Freesurfer August 2021

freesurfer@nmr.mgh.harvard.edu

73 participants
101 discussions

Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
by fsbuild 04 Aug '21

04 Aug '21

External Email - Use Caution Thanks Adam for pointing out different behavior at different screen resolutions.   I would be interested to know if those resolutions are not the native resolution of the external monitor.  The manual/info for any monitor should state what it’s native resolution is, e.g.., for a 4K monitor native resolution is  3840 X 2160.   If you don’t have the displays mirrored, I think when you select System Preferences -> Displays a window will appear on each monitor.  Under the Display tab try checking the box "default for display" for any external monitor and not the "scale" option for the hardware to scale the image up/down in size. - R. On Aug 2, 2021, at 16:08, Adam Martersteck <acmarter(a)gmail.com> wrote:        External Email - Use Caution        I started getting segfaults again but I was able to diagnose what was different.It turns out it was not the license file for me. I registered a new license file this morning --> it worked on my Mac and I assumed it was the new license; I went into the office --> plugged my MacBook into my external monitor --> segfaults.Having a display with resolution > 1600x900 caused segfaults. At both 2048x1152 or 2560x1440, I am able to 100% replicate segfault error. FreeView does not launch.When I downsample the monitor to 1600x900 or 720p or unplug the monitor, I can open FreeView without error.Hope this helps other people out there.My graphics card on the 13" MacBook Pro is the Intel Iris Plus Graphics (1536 MB) from the Quad-Core Intel i5.On Mon, Aug 2, 2021 at 10:28 AM Adam Martersteck <acmarter(a)gmail.com> wrote:I should add: I've used this license file for several years wtih FS v.5.1, v5.3, v6, v7+ and developer versions. It runs FreeSurfer perfectly on two MacOS computers and on a RedHat Linux cluster where it has run thousands of recons + additional processing.The license file continued to work -- I could run FreeSurfer commands with it and it never reported a missing or unreadable license file.So if you are getting segfaults and you think you have a good license -- try requesting a new one just in case.On Mon, Aug 2, 2021 at 10:10 AM Adam Martersteck <acmarter(a)gmail.com> wrote:Confirm, just requesting a new license file fixed my FreeView MacOS 11.4 segfault errors.Requesting a new license file with my same credentials produced an identical text file (same email, same license #, same two strings of random letter/digit/symbols).I didn't even need to download the new license file (as the identical one was already present) or move it into the /Applications/freesurfer/7.2.0 directory -- FreeView just began to work perfectly fine with my previously present license.This fixed my unusable FreeView in /Applications/freesurfer/7.1.1/ also. Same license file was present there, never needed to download the newly requested one. Just the act of requesting a new license file fixed it.Strange, right? Doesn't sound like a Mac OS permission problem, sounds like an issue with my license registration?On Mon, Aug 2, 2021 at 4:41 AM fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        After some feedback and some more testing, I can reproduce that freeview.app in the 7.2.0 release will segfault on MacOS 11.4 if the license file cannot be found or it cannot be read.  One user reported that he had to get a new license file in order for it to work.  The link for that is here,  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1MxE6xP8mPPjlSA8T50wRDKo-y1FrIDbXFfaR9… R..On Jul 29, 2021, at 14:34, Adam Martersteck <acmarter(a)gmail.com> wrote:        External Email - Use Caution        Here's a log from a completely clean install of FreeSurfer 7.2.0.On an Intel processor MacBook Pro, running macOS Big Sur (11.4).__Starting with a completely clean install of FreeSurfer 7.2.0__Copied license file over from 7.1.1.(Confirmed license file works by running mri_convert)MacBook-Pro:freesurfer adam$ freeview/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38945 Segmentation fault: 11  $FREESURFER_HOME/Freeview..app/Contents/MacOS/freeview "$@"MacBook-Pro:freesurfer adam$ freeview/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38951 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"MacBook-Pro:freesurfer adam$ freeview/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38954 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"MacBook-Pro:freesurfer adam$ freeview/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38974 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"MacBook-Pro:freesurfer adam$ freeview/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38977 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"(Line numbers that it faults at are linearly increasing?)With export QT_DEBUG_PLUGINS=1I have attached the output log from "freeview > freeview_QT_DEBUG_log.txt".The tail of it is:"loaded library "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqtiff.dylib"loaded library "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwbmp.dylib"loaded library "/Applications/freesurfer/7.2.0/Freeview..app/Contents/PlugIns/imageformats/libqwebp.dylib"/Applications/freesurfer/7.2.0/bin/freeview: line 2: 39147 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@""It perfectly replicates in FreeSurfer 7.1.1. Same error, same debug log.-AdamOn Wed, Jul 28, 2021 at 8:53 PM fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        If you have not already done so, see if you get a different result by double clicking on the Freeview.app icon under /Applications/freesurfer/7.2.0 with the mouse.You can try this variation on what's been previously suggested.1) run a bash shell$ bash2) setup freesurfer environment$ export FREESURFER_HOME=/Applications/freesurfer/7.2.0$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.2..0FSFAST_HOME       /Applications/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.2.0/subjectsMNI_DIR           /Applications/freesurfer/7.2.0/mni3) Locate your license file (I name mine license.txt) in your home directory and check you can read its contents,$ export FS_LICENSE=$HOME/license.txt$ cat $FS_LICENSE... check the output ....... first line should contain email address ...... followed by 3 more lines ...4) set environment variable for debug$ export QT_DEBUG_PLUGINS=15) run freeview with no arguments$ which freeview/Applications/freesurfer/7.2.0/bin/freeview$ freeview... an empty freeview window should appear and persist on the screen ...At this point the last few lines of output in the terminal window should now be:Got keys from plugin meta data ("svg", "svgz", "svg.gz")QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/MacOS/iconengines" ....QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/accessible" ...QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/MacOS/accessible" ...6) Use the freeview application "File" pull down menu to select "load volume".  In the window that comes up, click on the yellow folder icon to the r.h.s of the folder/file entry box under "Select Volume File".  In the Finder window that comes up, navigate to /Applications/freesurfer/7..2.0/subjects/bert/mri and select the brain.mgz file..  Click on OPEN. That path/filename will appear in the load volume text entry box.  Don't check/change any of the options for loading the volume and click OK.The steps above worked for me to load that volume using an Intel MacPro laptop with the 7.2.0 release running under either MacOS 10.15.7 (Catlaina) or MacOS 11.4 (Big Sur) w/o freeview exiting or producing any further output in the terminal window.  If it fails on your machine, you could send along the Qt debug output after the lines listed above.  Please do not send the output from cat'ing your license file though..- R.On Jul 28, 2021, at 14:53, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Please check in “energy saver” preferences that “automatic graphics switching” is not selected so that high performance graphics is always used.- R.On Jul 28, 2021, at 14:36, Sahil Bajaj <sahil.brain(a)gmail.com> wrote:        External Email - Use Caution        Hi Freesurfer team,I am also having a similar issue from the last few weeks. I hope we will get a solution soon.Thanks,Sahil On Wed, Jul 28, 2021 at 11:15 AM Tom Parker <tomparker59(a)gmail.com> wrote:        External Email - Use Caution        I have just installed Freesurfer 7.2.0 for Mac. When I attempt to open Freeview it crashes. Full details of error messages below.Any advice to correct would be much appreciated.Many thanks!_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1_b4Y2GYQnZYTkSO7Ee2AjmWBgfycwy70PTSw1… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<freeview_… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1_b4Y2GYQnZYTkSO7Ee2AjmWBgfycwy70PTSw1… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1_b4Y2GYQnZYTkSO7Ee2AjmWBgfycwy70PTSw1… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 2

