Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Deformed tksurfer results
by pfotiad＠nmr.mgh.harvard.edu 30 Jul '13

30 Jul '13

Hi, I ran tksurfer (with the inflated surface option) on a couple of my subjects that had a major deformation in their orig.mgz file and the inflated surface of tksurfer looked as if a chunk was missing off of it at the position where the deformation is located. Is that normal? I have attached two images to illustrate what I mean: One of an axial slab of the orig.mgz file where the deformation is shown, and one of the inflated surface of the same subject in tksurfer. Thank you for your time, Panos

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Unsegmented ventricles
by Victor Kovac 30 Jul '13

30 Jul '13

Dear Freesurfer experts, I am running recon-all on very atrophied brains with mixed results. Attached is an image of a brain where segmentation has gone awry. There is no message indicating talairach failure, and the segmentation appears to need WM and pial edits as well as the ventricles to be filled, so I am not sure how to proceed. If you have any recommendations as to how to fix these errors, I would very much appreciate it -- these data are past their deadline, and I am at a loss. Thank you! Sincerely, Victor

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Re: [Freesurfer] Deformed tksurfer results
by pfotiad＠nmr.mgh.harvard.edu 30 Jul '13

30 Jul '13

Sorry forgot the attachments. >> Hi, >> >> I ran tksurfer (with the inflated surface option) on a couple of my >> subjects that had a major deformation in their orig.mgz file and the >> inflated surface of tksurfer looked as if a chunk was missing off of it >> at >> the position where the deformation is located. Is that normal? >> >> I have attached two images to illustrate what I mean: One of an axial >> slab >> of the orig.mgz file where the deformation is shown, and one of the >> inflated surface of the same subject in tksurfer. >> >> Thank you for your time, >> Panos >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >

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Re: [Freesurfer] infant atlas segmentation
by Mark Plantz 30 Jul '13

