Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

Interior white matter surfaces
by Jason Reed 02 Jul '13

02 Jul '13

Dear FreeSurfer Experts, I am attempting to construct surfaces that are 1, 2, 3, and 4 mm interior from the GM/WM boundary (?h.white). So going gradually deeper into white matter from the GM/WM boundary. I have successfully used mris_fill to fill the ?h.white surface and mri_morphology to erode the resulting volume, but I'm not sure on the correct procedure to create the new surfaces. Any advice or suggestions on tools with options to use will be greatly appreciated! My eventual goal is to project coregistered DTI data onto these more interior white matter surfaces. Thanks! -Jason -- Jason Reed VA San Diego Healthcare System (116A-13) 3350 La Jolla Village Drive San Diego, CA 92161 Phone: (858) 552-8585 ext. 2946 Fax: (858) 642-3836 jreed(a)vapop.ucsd.edu

3 3

Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
by Martin Reuter 02 Jul '13

02 Jul '13

Not totally sure with 5.0, but I don't think it requires same voxel space for all time points (since 5.1), so it should work to run the analysis with 5.3 on that data. Cheers Martin Peter Bohn <bohn-peter(a)gmx.de> wrote: >Thanks a lot! Do I have to repeat >creating the base and the longitudinal runs once I use the new version >or are >they compatible concerning this aspect? > > > >Thank you very much! > > > >Best regards > > > >Peter > > > >From: mreuter(a)nmr.mgh.harvard.edu >Date: Thu, 20 Jun 2013 02:46:05 -0700 >To: bohn-peter(a)gmx.de; freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not >found > >Yes, those scripts are available since 5.2. You need to update to a >newer version. > >Best Martin > >Peter Bohn <bohn-peter(a)gmx.de> wrote: > > > >Hi Martin, > >thanks a lot fort he quick reply! When I type freesurfer into the >window it shows me v5.0.0 as the version. Sorry for my prior mistake >concerning the version’s name. All other commands I use run perfectly >fine. > >Thanks once again! > >Best regards > >Peter > >From: mreuter(a)nmr.mgh.harvard.edu >Date: Thu, 20 Jun 2013 05:21:39 -0400 >To: bohn-peter(a)gmx.de >CC: freesurfer(a)nmr.mgh.harvard.edu >Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not >found > >Hi Peter, >can you run any free surfer command at all? Looks to me that you did >not source free surfer. What happens if you typefreesurferinto the >terminal window? It should print the version. >Best, Martin >On Jun 20, 2013, at 5:17 AM, Peter Bohn <bohn-peter(a)gmx.de> wrote: > > >Dear Freesurfer experts, > >I was trying to run some longitudinal analysis but whenever I want to >use the commands “long_mris_slopes” or “long_qdec_table” I just get >“command not found” as an answer. When I try to look up a package that >might include the command, by typing “cnf long_mris_slopes”, >I also just get “command not found” as an answer. We are currently >using version v 1.313.2.6. > >Does anyone of you know if the two commands that I would like to run, >are included in this version? Where would I have to look for the >additional package if it exists? Or am I by any chance just typing the >commands incorrect? > >Many thanks for the help! > >Sincerely yours > >Peter_______________________________________________Freesurfer mailing >listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >---------------------------------Dr. Martin ReuterAssistant in >Neuroscience - Massachusetts General Hospital >Instructor in Neurology - Harvard Medical School >MGH / HMS / MIT > >A.A.Martinos Center for Biomedical Imaging >149 Thirteenth Street, Suite 2301 >Charlestown, MA 02129 > >Phone: +1-617-724-5652 >Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.eduWeb : >http://reuter.mit.edu > > > > >_______________________________________________ >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. > > >-- > >Sent from my phone, please excuse brevity. >_______________________________________________ >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. -- Sent from my phone, please excuse brevity.

2 9

CUDA Error when runnign freesurfer
by Salil Soman 01 Jul '13

01 Jul '13

Hi, I am running freesurfer 5.3 on an ubuntu 13.04 with a nvidia card and the the CUDA drivers installed. I am getting the following error when I try using the use-cuda command: Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Acquiring CUDA device Using default device ERROR: Unable to acquire a CUDA device! Linux Baldrick 3.5.0-27-generic #46-Ubuntu SMP Mon Mar 25 19:58:17 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux I am running the following freesurfer command: recon-all -i 242.nii.gz -s 242_FS -nuintensitycor-3T -nocanorm -openmp 8 -use-cuda -hippo-subfields -all Any suggestions on how I can fix this problem? Best wishes, Sal