Not able to find corresponding files for the paper: "Functional–anatomical validation and individual variation of diffusion tractography-based segmentation of the human thalamus"
by Sumit Sharma 04 Aug '21

04 Aug '21

External Email - Use Caution Hi Freesurfer Developers I am trying to reproduce your work in the below paper using freesurfer: Johansen-Berg, Heidi, et al. "Functional–anatomical validation and individual variation of diffusion tractography-based segmentation of the human thalamus." *Cerebral cortex* 15.1 (2005): 31-39. However, I am not able to find which find represents the c nding labels 9000 - 9006 as mentioned in the lookup table list: https://secure-web.cisco.com/1VgTGj_nBeRhSbdBymlZZQBlnh5ZmiJ_Bdb6vJu1i1grgz… Please share the details of the necessary files (mgz etc) after running the recon-all command. Thank you. Regads Sumit Sharma

2 1

mri_glmfit-sim error
by Harriet Cornwell 04 Aug '21

04 Aug '21

External Email - Use Caution Hi FreeSurfer team, I am currently trying to run a correlational analysis in FreeSurfer. I am able to run the preproc and mri_glmfit commands successfully, but I am getting error messages when running mri_glmfit-sim for lGI, thickness and area. An example error message is: ERROR: cannot find /usr/local/freesurfer6/freesurfer//average/mult-comp-cor/fsaverage/rh/cortex/fwhm55/abs/th40/mc-z.csd. I have attached the full terminal output so that you can see the variations of this error message that I am getting. Are you able to advise what the issue might be and how I might go about fixing the issue? Just for reference, I am using a smoothing value of 10 for volume, area and thickness, and 5 for lGI. I would also be happy to share my design matrix and scripts if that would make the troubleshooting easier. Thank you in advance for any help you can offer. Best wishes, Harriet Cornwell PhD Student | Department of Psychology University of Bath | 10 West 2.08

