Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

mcprextreg file structure and X
by Erik Jahner 15 Jul '21

15 Jul '21

External Email - Use Caution Dear all, I am trying to figure out the structure of X.dat and where the mcprextreg parameters are in the table. It is my understanding that the mcprextreg is the resulting PCA on the motion to generate a nuisance variable for motion. I see the following regressors clearly: my ROI, global regressor, PCA-wm, and PCA-csf. There are however, additional columns none of which line up with the mcprextreg file for that participant. Can someone explain how the mcprextreg file gets processed and entered into the X.dat file with it is used as a nuisance regressor? I have also checked the fmcpr.mcdat but I also cannot find this in the X.dat data set ~Erik Jahner

2 1

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 It seems, however, it is no longer maintained.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

Freesurfer not creating specific files
by Taylor, Lisa Marie 15 Jul '21

15 Jul '21

External Email - Use Caution Hi everyone, I could really use some help with figuring out an issue I've been struggling with the last few months. It seems that when I run recon-all on over 20 of my participants, not all freesurfer files are created. But I am not understanding why, and my technical capabilities are limited. Particularly, it seems there's an issue reading the lh.BA1_exvivo.label. I will attach the recon-all log file for any other information that it can provide. Also, I run a script for recon-all and these are the arguments: srun ${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all -hippocampal-subfields-T1 -brainstem-structures -qcache Not sure if this is pertinent, but our HPC has been updated, but I am unaware if that can impact how freesurfer is run. Thank you for any insight you can provide! Lisa (I previously sent an email with screen shots, but the email was waiting to be approved due to size) ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

2 1

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

Missing freesurfer files after running recon-all
by Taylor, Lisa Marie 15 Jul '21

15 Jul '21

External Email - Use Caution Hi everyone, I could really use some help with figuring out an issue I've been struggling with the last few months. It seems that when I run recon-all on over 20 of my participants, not all freesurfer files are created. But I am not understanding why, and my technical capabilities are limited. Particularly, it seems there's an issue reading the lh.BA1_exvivo.label. I will attach a screenshot of a participant who has all the expected files vs. a participant who is missing important files. I will also attach the recon-all log file for any other information that it can provide. Also, I run a script for recon-all and these are the arguments: srun ${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all -hippocampal-subfields-T1 -brainstem-structures -qcache Not sure if this is pertinent, but our HPC has been updated, but I am unaware if that can impact how freesurfer is run. Thank you for any insight you can provide! Lisa ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

2 1

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

One year position, working with ADNI data.
by ROBERT CARY WELSH 14 Jul '21

14 Jul '21

External Email - Use Caution Hi, Please see this posting. We are looking for an appropriate match for a 1-year NIH funded position. We are working on statistical modeling with ADNI data. We need a person that can hit the ground running. Only apply if eligible to work in the US as the lab does not have the resources to do any type of sponsorship. https://secure-web.cisco.com/1_4U_hvUopqCVLJhHNv0etmvHG3zmPupbHEEI8ATazfl-0… Do not send inquiries directly, as all materials must go via the portal above. Robert Welsh

1 0

Hiring a web developer
by Billah, Tashrif 14 Jul '21

14 Jul '21

The web developer will join a research laboratory at Harvard Medical School/Mass General Brigham. It is located in Boston, MA. Here is the job description: https://partners.taleo.net/careersection/ghc/jobdetail.ftl?job=3161646&tz=G… If you have any question, reach out to sylvain(a)bwh.harvard.edu. Otherwise, feel free to apply through the above. Best, Tashrif

1 0

RAM per CPU for running Freesurfer 7.1
by Ajay Kurani 14 Jul '21

14 Jul '21

External Email - Use Caution Hi Freesurfer Experts, I am designing some new hardware for a mini-cluster running Freesurfer and other neuroimaging toolboxes and wanted to better understand requirements from Freesurfer. 1) Is there a minimum amount of ram per core that is needed/recommended or is the amount of ram only defined per subject. Most of the threads I found say you need a minimum of 4 GB ram but these were from a long time ago and may not apply to the OPENMP code. Our compute node will have between 52-64 cores so I wanted to know what is the ratio for Ram to CPU (multithreading turned off) that is recommended as opposed to Ram per subject. 2) AMD vs Intel We will run jobs on an existing cluster that has Dual Intel Xeon 6230R and for our new minicluster we are debating between AMD and Intel. While AMD offers higher core-count per CPU, I am worried that results could potentially differ based on the CPU/underlying libraries. We plan on using docker images so from your perspective do you have a recommendation ? Best, Ajay

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Average intensity from functional image within a label along the surface
by Erik Jahner 12 Jul '21

12 Jul '21

External Email - Use Caution I am interested in obtaining the average intensity within a label from each frame of a functional image that has been smoothed on the surface (I have generated the label). However, the functional connectivity pipeline seems to use only volume based seeds. It seems to me that in using the FreeSurfer software we would want to take advantage of the surface based smoothing and not return to getting the average of voxels in aparc+aseg. (1) Am I incorrect in my thinking here? (2) Is there a way to get the mean intensity of a label (I have created) at each frame along the surface to get a timcourse for a particular region? I see there is a way to do this with anatomical features such as thickness, but I do not see a way to do this with functional data across frames for signal intensity. Thanks ~Erik Jahner

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