Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

recon-all finished with ERRORs
by Christine Smith 30 Oct '12

30 Oct '12

Hello, After successfully running a subject through freesurfer (recon-all -make all) several times as I fixed some pial and white matter edits, I now get the message that recon-all finished with errors. Inspection of the recon-all.log doesn't reveal any error messages to me in any particular step. What should I be looking for to track down the reason that errors were generated? I already examined the talairach transform and that looks great. I loaded the pial and white matter surfaces and they look fine. The segmentation aparc+aseg looks great too. Thanks, Christine -- Christine N. Smith, Ph.D. Department of Psychiatry University of California, San Diego

2 1

average lobar thickness
by Khalid Hamandi 30 Oct '12

30 Oct '12

Dear FSers I am looking for help in determining the average thickness for each lobe, frontal, temporal, parietal, occipital and cingulate by merging Desikan atlas ROI values. I have had a look at the parcellation wiki http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation and see the basic principles, i think.... I believe i could extract labels from each subject using mri_annotation2label, multiply the number of vertices per ROI by the average ROI thickness from asegstats and sum the lobar ROIs (no of vertices x av thickness), then divide by the total number of vertices in that lobe. I have 82 subjects. If mris_anatomical_stats is the way to go then i'm having trouble following the command line options. Is there an 'easy' way to do this, are there Freesurf command tools that help? or does someone already have a script they are willing to share? I'm using Freesurf version 4.4.0. so don't have --lobesStrict if that was going to be on offer. many thanks Khalid

2 1

fieldsign-sess problem in retinotopy
by Zhou, Wei 30 Oct '12

30 Oct '12

Dear freesurfers, I am trying retinotopy analysis in freesurfer. For "fieldsign-sess", I encounter the following problem when I type "fieldsign-sess -a rtopy.self.lh -occip -s SUBJ01" or "fieldsign-sess -a rtopy.self.lh -occip -sf sessid": /media/users/zhouw4/testf/retinotopy/SUBJ01/log/fieldsign-sess.log subject: Undefined variable. my structure of retinotopy fold is : retinotopy |--sessid |--SUBJ01 |--subjectname |--bold |--001 |--f.nii |--rtopy.par I really appreciate it if you could give me some idea about that problem. Thanks a lot in advance. Best Wei Zhou Medical Physics Ph.D. Student Diagnostic Imaging Track cgxzwwd(a)gmail.com<mailto:cgxzwwd@gmail.com> zhouw4(a)livemail.uthscsa.edu<mailto:zhouw4@livemail.uthscsa.edu>

2 1

Fwd: questions to qdec
by Daniel Klein 30 Oct '12

30 Oct '12

-----Ursprüngliche Mitteilung----- Von: Daniel Klein <dolphinede(a)aol.com> An: freesurfer-owner <freesurfer-owner(a)nmr.mgh.harvard.edu> Verschickt: So, 28 Okt 2012 11:58 am Betreff: questions to qdec Dear FreeSurfer experts, i want to test the effect of age square (in contrast to age) on cortical thickness in qdec. How can I do that? Am I right, that there is no possibility in qdec to use the per regressor-option to analyse the effects of cortical thickness on lGI vertex-wise? Many thanks Daniel

2 1

Re: [Freesurfer] average measure of cortical thickness
by Daniel Ferreira 30 Oct '12

30 Oct '12

So, as a measure of whole brain cortical thickness average is it better to "Mean Thickness" from aparc.stats file? > > > 2012/10/30 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> Hi Daniel >> >> the parcellations are not uniform in size, and therefore the average of >> them will not be the same as averaging over the cortex. >> >> cheers >> Bruce >> >> On Tue, 30 Oct 2012, Daniel Ferreira wrote: >> >> Hi, >>> I was wondering what should I use as an average of cortical thickness for >>> the whole cortex. >>> >>> The aparc.stats output gives a value of "Mean Thickness" for each >>> hemisphere. But this value does not coincide with the one I get if I >>> average >>> the 34 variables from aparc.stats. Do you know why? >>> >>> thanks so much in advance >>> >>> Daniel >>> >>> >>> >> >> 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<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. >> > >

