Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

recon-all -autorecon2 error.
by miracle ozzoude 29 Nov '16

29 Nov '16

Hello Freesurfer, I ran recon-all -autorecon 1 -s subjID on T1 (T1_nii) image and after that, I replaced the skull stripped volume generated from FS with the skull stripped volume from lesion explorer ( using mri_convert in_type analyze in_orientation LAS out-type img out_orientation LAS mgz; cp folder/brainmask.mgz folder/subjID/mri/brainmask.mgz). Then, I ran recon-all -autorecon2 -autorecon2 -s subjID. My recon-all is stucked at CORRECTION DEFECT 0 (vertices=49378, convex hull=3422, v0 =0) XL defect detected.... Please how do I resolve this problem? I am running freesurfer-6 development. I have attached the recon-all/recon-all status to the email. Thank you very much

4 15

Request for patch for mri_convert, nifti1Read(): unsupported slice timing pattern 5 error
by Jennifer Barredo 29 Nov '16

29 Nov '16

Hello Freesurfer experts, I'm trying to run the TRACULA preprocessing pipeline using data in NIFTI-1 format, but am receiving the following error: "nifti1Read(): unsupported slice timing pattern 5" Several other users have run into this problem. In the archives, there are a few links to dead file transfer protocols for a patch for mri_convert that might solve my problem. May I please have a patch for mri_convert? I'm using freesurfer-Darwin-lion-stable-pub-v5.3.0 and OSX Yosemite. Thank you, Jennifer -- Jennifer Barredo, PhD Staff Scientist Providence VA Medical Center Research Affiliate Brown Institute for Brain Sciences jlbarredo(a)gmail.com Jennifer.Barredo(a)va.gov

1 0

running freesurfer 5.3 on Ubuntu 16.04
by Parzer, Peter 28 Nov '16

28 Nov '16

Hi, there is an old thread about an recon-all error on Ubuntu 16.04, that is caused by an incompatibility between the MNI tools and the perl version 5.22 distributed with Ubuntu 16.04. This has been fixed in the development version. Has someone a more detailed description how this was fixed so that I could try to back-port this fix to freesurfer 5.3? Downgrading perl in Ubuntu 16.04 is not possible, there are to many packages depending on it and there is no other version of perl in the repositories. We have already about 100 subjects analyzed with version 5.3 and I hesitate to re-analyze all of them with the development version. Since we had to update Ubuntu to 16.04 for other reasons, we use freesurfer 5.3 now inside a virtual machine with Ubuntu 14.04 installed, which is not very efficient. Peter

2 1

recon-all error with nii file
by Htet, Aung Thu 28 Nov '16

28 Nov '16

Hi Everybody, I am trying to use an nii file in recon-all, where subject_dir does not exist yet. recon-all -subject <subject-name> -i <file.nii> -all But I am having this error: niiRead(): unsupported datatype 128 (with scl_slope != 0) in /home/fsuser/aung/18991230_000000s001a000A.nii Any help in understanding the error would be appreciated. Thanks in advance. Aung

2 1

Download latest version of mris_pmake
by Garikoitz Lerma-Usabiaga 28 Nov '16

28 Nov '16

Hi, I am using the 2011 of mris_pmake and I've seen in the list that there are newer versions. I am using both linux and mac. It's giving several errors when computing distances in fsaverage (just in some of the pairs), so I hope that the new version will be able to solve them. Thank you very much. Gari

