Freesurfer June 2021

freesurfer@nmr.mgh.harvard.edu

97 participants
140 discussions

Unit of the Numbers in cache.th40.neg.y.ocn.dat
by Na, Xiaoxu 17 Feb '24

17 Feb '24

External Email - Use Caution Dear Freesurfer Experts, As I'd like to extract the average value of each subject in the cluster after running group analysis, may I know the unit of these numbers? Since the one I'm running is surface area, and the cluster is 444mm^2, all the numbers in the file cache.th40.neg.y.ocn.dat is in the range of [0.55 1.05], may I know if this is correct and if so, how the unit is for those? Thanks a lot! ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx 1 -4.8321 40067 444.11 -58.1 -16.6 -23.9 0.0002 0 0.0004 670 -2784.11 Regards, Xiaoxu ---------------------------------------------------------------------- Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

4 11

Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

4 4

Reliability and sensitivity of two whole-brain segmentation approaches − ASEG and SAMSEG
by Donatas Sederevicius 28 Aug '22

28 Aug '22

External Email - Use Caution A new pre-print paper comparing two FreeSurfer’s whole-brain segmentation methods - ASEG and SAMSEG is now available (see the link below). The study is of great interest to many researchers in the field, providing new insights and guiding the selection of the processing method. https://www.biorxiv.org/content/10.1101/2020.10.13.335737v1

3 3

WM or Pial edits to correct surfaces
by Alexopoulos, Dimitrios 27 Sep '21

27 Sep '21

External Email - Use Caution Hi users, We're having some issues with running some of our 2-3yo data (0.8mm isotropic) through FS7 with and without the -hires flag. There are persistent issues with the frontal lobe regions where the pial has not extended to outer surface as illustrated below. The WM surface contour look reasonable but the pial has underestimated the outer cortex resulting in an incorrect surface (below). I don't think control points will work (low intensity values in the 50-60s), and no WM to add to the WM.mgz. Any suggestion on how to push the pial surface out to capture the cortical surface?? Thx. Jim [cid:image004.png@01D752FB.04011E10] [cid:image005.jpg@01D752FB.04011E10] [cid:image001.png@01D752F8.E6507AC0] [cid:image002.png@01D752F8.E6507AC0] [cid:image006.png@01D752FB.04011E10][cid:image007.jpg@01D752FB.04011E10] ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

3 30

Error in hippocampal subfields longitudinal processing
by Kaija Sander 29 Jul '21

29 Jul '21

External Email - Use Caution Hello all, I am attempting to obtain the hippocampal subfields segmentation in a small longitudinal dataset (18 participants, 2 time points each). I have successfully been able to run recon-all, recon-all -base and recon-all -long (or at least, these steps appear to be completed without errors). However, when trying to run segmentHA_T1_long.sh, I encountering the following error (I have also attached the full log file of one of the subjects): Open file failed because file '/tmp/MCR_511464988/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m' has invalid content. Details: 'file is closed.failbit is set.' The file "/tmp/MCR_511464988/.mcrCache8.4/Segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2/bin/kvlWriteImage.m" cannot be executed. Error in SegmentSubfieldsT1Longitudinal (line 1795) What is strange is that this has only happened for a couple of subjects, and has worked fine for the few others I did. Does anyone have any suggestions of what might be going wrong and how to fix it? Thank you very much, Kaija FreeSurfer version: freesurfer-local-build-dev-20200116 Platform: Ubuntu 18.04.5

3 9

Yeo atlas for children!
by Martin Juneja 16 Jul '21

16 Jul '21

External Email - Use Caution Dear experts, I used Yeo's 17-network parcellation to study the association between network-wise cortical volume and a clinical variable in adolescents. I received the following two questions from the reviewers regarding the use of Yeo's atlas. I would really appreciate if someone could help us in addressing these questions: *1) Could the author justify their choice to use a functional parcellation on structural data? How is using this parcellation helpful in understanding the brain? All in all, the authors need to justify the superiority of using Yeo's 17-area parcellations on structural data over other methods of parcellation/analysis. * *2) One issue with Yeo's parcellation also stems from the fact that this parcellation was derived from adult connectomes. Could the authors also address this issue and provide examples that justify their approach.* Thanks.

