Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

issues with registering MNI 152 to fsaverage on the right hemisphere
by Yune Lee 04 Aug '13

04 Aug '13

Hello freesurfer users -- I noticed an issue with registering MNI template to freesurfer surface, whereby a cluster located on the right hemisphere does not appear at all in the fsaverage rh.inflated template while the left cluster was clearly seen. [image: Inline image 1] The map was generated in SPM8, which indeed does not use MNI152 template. However, as far as I'm concerned, it should be more or less similar to MNI 152 template, so I can rule out the possibility of using a different template image instead of MNI152. Any way, I'd be grateful if you guys let me know any thoughts on this issue. -ysl fyi) below is the command line that I used. ----------- #for LH mri_vol2surf --mov rad4_regions.img --reg /usr/local/freesurfer/centos4_x86_64-stable-pub-v5.1.0/average/mni152.register.dat --trgsubject fsaverage --hemi lh --projfrac 0.5 --o rad4_lh.mgh #for RH mri_vol2surf --mov rad4_regions.img --reg /usr/local/freesurfer/centos4_x86_64-stable-pub-v5.1.0/average/mni152.register.dat --trgsubject fsaverage --hemi rh --projfrac 0.5 --o rad4_rh.mgh

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Re: [Freesurfer] GLM Analysis: ROI (--label)
by Rachel Jonas 04 Aug '13

04 Aug '13

Hi Doug, Thanks for the response. Here is my glmfit command: mri_glmfit \ --y lh.22q_age.thickness.10.mgh \ --fsgd 22q_age.fsgd dods\ --C 22q_age_2.mtx \ --surf fsaverage lh \ --label lh.orbitofrontal.label --cortex \ --glmdir lh.22q_age_OFC.glmdir And here is the error message: gdfReadHeader: reading 22q_age.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 age 12.7292 Class Means of each Continuous Variable 1 HC 12.8261 2 22Q 12.6400 INFO: gd2mtx_method is dods Reading source surface /u/home/FMRI/cbearden/data/22q/Analyses/sMRI/fsaverage/surf/lh.white ERROR: must specify GLM output dir [racheljo@login3 sMRI]$ --cortex \ ? --glmdir lh.22q_age_OFC.glmdir --cortex: Command not found. Thanks! Rachel

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identify the centroid of a volume
by John Richey 04 Aug '13

04 Aug '13

Dear freesurfer experts: I have a few MNI labels, and I need to identify the centroid of the volume in MNI coordinate space. These are binary files in compressed nifti format. At first, i thought could use mri_volcluster, and simply set the minimum to 0.01, which would capture the remaining voxels and then compute a centroid. However, this seems not to be the case. The coordinates refer only to the edge of the volume which is not correct. Has anyone done this before? Thanks in advance, John

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[tracula] error running trac-all -prep
by Borsodi Florian 01 Aug '13

01 Aug '13

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

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unpacksdcmdir error for resting state fMRI
by Eli Fredman 31 Jul '13

31 Jul '13

Hi all, I am following the FsFast tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkt…) for resting state data and I am stuck at the unpacksdcmdir step. When I try and run the command I get an error that says "ERROR: Run ## does not exist in session." I've tried several different combinations of numbers that I thought might be the run ## but I haven't had any success. All the data I am using are in .IMA format, not .dcm (ex. 000001.IMA 000002.IMA 000003.IMA...000140.IMA), so I am unfamiliar with how to find the scan acquisition number. Thanks for the help! P.S. Are there any good video tutorial's out there for resting state data? I have never done any fMRI analysis until now. -- Eli Fredman, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6118 Cell: (314) 952-8098 Fax: (617) 525-6150

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defect of cerebellar segmentation in the inferior part
by charles laidi 31 Jul '13

31 Jul '13

Dear Freesurfers, **** ** ** I am experiencing recurrent issue while performing cerebellar segmentation on T1 images.**** ** ** These are the characteristics of the acquisition:**** **§ **T1: field of view (FOV) = 230 mm**** **§ **repetition time (TR) = 1140 msec**** **§ **echo time (TE) = 4.38 msec**** **§ **matrix size 256 × 256** **§ ***interpolated to 512 × 512* **§ ***yielding an in-plane voxel size of 0.45 mm × 0.45 mm***** **§ **slice thickness of 0.9 mm**** ** ** After recon-all (ended without errors) I always end up with the same error in segmentation (see attached file) : there is the same defect of segmentation in the inferior part of cerebellum. **** ** ** Are you aware of any way to correct this defect ? (I think this might be related to the low resolution of my images)**** ** ** Thank you for your time. **** Best regards**** Charles**** **

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Fwd: infant atlas segmentation
by Mark Plantz 31 Jul '13