2 3

Trouble with Two Stage Longitudinal Analysis
by Timothy Hendrickson 28 Nov '16

28 Nov '16

I was able to figure out my design matrix issue. I had not originally appreciated that there were no data sets from a particular class. Thanks! -Tim FreeSurfer experts, I am attempting to use the two stage model for longitudinal analysis, however I keep receiving an error message that my design matrix is poorly scaled. I belive I have cross-checked my qdec, fsgd, design matrix, and contrast files and they all match so I do not think the problem is a mismatch. I am wondering if I made some sort of mistake in my script design or design matrix creation... Anyway here is the command line input: mri_glmfit --glmdir lh.AllSite.gender.group.Age.thickness.fwhm10.twoStage.glmdir --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat --y lh.testretest.thickness-pc1.stack.fwhm10.mgh --C age_AcctGroup_AcctSite_AcctGender_twoStage.DOSSDS.mtx --C DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_twoStage.DOSSDS.mtx --C DiffDiagnosis_ControlMore_AgeSlope_AcctSite_AcctGender_twoStage.DOSSDS.mtx --C DiffGender_MaleMore_AcctSite_AcctDiagnosis_AcctAge_twoStage.DOSSDS.mtx --C DiffGender_MaleMore_AgeSlope_AcctSite_AcctDiagnosis_twoStage.DOSSDS.mtx --label lh.testretest.fsaverage.cortex.label --surf fsaverage lh The error message is attached within file AllSite_twoStageLongitudinal_DsgnMtxErr.txt Additionally I've included my analysis script, all timepoint qdec file, temporal average qdec file, fsgd file, and design matrix. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) Design matrix ------------------ 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.600 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.800 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.500 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.200 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.295 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.800 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.495 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.095 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.895 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.665 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.745 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 12.500 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 13.995; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 14.740; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.265 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.240 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 13.415 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 14.835 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 14.240 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.835 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.825 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.835 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 15.820; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 13.675 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 15.420; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.245 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.695; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.400 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.310 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.450; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.400; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 10.955 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.410 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.905 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.210 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.500; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.200 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.305; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.435 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.895 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.795 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.500 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.900 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.985 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.390 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.180; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.380 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.200; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.090 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.790 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.090; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.090; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.685 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.085 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.810 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.885 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.900 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.995 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.595 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.200 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.950 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.490 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.495 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.295 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.595 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.415 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.605 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.605 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.600; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.600; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.005 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.705 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.585 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.795 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.690 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.190 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 14.400 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.605 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.210 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.090 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.495 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.195 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.595; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.400 0.000 0.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: *[image: Attachment:] <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/AllSite…> AllSite_longAnalysis_11_16_16_noYears.table.dat <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/AllSite…>* *Description:* Binary data *[image: Attachment:] <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/cross.A…> cross.AllSite_longAnalysis_11_16_16_noYears.table.dat <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/cross.A…>* *Description:* Binary data *[image: Attachment:] <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/DOSSDS.…> DOSSDS.twoStage_AllSite_Gender_Group_Age.dat <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/DOSSDS.…>* *Description:* Binary data *[image: Attachment:] <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/twoStag…> twoStageLongitudinal_AllSite_Gender_Group_Age.fsgd <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50287/twoStag…>* *Description:* Binary data #!/bin/bash #Author Timothy Hendrickson #Modified last -July 12, 2016 #This is a script which will run the two-stage model from Freesurfer. #debugging set -x # set nice priority to 19 for given job renice -n 19 -p $$ # set command argument to determine hemisphere hemi=$1 #will accept '$hemi' or 'lh' #set qdec file for first stage qdec=AllSite_longAnalysis_11_16_16_noYears.table.dat #set qdec file for second stage tempAvgQdec=cross.AllSite_longAnalysis_11_16_16_noYears.table.dat #set fsgd file for second stage, created in part by performing the following command to average covariates #fsgdfile=twoStageLongitudinal_AllSite_Gender_Group_StanAges.fsgd fsgdfile=twoStageLongitudinal_AllSite_Gender_Group_Age.fsgd #set data dir and SUBJECTS_DIR for freesurfer datadir=`pwd -P` SUBJECTS_DIR=$datadir #set base up to be used later when determining .mgh and .glmdir base=$hemi.AllSite.gender.group.Age.thickness.fwhm10.twoStage smooth=10 # First stage: Prepare the Data long_mris_slopes --qdec $qdec --meas thickness --hemi $hemi --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time age --qcache fsaverage --sd $SUBJECTS_DIR #Second stage: Perform tests on data. #long_mris_slopes: Computes slope maps (e.g. of thickness) in a longitudinal study. #The slope is computed within subject from the longitudinally processed #results (taken from the <tpNid>.long.<template> directories) and the #output is written into the subjects <template>/surf directory for further #processing long_mris_slopes --qdec $tempAvgQdec \ --meas thickness \ --hemi $hemi \ --sd $SUBJECTS_DIR \ --do-pc1 --do-label \ --generic-time \ --fwhm $smooth \ --qcache fsaverage \ --stack-pc1 $hemi.testretest.thickness-pc1.stack.mgh \ --isec-labels $hemi.testretest.fsaverage.cortex.label mri_glmfit \ --glmdir $base.glmdir \ --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat \ --y $hemi.testretest.thickness-pc1.stack.fwhm${smooth}.mgh \ --C age_AcctGroup_AcctSite_AcctGender_twoStage.DOSSDS.mtx \ --C DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_twoStage.DOSSDS.mtx \ --C DiffDiagnosis_ControlMore_AgeSlope_AcctSite_AcctGender_twoStage.DOSSDS.mtx \ --C DiffGender_MaleMore_AcctSite_AcctDiagnosis_AcctAge_twoStage.DOSSDS.mtx \ --C DiffGender_MaleMore_AgeSlope_AcctSite_AcctDiagnosis_twoStage.DOSSDS.mtx \ --label $hemi.testretest.fsaverage.cortex.label \ --surf fsaverage $hemi for i in abs pos neg do mri_glmfit-sim \ --glmdir ${base}.glmdir \ --cache 1.3 $i \ --cwp 0.05 \ --2spaces & done _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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 athttp://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. Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay)

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Re: [Freesurfer] Cohen's D = gamma.mgh / rstd.mgh?
by Elijah Mak 28 Nov '16

