Freesurfer

freesurfer@nmr.mgh.harvard.edu

30088 discussions

Skull strip
by irene saviozzi 18 Sep '13

18 Sep '13

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

1 0

(no subject)
by Gomar, Jesus 18 Sep '13

18 Sep '13

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.

2 2

mri_glmfit error: negative DOF -10
by Robert Schulz 18 Sep '13

18 Sep '13

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: +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +52.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +85.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.25000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +71.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +27.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.65200 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +63.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +12.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.78800 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +77.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +26.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.43800 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +61.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +13.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.71700 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +68.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +9.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.73000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +63.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +13.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.93400 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +29.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +12.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.17000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +46.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +12.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.96400 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +75.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +14.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.65500 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +68.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +13.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.09800 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +69.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +12.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.02800 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +40.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +20.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.69800 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +53.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +13.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.54700 +0.00000 +0.00000 +0.00000 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 56.0000 0.4510 2 CL 63.0000 12.0000 0.7880 3 WL 56.6667 19.6667 0.5610 4 WR 61.0000 13.0000 0.7170 5 IR 64.5000 11.7500 0.8442 6 IL 53.3333 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 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.196.2.6 2011/05/05 20:54:25 greve Exp $ cwd /home/schulz/dti/premotorstroke/02 cmdline mri_glmfit --glmdir /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l --y /home/schulz/dti/premotorstroke/wm-probe/fs_no3/l_average_all_smooth.mgh --fsgd /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.fsgd --C /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.mtx --surf fsaverage lh --cortex sysname Linux hostname BINS-Linux1 machine x86_64 user schulz FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/schulz/dti/premotorstroke/wm-probe/fs_no3/l_average_all_smooth.mgh logyflag 0 usedti 0 FSGD /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.fsgd labelmask /home/schulz/freesurfer/subjects/premotorstroke/fsaverage/label/lh.cortex.label maskinv 0 glmdir /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l Loading y from /home/schulz/dti/premotorstroke/wm-probe/fs_no3/l_average_all_smooth.mgh INFO: gd2mtx_method is dods Saving design matrix to /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/Xg.dat Normalized matrix condition is 1420.61 Matrix condition is 954196 Found 149955 points in label. Pruning voxels by thr: 0.000000 Found 136331 voxels in mask Saving mask to /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/mask.mgh Reshaping mriglm->mask... search space = 67992.449783 DOF = -10 ERROR: DOF = -10 -- Besuchen Sie uns auf: www.uke.de _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING

2 1

expanding pial surface
by Gabor Perlaki 18 Sep '13

18 Sep '13

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.gabor(a)gmail.com

2 1

How to convert a thickness file (i.e. lh.thickness) ti a 3D nifti file
by Fabrice Crivello 18 Sep '13

18 Sep '13

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

2 1

TALx coordinates
by Yang, Daniel 18 Sep '13

18 Sep '13

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

5 10

rewritten: updating the tables and volumes associated with aseg.mgz
by silver47＠gmx.com 18 Sep '13

18 Sep '13

Dear Freesurfer Experts, I'm sorry if I have not been clear with my question so far. I have completed the cortical analysis on a number of subjects using 5.3, with all requiring some editing and re-running. Now that I have the final surfaces, to update the aseg.mgz, I would like to run: recon-all -subjid subject -surfsegedit before examining the aseg.mgz more closely. Looking at one aseg.mgz (for example) I can see that edits could be made to label more of the cerebellar cortex as well as some relabelling of the brainstem. After performing edits such as these to aseg.mgz (and possibly to other subcortical structures) would I then run: recon-all -subjid subject -aparc2aseg -segstats -wmparc to update stats/aseg.stats, aparc+aseg.mgz, aparc.a2009s+aseg.mgz wmparc.mgz, and stats/wmparc.stats without changing the cortical stats files such as lh.aparc.stats? Using this approach, I'm hoping that I can begin the group analysis of the cortex using lh.aparc.stats (and the like) while the subcortical review is underway, without having to re-run this group analysis with subsequent updates of lh.aparc.stats that would occur by running -autorecon3 (or similar) to update aseg.stats, aparc+aseg.mgz, etc. Please let me know if this approach is valid, any suggestion would be appreciated. Thanks, P

1 0

"Nuisance factors" in Qdec
by ye tian 17 Sep '13

17 Sep '13

Dear Freesurfers, I have a question concerning the "nuisance factors" in the qdec dialogue. Suppose I have two independent variables x1 (discrete) and x2 (continuous), and only one observable y. I choose "Discrete (Fixed factor) = x1", "Continuous (covariate) = x2". If I further chose "Nuisance factor = x2", does that imply that 1) my contrast matrix is (0 1) 2) null hypothesis: Y is independent of x2 Thank you very much! Sincerely, Ye

3 4

Ventriculomegaly causing segmentation issues
by Victor Kovac 17 Sep '13

17 Sep '13

Dear FreeSurfer experts, There are a number of patients in my study with significant ventricular dilation, which is causing problems with segmentation of the ventricles and corpus callosum, in particular, after recon-all (image attached). I am using v5.3. I manually adjusted the talairach, but this did not fix the issue. Is there anything else I can try? It is very important that I get at least some volumetric data from these patients, as they are suffering from the worst neurologic disease. I appreciate any advice you can provide. Thanks, Victor

2 1

volume of subcortical structure calculation
by Subhabrata Chaudhury 17 Sep '13

17 Sep '13

Hello Where can I get information on how freesurfer calculates volumes of subcortical structures ? Is there a paper which provides insights into this method ? Is it that for certain subcortical structures, it just counts the number of voxels and adds them up since the voxels are 1mm3 ? Thanks Subha

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