Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

mri_segment optional flags problem
by Christopher Luna 05 Aug '11

05 Aug '11

Hello, I'm trying to run mri_segment with some custom values in the optional flags, such as -p for setting the percentage threshold with a float value. When I run the command though, "mri_segment -p 0.6 brain.mgz wm.seg.mgz" The command properly sets the threshold to 60%, but also takes the "0.6" to be in the input file name instead of brain.mgz. Is there another option I'm missing? Or have I unfortunately stumbled upon a small bug? Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT

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Nvidia upgrade considerations
by Andries R. Van Der Leij 05 Aug '11

05 Aug '11

Dear freesurfer team I'm currently investigating how to tweak 2 2 year old Dell 7400 Xeon machine's to run a large batch of fs jobs. Upgrading to Nehalem won't work, since it will require a new motherboard as well. However, we can replace our old non-fermi quadro card with a C2050. As an alternative, I was thinking about buying two GTX590 (two times 580 and 1.5 GB ram) or two palit GTX580 (1 times 580 with 3GB ram) and running them in SLI. This will save quite some money, and intuitively, it feels that more separate cards will work better if you start batching more recon scripts at the same time (1 per CPU). You'll end up with 6 gb of vram in both cases compared to the 3 for the C2050, with 4 processors for the 590 and 2 for the 580. As I don't understand cuda and sli well, I may very well be completely wrong. I'm not sure fi that running jobs under sli will work well. Do you have any ideas on this solution compared to a single c2050? thank you very much in advance, Andries van der Leij

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Error in preprocessing
by Eiran Vadim Harel 05 Aug '11

05 Aug '11

Hi, I am using stable5.0-env. I have run the pre[processing command: preproc-sess -s 1411_MC -surface fsaverage lhrh -mni305 -fwhm 5 -per-run I got this ERROR message: /autofs/space/shimshon_002/users/eiran/contproc/1411_MC RunList: 005 006 007 ------- ************************** ----------- ------- Motion Correcting Run 005 ----------- ------- ************************** ----------- sess = 1411_MC Fri Aug 5 11:51:17 EDT 2011 mc-afni2 --i 005/f.nii --t 005/template.nii --o 005/fmcpr.nii --mcdat 005/fmcpr.mcdat ERROR: cannot find AFNI command 3dvolreg My PROJECT DIR: /space/shimshon/2/users/eiran/contproc SUBJECTS_DIR: /space/shimshon/2/users/eiran/subjects Is there a way to solve it? Thanks, Eiran

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skull stripping and gcut error
by Jacquelynn Nicosia Copeland 05 Aug '11

05 Aug '11

Hi Freesurfers: I am trying to minimize the amount of skull stripping manual edits I need to make on Freesurfer outputs due to remaining dura. I've been trying both: adjusting the watershed parameters and using gcut. However, I noticed the output with and without gcut for the same participant were not different. So I went to the log file, and when I searched for gcut it says: " rm -f brainmask.gcuts.mgz mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz brainmask.gcuts.mgz INFO: Care must be taken to thoroughly inspect your data when using mri_gcut. In particular, inspect the edges of gm and cerebellum for over-aggressive cutting. Add -segmentation brainmask.gcuts.mgz to the tkmedit command string to view the voxels which gcut has removed. reading mask... white mean: 107.529232 threshold set to: 107.529232*0.400000=43.011693 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! masking... ** Gcutted brain is much smaller than the mask! ** Using the mask as the output instead! cp brainmask.auto.mgz brainmask.mgz " Thus, it does not appear to be using the brainmask with gcut edits. I added the "-segmentation brainmask.gcuts.mgz" to the tkmedit command and got an error basically saying that the file does not exist. This is the case for many of our participants. Why is this occurring? Isn't the purpose of gcut is to make the brainmask smaller (b/c it has less dura in it)? Also, any other suggestions for reducing remaining dura/skull? Thanks for any help you can provide, Jacquie Jacquelynn N. Copeland, M.A. Doctoral Candidate Medical/Clinical Psychology Program Department of Psychology University of Alabama at Birmingham Email:jcopeland@uab.edu

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convert .annot file to lable
by ZhiLiangLong 05 Aug '11

05 Aug '11

Hi all: Are there some FS commands that can convert .annot file to lable file? Thanks!

