Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

Re: [Freesurfer] How to extract a single subcortical structure from aseg+aparc.mgz file?
by Bruce Fischl 24 Nov '13

24 Nov '13

Hi Ran yes, mri_extract_label or mri_binarize --match should do the trick cheers Bruce On Sun, 24 Nov 2013, Ran Xu wrote: > Dear Freesurfer experts, > I got the aseg+aparc.mgz, and converted it into the individual T1 space. > Now, I am wondering if there is a way to extract the single subcortical > structure, like thalamus, from the converted aseg+aparc.mgz. I already know > the thalamus label, how to get thalamus.mgz file in this label. Could > someone help me out? > > Thank you very much! > > Ran > >

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Volume-defined ROI 'gone' after vol2surf
by Anita van Loenhoud 24 Nov '13

24 Nov '13

Hi all, I want to measure cortical thickness in 7 volume-defined ROIs (created in Marsbar). I followed the tutorial http://freesurfer.net/fswiki/VolumeRoiCorticalThickness. When I want to visualize my surface-based ROI after mri_vol2surf, for some reason ROI 6 and 7 do not appear in tksurfer (and with segstats, no segmentation is found). FreeSurfer does not seem to give any error message: $ mri_vol2surf --mov ~/Desktop/anita-vumc/7Rmidtempgyrus.nii --reg avg152T1_to_fsaverage.dat --projdist-max 0 1 0.1 --interp nearest --hemi rh --out rh.fsaverage.7Rmidtempgyrus.mgh --reshape srcvol = /home/guest/Desktop/anita-vumc/7Rmidtempgyrus.nii srcreg = avg152T1_to_fsaverage.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = 0.5 reshape = 1 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume Reading surface /data1/projects/ysbrand-vumc/pddatabase-freesurfer/fsaverage/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.1 0 1 using old 3 0.2 0 1 using old 4 0.3 0 1 using old 5 0.4 0 1 using old 6 0.5 0 1 using old 7 0.6 0 1 using old 8 0.7 0 1 using old 9 0.8 0 1 using old 10 0.9 0 1 using old Done mapping volume to surface Number of source voxels hit = 21723 Reshaping 7 (nvertices = 163842) Writing to rh.fsaverage.7Rmidtempgyrus.mgh Dim: 23406 1 7 Does anyone have an idea about what might have gone wrong? Thanks!

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Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit
by Douglas Greve 23 Nov '13

23 Nov '13

Hi Clark, mri_glmfit should work fine. If you have the ROIs in a volume format (eg, nifti or mgh) you can run mri_concat on them to create a stack, then just pass the stack to mri_glmfit with the --y flag (also add --no-est-fwhm). If you don't have them in a volume format, you can create a volume format in matlab, something like mri.vol = load('yourdata.dat'); mri.vol = vol(:)'; % make sure each ROI is in a different column instead of row MRIwrite(mri,'youdata.nii'); doug On 11/22/13 5:51 PM, Clark Fisher wrote: > Hi Freesurfers, > > I am working with fsfast, and interested in doing a 2nd-level fixed effects analysis over a number of subjects. However, the volumes I'm using aren't in a standard freesurfer space (native, talraich, etc.). They are nx1x1 volumes containing results from n ROIs. While I got first level analysis in fs-fast working, I don't think I'll get mri_glmfit to work in this space. > > What is the math that mri_glmfit carries out to do the fixed-effects analysis? Based on the inputs, it seems to rely upon the variance and degrees of freedom from each individual subject, and I can't find a formula in the general MRI literature (or in the freesurfer group analysis presentation) that uses both of these in a fixed-effects analysis. > > Thanks, > Clark > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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LONG stream question {Disarmed}
by Kirov, Ivan 22 Nov '13

22 Nov '13

Dear FreeSurfer group/Dr. Reuter, My questions are in regards to the LONG stream. My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 1) Error message During the creation of the BASE, I get the following error in the beginning of the recon: >>>WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s.<<<< What should I be aware of in regards to this error? The images were all acquired using the same MPRAGE protocol. All timepoints were fed MPRAGEs reconstructed in the axial orientation, but some may have been reconstructed at an angle. I was assured that this is not an issue for FreeSurfer, but could this be the reason for the error? 2) Conversion of LONG run aseg.mgz segmentations to native anatomical space Executing the commands for converting aseg.mgz to native space (http://freesurfer.net/fswiki/FsAnat-to-NativeAnat<http://freesurfer.net/fswiki/FsAnat-to-NativeAnat>) in the folder of a long run (me1.long.me_base) does not convert. It seems to me that (unlike the cross runs) the long runs are all in the same space (in the template/ base space?) and their rawavg.mgz does not match that of the corresponding cross run. Some insight on this would be appreciated. The question is how to convert an individual long run's aseg.mgz into native anatomical space. Perhaps using the rawavg.mgz from the corresponding cross run? Thank you very much! Ivan -- Ivan Kirov, PhD Postdoctoral fellow New York University School of Medicine Center for Biomedical Imaging 660 1st Ave, 4th floor, New York, NY 10016 Tel: 212-263-3337 Fax: 212-263-7541 ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