2 1

Re: [Freesurfer] Fwd: DTI questions
by Anastasia Yendiki 01 Jul '13

01 Jul '13

Hi Rotem - No problem. Were these scans by any chance acquired with a coronal slice prescription? In the axial views that you sent, the artifact that you're pointing to looks like misalignment between consecutive coronal slices, which could be due to head motion. a.y On Tue, 25 Jun 2013, Rotem Saar wrote: > Dear Anastasia, > > I tried several times to upload these images in a non-compressed way, but > they were too big and my posts were rejected, with no opportunity for any > other upload way. > Is there any other way for me to upload it so that everyone can see it ? > > Attached are the images in a non-compressed fashion. I will be very happy if > u will have a look, and post your answer to me and the list to save some > time, until I will be able to consider another way to upload them. > > I know that we should write to all the list, but at the moment if the images > are not visible this won't help - so I will really appreciate if u will have > a look but also tell me what is the best way to upload them so that all list > members will be able to see them. > > Thank u very much for your help. > > Rotem > > 2013/6/25 Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > > Sorry, can't open the image. > > On Sun, 23 Jun 2013, Rotem Saar wrote: > > Hi there, > > Long time:). Well I wrote to the list several times > regarding high FA values > I got when performing DTI analysis. > Today we know that the problem was an additional > direction (we had 17 > directions instead of 16 - we used a Philips > scanner,1.5T). So we deleted > the additional slices and the high values indeed > disappeared, but then > another problem came up (tried several subjects so > the problem is not > specific to a subject) - > > I noticed an artifact that I can't explain - please > see the attached > pictures. > > This artifact existed even before I deleted the > additional slices, also - I > see the artifact also when loading the masked > volume...It is cyclic - run > over all slices... > > any ideas ? > > I'm using version 5.2 and I know the command lines > are correct (send it to u > in the past). > > Thanks for your help > > Rotem > > > > > 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 2

Pial surface consistently misplaced
by Jonathan Holt 01 Jul '13

01 Jul '13

Hi all, I'm having a bit of trouble with one particular subject for which we brains for 4-5 different time points. The pial surface is consistently misplaced in the same area, see attached main/aux volume images. I'm hesitant to manually replace the white matter myself as I fear it wouldn't be as accurate. Suggestions on other methods to fix this? The problem is always in the LH temporal right around the lateral inferior ventricle and the fusiform and other subcortical structures.

3 16

Re: [Freesurfer] Xhemi question
by Douglas N Greve 01 Jul '13

01 Jul '13

Hi Daria, the only way is to map the individual curvature to the group space (fsaverage_sym) and see if the curvatures seem to align. doug ps. Please post questions to the FreeSurfer list. Thanks! On 06/07/2013 11:13 AM, Daria Boratyn wrote: > Hi Doug, > > We are experimenting with adding xhemi to our processing stream. Is there > is a way to QC the results at an individual subject level? > > Best, > Daria > > > Daria A. Boratyn, > Clinical Research Coordinator > MS Imaging Lab > Massachusetts General Hospital > 149 13th Street | Boston, MA 02129 > 617-726-7531 > > -- 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/

3 4

T1-weighted anatomical
by ye tian 01 Jul '13

01 Jul '13

Dear freesurfers, My data seems not to be T1-weighted by look ( http://www.youtube.com/watch?v=W8ZFGvGvHVc) Would you please help me further identify by reading the following experimental description? Images were acquired with blood-oxygen level dependent (BOLD) imaging on a 3 T Siemens Trio Scanner (Bandettini, Wong, Hinks, Tikofsky, and Hyde, 1992). A five-minute magnetization prepared, rapid-acquisition gradient echo image (*MPRAGE*) was acquired for anatomic overlays of *functional*data and spatial normalization (T1 MN1 Template). BOLD imaging used a 33-slice whole-brain, single-shot gradient echo (GE) echo-planar (EPI) sequence (TR/TE = 2000/25 ms, FOV = 240 mm, matrix = 64 x 64, slice thickness/gap = 4/0 mm). This sequence delivers a nominal voxel resolution of 3 x 3 x 3 mm. Also, if I do *mri_info *in freesurfer for the five sequences of the data, Series Number 1: TR: 8.6msec, TE: 4.00msec, T1: -1.00msec, Flip Angle: 20.00degrees Series Number 2: TR: 2000.00msec, TE: 25.0msec, T1: -1.00msec, Flip Angle: 90.00degrees Series Number 3: TR: 2300.00msec, TE: 2.96msec; T1: 900.00msec, Flip Angle: 90.00degrees Series Number 4&5: TR: 2000.00msec, TE: 25.00msec; T1: -1.00msec, Flipe Angle: 90.00degrees Is my data NOT T1-weighted for sure? Thank you very much! Sincerely, Ye * *

3 6

Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates
by Emily Boeke 01 Jul '13

