Freesurfer November 2012

freesurfer@nmr.mgh.harvard.edu

105 participants
177 discussions

tkregister2 error on lion
by Ritobrato Datta 14 Nov '12

14 Nov '12

Hi All, I have freesurfer 5.1 installed on my laptop running Lion. When I tried to use tkregister2, the program doesnt load up the GUI. It failed even after installing XQuartz. It loaded successfully in a machine running Snow Leopard. Any suggestions on how to get around it or are there any fixes available ? Thanks a lot Ri

1 0

aparc+aseg voxels labeled as "unknown"
by Nikhil Chandra 13 Nov '12

13 Nov '12

Hello, After completing the FreeSurfer Recommended Reconstruction, we have noticed that in aparc+aseg, many subjects exhibit small clusters of voxels in the medial temporal lobe that are labeled as "ctx-lh-unknown" or "ctx-rh-unknown". These clusters are mostly found on the boundaries between the amygdala, hippocampus, inferior lateral ventricles, and cerebral white matter. Please refer to the attached screen shot for an example. How can we deal with this problem? One possible solution that we thought of was to apply the corresponding label in aseg.mgz for each affected voxel in aparc+aseg.mgz, but we thought we would ask if there is a better way. Thank you, Nikhil Chandra

2 1

Fwd: bad acquisition and noise problem.
by youngmin huh 13 Nov '12

13 Nov '12

---------- Forwarded message ---------- From: youngmin huh <ymin1123(a)gmail.com> Date: 2012/11/14 Subject: Re: bad acquisition and noise problem. To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Thanks for your comment. I would appreciate if you could take a look. Do you want a whole folder of the subjects, or just 001.mgz and log file? Thanks, Youngmin. 2012/11/14 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > it's not a question of SNR, the problem appears to me to be that the B0 > distortions are so bad that a bunch of the temporal lobe is piled up on top > of itself. There's no way to fix that posthoc. If you upload the full > volume I'm happy to take a look > > > On Wed, 14 Nov 2012, youngmin huh wrote: > > I'm not engaged in obtaining images, so I don't have any details about the >> images.I wonder the method which you commented can be applied to images I >> >> already earned. >> If it's not, is there any way to recover SNR after image scanning? >> >> Thanks, >> >> Youngmin Huh. >> >> >> 2012/11/13 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> what is the bandwidth? The typical way to fix it is to increase >> the bandwidth. You can probably recover some of the SNR you will >> lose by reducing your flip angle, which is pretty far from the >> Ernst angle. >> Also, minimize your TE (if 4ms is not already the min) >> cheers >> Bruce >> >> >> On Tue, 13 Nov 2012, youngmin huh wrote: >> >> Hi, >> 3D SPGR sequences were used. (TR=22, TE=4, >> thickness=1.4, FOV=240*240, >> FA=40) >> If the artifacts are due to B0 distortion, I wonder >> how I can fix it. >> >> Thanks, >> Youngmin Huh >> >> >> >> 2012/11/12 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Can you give us the acquisition details? I >> suspect this is not >> noise, but rather B0 distortion. >> what is the acquisition? And what bandwidth? >> >> >> On Nov 8, 2012, at 2:53 AM, youngmin huh >> <ymin1123(a)gmail.com> >> wrote: >> >> > Dear all, >> > >> > I'm working with some images, and they have >> so much noises on >> temporal areas. >> > I just ran recon2, but not sure if they'll >> be segmented >> properly. >> > Does anyone have a recommendation for >> dealing with it? >> > I wonder if there is any flag or option for >> this occasion. >> > I would appreciate any comments or help. >> > I attached an example. >> > >> > Thanks, >> > >> > Youngmin Huh >> > <temporal_001.jpg> >> >> >> 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. >> >> >> >> >> >> >>