30 Jul '13

Sorry about that. I received the manual segmentations from a UNC medical group < http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlas…>. I actually asked the main researcher about the out of bounds regions. He thinks that as long as the segmented file lines up with the input volumes, a few out of bounds regions might be OK. However, these seg volumes look very different from a typical .aseg volume that I am used to seeing after recon-all is run. Maybe the segmentation is simply incompatible with FreeSurfer? Thanks for the help. These files are a nightmare! - MP On Mon, Jul 29, 2013 at 11:40 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > can you cc the list please? Maybe we should start over. Where did you get > the manual segmentations from? > > On Mon, 29 Jul 2013, Mark Plantz wrote: > > Ahh, right. So it looks like the red regions appear to be averaged around >> 248. I am not sure why that is the case or if it has >> any significance. I attached a screen shot for reference. >> >> >> On Mon, Jul 29, 2013 at 11:29 AM, Bruce Fischl < >> fischl(a)nmr.mgh.harvard.edu> wrote: >> it isn't a registration file. You should just specify it as a >> volume on the freeview command line, the same as >> brainmask.mgz >> >> On Mon, 29 Jul 2013, Mark Plantz wrote: >> >> I actually tried to view the brainmask.mgz file with the >> segmentation file [Freeview calls it >> 'registration file' I believe]. >> For some reason, the file will load without segmentation, but >> when I attempt to add the registration >> file, I get an error >> message: >> "Failed to load MRI ~/.../../../brainmask.mgz >> >> Could this potentially be part of the problem? >> >> Thanks >> >> MP >> >> >> On Mon, Jul 29, 2013 at 10:57 AM, Mark Plantz < >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> wrote: >> >> It looks like the values vary from 20-120 depending on >> which region I run the cursor over. >> However, aren't those the >> values that correspond to the brain.mgz regions? Is >> there another way to find the segmentation >> values? >> >> >> On Mon, Jul 29, 2013 at 10:37 AM, Bruce Fischl < >> fischl(a)nmr.mgh.harvard.edu> wrote: >> I mean the segmentation values that give you the "out >> of bounds" message >> On Mon, 29 Jul 2013, Mark Plantz wrote: >> >> Hi Bruce, >> Do you mean the brainmask.mgz values? I'm not >> sure what the segmentation #'s exactly are. >> >> Thanks! >> >> MP >> >> >> On Mon, Jul 29, 2013 at 10:17 AM, Bruce Fischl < >> fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Mark >> >> >> what #s are those segmentations? It should >> be trivial to just add them to the end of >> the >> LUT. I wouldn't let them be >> out of bounds as there might be code around >> that might ignore them then. >> >> cheers >> Bruce >> >> On Mon, 29 Jul 2013, Mark Plantz wrote: >> >> Hi Doug, >> Thanks for the reply. After >> doing some research, it looks like messing >> with the >> LUT might be a >> risky decision [and way >> out of my abilities!]. >> >> If I were to use this segmentation >> file to create a .gca atlas using the >> command >> mri_ca_train, do you >> think it would yield >> problems or be inaccurate? I guess >> what I am trying to figure out is if the >> color >> lookup values are even >> significant when using >> the segmentation file to create an >> atlas? >> >> Thanks for all of the help with this. >> >> Best, >> >> MP >> >> p.s. I attached the photo of the >> segmentation volume because this e-mail is sort >> of >> old >> >> >> On Wed, Jul 24, 2013 at 2:39 PM, >> Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> wrote: >> you need a new LUT. See my >> comment from a few emails ago. >> On 07/24/2013 03:29 PM, Mark >> Plantz wrote: >> I'm not actually quite sure >> what it means either. When I use the command >> line: >> >> tkmedit $Subject brain.mgz >> -segmentation <seg.mgz>, >> >> I can run the cursor over >> various regions and the name of the region >> should pop >> up. For some >> reason, the red >> regions are simply labeled as >> "out of bounds." >> >> I'll keep messing with tkmedit >> and let you know if I find out what the >> problem >> is. >> >> Thanks guys! >> >> MP >> >> >> On Wed, Jul 24, 2013 at 2:26 PM, >> Douglas N Greve <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> wrote: >> >> what do you mean that they are >> out of