2 1

How to extract individual structures after recon-all
by Ammar Shujaa 04 Aug '21

04 Aug '21

External Email - Use Caution Hello FreeSurfur Developers, A have completed the segmentation of T1 MRI image using recon all. I want to know how to get the segmentation of specific structures using mri and surf folders. For example, Thalamus, prefrontal lobe, grey matter and then save each one, so I can use them for machine learning later. Looking forward to hearing from you. Best regards,Ammar Shujaa Addin

3 3

Talairach Failure Detection
by Shymaa Darawshy 03 Aug '21

03 Aug '21

External Email - Use Caution Dear Freesurfer team, I'm running Fmriprep on patients with huge brain lesions, and I got this error for two of my patients. This is the code I'm running: fmriprep-docker /home/shymaa/Desktop/my_dataset/Participant /home/shymaa/Desktop/my_dataset/Participant/derivative participant --participant-label 07 --fs-license-file /home/shymaa/Desktop/license.txt --use-aroma --cifti-outputs Error: Node: fmriprep_wf.single_subject_07_wf.anat_preproc_wf.surface_recon_wf.autorecon1 Working directory: /tmp/work/fmriprep_wf/single_subject_07_wf/anat_preproc_wf/surface_recon_wf/autorecon1 Node inputs: FLAIR_file = T1_files = T2_file = args = big_ventricles = brainstem = directive = autorecon1 environ = {} expert = flags = hemi = hippocampal_subfields_T1 = hippocampal_subfields_T2 = hires = mprage = mri_aparc2aseg = mri_ca_label = mri_ca_normalize = mri_ca_register = mri_edit_wm_with_aseg = mri_em_register = mri_fill = mri_mask = mri_normalize = mri_pretess = mri_remove_neck = mri_segment = mri_segstats = mri_tessellate = mri_watershed = mris_anatomical_stats = mris_ca_label = mris_fix_topology = mris_inflate = mris_make_surfaces = mris_register = mris_smooth = mris_sphere = mris_surf2vol = mrisp_paint = openmp = 8 parallel = steps = subject_id = recon_all subjects_dir = talairach = use_FLAIR = use_T2 = xopts = Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node result["result"] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 419, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 814, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 745, in raise_exception ).format(**runtime.dictcopy()) RuntimeError: Command: recon-all -autorecon1 -i /data/sub-07/anat/sub-07_T1w.nii.gz -noskullstrip -openmp 8 -subjid sub-07 -sd /out/freesurfer Standard output: Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a INFO: SUBJECTS_DIR is /out/freesurfer Actual FREESURFER_HOME /opt/freesurfer Linux 1f98b6a77b48 5.8.0-45-generic #51 <https://secure-web.cisco.com/1PQtQcgjBkdpzGQxmcL0zU6EV4nHb3URJHEK3EDYTLj_vR…>~20.04.1-Ubuntu SMP Tue Feb 23 13:46:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux '/opt/freesurfer/bin/recon-all' -> '/out/freesurfer/sub-07/scripts/recon-all.local-copy' /out/freesurfer/sub-07 mri_convert /data/sub-07/anat/sub-07_T1w.nii.gz /out/freesurfer/sub-07/mri/orig/001.mgz mri_convert.bin /data/sub-07/anat/sub-07_T1w.nii.gz /out/freesurfer/sub-07/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/sub-07/anat/sub-07_T1w.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.990846, 0.00867391, -0.134721) j_ras = (-0.0205356, 0.996005, -0.086908) k_ras = (0.133429, 0.088879, 0.987065) writing to /out/freesurfer/sub-07/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Mon Apr 5 09:47:52 UTC 2021 Found 1 runs /out/freesurfer/sub-07/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /out/freesurfer/sub-07/mri/orig/001.mgz /out/freesurfer/sub-07/mri/rawavg.mgz /out/freesurfer/sub-07 mri_convert /out/freesurfer/sub-07/mri/rawavg.mgz /out/freesurfer/sub-07/mri/orig.mgz --conform mri_convert.bin /out/freesurfer/sub-07/mri/rawavg.mgz /out/freesurfer/sub-07/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /out/freesurfer/sub-07/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.990846, 0.00867391, -0.134721) j_ras = (-0.0205356, 0.996005, -0.086908) k_ras = (0.133429, 0.088879, 0.987065) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /out/freesurfer/sub-07/mri/orig.mgz... mri_add_xform_to_header -c /out/freesurfer/sub-07/mri/transforms/talairach.xfm /out/freesurfer/sub-07/mri/orig.mgz /out/freesurfer/sub-07/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Apr 5 09:48:04 UTC 2021 /out/freesurfer/sub-07/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/freesurfer/sub-07/mri /opt/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 1f98b6a77b48 5.8.0-45-generic #51 <https://secure-web.cisco.com/1PQtQcgjBkdpzGQxmcL0zU6EV4nHb3URJHEK3EDYTLj_vR…>~20.04.1-Ubuntu SMP Tue Feb 23 13:46:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Mon Apr 5 09:48:04 UTC 2021 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.548 /out/freesurfer/sub-07/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.548/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.548/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.548/nu0.mnc... ------------------------------ Iteration 1 Mon Apr 5 09:48:07 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.548/nu0.mnc ./tmp.mri_nu_correct.mni.548/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.548/0/ -iterations 1000 -distance 50 [root@1f98b6a77b48:/out/freesurfer/sub-07/mri/] [2021-04-05 