01 Jul '13

Sure, here it is: # Cluster Growing Summary (mri_volcluster) # $Id: mri_volcluster.c,v 1.38.2.3 2009/01/16 02:26:36 greve Exp $ # cwd /autofs/cluster/maury/users/gcoombs/College_Risk/ObjectLooming/allSBQ_061213/st4-obj_ns-4runs/face_v_car # cmdline mri_volcluster --in tal.sm.wls.pct.rfx//group/sig.mgh --csd tal.sm.wls.pct.rfx//csd/HvL.SBQ.2.pos.j001-group.csd --mask tal.sm.wls.pct.rfx//mask.mgh --cwsig tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.mgh --vwsig tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.voxel.mgh --sum tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.cluster.summary --ocn tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.sig.ocn.mgh --csdpdf tal.sm.wls.pct.rfx//group/HvL.SBQ.2.pos.pdf.dat # sysname Linux # hostname compute-0-114 # machine x86_64 # user eboeke01 # Input Volume: tal.sm.wls.pct.rfx//group/sig.mgh # Frame Number: 0 # Minimum Threshold: 2 # Maximum Threshold: inifinity # Threshold Sign: pos # AdjustThreshWhenOneTail 1 # Size Threshold: 0 mm^3 # Size Threshold: 0 voxels # Voxel Size: 8 mm^3 # Registration: None : Tal Coords invalid # Mask Vol: tal.sm.wls.pct.rfx//mask.mgh # Mask Thresh: 0.500000 # Mask Sign: abs # Mask Invert: 0 # AllowDiag: 0 # NClusters 192 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype mc-z # CSD contrast group # CSD confint 90.000000 # # Reporting Coordinates in Voxel Indices # Cluster Size(n) Size(mm^3) VoxX VoxY VoxZ Max# CWP CWPLow CWPHi 1 597 4776.0 30.00 50.00 65.00 5.94673 0.02490 0.02290 0.02690 2 730 5840.0 27.00 28.00 86.00 5.56628 0.00720 0.00610 0.00830 3 1124 8992.0 5.00 18.00 38.00 5.01850 0.00010 0.00000 0.00020 4 259 2072.0 59.00 20.00 78.00 5.01465 0.68360 0.67760 0.68960 5 279 2232.0 18.00 22.00 73.00 3.94952 0.58840 0.58210 0.59470 6 194 1552.0 35.00 66.00 76.00 3.94297 0.93630 0.93320 0.93940 7 664 5312.0 32.00 15.00 60.00 3.68551 0.01400 0.01250 0.01550 8 293 2344.0 28.00 5.00 58.00 3.66686 0.52560 0.51920 0.53200 9 49 392.0 12.00 52.00 58.00 3.63351 1.00000 -0.00010 1.00000 10 150 1200.0 5.00 4.00 28.00 3.62637 0.99560 0.99470 0.99640 11 298 2384.0 12.00 47.00 86.00 3.58250 0.50260 0.49620 0.50900 12 343 2744.0 13.00 39.00 60.00 3.57829 0.33900 0.33290 0.34510 13 467 3736.0 21.00 42.00 49.00 3.53307 0.09590 0.09210 0.09970 14 276 2208.0 49.00 36.00 56.00 3.51549 0.60280 0.59650 0.60910 15 134 1072.0 70.00 17.00 34.00 3.38623 0.99890 0.99850 0.99930 16 75 600.0 5.00 25.00 55.00 3.09334 1.00000 -0.00010 1.00000 17 74 592.0 13.00 10.00 49.00 3.03017 1.00000 -0.00010 1.00000 18 45 360.0 65.00 39.00 62.00 3.00205 1.00000 -0.00010 1.00000 19 15 120.0 72.00 7.00 42.00 2.96283 1.00000 -0.00010 1.00000 20 55 440.0 62.00 9.00 23.00 2.93121 1.00000 -0.00010 1.00000 21 79 632.0 46.00 60.00 87.00 2.92199 1.00000 -0.00010 1.00000 22 35 280.0 2.00 41.00 48.00 2.84065 1.00000 -0.00010 1.00000 23 44 352.0 6.00 35.00 27.00 2.80109 1.00000 -0.00010 1.00000 24 14 112.0 50.00 3.00 54.00 2.75399 1.00000 -0.00010 1.00000 25 71 568.0 0.00 22.00 9.00 2.75160 1.00000 -0.00010 1.00000 26 5 40.0 28.00 0.00 36.00 2.72535 1.00000 -0.00010 1.00000 27 130 1040.0 40.00 1.00 45.00 2.71826 0.99920 0.99880 0.99950 28 81 648.0 33.00 61.00 86.00 2.70040 1.00000 -0.00010 1.00000 29 73 584.0 67.00 26.00 52.00 2.68744 1.00000 -0.00010 1.00000 30 16 128.0 64.00 48.00 72.00 2.67636 1.00000 -0.00010 1.00000 31 28 224.0 75.00 35.00 88.00 2.65193 1.00000 -0.00010 1.00000 32 11 88.0 15.00 21.00 82.00 2.61771 1.00000 -0.00010 1.00000 33 5 40.0 45.00 0.00 27.00 2.61424 1.00000 -0.00010 1.00000 34 16 128.0 9.00 13.00 70.00 2.58842 1.00000 -0.00010 