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TRACULA exists uncompleted
by Emad Ahmadi 22 Nov '13

22 Nov '13

Hello, I'm using TRACULA for analyzing a number of cases, and I've made a file to successively run the three stages of pre-processing, model fitting, and pathways reconstruction which is attached (ter1.tcsh). I've also attached the configuration file I'm using (dmrircTer1.cshell). The problem is that TRACULA exists uncompleted. I've attached the log files. I'd really appreciate it if you let me know where I'm making some sort of a mistake. All the best, Emad

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affine registration with mri_robust_register
by Nathaniel Reynolds 22 Nov '13

22 Nov '13

Hi all, I can't find any explanation of how to perform an affine registration with mdi_robust_register. Could someone please explain? Thanks, Nathaniel

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Re: [Freesurfer] scale bar question
by Douglas N Greve 22 Nov '13

22 Nov '13

Just click on a point and look at the vertex RAS. At zoom=1, you have to translate the surface over to the scale bar. At zoom=1 I got about 10mm, but it did seem to change when I zoomed in. doug On 11/22/2013 12:23 PM, Cesar Echavarria wrote: > Actually, Doug can you tell me how to get the xyz coordinates on > Tksurfer so I can figure out the length of the bar as you did? > > Thanks > > Cesar > > > On Fri, Nov 22, 2013 at 12:19 PM, Cesar Echavarria > <cechavarria60(a)gmail.com <mailto:cechavarria60@gmail.com>> wrote: > > I meant zoom in on the brain. I guess I'll take Doug's approach > and estimate the scale of the bar with the xyz coordinates. > > Cesar > > > On Fri, Nov 22, 2013 at 12:16 PM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > wrote: > > Hi Cesar > > what do you mean by "scale the brain up"? > > Bruce > > On Fri, 22 Nov 2013, Cesar Echavarria wrote: > > Hi freesurfers, > Anyone know what the scale bar in TkSurfer represents? > >From past threads I > gathered that it represent 1 cm on the human brain. > However, the size of the > bar displayed gets smaller as I scale the brain up which > does not make sense > if the bar is supposed to represent a constant length. > > Cesar > > > > > 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. > > > > > -- > Cesar Echavarria > Research Assistant > Martinos Center for Biomedical Imaging, Harvard-MGH > Brain & Cognitive Sciences | MIT 2012 > > > > > -- > Cesar Echavarria > Research Assistant > Martinos Center for Biomedical Imaging, Harvard-MGH > Brain & Cognitive Sciences | MIT 2012 -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] scale bar question
by Cesar Echavarria 22 Nov '13

22 Nov '13

I meant zoom in on the brain. I guess I'll take Doug's approach and estimate the scale of the bar with the xyz coordinates. Cesar On Fri, Nov 22, 2013 at 12:16 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Cesar > > what do you mean by "scale the brain up"? > > Bruce > > On Fri, 22 Nov 2013, Cesar Echavarria wrote: > > Hi freesurfers, >> Anyone know what the scale bar in TkSurfer represents? >From past threads >> I >> gathered that it represent 1 cm on the human brain. However, the size of >> the >> bar displayed gets smaller as I scale the brain up which does not make >> sense >> if the bar is supposed to represent a constant length. >> >> Cesar >> >> >> > > 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. > > -- Cesar Echavarria Research Assistant Martinos Center for Biomedical Imaging, Harvard-MGH Brain & Cognitive Sciences | MIT 2012

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scale bar question
by Cesar Echavarria 22 Nov '13

22 Nov '13

Hi freesurfers, Anyone know what the scale bar in TkSurfer represents? From past threads I gathered that it represent 1 cm on the human brain. However, the size of the bar displayed gets smaller as I scale the brain up which does not make sense if the bar is supposed to represent a constant length. Cesar

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Order of edits for longitudinal data
by Rongxiang Tang 22 Nov '13

22 Nov '13

Dear All, I was would like to double check the order of edits for longitudinal data. I did edits for my cross-sectional data, and for my base data, I did the following: 1. skull strips edits (if necessary) 2. control points edits 3. white matter edits 4. pial edits 5.brain final surfs edits. I was also wondering if correction for topological defects is needed for the base data. Thanks, Rongxiang

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Freesurfer November 2013