Freesurfer August 2013

freesurfer@nmr.mgh.harvard.edu

145 participants
268 discussions

output orientations wrong
by Amy Bilderbeck 06 Aug '13

06 Aug '13

Dear FreeSurfer community, I've been unable to get my recon-all commands to work, and this appears to be because my output orientations are wrong. As input, I am using .nii.gz structural images (from 3 different scanners: a Siemens Sonata (1.5T), Siemens Trio (3T) GE Signa (1.5T)) Using FSLview, I've looked at the input structural images and I believe my input orientations are all fine and consistent across all the files. My output talairach.xfm, and orig.mgz, appear with the axial and coronal images "swapped" (one is labelled as the other) and my saggital images appear oddly too, with the nose down. I believe you have had reports of this problem before but I have not found a solution in my case. Thanks and my warm regards, Amy Dr Amy Bilderbeck D.Phil Experimental Psychology Department of Psychiatry, University of Oxford http://www.psych.ox.ac.uk/team/researchers/amy-bilderbeck

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trac-all inquiry
by Soto, David 06 Aug '13

06 Aug '13

thanks Anastasia, I have some problems however- could you help please? as said, I am not using the DICOMS, my diffusion data has been converted to nii and then to mnc my config file mostly accepts the defaults, and is simple as follows. There is a folder 'diffree' which contains the dmri config file, the becs and bvals and the mnc difffusion file $$$$$$$$ setenv SUBJECTS_DIR /home/dsoto/Documents/fmri/rsdtianawmgui set dtroot = /home/dsoto/Documents/fmri/rsdtianawmgui set subjlist = (02ST) set runlist = (1) set dcmroot = /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree set dcmlist = (diffdata.mnc) set bvecfile = /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/bvecs_t set bvalfile = /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/bvals_t set mnitemp = /usr/share/fsl/5.0/data/standard/MNI152_T1_1mm_brain $$$$$$$$ When i run trac-all -c tracula02ST.txt -prep I get some errors such as 1. fslmaths /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz -Tmean /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz Cannot open volume /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb for reading! bet /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain.nii.gz -m -f 0.3 Error: input image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb not valid mv -f /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain_mask.nii.gz /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff mv: cannot stat `/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain_mask.nii.gz': No such file or directory flirt -in /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain.nii.gz -ref /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/brain_anat.nii.gz -out /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain_anat.flt.nii.gz -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2anat.flt.mat -cost mutualinfo Image Exception : #22 :: ERROR: Could not open image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain terminate called after throwing an instance of 'RBD_COMMON::BaseException' Abort (core dumped) convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.flt.mat -inverse /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2anat.flt.mat Could not open matrix file /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2anat.flt.mat Cannot read input-matrix convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2diff.flt.mat -concat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.flt.mat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2anat.mat Could not open matrix file /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anat2diff.flt.mat Cannot read concat-matrix convert_xfm -omat /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/diff2anatorig.flt.mat -inverse /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2diff.flt.mat Could not open matrix file /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/xfms/anatorig2diff.flt.mat Cannot read input-matrix Intriguinly, the script completes with the message >>>trac-preproc finished without error at Tue Aug 6 03:02:08 BST 2013 HOWEVER, when I attempt the next step trac-all -c tracula02ST.txt -bedp it aborts saying "/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/nodif_brain_mask not found" I am running FSL 5.0.4 under Ubuntu 12.04 cheers ds http://www1.imperial.ac.uk/medicine/people/d.soto/ ________________________________________ From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] Sent: 02 August 2013 19:15 To: Soto, David Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] trac-all inquiry Hi David - You need to run each of the steps (-prep, -bedp, -path) separately. You can't run them all at the same time. See tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula Hope this helps, a.y On Fri, 2 Aug 2013, David Soto wrote: > Hi, > > I have successfully run recon-all in my dataset > and now am attempting to use trac-all on my diffusion data > obtained on a Siemens scanner. > > Diffusion dicoms were transformed to .nii using MRIConverter > and then to .mnc using > > nii2mnc output.nii output_t.mnc. > > I am trying to run trac-all on a single subject and for this I > have created the configuration file attached (tracula02ST) > > As you can see the SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui > and within each subject the T1 serving as input for recon-all are in > mri/orig > > while the diffusion images are in a folder call diffdata (named output_t.mnc) > which also contains the bvecs and bvals files, which were transposed and > organised > according to the tutorial (named as bvecs_t.txt and bvals_t.txt) > > When I run: > trac-all -c tracula02ST.txt > > I get: > ERROR: no analysis step (-{prep,bedp,path}) has been selected > > THEN I run: > trac-all -prep -bedp -path -c tracula02ST.txt which runs for 5 seconds or so > and then gives the long output text below with an error message. > > Segmentation fault (core dumped) > foreach: No match. > > The trac-all.log is attached also. > > Could you please help? > > Cheers > > David > > > 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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longitudinal stream percentage change
by Bastian Cheng 06 Aug '13