bounds? >> >> On 07/24/2013 03:25 PM, Mark >> Plantz wrote: >> >> I guess the problem is that >> those regions should not be out of >> bounds. Maybe I need to >> create a new Lookup Table for the >> infant mri's? Is that >> possible to do? >> >> >> On Wed, Jul 24, 2013 at 2:21 >> PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu<mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>> wrote: >> >> Hi Mark, please post to >> the list and not to me. >> thanks >> doug >> >> On 07/24/2013 03:21 PM, >> Mark Plantz wrote: >> >> I guess the problem >> is that those regions should not >> be out of >> bounds. Maybe I need >> to create a new Lookup Table for the >> infant mri's? Is that >> possible to do? >> >> >> On Wed, Jul 24, 2013 >> at 2:15 PM, Douglas N Greve >> < >> greve(a)nmr.mgh.harvard.edu >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>>> wrote: >> >> >> what is the >> problem exactly? The fact that there >> are red >> regions >> or that that the >> red regions are labeled as "Out of >> Bounds"? If >> the latter, you >> will need to create a LUT that >> matches your >> regions. the out >> of bounds means that the index in the >> volume does >> not match an >> index in the LUT. >> doug >> >> >> >> On 07/24/2013 >> 01:26 PM, Mark Plantz wrote: >> >> Finally got >> the registration to work. However, it >> looks like >> the out of >> bounds regions (in red) are still >> present (even >> though the >> regions are well within our >> boundaries). Is >> that >> expected >> since they were labeled in the original >> segmentation >> volume? Is >> there anyway to correct those? >> >> Thanks for >> all of the help! >> >> - Mark >> p.s. I >> attached a picture of the original >> brain.mgz file >> viewed with >> the corrected segmentation volume >> >> >> On Wed, Jul >> 24, 2013 at 12:22 PM, Mark Plantz >> < >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>> >> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>>>>> wrote: >> >> Finally >> got the registration to work. >> However, it >> looks >> like the >> out of >> bound regions (in red) are still >> prevalent. >> Is that >> expected >> since they were present in the >> original >> segmentation >> volume? >> Would there be anyway to correct >> those? >> >> Thanks >> for all the help! >> >> - MP >> >> >> On Wed, >> Jul 24, 2013 at 11:11 AM, Mark Plantz >> < >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>> >> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>>>>> wrote: >> >> >> Nevermind, it turned out to be a >> permissions >> issue. >> Thanks! >> >> >> On >> Wed, Jul 24, 2013 at 10:12 AM, Mark >> Plantz >> < >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>>> >> >> <mailto:markplantz2016@u.**northwestern.edu<markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>> >> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>> >> <mailto: >> markplantz2016(a)u.**northwestern.edu <markplantz2016(a)u.northwestern.edu> >> <mailto:markplantz2016@u.** >> northwestern.edu <markplantz2016(a)u.northwestern.edu>>>>>> wrote: >> >> >> Thanks for the reply Doug. I >> recently ran the >> bbregister >> >> command and attempted to view the >> results >> using >> >> tkregister2. I received the >> following error: >> >> >> dhcp-165-124-23-232 >> <tel:165-124-23-232> <tel: >> 165-124-23-232 <tel:165-124-23-232>> >> <tel:165-124-23-232<tel: >> 165-124-23-232> >> <tel:165-124-23-232 <tel: >> 165-124-23-232>>> >> <tel: >> 165-124-23-232 <tel:165-124-23-232> >> <tel:165-124-23-232 <tel: >> 165-124-23-232>> >> <tel:165-124-23-232<tel: >> 165-124-23-232> >> <tel:165-124-23-232 <tel: >> 165-124-23-232>>>>:Desktop >> >> >> >> IngvalsonLab$ tkregister2 --mov >> >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/** >> infant-1yr-mgz/mri/avgseg.mgz >> >> --reg >> >> /Users/IngvalsonLab/Desktop/**register.dat --surf >> >> >> tkregister_tcl >> /Applications/freesurfer/** >> tktools/tkregister2.tcl >> >> INFO: no target volume specified, >> assuming >> FreeSurfer >> orig >> >> volume. >> >> target volume orig >> >> movable volume >> >> /Volumes/Wong_Lab/**CochlearImplant/UNC_NiFTI/** >> infant-1yr-mgz/mri/avgseg.mgz >> >> reg file >> >> /Users/IngvalsonLab/Desktop/**register.dat >> >> LoadVol 1 >> >> ZeroCRAS 0 >> >> $Id: tkregister2.c,v 1.121.2.1 >> 2011/03/28 >> 20:25:16 >> greve Exp $ >> >> Diagnostic Level -1 >> >> regio_read_register(): Undefined >> error: 0 >> >> Error reading subject from >> /Users/IngvalsonLab/Desktop/* >> *register.dat >> >> ERROR: reading >> >> /Users/IngvalsonLab/Desktop/**register.dat >> >> dhcp-165-124-23-232 >> <tel:165-124-23-232> <tel: >> 165-124-23-232 <tel:165-124-23-232>> >> <tel:165-124-23-232<tel: >> 165-124-23-232> >> <tel:165-124-23-232 <tel: >> 165-124-23-232>>> >> <tel: >> 165-124-23-232 <tel:165-124-23-232> >> <tel:165-124-23-232 <tel: >> 165-124-23-232>> >> <tel:165-124-23-232<tel: >> 165-124-23-232> >> <tel:165-124-23-232 <tel: >> 165-124-23-232>>>>:Desktop >> >> >> >> IngvalsonLab$ >> >> I >> do not believe it is a >> permissions issue? >> >> >> Could it simply be that the >> register was >> bad? Is >> there an >> >> easy way to open up the >> register.dat.mincost >> file >> to check >> >> the registration? >> >> >> Thanks again, >> >> MP >> >> >> >> On Tue, Jul 23, 2013 at 9:32 PM, >> Douglas Greve >> < >> greve(a)nmr.mgh.harvard.edu >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>> >> >> <mailto:greve@nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>>>> wrote: >> >> >> >> You can try using bbregister. >> Normally, you >> don't use >> >> bbregister on a segmentation, >> but the >> segmentation >> >> index numbers just happen to be >> "T1-weighted". >> >> doug >> >> ps. Please remember to copy >> the list when >> responding. >> >> thanks! >> >> >> >> >> On 7/23/13 9:51 AM, Mark >> Plantz wrote: >> >> >> Hi Doug, >> >> >> Sorry about that vague >> explanation. So >> I received >> >> a series of infant brain >> atlases >> from a >> UNC >> medical >> >> research group >> >> (http://www.med.unc.edu/bric/** >> ideagroup/free-softwares/unc-**infant-0-1-2-atlases<http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlas…> >> ). >> >> I have a series of infant >> MRI's that I >> would >> like to >> >> segment (using the infant >> atlases, >> instead >> of the >> >> default adult atlas in >> FreeSurfer). >> >> >> As a preliminary step, >> I was >> attempting >> to check >> >> the alignment of one of >> the atlas >> files >> >> ('avgseg.mgz') with one of the >> input brains >> >> ('brain.mgz'). [I attached >> these two >> files, >> just in >> >> case]. >> >> >> So my command line would be: >> >> >> tkmedit $Subject brain.mgz >> -segmentation >> avgseg.mgz >> $FREESURFER_HOME/** >> FreeSurferColorLUT.txt >> >> >> The result was the >> previously attached >> image. I >> was >> >> just wondering if there is >> any way to >> shift the >> two >> >> images manually so the >> alignment is >> better? >> Or maybe >> >> the two files are simply not >> compatible >> with one >> another? >> >> >> Thanks for all the help! >> >> >> Best, >> >> >> Mark >> >> >> >> >> >> On Mon, Jul 22, 2013 at >> 3:53 PM, >> Douglas N >> Greve >> >> <greve(a)nmr.mgh.harvard.edu >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>> >> >> >> <mailto:greve@nmr.mgh.**harvard.edu<greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>> >> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu> >> <mailto: >> greve(a)nmr.mgh.harvard.**edu <greve(a)nmr.mgh.harvard.edu>>>>>> wrote: >> >> >> >> Hi Mark, I have no >> idea what >> you are >> doing. Can >> >> you send a command line? >> >> Are either of the images >> generated by FS? >> >> doug >> >> >> >> >> >> On 07/22/2013 03:56 >> PM, Mark >> Plantz wrote: >> >> > Hello FreeSurfers, >> >> > >> >> > I recently >> obtained a >> set of infant >> >> templates. Out of >> curiousity, >> >> > I decided to view >> one of the >> input >> brains >> with >> >> the provided segmented >> >> > volume file. It >> appears that >> there >> is some >> >> misalignment. I wouldn't >> >> > expect the alignment >> to be >> perfect, >> since I am >> >> basically overlaying an >> >> > average of multiple >> brains >> onto one. >> However, >> >> it looks like this >> >> > misalignment may be >> caused by >> either: >> 1.) the >> >> segmentation volume file >> >> > being shifted down >> or 2.) >> the slices >> not lining >> >> up properly (i.e. one >> >> > file starts before >> the other). >> >> > >> >> > Any ideas what >> could cause a >> problem >> like >> >> this? Could it be that >> >> > the segmented files are >> simply not >> compatible >> >> with FreeSurfer? >> >> > >> >> > Thanks for the help, >> >> > >> >> > Mark >> >> > > >