2 4

how to visualize statistical maps in FS7.1?
by Bernardoni, Fabio 15 Jul '21

15 Jul '21

External Email - Use Caution Dear Freesurfers I recently moved to FS7.1 and I was trying to reproduce my workflow I had with FS5.3. To visualize statistical maps, I had always used tksurfer. It seems, however, it is no longer maintained. When I launch it it fails to find out the tix, tcl, etc libraries. Following this thread: https://secure-web.cisco.com/1v7sQGKZgCQ9d6BT0fUpIf9QvmP5selhkoGYWs1-X9TSsF… I tried to use tksurferfv. However, when trying to overlay the sig.mgh output of mriglmfit, on an inflated fsaverage surface, the program shuts down, with this error: freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:curvature=/usr/local/freesurfer/subjects/fsaverage/surf/lh.curv -viewport 3d terminate called after throwing an instance of 'int' Abort (core dumped) What would you suggest to visualize statistical maps in FS7? Is my problem expected? Thank you in advance for your attention Fabio Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1fJ-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2Xh…; http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe… +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6E… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6E… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

3 6

trac-all -prep problem (error: corRead(): can't open file PATH/TO/DCMROOT/COR-.info)
by juergen.haenggi＠upd.unibe.ch 15 Jul '21

15 Jul '21

External Email - Use Caution Dear TRACULA experts I try to run trac-all -prep using the "Perform registration-based B0-inhomogeneity compensation“ option, but the following error occurred: mri_convert /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/ /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0mag.nii.gz mri_convert /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/ /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0mag.nii.gz reading from /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/... error: corRead(): can't open file /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/COR-.info Darwin upddkp224.unibe.ch 19.6.0 Darwin Kernel Version 19.6.0: Thu May 6 00:48:39 PDT 2021; root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Jun 29 13:55:16 CEST 2021 My magnitude and phase images are in NIFTI format. Do the magnitude and phase images have to be in DICOM format or does NIFTI format should also work? The full trac-all.log output is pasted below. Thanks in advance for any advise Regards Jürgen ——————————————— Tue Jun 29 13:52:16 CEST 2021 /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA /Applications/freesurfer/bin/trac-all -prep -c /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/tracula_config_IPS_all_with_eddy_with_fieldmap_test.txt Subject IPS_CO_007 SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 jurgenhanggi upddkp224.unibe.ch Darwin upddkp224.unibe.ch 19.6.0 Darwin Kernel Version 19.6.0: Thu May 6 00:48:39 PDT 2021; root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 11136 PhysMem: 64G used (5040M wired), 7908M unused. ######################################## Program versions: FreeSurferEnv.csh 7.1.1 mri_convert --all-info ProgramName: mri_convert ProgramArguments: mri_convert --all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41 BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi Machine: upddkp224.unibe.ch Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang CompilerVersion: 10.0.1 FLIRT version 6.0 bbregister 7.1.1 mri_cvs_register 7.1.1 ProgramName: dmri_motion ProgramArguments: /Applications/freesurfer/bin/dmri_motion --all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41 BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi Machine: upddkp224.unibe.ch Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang CompilerVersion: 10.0.1 ProgramName: dmri_train ProgramArguments: /Applications/freesurfer/bin/dmri_train --all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41 BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi Machine: upddkp224.unibe.ch Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang CompilerVersion: 10.0.1 ProgramName: dmri_paths ProgramArguments: /Applications/freesurfer/bin/dmri_paths --all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41 BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi Machine: upddkp224.unibe.ch Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang CompilerVersion: 10.0.1 ProgramName: dmri_pathstats ProgramArguments: /Applications/freesurfer/bin/dmri_pathstats --all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41 BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi Machine: upddkp224.unibe.ch Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang CompilerVersion: 10.0.1 ProgramName: dmri_mergepaths ProgramArguments: /Applications/freesurfer/bin/dmri_mergepaths --all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41 BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi Machine: upddkp224.unibe.ch Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang CompilerVersion: 10.0.1 ProgramName: dmri_group ProgramArguments: /Applications/freesurfer/bin/dmri_group --all-info ProgramVersion: 7.1.1 TimeStamp: 2021/06/29-11:52:17-GMT BuildTime: Aug 11 2020 19:06:41 BuildStamp: freesurfer-darwin-macOS-7.1.1-20200811-8b40551 User: jurgenhanggi Machine: upddkp224.unibe.ch Platform: Darwin PlatformVersion: 19.6.0 CompilerName: Clang CompilerVersion: 10.0.1 New invocation of trac-preproc jurgenhanggi upddkp224.unibe.ch Darwin upddkp224.unibe.ch 19.6.0 Darwin Kernel Version 19.6.0: Thu May 6 00:48:39 PDT 2021; root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 11136 PhysMem: 64G used (5024M wired), 7906M unused. #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Jun 29 13:52:17 CEST 2021 mri_convert --bvec-voxel /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/IPS_CO_007/DTI/dti4D.nii /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz mri_convert --bvec-voxel /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/IPS_CO_007/DTI/dti4D.nii /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz reading from /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/IPS_CO_007/DTI/dti4D.nii... TR=4400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997313, 0.0722762, 0.0119947) j_ras = (0.0714883, 0.995834, -0.0566035) k_ras = (0.0160358, 0.0555939, 0.998325) writing to /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz... mv -f /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvecs.tmp /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.bvecs mv -f /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvals.tmp /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.bvals orientLAS /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -10.6278 mri_convert -oni 96 -onj 96 -onk 64 -oid -0.997313 0.0722762 0.0119947 -ojd 0.0714883 0.995834 -0.0566035 -okd 0.0160358 0.0555939 0.998325 -oc 3.04031 28.5933 61.3756 -rt nearest /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.nii.gz mri_convert -oni 96 -onj 96 -onk 64 -oid -0.997313 0.0722762 0.0119947 -ojd 0.0714883 0.995834 -0.0566035 -okd 0.0160358 0.0555939 0.998325 -oc 3.04031 28.5933 61.3756 -rt nearest /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.997313, 0.0722762, 0.0119947) -> (-0.997313, 0.0722762, 0.0119947) normalizing out_j_direction: (0.0714883, 0.995834, -0.0566035) -> (0.0714883, 0.995834, -0.0566035) normalizing out_k_direction: (0.0160358, 0.0555939, 0.998325) -> (0.0160358, 0.0555939, 0.998325) reading from /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.nii.gz... TR=4400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997313, 0.0722762, 0.0119947) j_ras = (0.0714883, 0.995834, -0.0566035) k_ras = (0.0160358, 0.0555939, 0.998325) Reslicing using nearest writing to /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.nii.gz... INFO: found /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.bvals, copying INFO: found /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig.bvecs, converting to LAS mv -f /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.bvecs /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvecs mv -f /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.bvals /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvals eddy_correct /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_orig_las.nii.gz /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi.nii.gz 0 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0000 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0001 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0002 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0003 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0004 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0005 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0006 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0007 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0008 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0009 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0010 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0011 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0012 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0013 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0014 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0015 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0016 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0017 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0018 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0019 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0020 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0021 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0022 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0023 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0024 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0025 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0026 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0027 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0028 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0029 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0030 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0031 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0032 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0033 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0034 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0035 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0036 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0037 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0038 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0039 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0040 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0041 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0042 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0043 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0044 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0045 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0046 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0047 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0048 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0049 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0050 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0051 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0052 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0053 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0054 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0055 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0056 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0057 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0058 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0059 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0060 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0061 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0062 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0063 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0064 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0065 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0066 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0067 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0068 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0069 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0070 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0071 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0072 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0073 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0074 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0075 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0076 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0077 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0078 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0079 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0080 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0081 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0082 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0083 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0084 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0085 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0086 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0087 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0088 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0089 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0090 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0091 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0092 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0093 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0094 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0095 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0096 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0097 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0098 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0099 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0100 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0101 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0102 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0103 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0104 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0105 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0106 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0107 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0108 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0109 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0110 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0111 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0112 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0113 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0114 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0115 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0116 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0117 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0118 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0119 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0120 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0121 processing /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_tmp0122 mv -f /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvecs /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvecs.norot xfmrot /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi.ecclog /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvecs.norot /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/bvecs mv -f /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi.nii.gz /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/dwi_eddy.nii.gz mri_convert /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/ /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0mag.nii.gz mri_convert /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/ /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Results/IPS_CO_007/dmri/b0mag.nii.gz reading from /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/... error: corRead(): can't open file /Volumes/Datenspeicher/01_IPS/04_C_DTI_TRACULA/TRACULA_Prepared/COR-.info Darwin upddkp224.unibe.ch 19.6.0 Darwin Kernel Version 19.6.0: Thu May 6 00:48:39 PDT 2021; root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Jun 29 13:55:16 CEST 2021

