Freesurfer

freesurfer@nmr.mgh.harvard.edu

5 participants
30076 discussions

aseg.presurf edits are undone or incomplete when brainmask.mgz edits are involved
by Keefe, Sarah 12 Sep '22

12 Sep '22

External Email - Use Caution Hi FreeSurfer Team, Our group is in the process of switching to Freesurfer 7.1.1 from 5.3. We have been taking advantage of Freesurfer 7's aseg.presurf volume to add in correction of unlabeled cerebellum to our standard edit checklist rather than our previous workflow of having a Freesurfer fail our quality control standards and be excluded from analysis if too much cerebellum is unlabeled on aparc+aseg segmentation. We're consistently running into an issue when we have a Freesurfer that requires corrections to both brainmask.mgz and aseg.presurf.mgz. An example of when this happens is if the Freesurfer output labels dura as cerebellum cortex on aparc+aseg (which requires erasing the included dura from brainmask.mgz) and the output also has an exclusion of cerebellum from the aparc+aseg segmentation (which requires correctly labeling the excluded voxels on aseg.presurf.mgz). We have found that if we edit both the aseg.presurf.mgz and brainmask.mgz volumes and then rerun recon-all with both, the cerebellum exclusion segmentation fix does not "take" completely and individual voxels in the cerebellum that were corrected in the edited volume are still left unlabeled. We have 100% confirmed that our labeling edits to aseg.presurf are correct and complete before this happens. To reduce confusion and attempt some consistency across our editing team, we relaunch recon-all with the same flags every time: -autorecon2 -autorecon3 -qcache To work around this issue, we implemented a workflow where editors will make brainmask.mgz corrections, then rerun recon-all (rerun 1), and then make aseg.presurf corrections, and rerun recon-all again (rerun 2). This seems to work although it is frustrating since we are trying to minimize the number of reruns of recon-all and we typically tell people to stop and make a final quality control decision after 3 reruns. What we are finding is if another issue pops up on brainmask.mgz after rerun 2 that then needs corrections (e.g. other areas of dura are incorrectly included in the pial surface or aparc+aseg cerebellum labeling but weren't included before so weren't erased) then after making those edits and rerunning recon-all, the previously corrected aparc+aseg cerebellum segmentation shows "missing" unlabeled voxels, same as if we had run recon-all once with both aseg.presurf and brainmask volumes edited. The attached image shows an example of our process and the issues we're seeing. The end result (F) also happens if we edit both brainmask.mgz and aseg.presurf.mgz edits and rerun recon-all once with both included. screenshot A is the aparc+aseg.mgz of the original recon-all output (run 0) where cerebellum is unlabeled (red arrows). There is also visible dura labeled as cerebellum that we need to fix (yellow arrow). screenshot B is the aparc+aseg.mgz of the recon-all rerun output after just the brainmask.mgz was edited and saved (run 1). Additional segmentation issues have appeared in addition to the original ones (red arrows). This screenshot also shows an example of the type of edit we are doing to brainmask - we have erased dura from brainmask.mgz to correct the cerebellum cortex labeling and the edit worked (yellow arrow). screenshot C is the aseg.presurf.mgz volume after run 1 before editing for the cerebellum exclusion issue. screenshot D is our edited and saved aseg.presurf volume BEFORE we run the second recon-all relaunch. We have corrected the labeling (green arrows). screenshot E is the aparc+aseg.mgz after a recon-all relaunch with only the new edit to aseg.presurf. (run 2). The cerebellum exclusion error has been fixed in aparc+aseg (green arrows). This run 2 of recon-all caused more issues to show up that required more brainmask.mgz edits. screenshot F is what we see if we edit brainmask.mgz again and rerun recon-all (run 3). The output of run 3 shows missing voxels in the cerebellum where we had fixed them before. Unlabeled voxels appear throughout the areas that were edited in C and were corrected in D. We try to minimize edits and maintain consistency across our editing team by asking people to only erase dura from brainmask.mgz that has been erroneously included in the cerebellum labelling or in the pial surface (rather than other dura that also happens to be included in the brainmask.mgz). We also ask people to relaunch recon-all with the same -autorecon2 -autorecon3 -qcache flags each time for consistency across our data. We really really want to be able to cut down the number of times we are relaunching recon-all but we are unable to fix both these issues at once (it ends up like screenshot F after 1 rerun). Is there a way to prevent the aseg.presurf.mgz edits from "undoing" voxels when brainmask.mgz edits are included or done after aseg.presurf? Any assistance or alternative techniques for solving this would be much appreciated. We are primarily using the Freesurfer 7.1.1 Docker container but I have also been able to replicate this issue on CentOS 8 and Ubuntu 20.04 with build stamp freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551. Thanks so much, Sarah ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