09:48:07] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.548/0/ ./tmp.mri_nu_correct.mni.548/nu0.mnc ./tmp.mri_nu_correct.mni.548/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 40 CV of field change: 0.000988835 mri_convert ./tmp.mri_nu_correct.mni.548/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.548/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.548/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Mon Apr 5 09:50:29 UTC 2021 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Mon Apr 5 09:50:29 UTC 2021 Ended at Mon Apr 5 09:51:17 UTC 2021 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Apr 5 09:51:19 UTC 2021 /out/freesurfer/sub-07/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm *FAILED* (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://secure-web.cisco.com/1O_bVeK_eu-sCdteM_GAceKpdEU5JsnRs9jngy1A_pwUpSs… INFO: Retrying Talairach align using 3T-based atlas... #-------------------------------------------- #@# Talairach Mon Apr 5 09:51:19 UTC 2021 /out/freesurfer/sub-07/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/freesurfer/sub-07/mri /opt/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 1f98b6a77b48 5.8.0-45-generic #51 <https://secure-web.cisco.com/1PQtQcgjBkdpzGQxmcL0zU6EV4nHb3URJHEK3EDYTLj_vR…>~20.04.1-Ubuntu SMP Tue Feb 23 13:46:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Mon Apr 5 09:51:19 UTC 2021 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.4743 /out/freesurfer/sub-07/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4743/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.4743/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4743/nu0.mnc... ------------------------------ Iteration 1 Mon Apr 5 09:51:22 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.4743/nu0.mnc ./tmp.mri_nu_correct.mni.4743/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4743/0/ -iterations 1000 -distance 50 [root@1f98b6a77b48:/out/freesurfer/sub-07/mri/] [2021-04-05 09:51:23] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4743/0/ ./tmp.mri_nu_correct.mni.4743/nu0.mnc ./tmp.mri_nu_correct.mni.4743/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 40 CV of field change: 0.000988835 mri_convert ./tmp.mri_nu_correct.mni.4743/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.4743/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.4743/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Mon Apr 5 09:54:03 UTC 2021 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... Started at Mon Apr 5 09:54:04 UTC 2021 Ended at Mon Apr 5 09:54:49 UTC 2021 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Apr 5 09:54:52 UTC 2021 /out/freesurfer/sub-07/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4905, pval=0.1531 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /out/freesurfer/sub-07/mri/transforms/talairach_avi.log tal_QC_AZS /out/freesurfer/sub-07/mri/transforms/talairach_avi.log TalAviQA: 0.85645 z-score: -27 WARNING: Talairach QA check failed! z-score of -27 is <= threshold of -9 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://secure-web.cisco.com/1O_bVeK_eu-sCdteM_GAceKpdEU5JsnRs9jngy1A_pwUpSs… INFO: Trying MINC mritotal to perform Talairach align... #-------------------------------------------- #@# Talairach Mon Apr 5 09:54:52 UTC 2021 /out/freesurfer/sub-07/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/freesurfer/sub-07/mri /opt/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 1f98b6a77b48 5.8.0-45-generic #51 <https://secure-web.cisco.com/1PQtQcgjBkdpzGQxmcL0zU6EV4nHb3URJHEK3EDYTLj_vR…>~20.04.1-Ubuntu SMP Tue Feb 23 13:46:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Mon Apr 5 09:54:52 UTC 2021 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.6926 /out/freesurfer/sub-07/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6926/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.6926/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.6926/nu0.mnc... ------------------------------ Iteration 1 Mon Apr 5 09:54:55 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.6926/nu0.mnc ./tmp.mri_nu_correct.mni.6926/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.6926/0/ -iterations 1000 -distance 50 [root@1f98b6a77b48:/out/freesurfer/sub-07/mri/] [2021-04-05 09:54:55] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.6926/0/ ./tmp.mri_nu_correct.mni.6926/nu0.mnc ./tmp.mri_nu_correct.mni.6926/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 40 CV of field change: 0.000988835 mri_convert ./tmp.mri_nu_correct.mni.6926/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.6926/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.6926/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Mon Apr 5 09:57:40 UTC 2021 mri_nu_correct.mni done talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /out/freesurfer/sub-07/mri /opt/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.8 2016/02/16 17:17:20 zkaufman Exp $ Linux 1f98b6a77b48 5.8.0-45-generic #51 <https://secure-web.cisco.com/1PQtQcgjBkdpzGQxmcL0zU6EV4nHb3URJHEK3EDYTLj_vR…>~20.04.1-Ubuntu SMP Tue Feb 23 13:46:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux Mon Apr 5 09:57:40 UTC 2021 tmpdir is transforms/tmp.talairach.7643 /out/freesurfer/sub-07/mri mri_convert orig_nu.mgz transforms/tmp.talairach.7643/src.mnc mri_convert.bin orig_nu.mgz transforms/tmp.talairach.7643/src.