2 7

Problem with mri_glmfit-sim
by juergen.haenggi＠upd.unibe.ch 15 Jul '21

15 Jul '21

External Email - Use Caution Dear FS experts I have run stats using mri_glmfit (FS 7.1.1 on Mac) with the following command mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir --surf fsaverage lh --C IPS_2groups.mat --cortex and everything worked fine. When trying to run simulations with mri_glmfit-sim with the following command mri_glmfit-sim --glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim mc-z 500 1.302 lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25 the following error occurred Loading y from /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force error: mri_read(): couldn't determine type of file /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force ... done reading. ERROR: loading y /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force The entire output is shown below. I do not understand why after the —y option in the command reported by FS in the terminal, i.e. mri_glmfit --C IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx --sim mc-z 500 1.302 IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001 --sim-sign abs --fwhm 14.598750 --fsgd IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white the input file (IPS_2groups_n135_lh_thickness.10.mgh) is missed and hence the following option —perm-force is interpreted as input file. How can I fix this problem? Thanks in advance for any advise Regards Jürgen --------------------------------------------------- entire output: [upddkp224:average_IPS_FS7_Linux/stats/glm_group_n135] jurgenhanggi% mri_glmfit-sim --glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim mc-z 500 1.302 lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25 cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir --surf fsaverage lh --C IPS_2groups.mat --cortex SURFACE: fsaverage lh log file is IPS_2groups_n135_Thickness_LH.glmdir/lh_mc-z.abs_500p1.3.mri_glmfit-sim.log cd /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135 /Applications/freesurfer/bin/mri_glmfit-sim --glmdir IPS_2groups_n135_Thickness_LH.glmdir --sim mc-z 500 1.302 lh_mc-z.abs_500p1.3 --sim-sign abs --overwrite --cwpvalthresh 0.25 FreeSurferEnv.csh 7.1.1 Wed Jun 23 10:19:19 CEST 2021 Darwin upddkp224.unibe.ch<http://secure-web.cisco.com/1GJFlNOIRufFrF9EI_m9Z0M8ynVxVdXSTvLuBbjjKrTZTIr…> 19.6.0 Darwin Kernel Version 19.6.0: Thu May 6 00:48:39 PDT 2021; root:xnu-6153.141.33~1/RELEASE_X86_64 x86_64 jurgenhanggi setenv SUBJECTS_DIR /Applications/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Original mri_glmfit command line: cmdline mri_glmfit --y IPS_2groups_n135_lh_thickness.10.mgh --fsgd IPS_fsgd_2groups.txt --glmdir IPS_2groups_n135_Thickness_LH.glmdir --surf fsaverage lh --C IPS_2groups.mat --cortex DoSim = 1 UseCache = 0 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 14.598750 nSimPerJob = 500 1/1 Wed Jun 23 10:19:19 CEST 2021 mri_glmfit --C IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx --sim mc-z 500 1.302 IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001 --sim-sign abs --fwhm 14.598750 --fsgd IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed simbase IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001 FWHM = 14.598750 gdfRead(): reading IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd WARNING: carriage returns have been detected in file IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd Was it created on a Windows computer? This may cause an error in reading the FSGD file. If so, try running: cat IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd | sed 's/\r/\n/g' > new.IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd Then use new.IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/subjects/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 Surface smoothing by fwhm=14.598750, niters=157.000000 7.1.1 cwd /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135 cmdline mri_glmfit --C IPS_2groups_n135_Thickness_LH.glmdir/tmp.mri_glmfit-sim-96372/IPS_2groups.mtx --sim mc-z 500 1.302 IPS_2groups_n135_Thickness_LH.glmdir/csd/lh_mc-z.abs_500p1.3.j001 --sim-sign abs --fwhm 14.598750 --fsgd IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd dods --mask IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh --y --perm-force --surf fsaverage lh white sysname Darwin hostname upddkp224.unibe.ch<http://secure-web.cisco.com/1GJFlNOIRufFrF9EI_m9Z0M8ynVxVdXSTvLuBbjjKrTZTIr…> machine x86_64 user jurgenhanggi FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 14.598750 niters 157.000000 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force logyflag 0 usedti 0 FSGD IPS_2groups_n135_Thickness_LH.glmdir/y.fsgd mask IPS_2groups_n135_Thickness_LH.glmdir/mask.mgh maskinv 0 glmdir (null) IllCondOK 0 ReScaleX 1 DoFFx 0 Loading y from /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force error: mri_read(): couldn't determine type of file /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force ... done reading. ERROR: loading y /Applications/freesurfer/subjects/average_IPS_FS7_Linux/stats/glm_group_n135/--perm-force [upddkp224:average_IPS_FS7_Linux/stats/glm_group_n135] jurgenhanggi%

