[Freesurfer] How to convert a thickness file (i.e. lh.thickness) ti a 3D nifti file
Dear Freesurfer users, I am searching how to use the mri_surf2vol command in order to convert a lh.thickness file into a 3D .nii file (in the original subject space). Many Thanks, Fabrice ___ 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] expanding pial surface
Dear all, In the suggested workflow there is clear deescription of how to correct pial surface including non-cortex within the boundaries, but there is no description of how to expand the pial surface if it doesn't include the cortex within boundaries. Could anybody help me in this issue? Thanks, Gabor -- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-4098480 E-mail: petzinger.ga...@gmail.com ___ 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] mri_glmfit error: negative DOF -10
Hello, I am using mri_glmfit to perform a correlation analysis between some surface-based DTI measures and a behavioural outcome (grip), aiming to correct for scannertyp (C,I,W), handedness (R,L) as discrete variables and age (AGE) and duration (Mo) as continuous covariates. Please find the fsgd file, the contrast file and the calculated Xg down below. However, I get the follow error: DOF = -10 ERROR: DOF = -10 (the complete output is attached) I would be grateful if somebody could help. I already tried it with demeaned data, z-transformed data, it doesn't help. Thank you for your help, Robert fsgd file: GroupDescriptorFile 1 Title OSGM Class CR Class CL Class WL Class WR Class IR Class IL Variables Age Mo Grip Input c02 CR 52 85 0.250 Input c04 CR 71 27 0.652 Input c05 CL 63 12 0.788 Input c06 WL 77 26 0.438 Input c07 WR 61 13 0.717 Input c10 IR 68 9 0.730 Input c11 IL 63 13 0.934 Input c12 IL 29 12 1.170 Input c13 IR 46 12 0.964 Input c14 IR 75 14 0.655 Input c15 IL 68 13 1.098 Input c16 IR 69 12 1.028 Input c18 WL 40 20 0.698 Input c19 WL 53 13 0.547 contrast file: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 design matrix: +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +52.0 +0.0 +0.0 +0.0 +0.0 +0.0 +85.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.25000 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +71.0 +0.0 +0.0 +0.0 +0.0 +0.0 +27.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.65200 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +63.0 +0.0 +0.0 +0.0 +0.0 +0.0 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.78800 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +77.0 +0.0 +0.0 +0.0 +0.0 +0.0 +26.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.43800 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +61.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.71700 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +68.0 +0.0 +0.0 +0.0 +0.0 +0.0 +9.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.73000 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +63.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.93400 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +29.0 +0.0 +0.0 +0.0 +0.0 +0.0 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.17000 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +46.0 +0.0 +0.0 +0.0 +0.0 +0.0 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.96400 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +75.0 +0.0 +0.0 +0.0 +0.0 +0.0 +14.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.65500 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +68.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.09800 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +69.0 +0.0 +0.0 +0.0 +0.0 +0.0 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.02800 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +40.0 +0.0 +0.0 +0.0 +0.0 +0.0 +20.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.69800 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +53.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.54700 +0.0 +0.0 +0.0 output: gdfReadHeader: reading /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 59.6429 13.4462 1 Mo 20.0714 18.7444 2 Grip 0.762071 0.248599 Class Means of each Continuous Variable 1 CR 61.5000 56. 0.4510 2 CL 63. 12. 0.7880 3 WL 56.6667 19.6667 0.5610 4 WR 61. 13. 0.7170 5 IR 64.5000 11.7500 0.8442 6 IL 53. 12.6667 1.0673 INFO: gd2mtx_method is dods Reading source surface /home/schulz/freesurfer/subjects/premotorstroke/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267
Re: [Freesurfer] TALx coordinates
Hi Doug, I'm looking at the $FREESURFER_HOME/average/mni152.register.dat and I can see some relation with the formula you provided. It appears that y and z are swapped, and the offsets are all different. Do you know why they are so? By the way, is there a way I can ask mri_surfcluster to read mni152.register.dat? fsaverage 1.00 1.00 0.15 9.975314e-01 -7.324822e-03 1.760415e-02 9.570923e-01 -1.296475e-02 -9.262221e-03 9.970638e-01 -1.781596e+01 -1.459537e-02 -1.000945e+00 2.444772e-03 -1.854964e+01 0 0 0 1 tkregister Thanks a lot! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/15/13 3:53 PM, Douglas Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: That converts from MNI305 to MNI152 without going through the talairach itself. When FS computes Tal coords, it does so nonlinearly. doug On 9/11/13 12:08 PM, Yang, Daniel wrote: Hi Doug, It's pretty awesome. So accordingly, MNI152x = (0.9975) MNI305x + (-0.0073) MNI305y + (0.0176) MNI305z + (-0.0429) * 1 MNI152y = (0.0146) MNI305x + (1.0009) MNI305y + (-0.0024) MNI305z + (1.5496) * 1 MNI152z = (-0.0130) MNI305 + (-0.0093) MNI305y + (0.9971) MNI305z + (1.1840) * 1 The last row of the M (i.e., [-0.0429 1.5496 1.1840]') looks like some sort of offset to me, correct? In other words, we are obtaining MNI305 first, Freesurfer convert that to TAL by default (question: is it done linearly or non-linearly?), and then we can manually convert it to MNI152 also. Thanks so much! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 6:52 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu wrote: Hi Yang, I've computed a matrix that should do the trick. If you are in matlab, then M = [0.9975 -0.00730.0176 -0.0429 0.01461.0009 -0.00241.5496 -0.0130 -0.00930.99711.1840 0 0 01.] P305 = [MNI305x MNI305y MNI305z 1]'; P152 = M*P305 Can you give this a shot and see if it makes sense? It will probably be hard to tell since the matrix is pretty close to identity. doug On 09/10/2013 05:17 PM, Yang, Daniel wrote: Thanks, Doug. I am really hoping to get MNI152 (because I also use fsl). Are MNI305 and MNI152 the same? How can I obtain MNI152 coordinates? Best, Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 On 9/10/13 5:14 PM, Douglas N Greve gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu%3E wrote: It is an estimate of Tal coords from the MNI305. See http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach If you want MNI305, run mri_surfcluster with --nofixmni doug On 09/10/2013 05:08 PM, Yang, Daniel wrote: Hi all, The output of mri_surfcluster --sum shows TalX TalY TalZ. I am wondering if they are based on the Talairach system or some sort of MNI-Talairach system. If the latter, can you tell me something more about it? Like a webpage that describes its relationship between the MNI152 or the Talairach system? I find it confusing because mri_surfcluster said: INFO: fixing MNI talairach coordinates Thanks! Daniel -- Yung-Jui Daniel Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@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 gr...@nmr.mgh.harvard.edumailto:gr...@nmr.mgh.harvard.edu mailto:gr...@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.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@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
Re: [Freesurfer] How to convert a thickness file (i.e. lh.thickness) ti a 3D nifti file
Hi Fabrice, what would converting a thickness file (which has one value for each point on the surface) to a volume mean? Would you want just a strand of voxels with the thickness values at the gray/white boundary? At the pial surface? Would you want the ribbon filled with the same value? If you want the distance to either surface you can use mris_distance_transform. cheers Bruce On Wed, 18 Sep 2013, Fabrice Crivello wrote: Dear Freesurfer users, I am searching how to use the mri_surf2vol command in order to convert a lh.thickness file into a 3D .nii file (in the original subject space). Many Thanks, Fabrice ___ 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] expanding pial surface