1.00000 35 23 184.0 15.00 27.00 48.00 2.57410 1.00000 -0.00010 1.00000 36 28 224.0 15.00 31.00 44.00 2.57219 1.00000 -0.00010 1.00000 37 23 184.0 29.00 56.00 78.00 2.55890 1.00000 -0.00010 1.00000 38 7 56.0 0.00 42.00 92.00 2.55525 1.00000 -0.00010 1.00000 39 49 392.0 52.00 40.00 88.00 2.54894 1.00000 -0.00010 1.00000 40 42 336.0 7.00 31.00 63.00 2.52160 1.00000 -0.00010 1.00000 41 37 296.0 22.00 43.00 81.00 2.50557 1.00000 -0.00010 1.00000 42 21 168.0 22.00 58.00 72.00 2.49912 1.00000 -0.00010 1.00000 43 32 256.0 59.00 45.00 91.00 2.44918 1.00000 -0.00010 1.00000 44 12 96.0 31.00 29.00 36.00 2.42939 1.00000 -0.00010 1.00000 45 50 400.0 14.00 34.00 26.00 2.42102 1.00000 -0.00010 1.00000 46 22 176.0 6.00 15.00 55.00 2.41349 1.00000 -0.00010 1.00000 47 12 96.0 9.00 43.00 42.00 2.40593 1.00000 -0.00010 1.00000 48 27 216.0 64.00 17.00 31.00 2.38351 1.00000 -0.00010 1.00000 49 16 128.0 25.00 49.00 81.00 2.37500 1.00000 -0.00010 1.00000 50 37 296.0 12.00 18.00 54.00 2.36836 1.00000 -0.00010 1.00000 51 22 176.0 43.00 50.00 63.00 2.35072 1.00000 -0.00010 1.00000 52 39 312.0 31.00 39.00 46.00 2.31633 1.00000 -0.00010 1.00000 53 7 56.0 75.00 60.00 84.00 2.28945 1.00000 -0.00010 1.00000 54 6 48.0 33.00 25.00 67.00 2.28154 1.00000 -0.00010 1.00000 55 10 80.0 49.00 40.00 33.00 2.27301 1.00000 -0.00010 1.00000 56 13 104.0 26.00 65.00 88.00 2.27017 1.00000 -0.00010 1.00000 57 6 48.0 13.00 25.00 26.00 2.26583 1.00000 -0.00010 1.00000 58 15 120.0 54.00 9.00 20.00 2.25868 1.00000 -0.00010 1.00000 59 16 128.0 63.00 14.00 19.00 2.21490 1.00000 -0.00010 1.00000 60 4 32.0 9.00 25.00 61.00 2.21056 1.00000 -0.00010 1.00000 61 37 296.0 25.00 37.00 62.00 2.21055 1.00000 -0.00010 1.00000 62 10 80.0 59.00 51.00 51.00 2.20982 1.00000 -0.00010 1.00000 63 20 160.0 66.00 41.00 51.00 2.19863 1.00000 -0.00010 1.00000 64 2 16.0 53.00 66.00 72.00 2.18410 1.00000 -0.00010 1.00000 65 9 72.0 37.00 38.00 66.00 2.17739 1.00000 -0.00010 1.00000 66 6 48.0 6.00 44.00 62.00 2.17461 1.00000 -0.00010 1.00000 67 39 312.0 50.00 35.00 70.00 2.16322 1.00000 -0.00010 1.00000 68 11 88.0 52.00 6.00 21.00 2.16002 1.00000 -0.00010 1.00000 69 6 48.0 26.00 0.00 43.00 2.15030 1.00000 -0.00010 1.00000 70 8 64.0 41.00 16.00 19.00 2.14875 1.00000 -0.00010 1.00000 71 4 32.0 51.00 8.00 39.00 2.14592 1.00000 -0.00010 1.00000 72 3 24.0 47.00 9.00 21.00 2.14285 1.00000 -0.00010 1.00000 73 8 64.0 67.00 19.00 27.00 2.14034 1.00000 -0.00010 1.00000 74 12 96.0 3.00 59.00 86.00 2.13879 1.00000 -0.00010 1.00000 75 3 24.0 15.00 6.00 19.00 2.13024 1.00000 -0.00010 1.00000 76 9 72.0 59.00 41.00 41.00 2.12204 1.00000 -0.00010 1.00000 77 18 144.0 35.00 48.00 55.00 2.10334 1.00000 -0.00010 1.00000 78 6 48.0 40.00 57.00 92.00 2.08841 1.00000 -0.00010 1.00000 79 7 56.0 43.00 1.00 17.00 2.07371 1.00000 -0.00010 1.00000 80 6 48.0 41.00 55.00 69.00 2.07007 1.00000 -0.00010 1.00000 81 14 112.0 23.00 35.00 88.00 2.06307 1.00000 -0.00010 1.00000 82 11 88.0 40.00 73.00 82.00 2.05213 1.00000 -0.00010 1.00000 83 5 40.0 39.00 19.00 51.00 2.04809 1.00000 -0.00010 1.00000 84 10 80.0 38.00 24.00 69.00 2.04252 1.00000 -0.00010 1.00000 85 9 72.0 30.00 32.00 67.00 2.04237 1.00000 -0.00010 1.00000 86 7 56.0 54.00 58.00 72.00 2.03645 1.00000 -0.00010 1.00000 87 10 80.0 30.00 13.00 22.00 2.03577 1.00000 -0.00010 1.00000 88 8 64.0 0.00 25.00 72.00 2.03193 1.00000 -0.00010 1.00000 89 5 40.0 7.00 23.00 6.00 2.02805 1.00000 -0.00010 1.00000 90 4 32.0 59.00 28.00 21.00 2.02245 1.00000 -0.00010 1.00000 91 11 88.0 43.00 18.00 63.00 2.01764 1.00000 -0.00010 1.00000 92 5 40.0 14.00 41.00 87.00 2.01255 1.00000 -0.00010 