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dmri_train malloc error
by Dabbs (Kevin) 05 Aug '11

05 Aug '11

Freesurfer users, I have ran into a malloc error running trac-all. Looks like the same error that Stijn posted to the list on 17 Jun 2011. I did not see a solution posted. It occurs in dmr_train using trac-all -prep –c dmrirc.txt. Also tried using trac-all –prior –c dmrirc.txt with the same results. Reset the tcsh limits for datasize, …. ********* Loading segmentation from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/aparc+aseg.nii.gz Loading cortex mask from /Applications/freesurfer5_1/trctrain/trc029/dlabel/mni/cortex+2mm.nii.gz dmri_train(54615) malloc: *** mmap(size=159744) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(218, 182, 182): could not allocate 158704 bytes for 26th slice Cannot allocate memory ********** My system Model Name: Mac Pro Model Identifier: MacPro3,1 Processor Name: Quad-Core Intel Xeon Processor Speed: 2.8 GHz Number Of Processors: 2 Total Number Of Cores: 8 L2 Cache (per processor): 12 MB Memory: 18 GB System Version: Mac OS X 10.5.8 Thanks for any advice or suggestions! Kevin Dabbs SMPH/Neurology UW-Madison

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Retinotopy trouble shooting
by Michelle Umali 04 Aug '11

04 Aug '11

So when viewing with tksurfer I am assuming that -map angle shows the polar data. It looks ok. There's a lot of yellow and red, which I am assuming is the overall significance and not significance by position yes? tksurfer-sess -a rtopy.self.lh -s sj09 -map angle To view eccen data, is it -map eccen? thanks. michelle Quoting Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: [Hide Quoted Text] How do the eccen and polar look by themselves? You can look at them with tksurfer-sess doug Michelle Umali wrote: Hi Freesurfers, I'm troubleshooting my retinotopy data and am still having issues with wonky fieldsign data. The registration looked ok, so now I am trying to look at the retinotopy results using rtview. I got an error message saying it can't find the register.dof6.dat file. So, now I am stepping back to the beginning. Below are the commands I used for the analysis. -Does one need to specify starting position of wedge/size of wedge? Any help would be greatly appreciated. Michelle _____________ Here are the commands I used: recon-all -all ld09 tksurfer sj09 lh inflated and then for rh. Then I cut occipital patches. Then I registered the eccen and polar f.nii files: bbregister --s ld09 --mov f.nii --init-fsl --reg register.dat tkregister2 --mov f.nii --reg register.dat --surf mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj09 -force selxavg3-sess -a rtopy.self.lh -s sj09 selxavg3-sess -a rtopy.self.rh -s sj09 fieldsign-sess -a rtopy.self.lh -occip -s sj09 fieldsign-sess -a rtopy.self.rh -occip -s sj09 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --

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Can I use freesurfer to segment a phantom
by John Jan Drozd 04 Aug '11

04 Aug '11

Hi, I have MRI scans of a plastic polycarbonate ventricle that is an actual shape of a ventricle. It is in a brain mold of agar gel solution. I segmented the ventricle successfully using multiple seeds fuzzy connectedness in ITK. My segmentation was 97.2 % accurate. In ITK it had only single seed fuzzy connectedness but I adapted the code to work with multiple seeds. The reviewers of our paper want us to use FreeSurfer to segment the ventricles. Can I use freesurfer when the brain mold only has ventricles and grey matter (agar gel)? Or does Freesurfer require the brain to have the same number of brain parts as the Talairach atlas that it uses? My hunch us that it is the latter case. Thank you for your time. John John Drozd Post-Doctoral Fellow Robarts Research Institute University of Western Ontario London, Ontario, Canada http://publish.uwo.ca/~jdrozd2

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Re: [Freesurfer] [Error with mri_segtats
by Douglas N Greve 04 Aug '11