Hi Gabor, it depends on the cause. Typically we fix this by placing control points in the subjacent WM that is 110 cheers Bruce On Wed, 18 Sep 2013, Gabor Perlaki wrote: Dear all, In the suggested workflow there is clear deescription of how to correct pial surface including non-cortex within the boundaries, but there is no description of how to expand the pial surface if it doesn't include the cortex within boundaries. Could anybody help me in this issue? Thanks, Gabor -- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-4098480 E-mail: petzinger.ga...@gmail.com ___ 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] mri_glmfit error: negative DOF -10
It usually means that the number of subjects in the input is less (10 less) than the number of regressors. It looks like you have about 14 input subjects and 24=6*4 regressors. You need to add subjects or remove regressors (ie, classes or covariates) doug On 9/18/13 11:41 AM, Robert Schulz wrote: Hello, I am using mri_glmfit to perform a correlation analysis between some surface-based DTI measures and a behavioural outcome (grip), aiming to correct for scannertyp (C,I,W), handedness (R,L) as discrete variables and age (AGE) and duration (Mo) as continuous covariates. Please find the fsgd file, the contrast file and the calculated Xg down below. However, I get the follow error: DOF = -10 ERROR: DOF = -10 (the complete output is attached) I would be grateful if somebody could help. I already tried it with demeaned data, z-transformed data, it doesn't help. Thank you for your help, Robert fsgd file: GroupDescriptorFile 1 Title OSGM Class CR Class CL Class WL Class WR Class IR Class IL Variables Age Mo Grip Input c02 CR 52 85 0.250 Input c04 CR 71 27 0.652 Input c05 CL 63 12 0.788 Input c06 WL 77 26 0.438 Input c07 WR 61 13 0.717 Input c10 IR 68 9 0.730 Input c11 IL 63 13 0.934 Input c12 IL 29 12 1.170 Input c13 IR 46 12 0.964 Input c14 IR 75 14 0.655 Input c15 IL 68 13 1.098 Input c16 IR 69 12 1.028 Input c18 WL 40 20 0.698 Input c19 WL 53 13 0.547 contrast file: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 design matrix: +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +52.0 +0.0 +0.0 +0.0 +0.0 +0.0 +85.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.25000 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +71.0 +0.0 +0.0 +0.0 +0.0 +0.0 +27.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.65200 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +63.0 +0.0 +0.0 +0.0 +0.0 +0.0 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.78800 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +77.0 +0.0 +0.0 +0.0 +0.0 +0.0 +26.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.43800 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +61.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.71700 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +68.0 +0.0 +0.0 +0.0 +0.0 +0.0 +9.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.73000 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +63.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.93400 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +29.0 +0.0 +0.0 +0.0 +0.0 +0.0 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.17000 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +46.0 +0.0 +0.0 +0.0 +0.0 +0.0 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.96400 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +75.0 +0.0 +0.0 +0.0 +0.0 +0.0 +14.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.65500 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +68.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.09800 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +69.0 +0.0 +0.0 +0.0 +0.0 +0.0 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.02800 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +40.0 +0.0 +0.0 +0.0 +0.0 +0.0 +20.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.69800 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +53.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.54700 +0.0 +0.0 +0.0 output: gdfReadHeader: reading /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 59.6429 13.4462 1 Mo 20.0714 18.7444 2 Grip 0.762071 0.248599 Class Means of each Continuous Variable 1 CR 61.5000 56.