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LGI
by 이 정환 29 Jul '13

29 Jul '13

Hi, I am trying to computer the LGI local gyrification index with freesurfer. I have Matlab on my machine. I got the following error: < M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013a (8.1.0.604) 64-bit (maci64) February 15, 2013 ---------------------------------------------------- Your MATLAB license will expire in 10 days. Please contact your system administrator or MathWorks to renew this license. ---------------------------------------------------- To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> loading datas ... FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.03 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.01 sec) preparing outer mesh structure ... face 5000 / 128476 face 10000 / 128476 face 15000 / 128476 face 20000 / 128476 face 25000 / 128476 face 30000 / 128476 face 35000 / 128476 face 40000 / 128476 face 45000 / 128476 face 50000 / 128476 face 55000 / 128476 face 60000 / 128476 face 65000 / 128476 face 70000 / 128476 face 75000 / 128476 face 80000 / 128476 face 85000 / 128476 face 90000 / 128476 face 95000 / 128476 face 100000 / 128476 face 105000 / 128476 face 110000 / 128476 face 115000 / 128476 face 120000 / 128476 face 125000 / 128476 mesh_outer = vertices: [64240x3 double] faces: [128476x3 double] facesOfVertex: [64240x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (250.55 sec). ... creating path file for vertex 1 / 64240 area file for outer ROIs saved at 1 Improper assignment with rectangular empty matrix. Error in dsearchn (line 80) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); >> ERROR: make_roi_paths did not complete successfully! Darwin iui-MacBook-Pro.local 12.4.0 Darwin Kernel Version 12.4.0: Wed May 1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64 recon-all -s 20130219-01 exited with ERRORS at Tue Jul 30 09:35:07 KST 2013 For more details, see the log file /Users/jeonghwan/Documents/freesurfer/ADHD-re/20130219-01/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any suggestions to correct my error? Thanks, Jeonghwan

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Re: [Freesurfer] break up time course nifti (fwd)
by Louis Nicholas Vinke 29 Jul '13

29 Jul '13

Forwarding to the list so others can chime in. ---------- Forwarded message ---------- Date: Mon, 29 Jul 2013 18:19:38 -0400 From: Subhabrata Chaudhury <subha(a)scientist.com> To: Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu>, Aaron Tanenbaum <aaron.b.tanenbaum(a)gmail.com> Subject: Re: [Freesurfer] break up time course nifti Greetings Dr. Vinke and Dr. Tanenbaum, I saw your recent freesurfer posts. I have piped BOLD volumeetric nii files for each TR onto the subject's freesurfer surface using bbregister. The resulting surface files (1 for each TR) are in mgh format. Now I want to do a first level glm analysis on the surface files. I havent come across any tool that will allow me to conduct a first level glm analysis using the mgh files. So I was thinking if there is a way to convert these mgh files to nii files and then be able to read in these 'surface' nii files into fsl or spm or afni. Do you have some experience in this regard that you can share ? I will be highly obliged if you can help me with this and share your thoughts. Thank you for your help, Subha ----- Original Message ----- From: Louis Nicholas Vinke Sent: 07/29/13 05:46 PM To: Aaron Tanenbaum Subject: Re: [Freesurfer] break up time course nifti Hi Aaron, You can use the -f or -nth flags with mri_convert. -Louis On Mon, 29 Jul 2013, Aaron Tanenbaum wrote: > hola freesurfers, > I have a time course surface nii files. I would like to break up the time course into many nii > files for each time frame. Is there an easy way of doing this. > Thank you > Aaron Tanenbaum > > _______________________________________________ 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.