28 Nov '16

Hi Doug, This is my main objective. 1. PET in Group 1 vs Group 2 2. Thickness in the same sample, Group 1 vs Group 2 3. ASL in the same sample of Group 1 vs Group 2 4. Create a binary mask of the overlapping corrected sig voxels from 1-3. 5. This mask is therefore a site of co-localised atrophy, perfusion and PET changes in Group wrt Group 2. Now, I would like to look at how the effect sizes of 1-3 compare against one another, above and beyond the spatial overlap. I hope this is clearer, but let me know if I could provide more information. I thought about looking at *Z-scores* like some other studies, but I find that it is highly dependent on the range of the SD, which differed to a large extent (PET having a range of 1-10 vs 1-3 in atrophy). Hence I thought the Cohen's *D *might represent a more plausible workaround by pooling the SD across both groups, Thanks. Best Wishes, Elijah

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Re: [Freesurfer] Cohen's D = gamma.mgh / rstd.mgh?
by Elijah Mak 28 Nov '16

28 Nov '16

Dear Doug, Thanks. Do you mean use ROI averages as the samples and then test across ROIs? This would be unusual as the interpretation is problematic. I would probably compute a single number per subject that is a weighted sum/difference of the ROI values, then test whether this one number is different across subjects. Probably a silly question.. but how can I get the data at the subject-level as the effectsize.mgh is derived at the group-level after mri_glmft? On a similar note, if I want to simply report the effect size of a significant cluster, could I use mri_glmfit to extract the averaged effect size for the cluster by feeding it as a mask to mri_segstats? Best Wishes, Elijah

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Re: [Freesurfer] LME: contrast questions
by jorge luis 28 Nov '16

28 Nov '16

Yes, it was arbitrary. A linear trajectory was a sufficiently good model for the mean response over time for most of the cortex points in my analyses. Also if you only have at most three time points per user then you can only have at most two random effects in your mixed-model (intercept and time). Time squared, if considered, would be just a fixed effect. Best-Jorge De: Jordi Pegueroles <jordi(a)pegueroles.cat> Para: jorge luis <jbernal0019(a)yahoo.es> CC: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Enviado: Lunes 28 de noviembre de 2016 11:34 Asunto: Re: LME: contrast questions Thank you for your quickly answer Jorge. What is the rule for decide if we have to use a quadratic term in the model? That is, in your example you use the 80% of the length of the lh.cortex as a threshold. Is this value an arbitrary one? Thank you again, A 2016-11-28 16:05, jorge luis escrigué: > Hi Jordi > > You have implicitly included the reference group in your statistical > model by including an intercept term and a time variable: > > group0 intercept: ß1 > group0 time: ß2 > group1 intercept: ß1+ß3 > group1 time: ß2+ß4 > group2 intercept: ß1+ß5 > group2 time: ß2+ß6 > > From here you can quickly see that your proposed contrast for the > differences in the mean response over time between group1 and group2 > is correct. > > Finally the region growing estimation method should yield more > precise (lower variance) estimates for the ßs but I think it’s (might > be) too complicated to setup with the current scripts. The vw method > will produce good estimates too. So I recommend the vw estimation > method if things get too complicated for you with the region-wise > method. > > Cheers > -Jorge > >> ------------------------- >> DE: Jordi Pegueroles <jordi(a)pegueroles.cat> >> PARA: Freesurfer <freesurfer(a)nmr.mgh.harvard.edu>; >> jbernal0019(a)yahoo.es >> ENVIADO: Lunes 28 de noviembre de 2016 5:11 >> ASUNTO: LME: contrast questions >> >> Dear FS experts, >> >> I am trying to run a LME model for three groups (group0, group1 and >> group2) and (almost all) with three time points, all processed using >> the >> Longitudinal FS stream. >> >> Our intention is to compare the differences between group0 against >> group1 and group0 against group2. I have followed the online LME >> tutorial and I have adapted your code to my data. However, I think I >> have not well understood the steps and I have few questions that you >> will be able to answer me... >> >> i) In the X matrix I put the following columns: >> >> 1) intercept >> 2) time (years from baseline) >> 3) group1 (binary variable: 1 if belongs to group1) >> 4) group1.*time >> 5) group2 (binary variable: 1 if belongs to group2) >> 6) group2.*time >> >> I don't understand why I do not have to include the reference group >> (in my case group0 and group0.*time) in the design matrix. How I can >> see >> the progresion of the reference group if I did not include it in the >> design matrix? How I can compare both progressions if the time of the >> group0 subjects is not taking into account? >> >> ii) Linked to the previous question, if I want to compare the >> differences in time between group1 and group2... Should the contrast >> be >> C = [0 0 0 1 0 -1]? >> >> iii) Finally, between the vw method and the region growing method >> which >> one is more accurate? In other words, which one do you recommend to >> use? >> >> Thank you, >> >> -- >> Jordi. -- Jordi.

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using different versions of Freesurfer?
by Lee Subin Kristine 28 Nov '16

28 Nov '16

Hi Freesurfer team, I have currently used version 5.3. for all my cortical parcellations of MRI data, but for PET images of those same subjects I used the gtmseg, mri_coregister, gtmpvc of the 6.0 beta version to get partial volume effect-corrected SUVR(standard uptake value ratios). I am aware and heard that using different versions of Freesurfer is not recommended, and that any results from the developmental version should not be used for publication yet until it is officially released. However I was wondering if in my case(with the commands I used above), this would not be such an issue. Thanks a bunch, Kristine

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