1 0

Re: [Freesurfer] bad acquisition and noise problem.
by youngmin huh 13 Nov '12

13 Nov '12

Hi, 3D SPGR sequences were used. (TR=22, TE=4, thickness=1.4, FOV=240*240, FA=40) If the artifacts are due to B0 distortion, I wonder how I can fix it. Thanks, Youngmin Huh 2012/11/12 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Can you give us the acquisition details? I suspect this is not noise, but > rather B0 distortion. > what is the acquisition? And what bandwidth? > > > On Nov 8, 2012, at 2:53 AM, youngmin huh <ymin1123(a)gmail.com> wrote: > > > Dear all, > > > > I'm working with some images, and they have so much noises on temporal > areas. > > I just ran recon2, but not sure if they'll be segmented properly. > > Does anyone have a recommendation for dealing with it? > > I wonder if there is any flag or option for this occasion. > > I would appreciate any comments or help. > > I attached an example. > > > > Thanks, > > > > Youngmin Huh > > <temporal_001.jpg> > > > 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 4

Subgenual ACC - part of the Desikan rostral ACC?
by Amanda Schlesinger 13 Nov '12

13 Nov '12

Hello all - I'm unclear on whether the subgenual ACC gets included in the rostral ACC when running parcellations from the Desikan atlas. From the Desikan paper's description and images, it appears to me that the rACC area curves under the genu of the CC and that the caudal boundary there at the genu marks the rostral edge of the subgenual ACC/BA 25? Clarification would be much appreciated! thanks! - Amanda ---------------- Amanda Schlesinger, MD Department of Psychiatry University of Minnesota Medical School schle248(a)umn.edu

2 1

Re: [Freesurfer] Phase Encoding Direction and epidewarp.fsl
by Clark Fisher 13 Nov '12

13 Nov '12

Thanks Doug, Would the proper way to handle this then be to switch the rows and columns before unwarping, then switch them back before the further processing steps? -Clark

4 5

bankssts label
by Mensen, V.T. 13 Nov '12

13 Nov '12

Dear Freesurfers, Does anyone know why sometimes the "bankssts" (banks of the superior temporal sulcus) is only found in the sulcus, and sometimes occupies a sizeable part of an adjacent gyrus (superior temporal / inferior parietal)? The dark-green area is generally only visible in the inflated view, but every so often it is quite pronounced in the main (pial) view as well. Thanks! Vincent Mensen Utrecht ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

2 1

Re: [Freesurfer] pre-processing functional data error
by Douglas N Greve 13 Nov '12

13 Nov '12

The terminal output looks ok. Do you mean that there is something wrong with the output volume? What? doug On 11/12/2012 11:30 AM, Yangmei LUO wrote: > Hi Douglas, > > It appeared the same error as before. The picture of the results is > the same. I am so sorry. > Thanks again! > > Best, > Yangmei > > $ /usr/local/freesurfer/bin/mri_convert.linux I0001.dcm s105.run1.nii > /usr/local/freesurfer/bin/mri_convert.linux I0001.dcm s105.run1.nii > $Id: mri_convert.c,v 1.196 2012/07/11 17:50:50 fischl Exp $ > reading from I0001.dcm... > Getting Series No > Scanning Directory > INFO: Found 230 files in /home/fsl/data/emotion/s105/run1 > INFO: Scanning for Series Number 3 > INFO: found 228 files in series > INFO: loading series header info. > > INFO: sorting. > RunNo = 2 > INFO: ( 64 64 32), nframes = 228, ismosaic=1 > Could not parse NUMARIS version string syngo MR B17 > found in dicom tag 18,1020 (len = 3 != 6) > Repetition Time = 2000, TR = 2000 ms > PE Dir COL COL > AutoAlign matrix detected > AutoAlign Matrix --------------------- > 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; > > FileName /home/fsl/data/emotion/s105/run1/I0001.dcm > Identification > NumarisVer syngo MR B17 > ScannerModel TrioTim > PatientName LuoYangmei_s5^caoguoguo > Date and time > StudyDate 20121009 > StudyTime 084434.968000 > SeriesTime 090357.640000 > AcqTime 090309.732500 > Acquisition parameters > PulseSeq *epfid2d1_64 > Protocol run1 > PhEncDir COL > EchoNo 1 > FlipAngle 90 > EchoTime 30 > InversionTime -1 > RepetitionTime 2000 > PhEncFOV 192 > ReadoutFOV 192 > Image information > RunNo 2 > SeriesNo 3 > ImageNo 1 > NImageRows 384 > NImageCols 384 > NFrames 228 > SliceArraylSize 32 > IsMosaic 1 > ImgPos 99.3735 107.4917 -33.8349 > VolRes 3.0000 3.0000 3.9900 > VolDim 64 64 32 > Vc -1.0000 -0.0000 0.0000 > Vr -0.0000 -0.9999 0.0105 > Vs -0.0000 0.0105 0.9999 > VolCenter 3.3735 12.1655 31.0069 > TransferSyntaxUID 1.2.840.10008.1.2 > UseSliceScaleFactor 0 (slice 0: 1) > sagrev = 0, correv =1, trarev = 1 > Vs = -0 0.0104718 0.999945 > INFO: detected a Siemens slice order reversal in mosaic, so > I'm going to reverse them back to their 'original' order. > TR=2000.00, TE=30.00, TI=-1.00, flip angle=90.00 > i_ras = (-1, -0, 0) > j_ras = (-0, -0.999945, 0.0104718) > k_ras = (-0, 0.0104718, 0.999945) > writing to s105.run1.nii... > > > > > > > > > > On Mon, Nov 12, 2012 at 4:11 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > sorry, remove the slash from the end of the line > > > On 11/12/2012 10:49 AM, Yangmei LUO wrote: > > Hi Douglas, > > Thank you for your kind help. The command still can not work. > > $ /usr/local/freesurfer/bin/mri_convert.linux I0001.dcm > s105.run1.nii/ > > /usr/local/freesurfer/bin/mri_convert.linux I0001.dcm > s105.run1.nii/ > mri_convert.linux: can't determine type of output volume > ind = 86581; % bad > Ct0 = y(:,ind+1); > %Ct0 = load('tcp.dat'); > intCt0 = cumtrapz(t0,Ct0); > > HalfLifeMin = 20.4; %min > TDecayMin = -HalfLifeMin/log(.5); > TDecaySec = TDecayMin*60; > intDecay = t0.*exp(-t0/TDecayMin); > w = sqrt(intDecay/sum(intDecay)); > W = diag(w); > > > X0 = [Cr0 intCr0 -intCt0]; > X = W*X0; > WCt = W*Ct0; > beta = inv(X'*X)*X'*WCt; > R1 = beta(1); > k2 = beta(2); > k2a = beta(3); > BPnd0 = k2/k2a -1; > CtHatSRTM = X0*beta; > > psrtm0 = max([R1 k2 k2a],0) + eps; > if(BPnd0 > 7 | BPnd0 < 0) psrtm0(3) = abs(k2)/(6+1); end > psrtm = fminsearch('srtm_err',psrtm0,[],Ct0,t0,Cr0,w); > [err CtHatsrtm] = srtm_err(psrtm,Ct0,t0,Cr0,w); > BPndNL = psrtm(2)/psrtm(3)-1; > > k3Init = .35; > paramsInit = [beta(1) abs(beta(2)) k3Init k3Init/abs(BPnd0)]; > paramsInit = [beta(1) .066 0.3 0.06]; > params = fminsearch('frtm_err',paramsInit,[],Ct0,t0,Cr0,w); > [err CtHat] = frtm_err(params,Ct0,t0,Cr0,w); > BPndF = params(3)/params(4); > k2aF = params(2)/(1+BPndF); > betaF = [params(1:2) k2aF]'; > yhatF = X0*betaF; > > plot(t0,Ct0,t0,CtHat,t0,CtHatSRTM,t0,CtHatsrtm); > legend('Data','FRTM','SRTM','NL-SRTM') > > > > > when I typed the type of the output volume, there were some > errors. > > /usr/local/freesurfer/bin/mri_convert.linux --out_type nii > I0001.dcm s105.run1.nii/ > /usr/local/freesurfer/bin/mri_convert.linux --out_type nii > I0001.dcm s105.run1.nii/ > $Id: mri_convert.c,v 1.196 2012/07/11 17:50:50 fischl Exp $ > reading from I0001.dcm... > Getting Series No > Scanning Directory > INFO: Found 230 files in /home/fsl/data/emotion/s105/run1 > INFO: Scanning for Series Number 3 > INFO: found 228 files in series > INFO: loading series header info. > > INFO: sorting. > RunNo = 2 > INFO: ( 64 64 32), nframes = 228, ismosaic=1 > Could not parse NUMARIS version string syngo MR B17 > found in dicom tag 18,1020 (len = 3 != 6) > Repetition Time = 2000, TR = 2000 ms > PE Dir COL COL > AutoAlign matrix detected > AutoAlign Matrix --------------------- > 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; > > FileName /home/fsl/data/emotion/s105/run1/I0001.dcm > Identification > NumarisVer syngo MR B17 > ScannerModel TrioTim > PatientName LuoYangmei_s5^caoguoguo > Date and time > StudyDate 20121009 > StudyTime 084434.968000 > SeriesTime 090357.640000 > AcqTime 090309.732500 > Acquisition parameters > PulseSeq *epfid2d1_64 > Protocol run1 > PhEncDir COL > EchoNo 1 > FlipAngle 90 > EchoTime 30 > InversionTime -1 > RepetitionTime 2000 > PhEncFOV 192 > ReadoutFOV 192 > Image information > RunNo 2 > SeriesNo 3 > ImageNo 1 > NImageRows 384 > NImageCols 384 > NFrames 228 > SliceArraylSize 32 > IsMosaic 1 > ImgPos 99.3735 107.4917 -33.8349 > VolRes 3.0000 3.0000 3.9900 > VolDim 64 64 32 > Vc -1.0000 -0.0000 0.0000 > Vr -0.0000 -0.9999 0.0105 > Vs -0.0000 0.0105 0.9999 > VolCenter 3.3735 12.1655 31.0069 > TransferSyntaxUID 1.2.840.10008.1.2 > UseSliceScaleFactor 0 (slice 0: 1) > sagrev = 0, correv =1, trarev = 1 > Vs = -0 0.0104718 0.999945 > INFO: detected a Siemens slice order reversal in mosaic, so > I'm going to reverse them back to their 'original' order. > TR=2000.00, TE=30.00, TI=-1.00, flip angle=90.00 > i_ras = (-1, -0, 0) > j_ras = (-0, -0.999945, 0.0104718) > k_ras = (-0, 0.0104718, 0.999945) > writing to s105.run1.nii/... > niiWrite(): error opening file s105.run1.nii/ > ERROR: failure writing s105.run1.nii/ as volume type 24 > > > > > > On Mon, Nov 12, 2012 at 3:29 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > /Run this command line instead > mri_convert.linux I0001.dcm s105.run1.nii/ > doug > > On 11/09/2012 01:57 PM, Yangmei LUO wrote: > > Hi Dr, Douglas, > > > I attached the capture of the result using fslview. > > Thanks very much! > > Yangmei > > On Fri, Nov 9, 2012 at 12:51 PM, Yangmei LUO > <yangmeiluo(a)gmail.com <mailto:yangmeiluo@gmail.com> > <mailto:yangmeiluo@gmail.com <mailto:yangmeiluo@gmail.com>> > <mailto:yangmeiluo@gmail.com <mailto:yangmeiluo@gmail.com> > <mailto:yangmeiluo@gmail.com <mailto:yangmeiluo@gmail.com>>>> > > wrote: > > Hi Dr.Douglas, > > Thanks very much for your patient help. > MRI_convert can > work. It > is great. However, there was another problem about the > convert. > The results of the convert is unknown file and > there is a > warning. > Could you help me again? > > This the command : > //usr/local/freesurfer/bin/mri_convert.linux > --in_type dicom > --out_type nii I0001.dcm s105.run1.nii/ > > The result is: > > //usr/local/freesurfer/bin/mri_convert.linux > --in_type dicom > > --out_type nii I0001.dcm s105.run1.nii > $Id: mri_convert.c,v 1.196 2012/07/11 17:50:50 > fischl Exp $ > reading from I0001.dcm... > Starting DICOMRead2() > dcmfile = /home/fsl/data/emotion/s105/run1/I0001.dcm > dcmdir = /home/fsl/data/emotion/s105/run1 > Ref Series No = 3 > Found 231 files, checking for dicoms > Found 228 dicom files in series. > First Sorting > Computing Slice Direction > > > WARNING: it appears that the image position for all > slices is the > same. > This is a problem with the DICOM file. Using > direction > cosines > from col and row > to compute slice direction, but the output may be > misoriented. > > Vs: 0 -0.0104718 0.999945 > Vs: 0 -0.0104718 0.999945 > Second Sorting > Counting frames > nframes = 228 > nslices = 1 > ndcmfiles = 228 > PE Dir = COL (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2-- > Loading pixel data > TR=2000.00, TE=30.00, TI=0.00, flip angle=90.00 > i_ras = (-1, -0, 0) > j_ras = (-0, -0.999945, 0.0104718) > k_ras = (-0, 0.0104718, 0.999945) > writing to s105.run1.nii.../ > > > > Thank you so much! > > Best regards, > Yangmei > > > > > > On Fri, Nov 9, 2012 at 12:29 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > run these two lines then try again > chmod a+x mri_convert > reshash. > > > On 11/09/2012 01:04 PM, Yangmei LUO wrote: > > Hi Dr. Douglas, > > Thanks for your kind help. The version of > freesurfer is > stable v5.1.0 on CentOS 4 (32b). When I > download the > updated version you provided and switch > the file > in the > bin( I do not know what I did is correct). > When I > run the > command, the terminal appeared "permission > denied". > > What can I do next? > > Thanks so much! > > Best, > Yangmei > > > > > On Fri, Nov 9, 2012 at 11:29 AM, Douglas N > Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>>> wrote: > > The name is not important. I was able to > convert all > of those > files without a problem. What version > are you > using? > Maybe try an > updated version of mri_convert > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert.l… > > Also, please remember to include previous > correspondences in your > email to me. I always delete the > emails once I > answer > them. > thanks > doug > > > > On 11/09/2012 12:19 PM, Yangmei LUO wrote: > > > Hi Douglas, > > Thank you for your help. I change > the name > of the > dicom file > in order to process conveniently. > So, I > attached > two files of > with origin name and two files > with the > changed > name. I wish > it could help you figure out the > problem. > > > Thanks a million! > > > Best, > > > Yangmei > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> > Phone Number: 617-724-2358 > <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>> <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>> <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > <tel:617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > 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. > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > -- > 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 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

1 0

volume conversion problem
by Gabriel Gonzalez Escamilla 13 Nov '12

13 Nov '12

2 3

gstrobbe@ggmail.com, analysis-bugs@nmr.mgh.harvard.edu
by Azeez Adebimpe 13 Nov '12

13 Nov '12

Hi Freesurferers or Experts, I have been trying to convert the watershed bem brain surfaces to vol with mri_fill and mri_surf2vol but not succeed. My main aim is to create mask for outer_skull, inner_skull and other from their respective surfaces. Is there any other method to use? Azeez Azeez Adebimpe

2 1

← Newer
1
...
10
11
12
13
14
15
16
17
18
Older →

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 November 2012