Re: [Freesurfer] segmentation problem.
Can you try it without the expert opts? And what sequence is the data? On Nov 12, 2012, at 3:35 AM, youngmin huh ymin1...@gmail.com wrote: Hi I'm working with some images, and freesurfer didn't properly detect some of their white matter boundaries. I attached some examples. I ran recon2 with expert options(-b 20 -n 5). As you can see, they have inaccurate white matter boundaries in curved area. I think it's not that highly curved, though. Any comment will be appreciated. Thanks, Youngmin Huh image.jpegimage.jpeg ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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 . 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] volume conversion problem
Dear FS experts, I'm trying to convert one skull-stripped image from the FS segmentation to a nifti in native space, but I'm having some troubles with it.I'm doing everything with the a to d stepsa) cd /root/trabajo/freesurfer/subjects/s00x/mri/b) mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheaderc) mri_mask -T 2 rawavg.mgz brain2raw.mgz brainraw.mgzd) mri_convert -odt float brainraw.mgz brain.niibut in step b always get the following error:mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheadermovvol brain.mgztargvol rawavg.mgzoutvol brain2raw.mgzinvert 0tal 0talres 2regheader 1noresample 0interp nearest (0)precision float (3)Gdiag_no -1Synth 0SynthSeed 1352942991MRIalloc: could not allocate -512234304 frameCannot allocate memoryAny ideas how to solve this?Should I to re-run any recon?Many thanks in advanced,Gabriel ___ Freesurfer mailing list 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 . 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.
Re: [Freesurfer] pre-processing functional data error
/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 yangmei...@gmail.com mailto:yangmei...@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 0.45 Vs: 0 -0.0104718 0.45 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, -0.45, 0.0104718) k_ras = (-0, 0.0104718, 0.45) writing to s105.run1.nii.../ Thank you so much! Best regards, Yangmei On Fri, Nov 9, 2012 at 12:29 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@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.linux 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 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@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
Re: [Freesurfer] volume conversion problem
Can you send the result of mri_info brain.mgz mri_info rawavg.mgz doug On 11/12/2012 10:27 AM, Gabriel Gonzalez Escamilla wrote: Dear FS experts, I'm trying to convert one skull-stripped image from the FS segmentation to a nifti in native space, but I'm having some troubles with it. I'm doing everything with the a to d steps a) cd /root/trabajo/freesurfer/subjects/s00x/mri/ b) mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader c) mri_mask -T 2 rawavg.mgz brain2raw.mgz brainraw.mgz d) mri_convert -odt float brainraw.mgz brain.nii but in step b always get the following error: mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader movvol brain.mgz targvol rawavg.mgz outvol brain2raw.mgz invert 0 tal0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1352942991 MRIalloc: could not allocate -512234304 frame Cannot allocate memory Any ideas how to solve this? Should I to re-run any recon? Many thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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 ___ Freesurfer mailing list 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 . 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.
Re: [Freesurfer] pre-processing functional data error
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
NumarisVersyngo MR B17
ScannerModel TrioTim
PatientName LuoYangmei_s5^caoguoguo
Date and time
StudyDate 20121009
StudyTime 084434.968000
SeriesTime090357.64
AcqTime 090309.732500
Acquisition parameters
PulseSeq *epfid2d1_64
Protocol run1
PhEncDir COL
EchoNo1
FlipAngle 90
EchoTime 30
InversionTime -1
RepetitionTime2000
PhEncFOV 192
ReadoutFOV192
Image information
RunNo 2
SeriesNo 3
ImageNo 1
NImageRows384
NImageCols384
NFrames 228
SliceArraylSize 32
IsMosaic 1
ImgPos 99.3735 107.4917 -33.8349
VolRes 3. 3. 3.9900
VolDim 64 64 32
Vc -1. -0. 0.
Vr -0. -0. 0.0105
Vs -0. 0.0105 0.
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 0.45
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, -0.45, 0.0104718)
k_ras = (-0, 0.0104718, 0.45)
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
gr...@nmr.mgh.harvard.edu mailto:gr...@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
yangmei...@gmail.com mailto:yangmei...@gmail.com
mailto:yangmei...@gmail.com mailto:yangmei...@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.
[Freesurfer] The mismatched color in the tksurfer color bar for surface file
Hi, Doug and other FreeSurfer experts: I noticed that the color in a surface file I generated (*.mgh with the values ranging from 0 to 1) does not match that in the color bar. For example, the lowest value in the surface file has much darker red hue than the lowest values in the color bar (bright red). Is there any remedy for this mismatch? Also, I intended to attach an image in the email, but was told that the email contains blocked images. Thank you in advance! Longchuan___ Freesurfer mailing list 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 . 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.