06 Aug '13

Dear freesurfer-experts, I have successfully done a longitudinal analysis on cortical thickness changes over 2 timepoints (0 and 1 year). My question is: If I look at the -individual- overlays of perc. change (i.e. pc1fit), only positive values are shown. whereas at the -fsaverage- view, positve AND negative values are shown (i.e. thinning and thickening) I understood that long_mris_slopes calculates the "percent thinning per year". But is there a way to show both sides of the histogramm (i.e. from -2 to +2) also on the -individual- overlay? This might be a naive question, however, any help is greatly appreciated! Bastian.

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wmparc.stats
by Yang, Daniel 06 Aug '13

06 Aug '13

Dear FreeSurfer Experts, I'm looking at stats/wmparc.stats, and there are some inconsistencies between subjects. I am wondering what might be the cause. For one subject (say subject 1), part of the information appears to be: # NRows 66 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 3001 1869 1869.0 wm-lh-bankssts 101.6999 9.1445 69.0000 127.0000 58.0000 2 3003 1776 1776.0 wm-lh-caudalmiddlefrontal 98.1676 8.5074 75.0000 125.0000 50.0000 3 3005 710 710.0 wm-lh-cuneus 103.7088 10.1493 78.0000 134.0000 56.0000 4 3006 106 106.0 wm-lh-entorhinal 84.5902 9.0358 55.0000 96.0000 41.0000 For the other subject (subject 2), it appears to be: # NRows 70 # NTableCols 10 # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 3001 1012 1012.0 wm-lh-bankssts 93.6101 10.0971 71.0000 130.0000 59.0000 2 3002 1732 1732.0 wm-lh-caudalanteriorcingulate 104.3373 10.6871 58.0000 126.0000 68.0000 3 3003 4743 4743.0 wm-lh-caudalmiddlefrontal 95.2809 11.5139 66.0000 117.0000 51.0000 4 3005 1488 1488.0 wm-lh-cuneus 91.9310 10.1995 64.0000 126.0000 62.0000 5 3006 398 398.0 wm-lh-entorhinal 75.3343 9.0664 55.0000 101.0000 46.0000 Thus, in subject 1, there is no estimate for 3002, wm-lh-caudalanteriorcingulate, and the NRows is different. Could you please help? Both are analyzed by FreeSurfer 5.1.0. Thanks, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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Re: [Freesurfer] qdec question: discrepancy in sig. clusters (Douglas Greve)
by Maria Kharitonova 05 Aug '13

