Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

about correction of inhomogeneity
by Xiaoying Tang 26 Aug '11

26 Aug '11

Hi All, I am now trying to do inhomogeneity correction for T1 images. I find that there are two commands: nu_correct and mri_nu_correct.mni in Freesurfer. I am not sure about the difference between these two commands. To me, they seem to be the same.... I would be glad if someone could answer my question. Best, Xiaoying

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Freesursfer versions and Linux CentOS versions
by Alexopoulos, Dimitrios 26 Aug '11

26 Aug '11

I have a few questions related to Freesursfer versions and Linux CentOS versions. We have we processed some data (i.e. generated surfaces using -autorecon 1 -autorecon2, and then GM and WM surface-based volumes using mris_anatomical_stats and mris_wm_volume, respectively), using the build 'freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0' on our linux server that was running CentOS 4. We have recently upgraded the server OS to CentOS 5.6. We now would like to modify the segmentations/surfaces and was wondering whether we can use the same build (freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) on CentOS5.6 or do we need to install 'freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0' ? Are there any issues with processing data using 'freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0' on CentOs4 then modifying this data with 'freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 on CentOs5 Comments? Thanks. The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.

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DTI and Fresurfer
by Antonella Kis 26 Aug '11

26 Aug '11

Dear All, I would like to do DTI analysis on my subjects data. I finished the pre-processing using recon-all and also I used GLm for the group study. Can you please let me know how I can do DTI analysis using FSL in Freesurfer? What steps I need to follow? Many thanks, Antonella

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free surfer group analysis how to get cache-in thickness.fwhm10.fsaverage ?
by xian zhang 26 Aug '11

26 Aug '11

Dear Freesurfer: I am new in freesurfer. I have done recon-all for my subjects and the results are good. however in this tutorial the commands between recon-all the mirs-process are missing. Please advice what I have to after recon-all to have thickness.fshm10.fsaverage available? Appreciate your help. Xian http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#Assemblet… Previously Cached (qcached) Data When you have run recon-all with the -qcache option, recon-all will resample data onto the average subject (fsaverage) and smooth it at various FWHM (full-width/half-max), usually 0, 5, 10, 10, 20, and 25mm. This can speed later processing. The data for this tutorial have been cached, so run: mris_preproc --fsgd gender_age.fsgd \ --cache-in thickness.fwhm10.fsaverage \ --target fsaverage --hemi lh \ --out lh.gender_age.thickness.10.mgh

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help for further distribution (fwd)
by Bruce Fischl 26 Aug '11

26 Aug '11

FYI ---------- Forwarded message ---------- Date: Fri, 26 Aug 2011 15:48:33 +0200 From: Jorge Jovicich <jorge.jovicich(a)unitn.it> To: Jorge Jovicich <jorge.jovicich(a)unitn.it> Subject: help for further distribution Dear All, I'd appreciate your help to further distribute the attached advert for two MRI methods postdoctoral positions, or to bring it to the attention of potentially interested and qualified candidates. Below is the list of places where I have already posted the advert. Thanks!! jorge -ISMRM site, as well as the UK and German chapters -EEGlab list -MGH-all email list -- Jorge Jovicich, Ph.D. MR Lab Co-Director Center for Mind Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it http: //www.cimec.unitn.it/ http: //polorovereto.unitn.it/~jovicich

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Reference for tracula and enable mpi in tracula?
by Knut J Bjuland 26 Aug '11

26 Aug '11

Hi I am having trouble finding all reference to Tracula in the wiki. Could you please add them. I read in (Postelnicu, Zollei et al. 2009) that combined surface and volumetric algorithm could use MPI . Is the same true for tracula? Knut J Postelnicu, G., L. Zollei, et al. (2009). "Combined Volumetric and Surface Registration." Medical Imaging, IEEE Transactions on 28(4): 508-522. In this paper, we propose a novel method for the registration of volumetric images of the brain that optimizes the alignment of both cortical and subcortical structures. In order to achieve this, relevant geometrical information is extracted from a surface-based morph and diffused into the volume using the Navier operator of elasticity, resulting in a volumetric warp that aligns cortical folding patterns. This warp field is then refined with an intensity driven optical flow procedure that registers noncortical regions, while preserving the cortical alignment. The result is a combined surface and volume morph (CVS) that accurately registers both cortical and subcortical regions, establishing a single coordinate system suitable for the entire brain.

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epidewarp
by Marco Loggia, PhD 25 Aug '11

25 Aug '11

Dear Surfers, In the past couple of days epidewarp.fsl has been failing, reporting "vsm-smooth: Command not found" (see below). Epidewarp was run using the same parameters, and within the same script that I have been using with no problems for many months... Has there been a software update that I have missed? Thanks, Marco >> >> Marco >> >> >> bash-3.2$ /usr/local/freesurfer/stable/bin/epidewarp.fsl --mag >> $dirpath/$subjdir/fieldmap/fieldmap1.nii --dph >> $dirpath/$subjdir/fieldmap/fieldmap2.nii --epi bold.nii --tediff 2.54 >> --esp .48 --sigma 2 --vsm shiftmap --epidw bold_dw.nii >> FSLVersion 4.1.5 >> FSLVerMaj 4 >> Logfile is shiftmap.log >> FSLOUTPUTTYPE NIFTI >> Extension is nii >> nframes = 180, nmidframe = 90 >> fslroi /autofs/cluster/randy/2/cuff_FM/CuffFM_FM039/6min_rest/bold.nii >> ./tmp-epidewarp.26204.fsl/exf.nii 90 1 >> fslroi /autofs/cluster/randy/2/cuff_FM/CuffFM_FM039/fieldmap/fieldmap1.nii >> ./tmp-epidewarp.26204.fsl/mag 0 1 >> bet ./tmp-epidewarp.26204.fsl/mag.nii ./tmp-epidewarp.26204.fsl/brain.nii >> fslmaths ./tmp-epidewarp.26204.fsl/brain.nii -bin >> ./tmp-epidewarp.26204.fsl/brain.nii >> fslmaths ./tmp-epidewarp.26204.fsl/brain.nii -dilM >> ./tmp-epidewarp.26204.fsl/head.nii >> fslmaths ./tmp-epidewarp.26204.fsl/head.nii -dilM >> ./tmp-epidewarp.26204.fsl/head.nii >> fslmaths ./tmp-epidewarp.26204.fsl/head.nii -dilM >> ./tmp-epidewarp.26204.fsl/head.nii >> fslmaths >> /autofs/cluster/randy/2/cuff_FM/CuffFM_FM039/fieldmap/fieldmap2.nii -sub >> 2047.5 -mul 0.00153435539 ./tmp-epidewarp.26204.fsl/dph -odt float >> prelude -p ./tmp-epidewarp.26204.fsl/dph -a >> ./tmp-epidewarp.26204.fsl/mag.nii -o ./tmp-epidewarp.26204.fsl/dph -f -v >> -m ./tmp-epidewarp.26204.fsl/head.nii >> Loading volumes >> Phase loaded >> Magnitude loaded >> Mask loaded >> Number of phase splits = 8 >> Calculating starting matrices (5173 by 5173) >> Finished connection_matrices >> 13289 constraints left >> 7990 constraints left >> 6210 constraints left >> 4125 constraints left >> 2042 constraints left >> 174 constraints left >> Did while loop 5172 times >> fslmaths ./tmp-epidewarp.26204.fsl/dph -mul 0 >> ./tmp-epidewarp.26204.fsl/ph.zeros.nii >> fslmerge -t ./tmp-epidewarp.26204.fsl/ph.nii >> ./tmp-epidewarp.26204.fsl/ph.zeros.nii ./tmp-epidewarp.26204.fsl/dph >> Masking with ./tmp-epidewarp.26204.fsl/brain.nii >> fugue -i ./tmp-epidewarp.26204.fsl/mag.nii -u >> ./tmp-epidewarp.26204.fsl/magdw.nii -p ./tmp-epidewarp.26204.fsl/ph.nii >> --dwell=.48 --asym=2.54 --mask=./tmp-epidewarp.26204.fsl/brain.nii >> --saveshift=./tmp-epidewarp.26204.fsl/vsmmag.nii --smooth2=2 >> VSM Mean is -0.110589 >> fslmaths ./tmp-epidewarp.26204.fsl/vsmmag.nii -sub -0.110589 >> ./tmp-epidewarp.26204.fsl/vsmmag.nii >> fslmaths ./tmp-epidewarp.26204.fsl/vsmmag.nii -mul >> ./tmp-epidewarp.26204.fsl/brain.nii ./tmp-epidewarp.26204.fsl/vsmmag.nii >> fugue -i ./tmp-epidewarp.26204.fsl/mag.nii -w >> ./tmp-epidewarp.26204.fsl/magfw.nii >> --loadshift=./tmp-epidewarp.26204.fsl/vsmmag.nii >> --mask=./tmp-epidewarp.26204.fsl/brain.nii >> flirt.fsl -in ./tmp-epidewarp.26204.fsl/magfw.nii -ref >> ./tmp-epidewarp.26204.fsl/exf.nii -out >> ./tmp-epidewarp.26204.fsl/magfw-in-exf.nii -omat >> ./tmp-epidewarp.26204.fsl/magfw-in-exf.fsl.mat -bins 256 -cost corratio >> -searchrx -10 10 -searchry -10 10 -searchrz -10 10 -dof 6 -interp >> trilinear >> flirt.fsl -in ./tmp-epidewarp.26204.fsl/vsmmag.nii -ref >> ./tmp-epidewarp.26204.fsl/exf.nii -out shiftmap -init >> ./tmp-epidewarp.26204.fsl/magfw-in-exf.fsl.mat -applyxfm >> vsm-smooth --fwhm 10 --i shiftmap --o shiftmap >> vsm-smooth: Command not found. >> >> >> ______________________ >> >> Marco L. Loggia, PhD >> Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital >> Harvard Medical School >> >> Psychiatric Neuroimaging Research Program >> CNY Building 120, suite 100 >> Charlestown, Massachusetts 02129 >> Phone: (617) 643-7267 >> Fax: (617) 643-7340 >> marco(a)nmr.mgh.harvard.edu >> >> > > ______________________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 e-mail: marco(a)nmr.mgh.harvard.edu

