file for each anatomical label are 0s. Is that OK? what files are you checking for outliers against? My results are in agreement with the literature and i believe non of them should be outliers. Any suggestion what might be the problem? Thank you in advance, Efrat Left-Cerebral-Exterior 0 +/- 0 Left-Cerebral-White-Matter 0 +/- 0 Left-Cerebral-Cortex 0 +/- 0 Left-Lateral-Ventricle 0 +/- 0 Left-Inf-Lat-Vent 0 +/- 0 Left-Cerebellum-Exterior 0 +/- 0 Left-Cerebellum-White-Matter 0 +/- 0 Left-Cerebellum-Cortex 0 +/- 0 Left-Thalamus 0 +/- 0 Left-Thalamus-Proper 0 +/- 0 Left-Caudate 0 +/- 0 Left-Putamen 0 +/- 0 Left-Pallidum 0 +/- 0 3rd-Ventricle 0 +/- 0 4th-Ventricle 0 +/- 0 Brain-Stem 0 +/- 0 Left-Hippocampus 0 +/- 0 Left-Amygdala 0 +/- 0 Left-Insula 0 +/- 0 Left-Operculum 0 +/- 0 Line-1 0 +/- 0 Line-2 0 +/- 0 Line-3 0 +/- 0 CSF 0 +/- 0 Left-Lesion 0 +/- 0 Left-Accumbens-area 0 +/- 0 Left-Substancia-Nigra 0 +/- 0 Left-VentralDC 0 +/- 0 Left-undetermined 0 +/- 0 Left-vessel 0 +/- 0 Left-choroid-plexus 0 +/- 0 Left-F3orb 0 +/- 0 Left-lOg 0 +/- 0 Left-aOg 0 +/- 0 Left-mOg 0 +/- 0 Left-pOg 0 +/- 0 Left-Stellate 0 +/- 0 Left-Porg 0 +/- 0 Left-Aorg 0 +/- 0 Right-Cerebral-Exterior 0 +/- 0 Right-Cerebral-White-Matter 0 +/- 0 Right-Cerebral-Cortex 0 +/- 0 Right-Lateral-Ventricle 0 +/- 0 Right-Inf-Lat-Vent 0 +/- 0 Right-Cerebellum-Exterior 0 +/- 0 Right-Cerebellum-White-Matter 0 +/- 0 Right-Cerebellum-Cortex 0 +/- 0 Right-Thalamus 0 +/- 0 Right-Thalamus-Proper 0 +/- 0 Right-Caudate 0 +/- 0 Right-Putamen 0 +/- 0 Right-Pallidum 0 +/- 0 Right-Hippocampus 0 +/- 0 Right-Amygdala 0 +/- 0 Right-Insula 0 +/- 0 Right-Operculum 0 +/- 0 Right-Lesion 0 +/- 0 Right-Accumbens-area 0 +/- 0 Right-Substancia-Nigra 0 +/- 0 Right-VentralDC 0 +/- 0 Right-undetermined 0 +/- 0 Right-vessel 0 +/- 0 Right-choroid-plexus 0 +/- 0 Right-F3orb 0 +/- 0 Right-lOg 0 +/- 0 Right-aOg 0 +/- 0 Right-mOg 0 +/- 0 Right-pOg 0 +/- 0 Right-Stellate 0 +/- 0 Right-Porg 0 +/- 0 Right-Aorg 0 +/- 0 5th-Ventricle 0 +/- 0 Left-Interior 0 +/- 0 Right-Interior 0 +/- 0 Left-Lateral-Ventricles 0 +/- 0 Right-Lateral-Ventricles 0 +/- 0 WM-hypointensities 0 +/- 0 Left-WM-hypointensities 0 +/- 0 Right-WM-hypointensities 0 +/- 0 non-WM-hypointensities 0 +/- 0 Left-non-WM-hypointensities 0 +/- 0 Right-non-WM-hypointensities 0 +/- 0 Left-F1 0 +/- 0 Right-F1 0 +/- 0 Optic-Chiasm 0 +/- 0 Corpus_Callosum 0 +/- 0 Left-Amygdala-Anterior 0 +/- 0 Right-Amygdala-Anterior 0 +/- 0 Dura 0 +/- 0 Left-wm-intensity-abnormality 0 +/- 0 Left-caudate-intensity-abnormality 0 +/- 0 Left-putamen-intensity-abnormality 0 +/- 0 Left-accumbens-intensity-abnormality 0 +/- 0 Left-pallidum-intensity-abnormality 0 +/- 0 Left-amygdala-intensity-abnormality 0 +/- 0 Left-hippocampus-intensity-abnormality 0 +/- 0 Left-thalamus-intensity-abnormality 0 +/- 0 Left-VDC-intensity-abnormality 0 +/- 0 Right-wm-intensity-abnormality 0 +/- 0 