31 Jul '13

---------- Forwarded message ---------- From: Mark Plantz <markplantz2016(a)u.northwestern.edu> Date: Tue, Jul 30, 2013 at 8:39 AM Subject: Re: [Freesurfer] infant atlas segmentation To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Just opened up the default FreeSurferColorLUT.txt file. So it looks like all I have to change is the #No. column of the file, to match the ones in the other LUT used. I actually just received the MRIcro .lut file from the UNC group. [attached] Hopefully this will help with the conversion. However, I still have to figure out how to open the file. Any ideas? On Tue, Jul 30, 2013 at 8:25 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Mark > > creating a FreeSurfer LUT really isn't that hard. Have you looked at our > standard one? Probably we have the names you already want and you just need > to change our indices to match the ones in your segmentation file (and save > it as a different LUT) > > cheers > Bruce > > On Tue, 30 Jul 2013, Mark Plantz wrote: > > Turns out that the files had been labeled using a color LUT in a program >> called MRIcro. I am now installing this program simply to access the LUT. >> Will it be as simple as exchanging the index values from this LUT to a >> custom LUT in FreeSurfer? >> >> >> On Tue, Jul 30, 2013 at 12:35 AM, Douglas Greve < >> greve(a)nmr.mgh.harvard.edu> >> wrote: >> >> The problem is that you need to create a completely new LUT. The >> labels that get displayed with the standard LUT are going to be >> totally random with respect to what they should display. >> >> On 7/29/13 2:20 PM, Mark Plantz wrote: >> Hi Doug, >> Thanks for the reply. I will definitely go into the LUT and >> change those values to some specific region. My main concern is >> that I think all of these "out of bounds" labels are the >> symptoms of some larger problem. The segmentation looks very >> strange as compared to a typical segmentation (i.e. an >> 'aseg.mgz' file). In fact, the segmentation appears to be >> labeling "left-<region" in the right hemisphere. Have you seen a >> segmentation file that looks like the once I attached before? I >> am used to seeing segmentation files such as the one attached to >> this e-mail. >> >> - Mark >> >> >> On Mon, Jul 29, 2013 at 12:28 PM, Douglas Greve >> <greve(a)nmr.mgh.harvard.edu> wrote: >> >> Mark, the only thing that is wrong with the out of >> bounds regions is that they are not represented in >> the LUT. Once you add an index corresponding to the >> index of the segmentation to the LUT, it will not >> show up as "out of bounds". The brain mask has >> nothing to do with it. >> best >> doug >> >> >> >> On 7/29/13 12:50 PM, Mark Plantz wrote: >> 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-atla<http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atla> >> ses>. 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@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@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, >> > >

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Hand Segmenting White and Pial Layers
by Liv Wroblewski 31 Jul '13

31 Jul '13

Hi Freesurfer, Here at I-LABS we just finished making a couple new 6-month and 12-month infant templates for ourselves and the neuroscience community to use. When I run the template through the recon-all pipeline, there is significant blurring of the template as opposed to when I look at the original in FSL and the segmentation is not usable for our MEG source localization. I would like to create the grey matter and white matter masks completely by hand over the next week or two from the original nifti image, and then have freesurfer use those masks in the surface reconstructions. Is this possible? If so, how can I do it? Thanks so much in advance, Liv

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Re: [Freesurfer] hippo_subfields atlas
by Juan Eugenio Iglesias 31 Jul '13

31 Jul '13

Did you run recon-all -subjid bert -hippo-subfields? If so, there should be a log file with the output from the hippo-subfield code in $SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take a look at it to get an idea of what happened. Kind regards, /Eugenio On 07/31/2013 04:38 PM, Rajapillai Pillai wrote: > Thanks very much for the prompt response. The command I ran was > > $ kvlQuantifyPosteriorProbabilityImages > /Applications/freesurfer/data/GEMS/compressionLookupTable.txt > posterior_right_* posterior_Right-Hippocampus.mgz > > in $SUBJECTS_DIR/bert/mri > > And yeah, it's not in the mri directory. Any idea what might have gone > wrong and how I can try and fix it? > > Thanks, > Raja > > > On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias > <iglesias(a)nmr.mgh.harvard.edu <mailto:iglesias@nmr.mgh.harvard.edu>> > wrote: > > Hi Raja, > > >> >> I'm have a question regarding the GEMS hippocampal segmentation. >> I saw on the wiki how to run -hippo_subfields, but how do I >> access the atlas itself? What file is it under. > > That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz > > >> >> Also, I'm not sure if I'm missing some files: whenever I try to >> do one of the individual commands using, for example, >> posterior_Right_Hippocampus.mgz, it gives the following error: >> >> volumeInVoxels: >> terminate called after throwing an instance of 'itk::ExceptionObject' >> what(): itkMGHImageIO.cxx:216: >> itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file: >> posterior_Right-Hippocampus.mgz >> Abort trap >> > > What command is this? In any case, it's pretty clear that the file > is missing.... > > >> Also, upon searching through my freesurfer directory, I cannot >> find any posterior_Right-Hippocamus.mgz or >> posterior_Left-Hippocampus.mgz files. > It should be under the "mri" directory. If it isn't, there was > some problem running the algorithms. > > Cheers, > > /Eugenio > > > > >> >> Thanks very much for your time, >> Raja >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > ------------------------------------------------------------------------------------- > Juan Eugenio Iglesias, PhD > http://www.jeiglesias.com > iglesias(a)nmr.mgh.harvard.edu <mailto:iglesias@nmr.mgh.harvard.edu> > Athinoula A. Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, Massachusetts 2129 > U.S.A. > > 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. > > -- ------------------------------------------------------------------------------------- Juan Eugenio Iglesias, PhD http://www.jeiglesias.com iglesias(a)nmr.mgh.harvard.edu Athinoula A. Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, Massachusetts 2129 U.S.A.

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hippo_subfields atlas
by Rajapillai Pillai 31 Jul '13

31 Jul '13

Dear Freesurfers, I'm have a question regarding the GEMS hippocampal segmentation. I saw on the wiki how to run -hippo_subfields, but how do I access the atlas itself? What file is it under. Also, I'm not sure if I'm missing some files: whenever I try to do one of the individual commands using, for example, posterior_Right_Hippocampus.mgz, it gives the following error: volumeInVoxels: terminate called after throwing an instance of 'itk::ExceptionObject' what(): itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file: posterior_Right-Hippocampus.mgz Abort trap Also, upon searching through my freesurfer directory, I cannot find any posterior_Right-Hippocamus.mgz or posterior_Left-Hippocampus.mgz files. Thanks very much for your time, Raja

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Freesurfer July 2013