1.00000 93 3 24.0 28.00 50.00 55.00 2.01226 1.00000 -0.00010 1.00000 94 6 48.0 35.00 0.00 43.00 1.99869 1.00000 -0.00010 1.00000 95 1 8.0 59.00 57.00 79.00 1.99505 1.00000 -0.00010 1.00000 96 1 8.0 25.00 2.00 51.00 1.99394 1.00000 -0.00010 1.00000 97 4 32.0 55.00 4.00 36.00 1.98505 1.00000 -0.00010 1.00000 98 2 16.0 66.00 21.00 6.00 1.97461 1.00000 -0.00010 1.00000 99 3 24.0 31.00 51.00 90.00 1.97154 1.00000 -0.00010 1.00000 100 3 24.0 12.00 11.00 23.00 1.95664 1.00000 -0.00010 1.00000 101 5 40.0 38.00 43.00 50.00 1.95222 1.00000 -0.00010 1.00000 102 2 16.0 28.00 22.00 7.00 1.95066 1.00000 -0.00010 1.00000 103 4 32.0 20.00 17.00 69.00 1.94669 1.00000 -0.00010 1.00000 104 5 40.0 1.00 8.00 46.00 1.94587 1.00000 -0.00010 1.00000 105 4 32.0 42.00 15.00 49.00 1.94354 1.00000 -0.00010 1.00000 106 4 32.0 4.00 41.00 54.00 1.93906 1.00000 -0.00010 1.00000 107 3 24.0 15.00 9.00 33.00 1.93848 1.00000 -0.00010 1.00000 108 6 48.0 61.00 28.00 72.00 1.92516 1.00000 -0.00010 1.00000 109 1 8.0 49.00 26.00 88.00 1.92457 1.00000 -0.00010 1.00000 110 3 24.0 65.00 37.00 41.00 1.92365 1.00000 -0.00010 1.00000 111 3 24.0 69.00 29.00 25.00 1.91576 1.00000 -0.00010 1.00000 112 2 16.0 70.00 15.00 9.00 1.89931 1.00000 -0.00010 1.00000 113 2 16.0 65.00 24.00 70.00 1.89719 1.00000 -0.00010 1.00000 114 1 8.0 41.00 24.00 36.00 1.89653 1.00000 -0.00010 1.00000 115 7 56.0 71.00 32.00 91.00 1.89529 1.00000 -0.00010 1.00000 116 6 48.0 24.00 38.00 69.00 1.88993 1.00000 -0.00010 1.00000 117 4 32.0 6.00 22.00 34.00 1.88833 1.00000 -0.00010 1.00000 118 3 24.0 41.00 45.00 51.00 1.87881 1.00000 -0.00010 1.00000 119 2 16.0 18.00 58.00 91.00 1.87841 1.00000 -0.00010 1.00000 120 3 24.0 44.00 10.00 17.00 1.87792 1.00000 -0.00010 1.00000 121 4 32.0 7.00 38.00 71.00 1.87444 1.00000 -0.00010 1.00000 122 2 16.0 39.00 12.00 65.00 1.87242 1.00000 -0.00010 1.00000 123 7 56.0 25.00 35.00 38.00 1.87054 1.00000 -0.00010 1.00000 124 3 24.0 14.00 28.00 25.00 1.86776 1.00000 -0.00010 1.00000 125 4 32.0 64.00 23.00 76.00 1.86629 1.00000 -0.00010 1.00000 126 7 56.0 58.00 44.00 43.00 1.86598 1.00000 -0.00010 1.00000 127 1 8.0 40.00 44.00 63.00 1.86487 1.00000 -0.00010 1.00000 128 1 8.0 19.00 8.00 55.00 1.84677 1.00000 -0.00010 1.00000 129 1 8.0 59.00 58.00 80.00 1.84162 1.00000 -0.00010 1.00000 130 1 8.0 16.00 40.00 92.00 1.83828 1.00000 -0.00010 1.00000 131 2 16.0 21.00 42.00 63.00 1.83258 1.00000 -0.00010 1.00000 132 6 48.0 2.00 19.00 69.00 1.82733 1.00000 -0.00010 1.00000 133 1 8.0 25.00 45.00 73.00 1.81604 1.00000 -0.00010 1.00000 134 1 8.0 6.00 10.00 48.00 1.81496 1.00000 -0.00010 1.00000 135 2 16.0 9.00 7.00 43.00 1.80712 1.00000 -0.00010 1.00000 136 1 8.0 36.00 2.00 53.00 1.80667 1.00000 -0.00010 1.00000 137 1 8.0 19.00 43.00 60.00 1.80358 1.00000 -0.00010 1.00000 138 1 8.0 24.00 0.00 25.00 1.80337 1.00000 -0.00010 1.00000 139 2 16.0 25.00 5.00 42.00 1.79990 1.00000 -0.00010 1.00000 140 4 32.0 69.00 18.00 40.00 1.79854 1.00000 -0.00010 1.00000 141 1 8.0 62.00 48.00 85.00 1.79309 1.00000 -0.00010 1.00000 142 4 32.0 61.00 43.00 84.00 1.78916 1.00000 -0.00010 1.00000 143 1 8.0 13.00 13.00 34.00 1.78877 1.00000 -0.00010 1.00000 144 1 8.0 34.00 28.00 78.00 1.78826 1.00000 -0.00010 1.00000 145 3 24.0 69.00 32.00 83.00 1.78152 1.00000 -0.00010 1.00000 146 1 8.0 14.00 11.00 33.00 1.78004 1.00000 -0.00010 1.00000 147 1 8.0 70.00 19.00 25.00 1.77961 1.00000 -0.00010 1.00000 148 1 8.0 24.00 1.00 50.00 1.77625 1.00000 -0.00010 1.00000 149 1 8.0 3.00 35.00 84.00 1.77073 1.00000 -0.00010 1.00000 150 1 8.0 22.00 43.00 64.00 1.77048 1.00000 -0.00010 1.00000 151 1 8.0 25.00 63.00 83.00 1.76957 1.00000 -0.00010 1.00000 152 1 8.0 52.00 57.00 72.00 1.76913 1.00000 -0.00010 1.00000 153 1 8.0 6.00 24.00 31.00 1.76905 1.00000 -0.00010 1.00000 154 1 8.0 7.00 37.00 72.00 1.76885 1.00000 -0.00010 1.00000 155 2 16.0 75.00 24.00 12.00 1.76788 1.00000 -0.00010 1.00000 156 1 8.0 64.00 38.00 42.00 1.76533 1.00000 -0.00010 1.00000 157 1 8.0 54.00 32.00 84.00 1.76446 1.00000 -0.00010 1.00000 158 1 8.0 23.00 38.00 88.00 1.76098 1.00000 -0.00010 1.00000 159 1 8.0 6.00 40.00 33.00 1.75765 1.00000 -0.00010 1.00000 160 1 8.0 22.00 25.00 9.00 1.75009 1.00000 -0.00010 1.00000 161 2 16.0 67.00 3.00 52.00 1.74760 1.00000 -0.00010 1.00000 162 2 16.0 28.00 67.00 70.00 1.74531 1.00000 -0.00010 1.00000 163 1 8.0 4.00 33.00 30.00 1.74303 1.00000 -0.00010 1.00000 164 1 8.0 69.00 20.00 74.00 1.74160 1.00000 -0.00010 1.00000 165 1 8.0 18.00 21.00 55.00 1.74153 1.00000 -0.00010 1.00000 166 2 16.0 31.00 25.00 80.00 1.73939 1.00000 -0.00010 1.00000 167 2 16.0 22.00 40.00 63.00 1.73425 1.00000 -0.00010 1.00000 168 2 16.0 68.00 21.00 74.00 1.72982 1.00000 -0.00010 1.00000 169 2 16.0 7.00 18.00 27.00 1.72964 1.00000 -0.00010 1.00000 170 1 8.0 11.00 29.00 60.00 1.72963 1.00000 -0.00010 1.00000 171 1 8.0 25.00 65.00 86.00 1.72933 1.00000 -0.00010 1.00000 172 1 8.0 40.00 10.00 56.00 1.72897 1.00000 -0.00010 1.00000 173 2 16.0 40.00 56.00 61.00 1.72244 1.00000 -0.00010 1.00000 174 1 8.0 17.00 67.00 74.00 1.72103 1.00000 -0.00010 1.00000 175 1 8.0 42.00 67.00 70.00 1.71913 1.00000 -0.00010 1.00000 176 1 8.0 25.00 64.00 85.00 1.71646 1.00000 -0.00010 1.00000 177 1 8.0 9.00 38.00 73.00 1.71532 1.00000 -0.00010 1.00000 178 1 8.0 4.00 34.00 31.00 1.71458 1.00000 -0.00010 1.00000 179 1 8.0 3.00 22.00 7.00 1.71416 1.00000 -0.00010 1.00000 180 1 8.0 31.00 50.00 89.00 1.71002 1.00000 -0.00010 1.00000 181 1 8.0 51.00 7.00 19.00 1.70870 1.00000 -0.00010 1.00000 182 1 8.0 43.00 1.00 48.00 1.70621 1.00000 -0.00010 1.00000 183 1 8.0 22.00 36.00 41.00 1.70538 1.00000 -0.00010 1.00000 184 1 8.0 1.00 22.00 71.00 1.70431 1.00000 -0.00010 1.00000 185 1 8.0 65.00 20.00 5.00 1.70426 1.00000 -0.00010 1.00000 186 1 8.0 70.00 10.00 43.00 1.70299 1.00000 -0.00010 1.00000 187 1 8.0 11.00 17.00 62.00 1.70210 1.00000 -0.00010 1.00000 188 1 8.0 1.00 21.00 70.00 1.70207 1.00000 -0.00010 1.00000 189 1 8.0 35.00 26.00 63.00 1.70166 1.00000 -0.00010 1.00000 190 1 8.0 11.00 37.00 66.00 1.70059 1.00000 -0.00010 1.00000 191 1 8.0 22.00 37.00 70.00 1.70035 1.00000 -0.00010 1.00000 192 1 8.0 25.00 14.00 22.00 1.69897 1.00000 -0.00010 1.00000 Date: Tue, 25 Jun 2013 12:22:23 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <51C9C3BF.7000000(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed can you send the file? On 06/25/2013 10:08 AM, Emily Boeke wrote: > Hi All, > > I'm running Monte Carlo simulations on functional data, and the coordinate information outputted in the cluster.summary file isn't making sense. Usually the coordinates for the clusters listed are Talairach coordinates, but in the .summary files I'm getting, the coordinates are labeled "VoxX VoxY VoxZ" instead of "TalX TalY TalZ" and the numbers are clearly not Talairach coordinates. Above the table, it says "Reporting Coordinates in Voxel Indices." I also noted that in the descriptive information above the table, it says "Registration: None: Tal Coords invalid." > > However, the .nii files I'm seeing look like I would expect them too. > > I'm using the same command line I've run before, so I have no idea why the .summary file looks different. Does anyone know why this would be? > > Thanks, > Emily