Re: [Freesurfer] volume conversion problem
Here yu are:mri_info brain.mgzVolume information for brain.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: UCHAR (0) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 11.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWNras xform present xform info: x_r = -1., y_r = -0., z_r = 0., c_r = 2.1879 : x_a = -0., y_a = 0., z_a = 1., c_a = 11.6591 : x_s = -0., y_s = -1., z_s = -0., c_s = -17.2780talairach xfm :Orientation : LIAPrimary Slice Direction: coronalvoxel to ras transform: -1. -0. 0. 130.1879 -0. 0. 1. -116.3409 -0. -1. -0. 110.7220 0. 0. 0. 1.voxel-to-ras determinant -1ras to voxel transform: -1. 0. 0. 130.1879 0. -0. -1. 110.7220 -0. 1. -0. 116.3409 0. 0. 0. 1.mri_info rawavg.mgzMRIalloc: could not allocate -512234304 frameCannot allocate memoryAs I see, the problem comes from the rawavg.mgz, if I do convert the dicoms into mgz, would this solve the problem, right? or there's anything else I can do?Regards,GabrielEl 12/11/12, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:Can you send the result ofmri_info brain.mgzmri_info rawavg.mgzdougOn 11/12/2012 10:27 AM, Gabriel Gonzalez Escamilla wrote: Dear FS experts, I'm trying to convert one skull-stripped image from the FS segmentation to a nifti in native space, but I'm having some troubles with it. I'm doing everything with the a to d steps a) cd /root/trabajo/freesurfer/subjects/s00x/mri/ b) mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader c) mri_mask -T 2 rawavg.mgz brain2raw.mgz brainraw.mgz d) mri_convert -odt float brainraw.mgz brain.nii but in step b always get the following error: mri_vol2vol --interp nearest --mov brain.mgz --targ rawavg.mgz --out brain2raw.mgz --regheader movvol brain.mgz targvol rawavg.mgz outvol brain2raw.mgz invert 0 tal 0 talres 2 regheader 1 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1352942991 MRIalloc: could not allocate -512234304 frame Cannot allocate memory Any ideas how to solve this? Should I to re-run any recon? Many thanks in advanced, Gabriel ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Douglas N. Greve, Ph.D.MGH-NMR Centergr...@nmr.mgh.harvard.eduPhone Number: 617-724-2358Fax: 617-726-7422Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReportingFileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe information in this e-mail is intended only for the person to whom it isaddressed. If you believe this e-mail was sent to you in error and the e-mailcontains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in errorbut does not contain patient information, please contact the sender and properlydispose of the e-mail. ___ Freesurfer mailing list 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 . 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.
Re: [Freesurfer] segmentation problem.
Thanks. I'll try without expert opts. But i'm not sure if i can get better results. Before I found out these expert opts, I ran some images recon2 without expert opts. And they got poor segmentation. Actually, some images showed improvement with those options. I'm curious why these options work for some images and don't for others. And, 3D SPGR sequences were used. (TR=22, TE=4, thickness=1.4, FOV=240*240, FA=40) 2012/11/12 Bruce Fischl fis...@nmr.mgh.harvard.edu Can you try it without the expert opts? And what sequence is the data? On Nov 12, 2012, at 3:35 AM, youngmin huh ymin1...@gmail.com wrote: Hi I'm working with some images, and freesurfer didn't properly detect some of their white matter boundaries. I attached some examples. I ran recon2 with expert options(-b 20 -n 5). As you can see, they have inaccurate white matter boundaries in curved area. I think it's not that highly curved, though. Any comment will be appreciated. Thanks, Youngmin Huh image.jpegimage.jpeg ___ Freesurfer mailing list 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 . 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@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.
Re: [Freesurfer] bad acquisition and noise problem.
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 fis...@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 ymin1...@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. ___ Freesurfer mailing list 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 . 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.
Re: [Freesurfer] bad acquisition and noise problem.
Are you using a 32-channel coil? It looks like B1- receive field inhomogeneity to me. Peace, Matt. From: youngmin huh ymin1...@gmail.com Date: Monday, November 12, 2012 10:22 PM To: Bruce Fischl fis...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bad acquisition and noise problem. 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 fis...@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 ymin1...@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. ___ Freesurfer mailing list 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 . 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@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.