2 4

Ill-Conditioned/Badly Scaled Matrix Error
by Lurie, Lucy 11 Jul '21

11 Jul '21

External Email - Use Caution Hello I am trying to a whole brain analysis with one group and five covariates. I am getting an error that the design matrix may be ill-conditioned or badly scaled. I checked over the fsgd file in TextEdit and it seems to be formatted correctly. I am using Freesurfer version 5.3.0 and my platform is macOS Big Sur version 11.4. I would appreciate any help further troubleshooting this error. Thank you! ERROR: matrix is ill-conditioned or badly scaled, condno = 13065 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: 1. Your command line: mri_glmfit --y lh.eig_cgORCE_baselineORCE_teenCG.thickness.10.mgh --fsgd eig_cgORCE_baselineORCE_teenCG.fsgd dods --C eig_cgORCE3042_slope.mtx --C eig_cgORCEbaseline_slope.mtx --C eig_teenCGqual_slope.mtx --surf fsaverage lh --cortex --glmdir lh.eig_cgORCE_baselineORCE_teenCGagesex.glmdir 2. The FSGD file (if using one) 3. And the design matrix Design matrix ------------------ 1.000 0.000 16.660 2.950 2.200 0.000; 1.000 0.000 16.960 1.900 2.600 0.000; 1.000 0.000 17.390 2.450 2.800 0.000; 1.000 1.000 17.130 2.300 2.500 0.000; 1.000 1.000 16.980 2.400 2.300 0.000; 1.000 0.000 17.690 2.200 2.900 0.000; 1.000 1.000 16.870 2.750 2.900 1.000; 1.000 0.000 17.570 2.550 1.700 0.000; 1.000 0.000 17.130 2.150 1.928 0.000; 1.000 1.000 17.650 2.750 2.200 0.000; 1.000 1.000 17.210 2.450 2.500 1.000; 1.000 0.000 15.610 3.100 1.565 1.000; 1.000 0.000 16.440 2.650 2.300 0.000; 1.000 1.000 17.350 2.400 2.600 0.000; 1.000 0.000 16.800 1.600 1.400 0.000; 1.000 1.000 17.980 2.200 2.300 1.000; 1.000 1.000 16.890 2.800 1.600 1.000; 1.000 0.000 16.760 1.100 1.300 0.000; 1.000 1.000 16.790 2.500 1.400 0.000; 1.000 1.000 16.620 2.900 2.800 0.000; 1.000 1.000 16.500 2.500 1.200 0.000; 1.000 1.000 16.290 2.700 3.200 0.500; 1.000 0.000 16.440 3.100 2.500 1.000; 1.000 0.000 17.540 2.100 2.100 1.000; 1.000 1.000 16.810 1.900 2.600 1.000; 1.000 0.000 17.110 2.650 2.400 0.000; 1.000 1.000 16.520 2.000 2.300 0.000; 1.000 1.000 16.520 3.100 3.400 1.000; 1.000 0.000 16.320 3.300 2.800 0.500; 1.000 0.000 16.380 3.200 