3 11

Re: [Freesurfer] mri_binarize error for thalamic nuclei during trac-all prep
by Makenna B McGill 12 Sep '22

12 Sep '22

External Email - Use Caution Hi Freesurfer Developers, I believe I found a work around for the mri_binarize error I was running into regarding the thalamic nuclei segmentation during trac-all prep as described in greater detail in my previous message ( https://secure-web.cisco.com/1Rjl_EG-oXqOtVFNnzcnE1pzvr3JwoCtkvYdoNEBqGYqKM…) I'm using FS v7.3.2 on OS Monterey, with the segmentThalamicNuclei.sh script producing the segmentation file mri/ThalamicNuclei.v13.T1.FSvoxelSpace.mgz. From what I can tell, the error seems to arise from the following section from the trac-preproc script, specifically the line "set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`)": # Replace thalamus in main segmentation with nearest neighbor labels set ids = () foreach label (Left-Thalamus Right-Thalamus) set ids = ($ids `grep -i " ${label}[ \t]" $fslut | awk '{print $1}'`) end set cmd = mri_binarize set cmd = ($cmd --i $fsdir/mri/$segname.mgz) set cmd = ($cmd `printf "--replaceonly-nn %s 11 " $ids`) set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz) echo $cmd $cmd I made the following edits to print the $ids for the left and right thalamus, then input those values (10 49) as the window required by --replaceonly-nn: # Replace thalamus in main segmentation with nearest neighbor labels set ids = () foreach label (Left-Thalamus Right-Thalamus) set ids = ($ids `grep -i " ${label}[ \t]" $fslut | awk '{print $1}'`) printf "\n \n label is $label \n \n" printf "\n \n ids are $ids \n \n" end set cmd = mri_binarize set cmd = ($cmd --i $fsdir/mri/$segname.mgz) set cmd = ($cmd --replaceonly-nn 11 10-49) set cmd = ($cmd --o $labdir/anatorig/${segname}+thalnuc.nii.gz) echo $cmd $cmd This seems to successfully circumvent the error I was previously receiving ("printf: illegal option -- -"), which resulted in a missing --replaceonly-nn command and prevented the mri_binarize output file from being created. The rest of the script then runs without error, and the final trac-all output seems to have been successful. I'm not sure why I was receiving this printf error, but I would greatly appreciate any feedback or corrections to this potential solution. Thank you in advance for any guidance you are able to provide, and please let me know if any further information is needed. Best, Makenna *Makenna McGill *(she/her) Doctoral Student in Clinical Psychology The University of Texas at Austin

1 0

GLM error: matrix is ill-conditioned or badly scale
by Cao Yuan 12 Sep '22

12 Sep '22

External Email - Use Caution Dear experts, I would like to run mri_glmfit in a group analysis. However, I met the following error when I added the medicationload as variable in my fsgd file. Since I have 305 subjects and only 75 of these have medication load, it seems to this variable includes too many zero. Just I guess. The error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08\ \ \ --------------------------------\ -------- ERROR: READ THIS -----------------\ --vvvvvvvvvvvvvvvvvvvvvvvvvvvvvv-----\ Possible problem with experimental design:\ Check for duplicate entries and/or lack of range of\ continuous variables within a class.\ If you seek help with this problem, make sure to send:\ 1. Your command line:\ mri_glmfit --y lh.volume.BDHC3Study.10.mgh --fsgd FSGD/BDHC3Study.fsgd --C Contrasts/HC3-BD3.mtx --C Contrasts/BD3-HC3.mtx --surf fsaverage lh --cortex --glmdir lh.volume.BDHC3Study.10.glmdir \ 2. The terminal output of this program (ie, everything it prints to the screen)\ 3. The FSGD file (FSGD/BDHC3Study.fsgd)\ 4. The design matrix lh.volume.BDHC3Study.10.glmdir/Xg.dat\ Attempting to diagnose further \ SumSq: Min=6.368664 (col 8), Max=16.261612 (col 7)\ ... could not determine the cause of the problem\ --^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^----\ } I attached my terminal output, fsgd file, and design matrix Thanks Yuan