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fsaverage
by Antonella Kis 25 Aug '11

25 Aug '11

Dear All: I wonder if for a new FSGD file (e.g. age.fsgd) the resample of each subjects data to fsaverage (into a common space), as well as concatenating all the subjects' into a single file, will change my old fsaverage. Thank you. Antonella

2 1

tracula executables for snow leopard now online
by Anastasia Yendiki 25 Aug '11

25 Aug '11

Hi all - By popular demand we've posted the dmri_* executables compiled on snow leopard here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopar… This is not the entire FS distribution, just the commands that are called by trac-all. If you are a mac user with snow leopard and have been running into memory issues with the leopard version, you can download this, copy the new files into your $FREESURFER_HOME/bin, and try rerunning the part of the analysis that had errored out. Let us know if there are any problems, a.y

4 9

Intensity normalization parameters to fix dura included in pial surface
by Martina Ly 24 Aug '11

24 Aug '11

Hello freesurfers, Dura is being included in the pial surface of the superior section of the brain in about 80% of the subjects (about 200) that I'm processing in fs version 5.1 on Mac OS X 10.6.8. The T1s were acquired on a GE 3T scanner. It takes too much time to manually edit the dura and I would not like to do so much manual intervention on the other 2 time points. Adjusting the watershed parameters and the -gcut flag did not help. Would I be able to adjust nu_correct or mri_normalize (the intensity normalization steps prior to skull stripping)? I'm also thinking of using another intensity correction software (i.e. unicorr) to put back into the freesurfer pipeline but I would prefer a flag or parameter I can adjust within fs. Any suggestions would be appreciated! Best, Martina

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