1.900 1.000; 1.000 0.000 16.570 2.800 2.000 0.000; 1.000 1.000 16.250 2.200 1.600 0.000; 1.000 1.000 16.820 2.900 2.600 1.000; 1.000 0.000 16.580 2.600 2.800 0.000; 1.000 1.000 16.730 2.850 3.150 0.000; 1.000 0.000 16.310 2.600 1.900 0.000; 1.000 1.000 17.010 1.700 2.400 0.000; 1.000 1.000 16.360 3.200 3.200 0.000; 1.000 1.000 16.490 2.400 1.525 0.000; 1.000 0.000 16.300 2.400 1.450 1.000; 1.000 0.000 16.060 2.200 1.300 0.000; 1.000 1.000 16.600 2.200 2.000 0.000; 1.000 0.000 16.720 3.300 2.500 0.000; 1.000 1.000 16.160 2.300 2.200 0.000; 1.000 1.000 16.140 2.800 1.850 0.000; 1.000 1.000 16.550 3.100 2.950 1.000; 1.000 1.000 17.300 3.450 2.700 1.000; 1.000 0.000 16.940 3.000 2.200 1.000; 1.000 1.000 16.550 2.700 2.850 0.000; 1.000 0.000 17.170 3.000 2.900 1.000; 1.000 0.000 17.150 2.800 2.450 0.000; 1.000 0.000 16.650 3.100 1.900 0.500; 1.000 0.000 16.070 2.700 2.900 1.000; 1.000 1.000 16.720 1.800 1.450 1.000; 1.000 0.000 16.150 2.900 1.000 0.000; 1.000 1.000 16.120 2.400 2.200 1.000; 1.000 1.000 17.540 2.600 2.600 0.000; 1.000 1.000 16.840 2.900 1.100 0.000; 1.000 1.000 15.790 3.100 1.600 1.000; 1.000 1.000 16.430 2.800 1.500 0.000; 1.000 0.000 16.390 3.300 2.700 1.000; 1.000 0.000 16.480 3.350 3.000 0.000; 1.000 1.000 16.930 3.000 1.000 0.000; 1.000 1.000 15.550 2.200 2.600 0.000; 1.000 1.000 17.080 2.900 1.500 0.000; 1.000 0.000 16.850 2.500 2.200 0.500; 1.000 1.000 16.700 2.200 1.800 0.000; 1.000 1.000 15.930 2.600 2.000 1.000; 1.000 1.000 16.080 2.600 1.200 0.500; 1.000 0.000 16.130 3.150 1.400 1.000; 1.000 1.000 16.250 3.100 1.400 1.000; 1.000 0.000 16.040 3.250 3.200 1.000; 1.000 0.000 16.040 3.500 2.900 1.000; 1.000 0.000 16.070 1.400 1.000 1.000; 1.000 0.000 16.550 3.200 2.300 1.000; 1.000 0.000 16.120 2.800 2.000 0.500; 1.000 1.000 16.450 3.150 1.400 1.000; 1.000 0.000 15.910 3.400 1.600 1.000; 1.000 1.000 15.700 3.000 2.400 1.000; Best, Lucy Lurie (she/her/hers) Doctoral Student, Clinical Psychology Department of Psychology and Neuroscience University of North Carolina at Chapel Hill CIRCLE Lab<https://secure-web.cisco.com/18i_Rf4fzTTcqPA2OQAm3_CnM6qhNKl6D-xG6RO1PJGAuL…>

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