Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

Registration and Surface flatten
by Caka 19 May '14

19 May '14

Hi Doug, Thanks for your suggestion on tksurfer, it works. I would like to map all the subjects into a flat map because I am curious about the 2-D thickness patterns between different groups. I think there will be some distinctions. But if I flatten fsaverage, how can I map everyone?s 3D surface onto the fsaverage?s 2D map? Is there a command? Best, Qiongmin On 05/13/2014 11:19 PM, Caka wrote: > Dear Doug and all, I have already done two things: (1) 'recon-all? to > the segmentation for 140 subjects; (2) surface registration to > fsaverage template for 1 subject using: mri_surf2surf --hemi lh > --srcsubject sub001 --srcsurfval thickness --src_type curv > --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.mgz Now I > have got the 'sub001-thickness-lh.mgz' file. I have two questions: (1) > Is this 'sub001-thickness-lh.mgz? a surface file or a volume file? How > can I read it? I used ?freeview sub001-thickness-lh.mgz? to read it, > but a dark scene was shown, nothing can be found. I also used > ?mris_convert -c $SUBJECTS_DIR/sub001/sub001-thickness-lh.mgz > $SUBJECTS_DIR/sub001/surf/lh.orig lh.thickness.asc?, an error occurred > like ?ERROR: number of vertices in > /disk250/data_analysis/sub001/sub001-thickness-lh.mgz does not match > surface (163842, 132230)?. Try tksurfer fsaverage lh inflated -aparc -overlay sub001-thickness-lh.mgz -fminmax .01 4 > (2) After the registration, I want to flatten the surface of curvature > or thickness into a full plane. The wiki says we should first specify > 5 vertices and cut the whole area without the midline region, then > ?kris_flatten? can be used. Indeed, this procedure requires quite a > lot manually operation. I am wondering if there are some automatically > commands that can do this flatten projects for 140 subject? Any reply > would be really appreciated! Qiongmin > _______________________________________________ Freesurfer mailing > list Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer I don't think so, though I think bruce was working on something. You could just flatten fsaverage and then map everyone to fsaverage (as you have already done). Why do you want to map everyone to a flat map? doug

2 1

LGI qdec analysis on longitiudinal data
by Jon Wieser 19 May '14

19 May '14

Hi freesurfer experts I am trying to analyze the longitudinal effects on LGI. I've run all my subject's through the longitudinal processing stream. I set-up my qdec dat file: fsid fsid-base years 100674-0107 100674_base 1.6 100674-0408 100674_base 2.8 100674-0605 100674_base 0 100712-0505 100712_base 0 100712-0708 100712_base 3.2 100712-1006 100712_base 1.4 100724-0605 100724_base 0 100724-0808 100724_base 3.2 100724-1206 100724_base 1.5 100733-0106 100733_base 0 100733-0507 100733_base 1.3 100733-1008 100733_base 2.8 I ran long_mris_slopse for both hemispheres: long_mris_slopes --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --meas pial_lgi --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Studies/UCSDsubjects-NIDA/Cluster_Proc long_mris_slopes --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --meas pial_lgi --hemi rh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd /Studies/UCSDsubjects-NIDA/Cluster_Proc i also ran long_qdec_table long_qdec_table --qdec ./UCSD_subj_NIDA_LGI.qdec.dat --cross --out ./qdec/cross.qdec.table.dat then I ran qdec: qdec --table ./qdec/cross.qdec.table.dat I specified pial_lgi as the Measure, and selected years as the covariate when I press Analyze, I get the following error: Error in Analyze: Couldn't open 100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgz or mgh file when looking in the directories, I have lh.pial_lgi.fwhm10.fsaverage.mgh files in the 100674-0107.long.100674_base directories: \100674-0107.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-0605.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0107.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-0605.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100674-0408.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-0808.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0408.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-0808.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100674-0605.long.100674_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100724-1206.long.100724_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100674-0605.long.100674_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100724-1206.long.100724_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-0505.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-0106.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-0505.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-0106.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-0708.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-0507.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-0708.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-0507.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100712-1006.long.100712_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100733-1008.long.100733_base/surf/lh.pial_lgi.fwhm10.fsaverage.mgh 100712-1006.long.100712_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh 100733-1008.long.100733_base/surf/rh.pial_lgi.fwhm10.fsaverage.mgh but not in the following directories 100674_base/surf 100712_base/surf 100724_base/surf 100733_base/surf How can I fix this? Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

2 4

bbregister to convert .labels to MNI space
by Nathan Hutcheson 19 May '14

19 May '14

Hello, I am trying to use bbregister to take an .annot file of a particular structure and register it to MNI space. I want to be able to use one of the FreeSurfer parcellations of the ACC (lh.caudalanteriorcingulate.label) and do a fMRI BOLD extraction in FSL in MNI space. Below is the command I used and the error message I am getting. Please let me know if what I am doing makes any sense or if I am way off base. Input > bbregister --s fsaverage --mov > /u/home/n/nhutche/temp/labels/lh.caudalanteriorcingulate.label --t1 > --init-fsl --reg register.dat > > Output > mkdir: cannot create directory `./tmp.bbregister.6489': Permission denied > > Log file is register.dat.log > > register.dat.log: Permission denied. > Take care, Dr. Nathan Hutcheson Postdoctoral Researcher University of California Los Angeles Semel Institute 760 Westwood Plaza C8-202 Los Angeles, CA 90024 T: 770.841.1694 nathanhutcheson.com <http://www.linkedin.com/pub/nathan-hutcheson/3a/7a8/a46>