2 2

Issues with recon-all
by Hitesh Pradhan 12 Sep '22

12 Sep '22

External Email - Use Caution Hello Developers, I am facing the recon-all command which exits with premature exit. I have attached the recon-all log file. I have also attached my license file for your reference. 1. I am using UBUNTU 18 as my platform. 2. I have attached the recon-all log file. Please get back to me at your earliest convenience. Thank you and best regards. -- Hitesh Pradhan M.Sc. Cognitive Science Centre for Cognitive and Brain Sciences Indian Institute of Technology Gandhinagar LinkedIn <https://secure-web.cisco.com/13VrVZScSFZgTtwJnKzvDKGc6Y7MsVyq6ChC78NAKxCr8q…> | CCBS <https://secure-web.cisco.com/1kQt58ynwE9ki5pHwGOx_x8m7sW3h7SrKWfetpp-nnkh_n…> | GitHub <http://secure-web.cisco.com/1JHLsfRYu6iRsIz35H_9d38JOMYz_8oYgBH1Cuv-rVzNBPN…>

2 1

recon-all error: ERROR: recon-all command failed with return_code: 1
by Estephan Moana Filho 12 Sep '22

12 Sep '22

External Email - Use Caution Hello, I am using QuNex to process MRI data with the HCP pipelines. I was able to complete the hcp_pre_freesurfer without problems, but I am having trouble completing the hcp_freesurfer step. I tried processing 10 participants, and they all fail after several hours of processing. The qunex log reports the error "ERROR: recon-all command failed with return_code: 1". The recon-all.log is not clear about what went wrong (at least to me). I attached here both log files. Please let me know your thoughts on this. Thank you. Estephan -- Estephan J. Moana-Filho, DDS, MS, PhD Assistant Professor Division of TMD, Orofacial Pain and Dental Sleep Medicine Graduate Faculty in Oral Biology Department of Diagnostic and Biological Sciences UMN School of Dentistry moana004(a)umn.edu 6-320d Moos Tower 515 Delaware St. SE Minneapolis, MN 55455-0329 Office: (612) 624-3338 Clinic: (612) 626-0140 Fax: (612) 626-0138 Clinical referrals: z.umn.edu/TMDrefer UMN profile: https://secure-web.cisco.com/1BluccjzH3-KDTRdy4AY9mJxa3QFjRrZfgNGYogzNmymzc… ORCID ID: http://secure-web.cisco.com/1kWXy7S9i2NP1dVe5fSw4QHrsALsBPTsDyl3WsasxISwIXg… Publons: https://secure-web.cisco.com/1COoH1uI40MMWj6AieYoBdFPeLpi8j-IPG1MGvT1nWz6Qi… My Bibliography (NCBI): https://secure-web.cisco.com/10i4Yv5gmnclIOBTdnC7Px0JYiS0Sd0QPMcZUFY06jZGLV… The information transmitted in this e-mail is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material, including "protected health information." If you are not the intended recipient, you are hereby notified that any review, retransmission, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please destroy and delete this message from any computer and contact us immediately by return e-mail.

2 2

Re: [Freesurfer] Enabling AVX instructions on Windows 10 (was Re: Illegal Instruction (mri_segment_hypothalamic_subunits) - VM 7.2.0
by fsbuild 11 Sep '22