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break up time course nifti
by Aaron Tanenbaum 29 Jul '13

29 Jul '13

hola freesurfers, I have a time course surface nii files. I would like to break up the time course into many nii files for each time frame. Is there an easy way of doing this. Thank you Aaron Tanenbaum

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Re: [Freesurfer] recon-all stopped with error
by Louis Nicholas Vinke 29 Jul '13

29 Jul '13

ok, that's good. Just make a symlink to the fsaverage dir from your subjects dir (/home/pom/Software/freesurfer/subjects) i.e. cd /home/pom/Software/freesurfer/subjects ln -s ./fsavg/fsaverage . -Louis On Mon, 29 Jul 2013, Pom Sailasuta wrote: > fsavg dir contains several directories. > > [pom@PomLinux /home/pom]% cd fsavg > [pom@PomLinux /home/pom]% ls > fsaverage fsaverage3 fsaverage4 fsaverage5 fsaverage6 lh.EC_average rh.EC_average V1_average > > > thanks again. > > On Mon, Jul 29, 2013 at 1:23 PM, Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> wrote: > what is fsavg in that same directory? Maybe fsaverage was renamed to fsavg? > > You would just need to copy the fsaverage recon folder back into > /home/pom/Software/freesurfer/subjects, no need to reinstall. > -Louis > > On Mon, 29 Jul 2013, Pom Sailasuta wrote: > > hi, > > yes, but it is a link, not sure how is this happen. > > /////////////////////////////////// > [pom@PomLinux /home/pom]% pwd > /home/pom/Software/freesurfer/subjects > [pom@PomLinux /home/pom]% ls -al > total 10981644 > drwxr-xr-x 9 pom pom 4096 2013-07-29 07:24 . > drwxr-xr-x 17 pom pom 4096 2013-07-28 20:07 .. > drwxr-xr-x 12 pom pom 4096 2012-04-21 11:46 bert > drwxr-xr-x 3 pom pom 4096 2012-04-22 06:37 buckner_data > -rw-r--r-- 1 pom pom 11245151143 2012-04-21 23:33 > buckner_data-tutorial_subjs.tar.gz > lrwxrwxrwx 1 pom pom 48 2013-07-29 07:24 fsaverage -> > /home/pom/Software/freesurfer/subjects/fsaverage > drwxr-xr-x 10 pom pom 4096 2012-04-21 15:32 fsavg > drwxr-xr-x 12 pom pom 4096 2011-08-16 11:27 harris > drwxr-xr-x 13 pom pom 4096 2012-04-21 15:13 LarryR > -rw-r--r-- 1 pom pom 1512 2011-05-22 08:12 README > drwxr-xr-x 13 pom pom 4096 2013-07-28 20:09 S009002A > drwxr-xr-x 2 pom pom 4096 2012-04-21 15:33 sample > -rw-rw-rw- 1 pom pom 492 2012-04-21 18:43 .xdebug_tkmedit > ///////////////////////////////////////////// > > I think it linked to itself, should I re-install freesurfer. > > thanks > Pom > > On Mon, Jul 29, 2013 at 1:09 PM, Louis Nicholas Vinke > <vinke(a)nmr.mgh.harvard.edu> wrote: > Hi Pom, > Does the following path exist? > /home/pom/Software/freesurfer/subjects/fsaverage/label/ > > if so, do it contain lh.BA1.label? It probably has something do with > the fsaverage > symbolic link. A few lines up in your error log it prints "Too many > levels of symbolic > links". > -Louis > > On Mon, 29 Jul 2013, Pom Sailasuta wrote: > > Hi, > > I am wondering the errors I got from recon-all is from my > FreeSurfer > installation, please comments. > > Here is my error: > //////////////////////// > Reporting on 70 segmentations > /home/pom/Software/freesurfer/subjects/S009002A/label > #-------------------------------------------- > #@# BA Labels lh Mon Jul 29 07:24:35 PDT 2013 > INFO: fsaverage subject does not exist in SUBJECTS_DIR > INFO: Creating symlink to fsaverage subject... > > cd /home/pom/Software/freesurfer/subjects; ln -s > /home/pom/Software/freesurfer/subjects/fsaverage; > cd - > > > mri_label2label --srcsubject fsaverage --srclabel > > /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label > --trgsubject S009002A > --trglabel ./lh.BA1.label --hemi lh --regmethod surface > > Too many levels of symbolic links > mri_label2label: could not open label file > > /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label > > srclabel = > > /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label > srcsubject = fsaverage > trgsubject = S009002A > trglabel = ./lh.BA1.label > regmethod = surface > > srchemi = lh > trghemi = lh > trgsurface = white > srcsurfreg = sphere.reg > trgsurfreg = sphere.reg > usehash = 1 > Use ProjAbs = 0, 0 > Use ProjFrac = 0, 0 > DoPaint 0 > > SUBJECTS_DIR /home/pom/Software/freesurfer/subjects > FREESURFER_HOME /home/pom/Software/freesurfer > Loading source label. > Invalid argument > ERROR reading > > /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label > Linux PomLinux 2.6.32-45-generic-pae #104-Ubuntu SMP Tue Feb 19 > 21:36:53 > UTC 2013 i686 GNU/Linux > > recon-all -s S009002A exited with ERRORS at Mon Jul 29 07:24:35 > PDT 2013 > > For more details, see the log file > > /home/pom/Software/freesurfer/subjects/S009002A/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > ////////////////////////////// > > thanks > > Pom > > > > 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. > > > > > -- > Pom > > > > > -- > Pom >