Right-caudate-intensity-abnormality 0 +/- 0 Right-putamen-intensity-abnormality 0 +/- 0 Right-accumbens-intensity-abnormality 0 +/- 0 Right-pallidum-intensity-abnormality 0 +/- 0 Right-amygdala-intensity-abnormality 0 +/- 0 Right-hippocampus-intensity-abnormality 0 +/- 0 Right-thalamus-intensity-abnormality 0 +/- 0 Right-VDC-intensity-abnormality 0 +/- 0 Epidermis 0 +/- 0 Conn-Tissue 0 +/- 0 SC-Fat/Muscle 0 +/- 0 CSF-SA 0 +/- 0 Muscle 0 +/- 0 Ear 0 +/- 0 Adipose 0 +/- 0 Spinal-Cord 0 +/- 0 Soft-Tissue 0 +/- 0 Nerve 0 +/- 0 Bone 0 +/- 0 Air 0 +/- 0 Orbital-Fat 0 +/- 0 Tongue 0 +/- 0 Nasal-Structures 0 +/- 0 Globe 0 +/- 0 Teeth 0 +/- 0 Left-Caudate/Putamen 0 +/- 0 Right-Caudate/Putamen 0 +/- 0 Left-Claustrum 0 +/- 0 Right-Claustrum 0 +/- 0 Cornea 0 +/- 0 Diploe 0 +/- 0 Vitreous-Humor 0 +/- 0 Lens 0 +/- 0 Aqueous-Humor 0 +/- 0 Outer-Table 0 +/- 0 Inner-Table 0 +/- 0 Periosteum 0 +/- 0 Endosteum 0 +/- 0 Left-Cerebral-Exterior 0 +/- 0 Left-Cerebral-White-Matter 0 +/- 0 Left-Cerebral-Cortex 0 +/- 0 Left-Lateral-Ventricle 0 +/- 0 Left-Inf-Lat-Vent 0 +/- 0 Left-Cerebellum-Exterior 0 +/- 0 Left-Cerebellum-White-Matter 0 +/- 0 Left-Cerebellum-Cortex 0 +/- 0 Left-Thalamus 0 +/- 0 Left-Thalamus-Proper 0 +/- 0 Left-Caudate 0 +/- 0 Left-Putamen 0 +/- 0 Left-Pallidum 0 +/- 0 3rd-Ventricle 0 +/- 0 4th-Ventricle 0 +/- 0 Brain-Stem 0 +/- 0 Left-Hippocampus 0 +/- 0 Left-Amygdala 0 +/- 0 Left-Insula 0 +/- 0 Left-Operculum 0 +/- 0 Line-1 0 +/- 0 Line-2 0 +/- 0 Line-3 0 +/- 0 CSF 0 +/- 0 Left-Lesion 0 +/- 0 Left-Accumbens-area 0 +/- 0 Left-Substancia-Nigra 0 +/- 0 Left-VentralDC 0 +/- 0 Left-undetermined 0 +/- 0 Left-vessel 0 +/- 0 Left-choroid-plexus 0 +/- 0 Left-F3orb 0 +/- 0 Left-lOg 0 +/- 0 Left-aOg 0 +/- 0 Left-mOg 0 +/- 0 Left-pOg 0 +/- 0 Left-Stellate 0 +/- 0 Left-Porg 0 +/- 0 Left-Aorg 0 +/- 0 Right-Cerebral-Exterior 0 +/- 0 Rig
[Freesurfer] Surface to native space
Dear freesurfer expert, We have preformed the full autorecon command using freesurfer and want to view the results in Slicer, When we load the pial surface onto slicer it doesn't seem to be coregister to the original MR image, how can we bring back the surface to the original native space or alternatively, how can we preforme the transformation on the original MRI so it will fit the surface that we gut. We found in the wiki a way to do that with volumes (mri_vol2vol --mov brain.mgz --targ rawavg.mgz --regheader --o brain-in-rawavg.mgz) but what about surface? We have also found the command mri_surf2surf, but not sure how to use it because we don't have surface in the native space? thank you in advance Efrat ___ 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] QATools
Dear FreeSurfer expert, I am trying to run QA tools for verifying all steps of the FreeSurfer recon-all stream. I am working with FreeSurfer version 4.5.0. I don't see any optional flagged arguments in which i can specify the version i am working with (the default version is 5.1.). I will be grateful if you can help me with that. Thanks a lot efrat ___ 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] Question about version upgrade
