Freesurfer

freesurfer@nmr.mgh.harvard.edu

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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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Freesurfer Wiki down?
by Caspar M. Schwiedrzik 29 Jul '13

29 Jul '13

not sure whether others are experiencing this as well, but the freesurfer wiki seems to be down. caspar

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Fwd: infant atlas segmentation
by Mark Plantz 29 Jul '13

29 Jul '13

---------- Forwarded message ---------- From: Mark Plantz <markplantz2016(a)u.northwestern.edu> Date: Mon, Jul 29, 2013 at 11:33 AM Subject: Re: [Freesurfer] infant atlas segmentation To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@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@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@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@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@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@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@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@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>>>>>> 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@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@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@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>>>>>> 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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>> >> >> <mailto:greve@nmr.mgh.**harvard.edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@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 >> > >> > >> > >> > >> >> _____________________________**__________________ >> > >> Freesurfer mailing list >> > >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> <mailto: >> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >>> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto: >> Freesurfer(a)nmr.mgh.**harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >>>> >> >> > >> https://mail.nmr.mgh.harvard.** >> edu/mailman/listinfo/**freesurfer<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(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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>> >> <mailto:greve@nmr.mgh.**harvard.edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>>> >> >> Phone Number: >> 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel: >> 617-724-2358>> >> <tel:617-724-2358<tel: >> 617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>>> >> <tel:617-724-2358 <tel: >> 617-724-2358> <tel:617-724-2358 >> <tel:617-724-2358>> <tel:617-724-2358<tel: >> 617-724-2358> >> <tel:617-724-2358 <tel: >> 617-724-2358>>>> >> >> Fax: 617-726-7422 >> <tel:617-726-7422> >> <tel:617-726-7422 <tel: >> 617-726-7422>> >> <tel:617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 >> <tel:617-726-7422>>> >> <tel:617-726-7422<tel: >> 617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> <tel:617-726-7422 <tel: >> 617-726-7422> <tel:617-726-7422 >> <tel:617-726-7422>>>> >> >> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/** >> fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.** >> harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> <http://surfer.nmr.mgh.** >> harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> <http://surfer.nmr.mgh.** >> harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> >> FileDrop: >> https://gate.nmr.mgh.harvard.** >> edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/** >> facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> < >> http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> > >

1 0

cvs_avg35
by SHAHIN NASR 29 Jul '13

29 Jul '13

Hi, Would you tell me where I can find cvs_avg35 brain template. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

Fwd: infant atlas segmentation
by Mark Plantz 29 Jul '13

29 Jul '13

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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@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@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@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@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@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@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@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@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@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@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@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@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>>>>>> >> 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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@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 >> > >> > >> > >> > >> >> _____________________________**__________________ >> > Freesurfer >> mailing list >> > >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >>> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >>>> >> >> > >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/* >> *freesurfer<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(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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>> >> <mailto:greve@nmr.mgh.**harvard.edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto:greve@nmr.mgh.harvard.** >> edu <greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>>> >> Phone Number: >> 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> <tel:617-724-2358 <tel: >> 617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>>> >> <tel:617-724-2358 <tel:617-724-2358> <tel: >> 617-724-2358 >> <tel:617-724-2358>> <tel:617-724-2358 <tel: >> 617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>>>> >> Fax: >> 617-726-7422 >> <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> <tel:617-726-7422 <tel:617-726-7422> <tel: >> 617-726-7422 >> <tel:617-726-7422>>> >> <tel:617-726-7422 <tel: >> 617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> <tel:617-726-7422 <tel:617-726-7422> <tel: >> 617-726-7422 >> <tel:617-726-7422>>>> >> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/* >> *BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> < >> http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/** >> facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> < >> http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.** >> edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> _____________________________** >> __________________ >> Freesurfer >> mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >>> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >> >> >> <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> >>>> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/* >> *freesurfer<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<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. >> >> >> >> >> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> 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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >>> >> >> Phone Number: 617-724-2358 <tel: >> 617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> <tel:617-724-2358 <tel:617-724-2358> <tel: >> 617-724-2358 >> <tel:617-724-2358>>> >> Fax: 617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> <tel: >> 617-726-7422 >> <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>>> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/* >> *BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> <http://surfer.nmr.mgh.** >> harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: https://gate.nmr.mgh.harvard.** >> edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/** >> facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.** >> edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> 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@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> >> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel: >> 617-726-7422 >> <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/** >> fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> FileDrop: https://gate.nmr.mgh.harvard.** >> edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/** >> facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.** >> edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.* >> *edu <greve(a)nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >> BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>> >> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.** >> edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.** >> edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >

2 2

Error "Cannot allocate memory"
by Annemarie Brandhofe 29 Jul '13

29 Jul '13

Dear freesurfer community, we are conducting cortical-thickness analysis using freesurfer-5.1.0 and have been experiencing some problems with the automatic recognition of the control points. For several subjects, we run the recon-all command and after about 40 hours of computations, we receive the error message “Excessive topologic defect encountered: could not allocate 171060256 edges for retessellation Cannot allocate memory”. After the occurrence of the error message, the computation is stopped. Below, we provide the details of our setup and the exact error message for one subject. Feel free to ask for more information. Thank you very much for your help! Yours sincerely, Annemarie $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-5.1.0 Build stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Debian version: 5.0.6 Kernel info: Linux 2.6.27.39-1-ql-beowulf i686 $ which freesurfer -> /apps/prod/i486/freesurfer-5.1.0/bin/freesurfer Used command: recon-all –autorecon2-cp –subjid IB34_mdeft. Error message: CORRECTING DEFECT 0 (vertices=72621, convex hull=6983) Excessive topologic defect encountered: could not allocate 171060256 edges for retessellation Cannot allocate memory Linux beo-08 2.6.27.39-1-ql-beowulf #1 SMP Mon Nov 23 10:55:10 CET 2009 i686 GNU/Linux recon-all -s IB34_mdeft. exited with ERRORS at Sat Jul 27 00:01:52 CEST 2013

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