2 1

aparcstats2table for functional overlay
by Jonathan DuBois 19 May '14

19 May '14

Hi all, I was wondering if there was a script like aparcstats2table that would accept a functional overlay file that has been sampled to the surface as a measure instead of the available options for structural measures? In tksurfer there is a manual way to average over an ROI using the sig.mgh and the y.fsgd file, marking the label and exporting the average graph. I would like to do something similar. Is there anything like this avaiable? Thanks, Jonathan

2 1

regarding contrast vector in qdec analysis
by Santosh Yadav 19 May '14

19 May '14

Dear FreeSurfer Experts, I am running an analysis in Qedc that include 2 groups (Control and Heart Failure). I want to see the cortical thickness difference between these 2 groups, with age and gender as a co-variate, not interested in any correlation analysis. In Qdec, Model factors have three options that include the fixed factor, continuous factor (Co-variate) and Nuisance. So groups (control and heart failure) belongs to fixed factor while age and gender belongs to both continuous factor and Nuisance. When I am running this analysis in Qdec by selecting the model that include only group in the model the contrast vector in the Qdec terminal is 1, -1, and its fine. But when I am selecting the model that includes age and gender as a nuisance, the contrast vector showing 1, -1, 0, 0, 0, 0. So my question is why we have two extra 0, 0 in contrast vector, it should be 1 -1 0 0. Another question: When I finished the analysis in Qdec and got the state data tables, that have 18 files, with volume, area, curv and thickness from both sides. I am interested in thickness and its have four files with left and right. lh.aparc.a2009s and lh.aparc, I am not sure what file should i used for the analysis. I believe for left side qdec is using lh.aparc, Is I am right? With Regards, Santosh K. Yadav -- With Best Regards, Post Doctoral Fellow, Department of Anesthesiology University of California, Los Angeles, CA 90034 Phone No. 808-5896940

2 1

Small volume correction in qdec
by Narly Golestani 19 May '14

19 May '14

Dear all, I would like to follow up on several posts that have already been made regarding how to restrict the search volume (i.e. do a small volume correction) to a particular region (e.g. to a freesurfer label) within qdec. As far as I can see this query was not answered on the list: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg13770.html How exactly can this be implemented in qdec please? Thanks in advance and best wishes, Narly.

2 1

Re: [Freesurfer] Registration and Surface flatten
by Caka 19 May '14

19 May '14

Hi Doug, Thanks for your suggestion on tksurfer, it works. I would like to map all the subjects into a flat map because I am curious about the 2-D thickness patterns between different groups. I think there will be some distinctions. But if I flatten fsaverage, how can I map everyone’s 3D surface onto the fsaverage’s 2D map? Is there a command? Best, Qiongmin On 05/13/2014 11:19 PM, Caka wrote: > Dear Doug and all, I have already done two things: (1) 'recon-all? to > the segmentation for 140 subjects; (2) surface registration to > fsaverage template for 1 subject using: mri_surf2surf --hemi lh > --srcsubject sub001 --srcsurfval thickness --src_type curv > --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.mgz Now I > have got the 'sub001-thickness-lh.mgz' file. I have two questions: (1) > Is this 'sub001-thickness-lh.mgz? a surface file or a volume file? How > can I read it? I used ?freeview sub001-thickness-lh.mgz? to read it, > but a dark scene was shown, nothing can be found. I also used > ?mris_convert -c $SUBJECTS_DIR/sub001/sub001-thickness-lh.mgz > $SUBJECTS_DIR/sub001/surf/lh.orig lh.thickness.asc?, an error occurred > like ?ERROR: number of vertices in > /disk250/data_analysis/sub001/sub001-thickness-lh.mgz does not match > surface (163842, 132230)?. Try tksurfer fsaverage lh inflated -aparc -overlay sub001-thickness-lh.mgz -fminmax .01 4 > (2) After the registration, I want to flatten the surface of curvature > or thickness into a full plane. The wiki says we should first specify > 5 vertices and cut the whole area without the midline region, then > ?kris_flatten? can be used. Indeed, this procedure requires quite a > lot manually operation. I am wondering if there are some automatically > commands that can do this flatten projects for 140 subject? Any reply > would be really appreciated! Qiongmin > _______________________________________________ Freesurfer mailing > list Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer I don't think so, though I think bruce was working on something. You could just flatten fsaverage and then map everyone to fsaverage (as you have already done). Why do you want to map everyone to a flat map? doug

2 1

Cortical Lesions
by Maia Pujara 19 May '14

19 May '14

Hi all, I'm having similar issues that were brought up in this post regarding subjects with cortical lesions: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-January/004359.h… Would these lesions would affect the way the brain is labeled and the measurements for cortical thickness? If so, how would this affect group comparisons of lesion patients to healthy controls? I've attached an example of what one of the lesion subjects looks like. Thanks, Maia

2 1

automatically expand surface label along the surface
by Martha Shiell 19 May '14

19 May '14

Hello Freesurfer users, Does anyone know a command to automatically expand (grow/dilute) a label file along the surface, e.g. add neighbouring vertices to the label? Thanks, Martha Shiell Ph.D. Candidate, Neuroscience McGill University

3 2

labels of surface vertices
by Tanya 19 May '14

19 May '14

Hi Freesurfers, I'm confused about surface vertices labels. One of the tutorial mentions that: " There is a one-to-one correspondence between surfaces which allows the user to cross-reference vertices from one surface to another (even across subjects) and to the volume." So there is a map between vertex index and label and it is universal for all subjects and all surfaces? Where can I find this map and is there a script to use it? Thank you! Tanya

2 1

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