Dear FreeSurfer expert, I am currently working on FreeSurfer Version 4.5.0 and already performed an analysis for approximately 200 subjects. Is there a way to change the version that I am working on (4.5.0) to 5.0.1 without the need to run recon-all again in the new version? Thanks in advanced, efrat ___ 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] Cortical Thickness of a Volume-defined ROI
Dear FreeSurfer expert I am trying to create a mask for the right hemisphere frontal lobe cortex in order to calculate the mean cortical thickness for this specific ROI. I am using the following commands: To create a mask for the specific region: mri_binarize --i /mri/aparc+aseg --match 2028 --match 2027 --match 2003 --match 2024 --match 2018 --match 2020 --match 2019 --match 2014 --match 2032 --match 2002 --match 2026 --o /mri/rh_frontal_ctx.mgz But I am not sure what the next step is - I tried to follow this link: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness(Cortical Thickness of a Volume-defined ROI) fslregister --s fsaverage --mov /mri/T1.mgz --reg T1_to_fsaverage.dat but I am not sure if that is the correct way, and also my ROI in the fsaverage subject volume is not perfectly matched to what I expect it to be - how can I fix that? They are very different. I also tried the mri_tessellate command to create surface by tessellating given input volume: mri_tessellate /data/Temp_efrat/subjects/TB_281_test/mri/rh_frontal_ctx_1.mgz -a 2028 2027 2003 2024 2018 2020 2019 2014 2032 2002 2026 frontal_ctx_test I get this massage: changing type of input volume to 8 bits/voxel... $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ slice 110: 431 vertices, 495 faces slice 120: 2986 vertices, 3215 faces slice 130: 6636 vertices, 7037 faces slice 140: 12817 vertices, 13506 faces slice 150: 22361 vertices, 23291 faces slice 160: 32454 vertices, 33549 faces slice 170: 44058 vertices, 45346 faces slice 180: 56174 vertices, 57633 faces slice 190: 67020 vertices, 68612 faces slice 200: 75820 vertices, 77402 faces slice 210: 78847 vertices, 80236 faces slice 220: 78900 vertices, 80278 faces slice 230: 78900 vertices, 80278 faces slice 240: 78900 vertices, 80278 faces slice 250: 78900 vertices, 80278 faces using the conformed surface RAS to save vertex points... writing 2028 using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; But I can not find the output file of that command. And then to calculate the thickness of the frontal cortex by using the mris_anatomical_stats TB_281_test rh -t frontal_ctx_test I am a little confused, I will be grateful if you can help me with that. Thanks a lot Efrat ___ 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.