05 Aug '13

Hi Doug, Thanks. Per your advice, I'm trying to visualize output in tksurfer but it would help me to do what the different overlays refer to. Could you clarify what the differences are between: mc-z.abs.tho20.sig.cluster.mgh vs mc-z.abs.tho20.sig.ocn.mgh vs mc-z.abs.tho20.sig.vertex.mgh I think .ocn.mgh draws the regions that I see output in the terminal when I run qdec, but am not 100% sure. I searched the archives/tutorials and couldn't find the explanation of these different files. Thanks! Maria > > > Message: 14 > Date: Fri, 26 Jul 2013 13:47:41 -0400 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] qdec question: discrepancy in sig. clusters > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <51F2B63D.6020706(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Maria, can you tar up the qdec output folder and send it to our file > drop? I'm traveling now, so it might be the 1st week of august before I > can take a look. You can also go into the qdec output folder and run > tksurfer to show you the results. > > doug > > > On 7/26/13 1:37 PM, Maria Kharitonova wrote: >> Hello, >> >> I have another newbie question. I'm running qdec, trying to compare cortical thickness in children with and without ADHD. However, I'm seeing a discrepancy between the clusters that are significant according to the terminal (after applying the Monte-Carlo simulation with default parameters; output below) and the ones that pop up when I hit "Find clusters and goto Max". For example, I'm seeing 4 regions in the terminal: medialorbitalfrontal, inferiorparietal, caudalmiddlefrontal, and precentral. However, when I hit "Find clusters and goto Max", I only see the Frontalpole. >> >> Using mri_surfcluster to extrat thickness measures only extracts it for the frontalpole, and not for the 4 ROIs listed in the terminal. I would like to be able to extract stats on those 4 that are listed in the terminal, if possible. >> >> Can you please help me reconcile the 2 types of output? Thanks! >> >> *** terminal output: >> >> # Input /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final/qdec/dx_age_icv_nuis_lh/rh-Diff-CONTROL-ADHD-Cor-thickness-age/sig.mgh >> # Frame Number 0 >> # srcsubj fsaverage >> # hemi rh >> # surface white >> # annot aparc >> # SUBJECTS_DIR /net/rc-fs-nfs/ifs/data/Shares/DMC-Sheridan2/projects/FOCUS/FreeSurfer/FS_5.3_final >> # Minimum Threshold 2 >> # Maximum Threshold infinity >> # Threshold Sign abs >> # AdjustThreshWhenOneTail 1 >> # CW PValue Threshold: 0.05 >> # Area Threshold 0 mm^2 >> # CSD thresh 2.000000 >> # CSD nreps 10000 >> # CSD simtype null-z >> # CSD contrast NA >> # CSD confint 90.000000 >> # Overall max 4.75828 at vertex 134555 >> # Overall min -2.56762 at vertex 93241 >> # NClusters 4 >> # Total Cortical Surface Area 65020.8 (mm^2) >> # FixMNI = 1 >> # >> # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot >> 1 4.758 134555 1015.59 8.7 58.2 -5.8 0.00010 0.00000 0.00020 1292 medialorbitofrontal >> 2 3.968 135840 466.91 40.0 -66.8 25.9 0.01790 0.01620 0.01960 750 inferiorparietal >> 3 3.954 115431 497.60 29.3 21.4 39.9 0.01150 0.01010 0.01290 900 caudalmiddlefrontal >> 4 3.242 133890 439.44 49.4 -5.1 22.0 0.02520 0.02320 0.02720 932 precentral >> >> Simulation complete. >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > > ------------------------------ > > Message: 15 > Date: Fri, 26 Jul 2013 13:56:13 -0400 > From: Satrajit Ghosh <satra(a)mit.edu> > Subject: Re: [Freesurfer] Freesurfer surface circle of pre-defined > size > To: sarahp(a)nmr.mgh.harvard.edu > Cc: Freesurfer Mailing List <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CA+A4wO=cfM+7MnCVi-GvadUT5s4NFNGASU_+DS4nUStUoQ4frQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > hi sarah, > > you'll get a much quicker response posting PySurfer related questions to: > > nipy-devel(a)neuroimaging.scipy.org > > cheers, > > satra > > On Fri, Jul 26, 2013 at 12:57 PM, <sarahp(a)nmr.mgh.harvard.edu> wrote: > >> Hello Freesurfer Experts, >> >> We would like to use PySurfer's function plot_label_foci.py to >> automatically create circular labels of a pre-defined radius (eg. 14mm) on >> the fsaverage surface of freesurfer. >> >> What are the specified units of "n_steps" in the command line argument >> "utils.coord_to_label(subject_id, coord, label='coord', hemi='lh', >> n_steps=50"? >> >> Thank you, >> Sarah >> _______________________________________________ >> 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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Re: [Freesurfer] function that do the same step like qcache?
by Bruce Fischl 05 Aug '13