2 3

Re: [Freesurfer] mri_label2vol problem
by LAOUCHEDI MAKHLOUF 01 Jul '13

01 Jul '13

excuse me Doug. i gathered previous correspondences (i wrote your replies are in bold) : june, 28 at 16:41 here is the command and it's terminal : mri_label2vol --annot G_and_S_cingul-Ant.annot --temp /home/mlaouche/makh_free/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity --fillthresh 0 --o /home/mlaouche/G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1 Number of labels: 0 Annot File: G_and_S_cingul-Ant.annot Template Volume: /home/mlaouche/makh_free/ctr2/mri/brain.mgz Outut Volume: /home/mlaouche/G_and_S_cingul-Ant.nii.gz Registration File: (null) Fill Threshold: 0 Label Vox Vol: 1 ProjType: frac ProjTypeId: 2 ProjStart: 0 ProjStop: 1 ProjDelta: 0.1 Subject: ctr2 Hemi: lh UseNewASeg2Vol: 1 DoLabelStatVol 0 $Id: mri_label2vol.c,v 1.34.2.1 2011/03/22 18:09:04 greve Exp $ Template RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; -0.000 -0.000 -1.000 128.000; -0.000 1.000 -0.000 128.000; 0.000 0.000 0.000 1.000; Template Voxel Volume: 1 nHits Thresh: 0 Using Identity Matrix RegMat: -------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; Label RAS-to-Vox: -------- -1.000 0.000 0.000 128.000; 0.000 0.000 -1.000 128.000; 0.000 1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading surface /home/mlaouche/makh_free/ctr2/surf/lh.white nvertices = 138786 Reading thickness /home/mlaouche/makh_free/ctr2/surf/lh.thickness Loading annotations from G_and_S_cingul-Ant.annot reading colortable from annotation file... colortable with 14176 entries read (originally /home_cluster/amesse/software/freesurfer5.1/FreeSurferColorLUT.txt) annotidmax = 1 Allocating Hit Volume (16777216) voxels nlabels = 1 PVF (null) Thesholding hit volume. done june, 28 at 16:41 The terminal output, ie, what gets printed to the screen after your run the program. june, 28 at 16:39 excuse me but i don't understand what you mean by "terminal of mri_label2volume" Thank you for help june, 28 at 16:33 please post responses to the list doug btw, there is no terminal output below june, 28 at 16:29 i used tksurfer to display the volume and i imported the annotation file created, it looks ok. about the full terminal ouput of mri_label2vol : /home/mlaouche/lh.G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1 Thanks (in fact i used to assemble individual labels to make some annotation files for some parts of the brain, which i used to transform to nifti using mri_label2vol without problem) june, 28 at 16:49 Doug How does the annot look on the surface (ie, intksurfer)? What is the full terminal output of mri_label2vol? june, 28 at 16:19 Hi i run mri_label2annot to get individual annot files for all labels, then i run mri_label2vol to get nifti volumes of my labels using the following command : mri_label2vol --annot lh.G_and_S_cingul-Ant.annot --temp SUBJ_DIR/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity --fillthresh .5 --o ~/lh.G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1 but the result is a volume with zero values (i changed --fillthresh .5 to --fillthresh 0 and i got the same probleme) Thanks ________________________________ De : Douglas N Greve <greve(a)nmr.mgh.harvard.edu> À : LAOUCHEDI MAKHLOUF <laoumakhl(a)yahoo.fr> Envoyé le : Vendredi 28 juin 2013 18h41 Objet : Re: [Freesurfer] mri_label2vol problem Hi Laouchedi, I have asked you two times now to include all previous correspondences in each email. This is the 3rd time. If you are going to make it hard for us to answer your question, then the result will be that they won't be answered. thanks doug On 06/28/2013 12:12 PM, LAOUCHEDI MAKHLOUF wrote: > here is the command and it's terminal : > > mri_label2vol --annot G_and_S_cingul-Ant.annot --temp > /home/mlaouche/makh_free/ctr2/mri/brain.mgz --subject ctr2 --hemi lh > --identity --fillthresh 0 --o /home/mlaouche/G_and_S_cingul-Ant.nii.gz > --proj frac 0 1 .1 > > Number of labels: 0 > Annot File: G_and_S_cingul-Ant.annot > Template Volume: /home/mlaouche/makh_free/ctr2/mri/brain.mgz > Outut Volume: /home/mlaouche/G_and_S_cingul-Ant.nii.gz > Registration File: (null) > Fill Threshold: 0 > Label Vox Vol: 1 > ProjType: frac > ProjTypeId: 2 > ProjStart: 0 > ProjStop: 1 > ProjDelta: 0.1 > Subject: ctr2 > Hemi: lh > UseNewASeg2Vol: 1 > DoLabelStatVol 0 > $Id: mri_label2vol.c,v 1.34.2.1 2011/03/22 18:09:04 greve Exp $ > Template RAS-to-Vox: -------- > -1.000 0.000 0.000 128.000; > -0.000 -0.000 -1.000 128.000; > -0.000 1.000 -0.000 128.000; > 0.000 0.000 0.000 1.000; > Template Voxel Volume: 1 > nHits Thresh: 0 > Using Identity Matrix > RegMat: -------- > 1.000 0.000 0.000 0.000; > 0.000 1.000 0.000 0.000; > 0.000 0.000 1.000 0.000; > 0.000 0.000 0.000 1.000; > Label RAS-to-Vox: -------- > -1.000 0.000 0.000 128.000; > 0.000 0.000 -1.000 128.000; > 0.000 1.000 0.000 128.000; > 0.000 0.000 0.000 1.000; > INFO: loading surface /home/mlaouche/makh_free/ctr2/surf/lh.white > nvertices = 138786 > Reading thickness /home/mlaouche/makh_free/ctr2/surf/lh.thickness > Loading annotations from G_and_S_cingul-Ant.annot > reading colortable from annotation file... > colortable with 14176 entries read (originally > /home_cluster/amesse/software/freesurfer5.1/FreeSurferColorLUT.txt) > annotidmax = 1 > Allocating Hit Volume (16777216) voxels > nlabels = 1 > > PVF (null) > Thesholding hit volume. > done > > > ------------------------------------------------------------------------ > *De :* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *À :* freesurfer(a)nmr.mgh.harvard.edu > *Envoyé le :* Vendredi 28 juin 2013 16h49 > *Objet :* Re: [Freesurfer] mri_label2vol problem > > How does the annot look on the surface (ie, intksurfer)? What is the > full terminal output of mri_label2vol? > > On 06/28/2013 10:19 AM, LAOUCHEDI MAKHLOUF wrote: > > Hi > > i run mri_label2annot to get individual annot files for all > > labels, then i run mri_label2vol to get nifti volumes of my labels > > using the following command : > > mri_label2vol --annot lh.G_and_S_cingul-Ant.annot --temp > > SUBJ_DIR/ctr2/mri/brain.mgz --subject ctr2 --hemi lh --identity > > --fillthresh .5 --o ~/lh.G_and_S_cingul-Ant.nii.gz --proj frac 0 1 .1 > > > > but the result is a volume with zero values (i changed --fillthresh .5 > > to --fillthresh 0 and i got the same probleme) > > > > Thanks > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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 > <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. > > > -- 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/

2 2

Re: [Freesurfer] tksurfer display problem
by Xiangzhen Kong 29 Jun '13

29 Jun '13

Actually when I just use "tksurfer fsaverage lh inflated", there is the similar problem. And fsaverage was copied from freesufer by recon-all. So I think there might be something wrong with using tksurfer, e.g., config. 【小孔成像】http://www.conxz.net From: Bruce Fischl Date: 2013-06-28 10:28 To: Xiangzhen Kong CC: freesurfer Subject: Re: [Freesurfer] tksurfer display problem Are you sure you didn't accidentally copy the rh over lh On Jun 27, 2013, at 9:31 PM, "Xiangzhen Kong" <bnucon(a)gmail.com> wrote: Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. 【小孔成像】http://www.conxz.net <test.jpg> _______________________________________________ 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.

3 10

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer June 2013