1 0

Re: [Freesurfer] Talairach Failure Detection
by Daniel Ferreira 30 Oct '12

30 Oct '12

Thanks Nick very much for your suggestion. Unfortunately it did not fix the error. I run the mri_nu_correct command trying several -n values (1, 5, 20), then I -talairach, but the output is always the same. Talairach finish but when I check it the brain and standars are slided down to the bottom of the window. See a new output attached. What can be happening here? Any idea to fix it? thanks Daniel > > > > 2012/10/17 Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > >> Daniel, >> >> See this page which i just created which describes a workaround to a >> problem some people are having with the Talairach stage in the v5.1 >> release: >> >> https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 >> >> Nick >> >> >> On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote: >> > Dear experts, >> > >> > Please, I'm getting the Talairach Failure Detection problem in one of >> > my subjects (message enclosed below). >> > >> > >> > I tried to follow the tutorial to fix a bad Talairach with: >> > >> > >> > 1) tkregister2 --mgz -s <id> --fstal --> not green lines appear, I >> > attach a screenshot. Both the standard and my MRI are slided down to >> > the bottom of the window. See also attached tkmedit file. >> > >> > >> > 2) Anyway, I tried also -notal-check to see if something changed in >> > spite Talairach failed, but it fails also (off course). >> > >> > >> > 3) I used -use-mritotal but I still get the same. However, this time >> > processing finishes without errors, but my MRI is still at the bottom >> > of the window and output cut all what is between middle temporal >> > regions and neck. >> > >> > >> > Please, any idea? >> > >> > >> > Thanks a lot >> > >> > >> > Daniel >> > >> > >> > >> > #@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 >> > /home/daniel/FreeSurfer/subjects/N001511_d2/mri >> > >> > talairach_afd -T 0.005 -xfm transforms/talairach.xfm >> > >> > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >> > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) >> > Manual Talairach alignment may be necessary, or >> > include the -notal-check flag to skip this test, >> > making sure the -notal-check flag follows -all >> > or -autorecon1 in the command string. >> > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach >> > Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC >> > 2011 x86_64 GNU/Linux >> > >> > recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST >> > 2012 >> > >> > To report a problem, see >> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> > >> > >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)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. >> > >

3 8

average measure of cortical thickness
by Daniel Ferreira 30 Oct '12

30 Oct '12

Hi, I was wondering what should I use as an average of cortical thickness for the whole cortex. The aparc.stats output gives a value of "Mean Thickness" for each hemisphere. But this value does not coincide with the one I get if I average the 34 variables from aparc.stats. Do you know why? thanks so much in advance Daniel