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Re: [Freesurfer] [tracula] error running trac-all -prep
by Borsodi Florian 29 Jul '13

29 Jul '13

Hello, Thank you for your quick answer. I already run tracula with the transposed bvec and bval files but i keep getting the same kind of error. With kind regards, Florian Borsodi >>> Chris Watson 29.07.13 19.12 Uhr >>> You may have to transpose the bval and bvec files. On 07/29/2013 11:17 AM, Borsodi Florian wrote: Hello, I have been trying to run tracula on my data and i keep getting the same kind of error repeatedly. For my imput I am using dicoms from a Siemens scanner with a stadard diffusion protocol. However, tracula cannot read the bvec and bval data out of the dicom header. Therefore, I implemented bvec and bval files into the config file. After doing so, I got the error which says that tracula cannot find the "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. I have tried many options, but still cannot find a solution. I am hoping to get some troubleshooting help. I have atteched my log- and config- files, as well as my bvec and bval files. To uphold patient confidentiality, I have encode the name patient's data as "AAAAAA". I believe the problems are the bvec and bval files or their structures. The log-file lete me assume this, especially the lines 202 - 205, 264 - 268 and 1480 - 1484. Thank you in advance for your help, and your speedy response. With kind regards, Florian Borsodi Department of Neurology Medical University of Graz _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail.

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recon-all stopped with error
by Pom Sailasuta 29 Jul '13

29 Jul '13

Hi, I am wondering the errors I got from recon-all is from my FreeSurfer installation, please comments. Here is my error: //////////////////////// Reporting on 70 segmentations /home/pom/Software/freesurfer/subjects/S009002A/label #-------------------------------------------- #@# BA Labels lh Mon Jul 29 07:24:35 PDT 2013 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /home/pom/Software/freesurfer/subjects; ln -s /home/pom/Software/freesurfer/subjects/fsaverage; cd - mri_label2label --srcsubject fsaverage --srclabel /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label --trgsubject S009002A --trglabel ./lh.BA1.label --hemi lh --regmethod surface Too many levels of symbolic links mri_label2label: could not open label file /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label srclabel = /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = S009002A trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /home/pom/Software/freesurfer/subjects FREESURFER_HOME /home/pom/Software/freesurfer Loading source label. Invalid argument ERROR reading /home/pom/Software/freesurfer/subjects/fsaverage/label/lh.BA1.label Linux PomLinux 2.6.32-45-generic-pae #104-Ubuntu SMP Tue Feb 19 21:36:53 UTC 2013 i686 GNU/Linux recon-all -s S009002A exited with ERRORS at Mon Jul 29 07:24:35 PDT 2013 For more details, see the log file /home/pom/Software/freesurfer/subjects/S009002A/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ////////////////////////////// thanks Pom

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