Re: [Freesurfer] (no subject)
Hi again Doug, I'm looking at the stats file associated to aparc and perirhinal is not there. I have looked for perirhinal and I found it in ?h.BA.stats, so I guess what I need to update is the BA annot, right? Thanks a lot! Jesus From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Tuesday, September 17, 2013 5:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject) That should have done it. You are looking at the ?h.aparc.annot, right? Send me the recon-all.log file doug On 9/17/13 10:34 PM, Gomar, Jesus wrote: Hi Doug, I have run recon-all -s subject -cortparc -parcstats and the process finished without errors, but the aparc files do not have the perirhinal cortex on it. I have noticed that when I recon with 5.3 perirhinal labels are created on the label folder, but when I run recon-all -s subject -cortparc -parcstats (to update 5.1 to 5.3) no perirhinal labels are created. Do I need to add an additional flag to recon-all -s subject -cortparc -parcstats to obtain perirhinal measures? Thanks for your help! Jesus The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this communication is not the intended recipient, or the employee or agent responsible for delivering this communication to the intended recipient, you are hereby notified that any dissemination, distribution, copying or disclosure of this communication and any attachment is strictly prohibited. If you have received this transmission in error, please notify the sender immediately by telephone and electronic mail, and delete the original communication and any attachment from any computer, server or other electronic recording or storage device or medium. Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege.___ 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] Skull strip
Hi, I am learning to use the program. I have some questions about how to edit skull strip manually. In this procedure is correct to remove only the residual skull or even other non-cerebral elements (eg meninges)? So far I have never found remaining skull but small residual portions of meninges. Also, I have to correct it inside and/or outside the red line of brainmask? I noticed that by removing the small remaining portions of the meninges ( outside of the red line), during the subsequent processing are cut pieces of brain cortex, and also sucortical volumes changes (i.e. callosal volume). Thank you, Irene ___ 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] High intensity GM being omitted
Attached is an image that describes my issue. WM in the temporal region is being omitted after running recon-all. Most of the omitted voxels are in the 120-130 range. It's causing an issue with the underlying WM voxels as well, they've simply disappeared. I can see how this voxel intensity limit would help omit dura, vessels, and other high intensity objects but in this case it's a bit of an issue and I'm not sure how to A) rectify it (I could replace the WM voxels?) B) keep it from happening again. Is there a way to give freesurfer an intensity threshold to work with? Please advise! Jon attachment: Screen Shot 2013-09-18 at 3.08.59 PM.png___ 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] make_average_subject without aparc and talairach.xfm
Hi Doug, just a quick follow-up on my previous questions regarding custom average surfaces. I guess I am a bit confused regarding the relationship of custom templates and custom average surfaces. I made a custom template and a custom average surface. However, I don't understand how they are related to each other. Furthermore, I am wondering which is used when I use rawfunc2surface-sess. Thanks, Caspar 2013/8/19 Douglas Greve gr...@nmr.mgh.harvard.edu You can just copy in the T1.mgz from fsaverage (won't matter that it is human), or you can try running make_average_volume to make a NHP volume. Not sure that will work, but make sure to use --no-aseg doug On 8/19/13 8:43 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I ran make_average_surface.no-aparc and identity matrices on my data, and I seems to have completed the averaging without an error. However, when I try to view the result with tksurfer, I get an error because there is no average T1 for the average subject. How would you recommend I go about this? Do you have a make_average_volume.no-aparc as well, shall I make an average T1 manually, or can I skip the average T1? Thanks! Caspar 2013/8/19 Douglas N Greve gr...@nmr.mgh.harvard.edu I would probably just try to do it by hand. Copy a file with the identity matrix into the right folder, then run tkregister2 --fstal --s subject It will bring the human atlas up. I would then play with it a little bit to get it to look ok. For surface-based applications, it will have no effect on statistics, but it will affect the appearance of the pial and white surfaces (if you display your results on those instead of on the inflated). If you are not going to display on the white or the pial, then you can just leave it as the identity doug On 08/19/2013 03:57 PM, Caspar M. Schwiedrzik wrote: Hi Doug, that's great, thank you very much. From the previous posts I assume that this does not solve the issue with the missing Talairach.xfm. Do you have a recommendation for that? Thanks, Caspar 2013/8/19 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto: gr...@nmr.mgh.harvard.edu I've put that script here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote: Hi Freesurfer experts, I am trying to make an average surface from several monkey surfaces, and I ran into a problem with make_average_subject. Specifically, I do not have an aparc file nor a talairach.xfm. It seems that these problems have come up on the list before ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html ). I tried to download make_average_surface.no-aparc, however, the link seems to be broken. Also, I couldn't find a solution to the missing talairach.xfm on the list. It would be great if you could provide me with a working link to make_average_surface.no-aparc; any suggestions regarding making an average surface without talairach.xfm would be appreciated. I already made a new template and aligned all individual surfaces to this template. Thanks! Caspar ___ Freesurfer mailing list Freesurfer@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 gr...@nmr.mgh.harvard.edu mailto:gr...@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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@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 . 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop:
[Freesurfer] talairach transforms
Trying autorecon1 with the example data set Bert,there is error in talairach transforms.What would be the problem? ___ 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.