2 1

Re: [Freesurfer] cortical parcellation question
by Daniel Ferreira 30 Oct '12

30 Oct '12

Hello again, Thanks for all the information Bruce. Is it not possible to back-project the regions defined in the 2D surface-based spherical coordinate system onto the mean_intensity.nii image? As those regions in the 2D surface-based coordinate system would have been initially defined on a 3D volume(s) and transformed (inflated) to the 2D spherical surface? Daniel ---------- Forwarded message ---------- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: 2012/10/11 Subject: Re: [Freesurfer] cortical parcellation question To: Daniel Ferreira <daniferp(a)gmail.com> Cc: freesurfer(a)nmr.mgh.harvard.edu Hi Daniel, no, sorry. The gca is not a cortical atlas. Those labels are stored in the .gcas file and aren't in the same space (in fact, they are in a surface-based spherical coordinate system and not in the volume at all, so not easily combinable). Bruce On Thu, 11 Oct 2012, Daniel Ferreira wrote: Thanks for the detailed information. > > The mean intensity image (mean_intensity.nii) generated from frame #1 is > almost exactly what I need. This image has all the sub-cortical regions > assigned a discrete integer number (i.e. all the voxels in the left > cerebelllar grey matter = 8 and right = 47). However the whole of the > neocortex is defined as left (intensity = 3) and right (intensity = 42) > only, there are no cortical sub-divisions. > > Is it possible to have the individual neocortical regions assigned a > discrete integer number; (obviously not one already assigned to the other > regions in the mean_intensity.nii image)? For example all inferior temporal > voxels = 9; middle temporal voxels = 10; superior temporal voxels = 11. So > each of the regions defined in the "colortable_desikan_killiany.**txt" > file > found in the FREESURFER_HOME/average/ directory are also defined in the > mean_intensity.nii image? > > Thanks > > > 2012/10/6 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Daniel > > it's in .gca format, and includes information that wouldn't fit > in a nifti file (e.g. markov relationships). You can use > mri_convert to extract some of the basic info though (e.g. the > most likely class at each location and the mean intensity of the > most likely class) using mri_convert. For example: > > mri_convert $FREESURFER_HOME/average/RB_**all_2008-03-26.gca#0 > ./labels.nii > mri_convert $FREESURFER_HOME/average/RB_**all_2008-03-26.gca#1 > ./mean_intensity.nii > > > where the #<n> syntax mean extract the nth frame from the 4D gca > volume. Frame 0 is the most likely label and frame 1 is the mean > intensity. Note however that there is lots more info in the .gca > that this doesn't capture such as the MRF parameters I mentioned > above, class variances, other class probabilities, etc.... > cheers > Bruce > > > > > On Thu, 4 Oct 2012, Daniel Ferreira wrote: > > Thanks Bruce, > When you say the atlas itself is included in the > Freesurfer distribution, do > you mean there is a 3D version of it available in > the download? > Also, I am not looking for the individual subjects' > images, I just want a > copy of the final atlas as a 3D image in > analyze/nifti format. (i.e. in the > same format as the Harvard-Oxford atlas that is > downloaded with FSL). > > Thanks a lot. > > Daniel Ferreira > > > > 2012/10/3 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Daniel, > > 1. Do you mean the atlas or the parcellation > of your subjects? > We cannot distribute the individual subjects > in the atlas as the > data was collected under an IRB long ago that > didn't include > this. The atlas itself (summary statistics > derived from those > subjects) is included in the FreeSurfer > distribution. > > 2. The subcortical areas are the same, but not > the cortical > ones. That cortical parcellation is quite > coarse, and while we > did implement it we were never given > permission to distribute > the automated version, so it is not part of > FreeSurfer. The > boundaries that we define are thus different > than that one (and > since the Harvard-Oxford one is based on > volumetric labeling of > folding patterns we found that it contained a > bunch of errors in > which e.g. the wrong side of a sulcus was > labeled) > > cheers > Bruce > > > On Wed, 3 Oct 2012, Daniel Ferreira wrote: > > Dear experts, > I have a couple of questions regarding > the cortical > parcellation atlas that > is used in Freesurfer: > > 1) I would like to know if it is > possible to obtain > the Desikan-Killiany > atlas in 3D analyze/nifti format. With > each region > of the brain assigned a > discrete integer number (for example the > all of the > voxels of the left > inferior temporal lobe have an intensity > = 1, or > the whole of the left > hippocampus = 2). > > 2) Are the Harvard-Oxford cortical and > subcortical > atlases that can be > downloaded with FSL the same as the > cortical > parcellation atlas that is used > in Freesurfer? (i.e. are the > neuroanatomical > boundaries the same; does the > left inferior temporal cortex in the > Freesurfer > cortical parcellation = the > left inferior temporal cortex in the > Harvard-Oxford > atlas downloaded with > FSL) > > Many thanks > > Daniel Ferreira > > > > > > > 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<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. > > > > > >

2 2

which version of FS to use?
by Chunhui Chen 29 Oct '12

29 Oct '12

Dear Freesurfers, I just read this paper about freesurfer version and operating system matters: Gronenschild EHBM, Habets P, Jacobs HIL, Mengelers R, Rozendaal N, et al. (2012) The Effects of FreeSurfer Version, Workstation Type, and Macintosh Operating System Version on Anatomical Volume and Cortical Thickness Measurements. PLoS ONE 7(6): e38234. doi:10.1371/journal.pone.0038234 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038234 I am running freesurfer on linux system, and installed both version 4.5 and 5.1, and currently using 5.1. So which version is most recommended? should I use other versions like 5.0 or the coming 5.2? Any suggestion is appreciated

2 4

Problems to create my own template
by Bernd Merkel 29 Oct '12

29 Oct '12

Dear all, just having started using Freesurfer, I have the following question which has also been touched by other people but I couldn't find a solution for my problem. I have about 100 subjects from which I want to create my own template to be used by Freesurfer. These have been my steps: 1. recon-all (on all my subjects) 2. make_average_subject --subjects (list of all subjects) 3. I wanted to use the code provided on the Wiki: for subject in 'subjectList.txt'; do cd $SUBJECTS_DIR/subject mris_register -curv surf/lh.sphere $SUBJECTS_DIR/newtemplate/lh. reg.template.tif surf/lh.sphere.reg.newtemplate end The first two steps went fine. But I do not know how to handle that template.tif-File, because that hasn't been created as a result during my second step. Have I missed something ? Furthermore there is this other command mris_make_template but I do not know whether (and where in my processing) I should use that (perhaps instead of make_average_subject) ? Thanks for any help, Bernd

2 1

← Newer
1
2
3
4
5
6
7
...
20
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer October 2012