04 Aug '11

try this mri_segstats --annot bert lh aparc --i lh.thickness --sum lh.aparc.thickness.stats Antonella Kis wrote: > Dear Doug, > > I was running the mri_segstats as you suggested but I got an error: > > Constructing seg from annotation > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > Seg base 1000 > Loading lh.aparc.stats > mri_read(): couldn't determine type of file > /usr/local/freesurfer/subjects/bert/stats/lh.aparc.stats > ERROR: loading lh.aparc.stats > > This is what I did: > > setenv FREESURFER_HOME /usr/local/freesurfer > setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/bert/stats > mri_segstats --annot bert lh aparc --i lh.aparc.stats --sum > lh.aparc.stats > > Please help! > Thanks Antonella > > > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com>; freesurfer > <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Thursday, August 4, 2011 10:39 AM > *Subject:* Re: [Freesurfer] Error with aparcstats2table > > You can use mri_segstats with the --annot option. The output summary > table will have a column with the number of "voxels". In this case, it > will actually be number of vertices. > > doug > > Antonella Kis wrote: > > Hi Doug, > > > > Thank you for your help. Based on your answer my questions is: Do I > have to install the MATLAB software on my computer an load the > read_annotation.m file from FS? I know MATLAB is not a free software > so I wonder if there is another way. > > > > Thanks, > > Antonella > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com>>; > freesurfer <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Thursday, August 4, 2011 9:58 AM > > *Subject:* Re: [Freesurfer] Error with aparcstats2table > > > > you can load the annotation into matlab with read_annotation.m > > doug > > > > Antonella Kis wrote: > > > Hi Doug, > > > > > > Thank you very much for your answer. I need to prepare a table > here to include the number of vertex and the cortical thickness, for > some further studies. Is there a way to do it in MATLAB? How can I run > MATLAB using FS under Linux? I have the startup.m file and a MATLAB > directory installed in the freesurfer folder but I don't know how I > can run MATLAB using FS. > > > > > > Thank you very much for your help. > > > Antonella > > > > > > > > > > ------------------------------------------------------------------------ > > > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > > > *To:* Antonella Kis <atorok9(a)yahoo.com <mailto:atorok9@yahoo.com> > <mailto:atorok9@yahoo.com <mailto:atorok9@yahoo.com>>> > > > *Cc:* Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>; "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>" > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > > *Sent:* Wednesday, August 3, 2011 10:55 AM > > > *Subject:* Re: [Freesurfer] Error with aparcstats2table > > > > > > Hi Antonella, there is not an option for getting the number of > vertices because that is not a meaningful quantity. Why do you want it? > > > doug > > > > > > Antonella Kis wrote: > > > > > > > > Hi Bruce, > > > > > > > > Sorry to bother you again with the same question. Unfortunately > I did not get any reply from the freesurfer list (from Doug and/or > Nick as you mentioned) so I will really appreciate if you can help me > with the same question: > > > > in the aparc stats I have for each segmentation the Number of > Vertices, Surface Area, etc. > > > > I want this data to be exported in a table where in the first ro > I will have the thickness of each segmentation(bankssts , etc) and > the second row I want the Number of Vertices, for each subject. > > > > > > > > > > > > Many thanks, > > > > Antonella > > > > *From:* Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>> > > > > *To:* Antonella Kis <atorok9(a)yahoo.com > <mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com>> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com>>>> > > > > *Sent:* Friday, July 29, 2011 5:24 PM > > > > *Subject:* Re: [Freesurfer] Error with aparcstats2table > > > > > > > > doug and nick can help with that > > > > On Fri, 29 Jul 2011, Antonella Kis wrote: > > > > > > > > > Hi Bruce, > > > > > > > > > > Thanks again for helping. I mean in the aparc stats I have for > each segmentation the Number of Vertices, Surface Area, etc. I want > this data > > > > > to be exported in a table where in the first ro I will have > the thickness of each segmentation(bankssts , etc) and the second > row I want the > > > > > Number of Vertices, for each subject. > > > > > > > > > > Thanks. > > > > > Antonella > > > > > > > > > > > _______________________________________________________________________________________________________________________________________________ > > > > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>> > > > > > To: Antonella Kis <atorok9(a)yahoo.com > <mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com>> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com>>> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com>> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com> <mailto:atorok9@yahoo.com > <mailto:atorok9@yahoo.com>>>>> > > > > > Cc: "freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>>" > <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>>>> > > > > > Sent: Friday, July 29, 2011 3:18 PM > > > > > Subject: Re: [Freesurfer] Error with aparcstats2table > > > > > > > > > > Hi Antonella, > > > > > > > > > > what do you mean by no. of vertices? The total # in the > surface? You can get that with mri_info. It's loosely related to > surface area, but not > > > > > that interested a quantity. > > > > > > > > > > Bruce > > > > > > > > > > > > > > > On Fri, 29 Jul 2011, Antonella Kis wrote: > > > > > > > > > > > Hello everyone, > > > > > > > > > > > > > > > > > > I was trying to create a table with my statistical results > (the cortical thickness and the number of vertices) and I was running: > > > > > > > > > > > > aparcstats2table --hemi lh --subjects bert NPI001 --meas > thickness -t lh.aparcstas.THICKNESS.txt > > > > > > > > > > > > When I tried to also get the number of vertices a table by > running: aparcstats2table --hemi lh --subjects bert NPI001 --meas > vertices -t > > > > > > lh.aparcstas.VERTICES.txt I got the following error: > > > > > > > > > > > > aparcstats2table: error: option --measure: invalid choice: > 'Voxels' (choose from 'area', 'volume', 'thickness', 'thicknessstd', > 'meancurv') > > > > > > > > > > > > I Why I don't have an option for the no. of vertices? > > > > > > > > > > > > Can I get a table with both data: cortical thickness and no. > of vertices? > > > > > > > > > > > > Many thanks, > > > > > > Antonella > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 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(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- Douglas N. Greve, Ph.D. > > > MGH-NMR Center > > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > > > > > > > > > > > > > -- Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 > > > > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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 > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)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

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Which hemisphere is in the sagital view of the wm
by Antonella Kis 04 Aug '11

04 Aug '11

Hi, When visualizing the wm.mgz in the coronal view we can see both hemispheres: lh and rh. How do I know which hemisphere I am visualising in a sagittal view? Do I have a transition from lh to the rh while passing through the slices? Thank you, Antonella

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Freesurfer August 2011