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 7.45058e-09, -1) k_ras = (-9.31323e-10, 1, -7.45058e-09) writing to transforms/tmp.talairach.7643/src.mnc... mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.7643/src.mnc transforms/talairach.auto.xfm Transforming slices:................................................................................................................................Done Copying chunks:......................................................................................................................................................Done. Copying chunks:..........................................................................................................Done. Transforming slices:......................................................................................................................................................Done Copying chunks:....................................................................................................................Done. Copying chunks:....................................................................................................................Done. Source volume size: 74 by 106 by 106 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 157.547 Source min/max voxel= -0.000 157.547 Target volume size: 58 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.970 123.710 Target min/max voxel = -0.000 123.710 AFTER init_params() Transform matrix = 1.0000 0.0000 0.0000 4.1908 0.0000 1.0000 0.0000 -10.2661 0.0000 0.0000 1.0000 33.3827 Transform center = -3.863 -7.325 -23.928 Transform rotations = 0.000 0.000 0.000 Transform trans = 4.191 -10.266 33.383 Transform scale = 1.000 1.000 1.000 Transform shear = 0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -85.095 -125.510 -47.250 Lattice count = 43 55 29 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 214.907 Source min/max voxel= -0.000 214.907 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= -0.000 144.070 Target min/max voxel = -0.000 144.070 AFTER init_params() Transform matrix = 0.8973 -0.2092 -0.1398 -1.3581 0.1477 0.8571 -0.3348 -11.7152 0.2037 0.3002 0.8584 46.4240 Transform center = -3.863 -7.325 -23.928 Transform rotations = 0.336 -0.220 0.163 Transform trans = 3.916 -3.227 46.826 Transform scale = 0.932 0.932 0.932 Transform shear = -0.000 0.000 -0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -85.095 -125.510 -57.250 Lattice count = 43 55 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.023 24.915 Source min/max voxel= 0.023 24.915 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.8493 -0.3524 -0.1329 -1.8151 0.2467 0.7682 -0.4605 -13.8695 0.2846 0.3857 0.7959 37.7361 Transform center = -3.863 -7.325 -23.928 Transform rotations = 0.451 -0.311 0.283 Transform trans = 4.529 -2.106 38.697 Transform scale = 0.929 0.929 0.929 Transform shear = -0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.023 24.915 Source min/max voxel= 0.023 24.915 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.8413 -0.3229 0.1654 -19.8003 0.3494 0.8335 -0.1501 23.9121 -0.0976 0.2009 0.8885 10.4402 Transform center = -3.863 -7.325 -23.928 Transform rotations = 0.222 0.107 0.394 Transform trans = -20.779 27.373 12.013 Transform scale = 0.916 0.916 0.916 Transform shear = -0.000 -0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.023 24.915 Source min/max voxel= 0.023 24.915 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.7832 -0.3616 0.0905 -12.9926 0.5471 1.1481 -0.1464 21.9242 -0.0406 0.1307 0.8739 2.7341 Transform center = -3.863 -7.325 -23.928 Transform rotations = 0.149 0.046 0.442 Transform trans = -11.671 22.228 4.950 Transform scale = 0.867 1.280 0.885 Transform shear = 0.000 0.000 -0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.023 24.915 Source min/max voxel= 0.023 24.915 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.7722 -0.3700 0.0882 -13.1052 0.5643 1.1383 -0.1659 21.3297 -0.0313 0.1427 0.8723 3.0791 Transform center = -3.863 -7.325 -23.928 Transform rotations = 0.162 0.035 0.456 Transform trans = -11.625 22.108 5.209 Transform scale = 0.861 1.281 0.884 Transform shear = -0.000 -0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Mon Apr 5 09:57:52 UTC 2021 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Apr 5 09:57:54 UTC 2021 /out/freesurfer/sub-07/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm *FAILED* (p=0.0442, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See: http://secure-web.cisco.com/1O_bVeK_eu-sCdteM_GAceKpdEU5JsnRs9jngy1A_pwUpSs… ERROR: Talairach failed! Linux 1f98b6a77b48 5.8.0-45-generic #51 <https://secure-web.cisco.com/1PQtQcgjBkdpzGQxmcL0zU6EV4nHb3URJHEK3EDYTLj_vR…>~20.04.1-Ubuntu SMP Tue Feb 23 13:46:31 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-07 exited with ERRORS at Mon Apr 5 09:57:55 UTC 2021 For more details, see the log file /out/freesurfer/sub-07/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/11XvQqKiZyaLMNPzU4XdOq3SOmKku2aCtVDeUlmEBOXfPoP… Standard error: Return code: 1 How can I fix this error? Also attached an image of the lesions [image: image.png][image: image.png] thank you, Shaymaa