11 Sep '22

External Email - Use Caution Thank you Randy for the feedback and glad to hear things are working for you. Juts FYI, If you want to use the Windows Subsystem for Linux (WSL), e.g., to run Ubuntu Linux, then you will need to re-enable Hyper-V on your Windows machine.  I have not consistently seen a conflict with running Windows Hyper-V and Virtualbox, and this seems to happen only with Virtualbox.  Virtualization software from VMware apparently does not have a conflict with Windows Hyper-V.   Going forward we can look into providing a VMware image of a Freesurfer VM as well.  It's just that VirtualBox is free and that has not always been the case with VMware and other vendors virtualization software. - R.On Sep 8, 2022, at 14:20, daedalus39(a)aol.com wrote:        External Email - Use Caution        Thank you so much for these incredibly clear instructions.  I was able to “enable” AVX, disable hypervisor, and import tensorflow.Since these posts are publicly visible, I'm hoping this thread will be useful for all others who face these issues.Thanks again-Randyxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxdeveloper@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$ mri_segment_hypothalamic_subunits --s WBI-FES_S_0862 --write_posteriorsPosteriors will be saved in each subject's directory. using 1 threadprocessing 1/1segmentation saved in: /usr/local/freesurfer/7.2.0/subjects/WBI-FES_S_0862/mri/hypothalamic_subunits_seg.v1.mgzposteriors saved in:   /usr/local/freesurfer/7.2.0/subjects/WBI-FES_S_0862/mri/hypothalamic_subunits_posteriors.v1.mgzvolumes saved in:      /usr/local/freesurfer/7.2.0/subjects/WBI-FES_S_0862/mri/hypothalamic_subunits_volumes.v1.csv If you use this tool in a publication, please cite:Automated segmentation of the hypothalamus and associated subunits in brain MRIB. Billot, M. Bocchetta, E. Todd, A. V. Dalca, J. D. Rohrer, J. E. IglesiasNeuroImage (in press) developer@developer-VirtualBox:/usr/local/freesurfer/7.2.0/subjects$xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx-----Original Message-----From: fsbuild <fsbuild(a)contbay.com>To: freesurfer(a)nmr.mgh.harvard.eduCc: daedalus39(a)aol.comSent: Sun, Sep 4, 2022 12:35 amSubject: [Freesurfer] Enabling AVX instructions on Windows 10 (was Re: Illegal Instruction (mri_segment_hypothalamic_subunits) - VM 7.2.0        External Email - Use Caution        The lscpu output in the VM not listing AVX and AVX2 does not necessarily mean something is missing from the VM to run AVX instructions.The Intel processor listed in your output, i7-8700K, does support AVX instructions.  But AVX instructions could be disabled on your host (windows) machine preventing the VM from running them.  Microsoft's own virtualization or “hyper-v” software may also be interfering with Virtualbox.If you start the VM and open the terminal window you should see the output from the freesurfer startup script list SUBJECTS_DIR, etc.  You can run the included python distribution by typing “fspython” .  At the next prompt, type “import tensorflow”.   I think you will get an illegal instruction error and a core dump when you do that since the VM cannot currently run AVX instructions.developer#developer-VirtualBox:~$ fspythonPython 3.6.8 (default, Apr 10 2020, 02:08:58)[GCC 4.4.7 20120313 (Red Hat 4.4.7-23)] on linuxType “help”, “copyright”, “credits” or “license” for more information.>>> import tensorflow… Illegal instruction … (core dumped) ...This post describes what I think you are seeing on a Windows machine hosting an Ubuntu VM,https://secure-web.cisco.com/1Z2p4OueSZVcRiWfZ62YUUMfKkWvThyO-5u6sBN2u-M… and this lists how to enable/disable AVX instructions …https://secure-web.cisco.com/1e3vbXGbSnNejaHXRJmtGrQUvmpBB5E7o6CVNbXMNgppS04-dAu7jOPS3NGH8FSRrWNMWtR3RjuwAGZIrBlerpJLOMMOR4j6xjLVM1yiEFgQBD4NHWs8siIz1tG_1hYJaL_1bCripok8KxU4iOWT6PMW7xyxAJwYVZj9it1ojM-WC4BDbj3seHnHkzB_R60TCbZZac5qnbROwwFuepcYdfggI6k5V0j-3xkWbVKi_vtMUZMMl_6zPNmUnSq0rxdIjjmQ4DlyZ6ss5OWHR8hv96YRz_UVeS-R4fBEwE69QcKqpqA5RdMNgMgkB7Y7Pvy9Smf1BOKkfE0dbLGQ_e80yJw/https%3A%2F%2Fsuperuser.com%2Fquestions%2F244213%2Fhow-can-i-check-whether-intels-avx-is-enabled-on-my-computerFrom those and other posts I would try the following on your Windows (host) machine:1) Open the windows terminal or command line window in administrator mode2) Enable AVX instructions with the command   BCDEDIT /set xsavedisable 03) Disable launching the Microsoft hypervisor   BCDEDIT /set hypervisorlaunchtype off4) Shut down the VM and quit Virtualbox.  