05 Aug '13

can you cc the list so that others can answer or see the answer? You need to specify the source and target subjects with --srcsubject and --trgsubject cheers Bruce On Mon, 29 Jul 2013, fatma zribi wrote: > mri_surf2surf --hemi lh --s s000_open_brain_sanlm_+TIR_normlalized --sval curv --src_type curv --fwhm 10 --trg_type curv --tval > curv.10 > > > 2013/7/29 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > what is your full command line? You can smooth and map with it (use -fwhm-src or fwhm-trg to smooth in either the > source or target space) > On Mon, 29 Jul 2013, fatma zribi wrote: > > Dear Bruce, > I have tried mri-surf2surf, it makes the result (smoothed curv for example) with the same dimension of > the subject. But I would > like a smoothed file with the dimesion of fsaverage. > > Thank you for your help. > > With best regards, > > Fatma > > > 2013/7/29 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Fatma > > you can use mri_surf2surf within subject I believe, but Doug can confirm (although he's traveling > so it may be a > bit). You can also do it interactively in tksurfer. > > cheers > Bruce > > > On Mon, 29 Jul 2013, fatma zribi wrote: > > Dear Bruce, > > Would you mind tell me if there is a function of freesurfer that I can use to do the same > step of > qcache to smooth and > interpolate in the fsaverage one subject > with mri_surf2surf I can smooth only or align one subject with an average. > thank you for you help. > with best regards, > Fatma > > > > > 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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Re: [Freesurfer] dPSD and ev duration
by Ella Hinton 05 Aug '13

05 Aug '13

Hi Doug Thanks for your email. I gave your suggestion a try - reduced the dPSD to 0.5 (as well as adjusted the PSDMAX, and no. of volumes to reflect the new TR - see full command line below). Unfortunately the efficiency is way down (0.03) and the VRF you previously suggested should be between 20-40 is 4.5! I now wonder if Optseq is trying to tell me this is now a bad design!! Would be very grateful for any ideas for improvement? optseq2 --ntp 240 --tr 2.5 --psdwin 0 20 0.5 --ev hf 3 50 --ev lf 3 50 --ev nf 3 50 --nkeep 3 --o test14 --nsearch 10000 --focb 100 many thanks Ella Date: Sun, 28 Jul 2013 23:33:07 -0400 From: greve(a)nmr.mgh.harvard.edu To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] dPSD and ev duration Hi Ella, it has an internal clock that events have to be syncrhonized to. Try setting the dPSD to 0.5 doug On 7/28/13 4:05 PM, Ella Hinton wrote: Hi Quick question - why must the duration of the EVs be an integer multiple of the dPSD, which is also tied to the TR? I have event duration of 3 seconds, but would like to reduce my TR from 3 down to 2.5, but I can't seem to input the correct numbers for optseq to help me. thanks in advance Ella _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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. _______________________________________________ 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.

2 1

Binary mask
by pfotiad＠nmr.mgh.harvard.edu 05 Aug '13

05 Aug '13

Hi FS Community, Is there a way to create a binary mask of everything that is inside the cortical ribbon of a subject (including the cortical ribbon)? I ran: mri_binarize --i aseg.mgz --match 3 --match 42 --o test.mgz which gave me a binary mask of the cerebral cortex, but I was wondering whether there is a way to create a binary mask of the cerebral cortex as well as everything inside of it. Thank you for your time. Best, Panos

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Group thickness means
by Worker, Amanda 05 Aug '13

05 Aug '13

Hello, I just have a quick question about how to find the group mean of a significant cluster found in thickness analysis in QDEC. I have run comparison of a number of clinical groups with healthy controls and found several clusters of significant thinning. In the stats table generated by QDEC I can see individual subjects mean thickness but I'm not sure how to get the group mean? If you could help with this it would be much appreciated. Thank you in advance. Amanda

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tksurfer and mountain lion problem / question
by Salil Soman 05 Aug '13

05 Aug '13

Hi, I can run freeview using my current install on Mountain Lion, however when I run tkmedit or tksurfer I get the following error: GLUT: Fatal Error in tksurfer.bin: could not open display: :0.0 my /etc/profile has the setting export DISPLAY=:0.0 for a different program. Is there settings I should add / change to allow tkmedit or tksurfer to run? Thanks! Sal

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Freesurfer August 2013