2 1

mri_glmfit-sim ERROR
by Boa Sorte Silva, Narlon 03 Aug '21

03 Aug '21

External Email - Use Caution Dear experts, I am running this command to apply correction for multiple comparisons on my data: mri_glmfit-sim --glmdir a_glm_results/lh.thickness.velocity.10.glmdir \ --cache 1.3 abs \ --cwp 0.05 \ --2spaces However, I receive the following error: INFO: unrecognized mri_glmfit cmd option doss ... probably not a problem SURFACE: fsaverage lh log file is a_glm_results/lh.thickness.velocity.10.glmdir/cache.mri_glmfit-sim.log cd /Users/narlonsilva/Desktop/freesufer_subjects /Applications/freesurfer/7.1.1/bin/mri_glmfit-sim --glmdir a_glm_results/lh.thickness.velocity.10.glmdir --cache 1.3 abs --cwp 0.05 FreeSurferEnv.csh 7.1.1 Mon Jul 26 10:02:49 EDT 2021 Darwin Narlons-MacBook-Pro.local 20.4.0 Darwin Kernel Version 20.4.0: Thu Apr 22 21:46:47 PDT 2021; root:xnu-7195.101.2~1/RELEASE_X86_64 x86_64 narlonsilva setenv SUBJECTS_DIR /Users/narlonsilva/Desktop/freesufer_subjects FREESURFER_HOME /Applications/freesurfer/7.1.1 Original mri_glmfit command line: cmdline mri_glmfit --y a_cat_data/lh.thickness.velocity.10.mgh --fsgd a_fsgd/velocity.fsgd doss --C a_contrasts/velocity_sex_age.mtx --surf fsaverage lh --cortex --glmdir a_glm_results/lh.thickness.velocity.10.glmdir DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = doss fwhm = 1240.684619 ERROR: cannot find /Applications/freesurfer/7.1.1/average/mult-comp-cor/fsaverage/lh/cortex/fwhm1241/abs/th13/mc-z.csd I was wondering how to fix the error? Thank you! I have a MacBook Pro: macOS Big Sur version 11.3.1. Best regards, Nárlon Cássio Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon

2 2

ERROR- input(s) cannot have multiple frames on Recon-all
by Frank Chau 03 Aug '21

03 Aug '21

External Email - Use Caution Dear Freesurfer experts, I tried to run Recon-all on a T1 series .nii file. A error occurred: "ERROR: input(s) cannot have multiple frames!". I tried to google the method of converting multi frame dicom to single frame dicom. I found software of "dicom2" stated that it could perform the conversion but their manual guide are too hard for me to understand. May I know there are any easier method to perform the conversion? Thank you. Regards Frank --------------------------- FRANK C Y CHAU Research assistant Division of Neurology Department of Medicine Tel: +852 6340 2553 Fax: 2872 5828 E-mail : cyfrank(a)hku.hk<mailto:cyfrank@hku.hk> Rm 304, 3/F, New Clinical building, Queen Mary Hospital, 102 Pokfulam Road, Hong Kong

4 4

Prototype of new tool: SynthSR
by Iglesias Gonzalez, Juan E. 03 Aug '21

03 Aug '21

Dear users, We have added to the development version of FreeSurfer a tool to turn a clinical scan of any resolution and contrast intro a synthetic 1mm T1 MPRAGE that you can segment, register, etc with FreeSurfer (or any other tool, really). The tool has a dedicated mode for low-field Hyperfine scans (which are becoming increasingly popular) and also works to some extent with CT scans. Early feedback on the tool is greatly appreciated. Wiki page of SynthSR: https://surfer.nmr.mgh.harvard.edu/fswiki/SynthSR Link to download the development version of FreeSurfer: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ Link to publication describing the method: https://www.sciencedirect.com/science/article/pii/S1053811921004833 Pretty picture showing what SynthSR can do: attached. Kind regards, Eugenio [cid:BEEBC773-0D95-46C6-B33D-7CEA40DA9F74@partners.org] Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

1 0

Contrast for continuous-by-continuous interactions
by Avi Gharehgazlou 03 Aug '21

03 Aug '21

External Email - Use Caution Hi experts, I am using the command line stream on Freesurfer for my analyses. Although I have successfully designed all my contrasts, I wanted confirmation from you regarding one contrast that I am unsure about. Will you please check if the below contrast appropriately investigates age-by-IQ interaction effects across my two groups (TD and NDDs)? I am also copying here information regarding my regressors and the first few lines of my FSGD file for further detail. *Contrast:* To examine age-by-IQ interaction effects across groups (TD and NDDs): agexIQinteraction_acrossgroups.mtx 0 0 0 0 0.5 0.5 0.5 0.5 0 0 0 0 -0.5 -0.5 -0.5 -0.5 My regressors: · 2 discrete factors: Diagnosis, sex · 4 groups/levels/classes: TD M, TD F, NDD M, NDD F · 3 continuous covariates: age, SA, IQ · Number of classes: 4 · Number of variables: 3 · NregressorsDODS= Nclasses*(Nvariables+1)= 4*(3+1)= 16 · Regressor 1: ones for TDM subjects, 0 otherwise. Codes intercept for TDM · Regressor 2: ones for TDF subjects, 0 otherwise. Codes intercept for TDF · Regressor 3: ones for NDDM subjects, 0 otherwise. Codes intercept for NDDM · Regressor 4: ones for NDDF subjects, 0 otherwise. Codes intercept for NDDF · Regressor 5: age for TDM subjects, 0 otherwise. Codes for TDM · Regressor 6: age for TDF subjects, 0 otherwise. Codes for TDF · Regressor 7: age for NDDM subjects, 0 otherwise. Codes for NDDM · Regressor 8: age for NDDF subjects, 0 otherwise. Codes for NDDF · Regressor 9: SA for TDM subjects, 0 otherwise. Codes for TDM · Regressor 10: SA for TDF subjects, 0 otherwise. Codes for TDF · Regressor 11: SA for NDDM subjects, 0 otherwise. Codes for NDDM · Regressor 12: SA for NDDF subjects, 0 otherwise. Codes for NDDF · Regressor 13: IQ for TDM subjects, 0 otherwise. Codes for TDM · Regressor 14: IQ for TDF subjects, 0 otherwise. Codes for TDF · Regressor 15: IQ for NDDM subjects, 0 otherwise. Codes for NDDM · Regressor 16: IQ for NDDF subjects, 0 otherwise. Codes for NDDF My FSGD file: GroupDescriptorFile 1 Title TD_vs_NDDs_sex_age_SA_IQ Class TDM Class TDF Class NDDM Class NDDF Variables age SA IQ Input 100092_01 TDM 0.060861784 1.747581397 0.386693428 … I'd really appreciate your confirmation of my contrast, Thanks so much, Avi