You may want to quit all other applications as this next command may ask to reboot your machine (say yes).  If you are not prompted to reboot, then manually reboot the Windows host.5) Disable Microsoft Hyper-V   DISM /Online /Disable-Feature:Microsoft-Hyper-V6) After your machine reboots, login and start the VM7) In the VM Ubuntu terminal window, run “lscpu | grep avx” again and see if it lists avx, avx28) IF IT DOES REPORT AVX NOW, try the lines above again where you typed “fspython” followed by “import tensorflow”.  This time you should not get an illegal instruction error.  You can ignore any error you see about a missing library for libcuda and/or no GPU support.- R.On Sep 3, 2022, at 13:46, daedalus39(a)aol.com wrote:        External Email - Use Caution        OK.  It appears this VM (provided by the FreeSurfer developers) does not include "AVX".That is, "freesurfer_7.2.0_amd64.deb" can't run mri_segment_hypothalamic_subunits without additional setup?  Is it even possible?  If so, can anyone in the FS community provide some simple guidance.  I am not horribly facile with Linux to begin with, but I'd really like to test the hypothal function..-Randydeveloper@developer-VirtualBox:/$ lscpu | grep avxdeveloper@developer-VirtualBox:/$ lscpu | grep avx2developer@developer-VirtualBox:/$ lscpuArchitecture:        x86_64CPU op-mode(s):      32-bit, 64-bitByte Order:          Little EndianCPU(s):              4On-line CPU(s) list: 0-3Thread(s) per core:  1Core(s) per socket:  4Socket(s):           1NUMA node(s):        1Vendor ID:           GenuineIntelCPU family:          6Model:               158Model name:          Intel(R) Core(TM) i7-9700K CPU @ 3.60GHzStepping:            13CPU MHz:             3599.998BogoMIPS:            7199.99Hypervisor vendor:   KVMVirtualization type: fullL1d cache:           32KL1i cache:           32KL2 cache:            256KL3 cache:            12288KNUMA node0 CPU(s):   0-3Flags:               fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid tsc_known_freq pni ssse3 cx16 pcid sse4_1 sse4_2 hypervisor lahf_lm invpcid_single ibrs_enhanced fsgsbase invpcid md_clear flush_l1d arch_capabilitiesdeveloper@developer-VirtualBox:/$ -----Original Message-----From: fsbuild <fsbuild(a)contbay.com>To: freesurfer(a)nmr.mgh.harvard.eduCc: daedalus39(a)aol.comSent: Fri, Sep 2, 2022 10:12 pmSubject: Re: [Freesurfer] Illegal Instruction (mri_segment_hypothalamic_subunits) - VM 7.2.0        External Email - Use Caution        Hello Randy,The mri_segment_hypothalamic_subunits command is a python script that uses tensorflow which in turn is coded to use AVX instructions.  If the VM host processor does not support AVX instructions, then you will get an illegal instruction error.You can check to see if AVX instructions are supported if this commands shows "avx" or "avx2" in the output (see screenshot for where that is the case).$ lscpu | grep avxIf AVX instructions are supported, then error can also happen if the command is incomplete.- R._______________________________________________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/19QcljupuVmx74lbRGbM58XsgPurzxhIXR41Y-… information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1JMGwjYsWBR4R7YizFXlyvg61zGiGWBCoLVytA… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1qLkCNQM8H-GA9PnGqXjOlOlYDKhiP4OZXyBN8…; .Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________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/19QcljupuVmx74lbRGbM58XsgPurzxhIXR41Y-… information in this e-mail is intended only for the person to whom it is addressed.  If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1JMGwjYsWBR4R7YizFXlyvg61zGiGWBCoLVytA… has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1mBYjOg9rwrAmLnsaW5YyqCsJ5FKXVXgXIV-gO…; .Please note that this e-mail is not secure (encrypted).  If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately.  Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Talairach failed error
by Romeo Penheiro 11 Sep '22