2 3

Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
by fsbuild 02 Aug '21

02 Aug '21

External Email - Use Caution After some feedback and some more testing, I can reproduce that freeview..app in the 7.2.0 release will segfault on MacOS 11.4 if the license file cannot be found or it cannot be read.  One user reported that he had to get a new license file in order for it to work.  The link for that is here,  https://secure-web.cisco.com/1wLe38Ld2-MJosql9_igECcekBov1nUay8lBJ4gNTyOy7CMKYpu0qhOebXHKkjJcq50BBjrmG1r0LVvavWylVU7gtzxzH-H0TwRBJnWZtIxnTEp0PXkzqmAryNMlqopJhQ96A5QROiaGzPNVj1lIMcieRGjjyt9xhXMEH7GTbJnvCpxNV2Ncf0mSHHUiMPyznxSP0HYeUw9xpwrQsquBDiHr3zkgVMVc-gBH5_RLzCTQCSS7mnT6tOetgNsfkZiN32shJYQrHz9fEuTFD4fSosg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html - R. On Jul 29, 2021, at 14:34, Adam Martersteck <acmarter(a)gmail.com> wrote:        External Email - Use Caution        Here's a log from a completely clean install of FreeSurfer 7.2.0..On an Intel processor MacBook Pro, running macOS Big Sur (11.4).__Starting with a completely clean install of FreeSurfer 7.2.0__Copied license file over from 7.1.1.(Confirmed license file works by running mri_convert)MacBook-Pro:freesurfer adam$ freeview/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38945 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"MacBook-Pro:freesurfer adam$ freeview/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38951 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"MacBook-Pro:freesurfer adam$ freeview/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38954 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"MacBook-Pro:freesurfer adam$ freeview/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38974 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"MacBook-Pro:freesurfer adam$ freeview/Applications/freesurfer/7.2.0/bin/freeview: line 2: 38977 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"(Line numbers that it faults at are linearly increasing?)With export QT_DEBUG_PLUGINS=1I have attached the output log from "freeview > freeview_QT_DEBUG_log.txt".The tail of it is:"loaded library "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqtiff.dylib"loaded library "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwbmp.dylib"loaded library "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwebp.dylib"/Applications/freesurfer/7.2.0/bin/freeview: line 2: 39147 Segmentation fault: 11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@""It perfectly replicates in FreeSurfer 7.1.1. Same error, same debug log.-AdamOn Wed, Jul 28, 2021 at 8:53 PM fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        If you have not already done so, see if you get a different result by double clicking on the Freeview..app icon under /Applications/freesurfer/7.2.0 with the mouse.You can try this variation on what's been previously suggested.1) run a bash shell$ bash2) setup freesurfer environment$ export FREESURFER_HOME=/Applications/freesurfer/7.2.0$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.2.0FSFAST_HOME       /Applications/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.2.0/subjectsMNI_DIR           /Applications/freesurfer/7.2.0/mni3) Locate your license file (I name mine license.txt) in your home directory and check you can read its contents,$ export FS_LICENSE=$HOME/license.txt$ cat $FS_LICENSE... check the output ...... first line should contain email address ...... followed by 3 more lines ...4) set environment variable for debug$ export QT_DEBUG_PLUGINS=15) run freeview with no arguments$ which freeview/Applications/freesurfer/7.2.0/bin/freeview$ freeview... an empty freeview window should appear and persist on the screen ...At this point the last few lines of output in the terminal window should now be:Got keys from plugin meta data ("svg", "svgz", "svg.gz")QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/MacOS/iconengines" ...QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/accessible" ...QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/MacOS/accessible" ...6) Use the freeview application "File" pull down menu to select "load volume".  In the window that comes up, click on the yellow folder icon to the r.h.s of the folder/file entry box under "Select Volume File".  In the Finder window that comes up, navigate to /Applications/freesurfer/7.2.0/subjects/bert/mri and select the brain.mgz file..  Click on OPEN. That path/filename will appear in the load volume text entry box.  Don't check/change any of the options for loading the volume and click OK.The steps above worked for me to load that volume using an Intel MacPro laptop with the 7.2.0 release running under either MacOS 10.15.7 (Catlaina) or MacOS 11.4 (Big Sur) w/o freeview exiting or producing any further output in the terminal window.  If it fails on your machine, you could send along the Qt debug output after the lines listed above..  Please do not send the output from cat'ing your license file though.- R.On Jul 28, 2021, at 14:53, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution        Please check in “energy saver” preferences that “automatic graphics switching” is not selected so that high performance graphics is always used.- R.On Jul 28, 2021, at 14:36, Sahil Bajaj <sahil.brain(a)gmail.com> wrote:        External Email - Use Caution        Hi Freesurfer team,I am also having a similar issue from the last few weeks. I hope we will get a solution soon.Thanks,Sahil On Wed, Jul 28, 2021 at 11:15 AM Tom Parker <tomparker59(a)gmail.com> wrote:        External Email - Use Caution        I have just installed Freesurfer 7.2.0 for Mac. When I attempt to open Freeview it crashes. Full details of error messages below.Any advice to correct would be much appreciated.Many thanks!_______________________________________________Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1oDn4gf3V6EWu2tGEdhRuEDdFnBvCgTb7firJ_… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_____________… mailing listFreesurfer(a)nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<freeview_… mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 3

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2021