11 Sep '22

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute the FreeSurfer outputs for one of my subjects. I get the following error when I run the recon-all command: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0077, pval=0.0000 < threshold=0.0050) I've searched the list and one similar error has been reported<https://secure-web.cisco.com/1mb7ICnEk6d7MX8y2VUywYPvb7bDBqwKBiUBJRRl0MYz9P…> in fMRIPrep. However, I am not sure how to implement this on the platform. Does anyone have any thoughts on how to troubleshoot this one? Also, I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: v7.2.0 2) Platform: CBRAIN 3) uname -a: Linux cdr854.int.cedar.computecanada.ca<http://secure-web.cisco.com/1S0ZPkqWcDQh46lUo_Qq5ag8EA7S14eBo9cHG1xCnN5nATS…> 3.10.0-1160.53.1.el7.x86_64 #1 SMP Fri Jan 14 13:59:45 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Romeo Penheiro Master's Student - Cognitive Science Program Carleton University This email contains links to content or websites. Always be cautious when opening external links or attachments. Please visit https://secure-web.cisco.com/1PY_amCYECNNWCwzy3R4JIwB68nuCzqGc5BQ-T7BjvfW8o… for information on reporting phishing messages. When in doubt, the ITS Service Desk can provide assistance. https://secure-web.cisco.com/1RwAwHBYZhklMOEk6WUWXJsqLCukS6Gr7jS6yOEgcPy-3n… -----End of Disclaimer-----

1 0

Re: [Freesurfer] problem with autorecon2-cp
by Mostafa Fakhri 10 Sep '22

10 Sep '22

External Email - Use Caution Thank you for sharing your expertise. Mostafa

1 0

ls: *.nii: No such file or directory
by Ellie Shaw 09 Sep '22

09 Sep '22

External Email - Use Caution i there, I am attempting to perform the recon-all in parallel command. When I run this command I get the following message: ls: *.nii: No such file or directory The following command is: bash-3.2$ export SUBJECTS_DIR=/Applications/freesurfer/7.2.0/tbi/TBN bash-3.2$ echo $SUBJECTS_DIR /Applications/freesurfer/7.2.0/tbi/TBN bash-3.2$ ls *.nii | parallel --jobs 8 recon-all -s {.} -i {} -all -qcache ls: *.nii: No such file or directory Academic tradition requires you to cite works you base your article on. If you use programs that use GNU Parallel to process data for an article in a scientific publication, please cite: Tange, O. (2022, August 22). GNU Parallel 20220822 ('Rushdie'). Zenodo. https://secure-web.cisco.com/1mGw517t0yBXkztNqf01JZCPURoO6_GwJZcmOf9XN0Bit3… This helps funding further development; AND IT WON'T COST YOU A CENT. If you pay 10000 EUR you should feel free to use GNU Parallel without citing. More about funding GNU Parallel and the citation notice: https://secure-web.cisco.com/1qeJBgbE0rR_XWDJGaS_dtrryFt6t984jQGxAubuxxJ-dk… To silence this citation notice: run 'parallel --citation' once. I have also attached a screenshot of the file with the nii files to help. I am seeking some support to overcome this issue. Freesurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b Platform: OSX 7.2.0 Thank you in advance! Kind regards, Ellie

2 1

equest for password to open FS_7_2_0_Ubuntu_18_04_06.ova.7z, reg:-
by PRASAD D 09 Sep '22

09 Sep '22

External Email - Use Caution Dear sir/madam. My name is D.Prasad from PTU university, Puducherry, INDIA. I'm a research scholar at PTU university. my research area deals with Brain MRI Images. to work on that, i have downloaded (Ubuntu 18.04.06 compressed image with the *FreeSurfer <https://secure-web.cisco.com/1QXoCtx-MIiYDhd3WUA3RA2DLeZHX5T78Sq0bvhIq3vqTy…> 7.2.0 release installed)* FS_7_2_0_Ubuntu_18_04_06.ova.7z <https://secure-web.cisco.com/10p_AiCmfuT7rYhn0VynvFaHc0KgMJaRONhMsmtslzUKju…> When I'm trying to open the above file, it is asking for Password. I kindly request you to send the Password at the earliest. Thank you Yours Sincerely D.Prasad Fulltime Research Scholar

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer