Freesurfer July 2022

freesurfer@nmr.mgh.harvard.edu

90 participants
122 discussions

Re: [Freesurfer] recon-all finished without error but no results
by Boa Sorte Silva, Narlon 16 Jul '22

16 Jul '22

External Email - Use Caution Hi Zixuan, I would try keeping the input and output folders separate (i.e., use a different output folder). Also, usually we don’t need to specific the subject’s directory in the command line if it’s already set up in the environment. Nárlon Cássio From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Zixuan Lin <zlin14(a)outlook.com> Reply-To: Freesurfer support list <Freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, July 13, 2022 at 8:53 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <Freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] recon-all finished without error but no results [CAUTION: Non-UBC Email] External Email - Use Caution Hello! I am trying to run recon-all but it only converted the original image to .mgz and finished without error. I checked all other folders and it's empty. Attached please find the recon-all.log. The command line I used is recon-all -i hc01.nii -s hc01 -sd /home/zlin/Documents/MDD_CVR/control Could you please help me check what happens here? Thanks a lot, Zixuan.

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Image Edits
by Rachel Wagner 15 Jul '22

15 Jul '22

External Email - Use Caution Hello all! I hope you are all keeping well. I was wondering if there was a way to save images from freeview that are higher quality than png? In addition, is there a way to set the color bar scale from 0 to 1 and hopefully at 10 internals 0, 0.1, 0.2, 0.3...1? Even when selecting the ‘fixed axis’ option, it seems to automatically adjust. Thanks! Rachel Wagner

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Re: [Freesurfer] FSLOUTPUTTYPE=NIFTI_PAIR: Command not found
by fsbuild 15 Jul '22

15 Jul '22

External Email - Use Caution Hello Deanna, Something is executing the “export” command which is fine in bash or sh, but not in csh or tcsh (which needs “setenv”). export: Command not found.You could try manually running the scripts that get sourced with “tcsh -xf” to better see if they return that error, e.g., % tcsh -xf  $HOME/.afni/help/all_progs.COMP% tcsh -xf  ${FSLDIR}/etc/fslconf/fsl.csh You may want to temporarily rename your .cshrc or comment out the contents before running what’s in $HOME/.cshrc manually.  But if something gets run that does an export command, then it won’t matter what is currently set in your environment. - R. On Jul 15, 2022, at 12:48, Deanna Aghbashian <daghbashian07(a)gmail.com> wrote:        External Email - Use Caution        Hello FreeSurfer Developers, I have set up with terminal in tcsh, and it was working without error. However, when I logged on late last week I got an error in setting up environment for FreeSurfer on Mac OS Monterey Version 12.4 -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSLOUTPUTTYPE=NIFTI_PAIR: Command not found. export: Command not found.. FSL_DIR /usr/local/fsl [MacBook-Pro:~] deanna% nano ~/.cshrc Within my tcsh profile, I do not have anything to indicate to have FSLOUTPUTTYPE to be NIFTI_PAIR, nor do I have a line to export. I have also checked the SetUpFreeSurfer.csh, FreeSurferEnv.csh. I have tried clearing out my profile and recreating it, deleting and reinstalling FSL and FreeSurfer. When I use echo $FSLOUTPUTTYPE it comes back as NIFTI_GZ. My profile is below: # auto-inserted by @update..afni.binaries : setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace # set up tab completion for AFNI programs if ( -f $HOME/..afni/help/all_progs.COMP ) then    source $HOME/.afni/help/all_progs.COMP endif if ( $?DYLD_LIBRARY_PATH ) then   setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace else   setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace endif set path = ( $path $HOME/abin ) # include directories for FSL setenv FSLDIR /usr/local/fsl source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH} setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh Does anyone have any suggestions? Thanks, Deanna _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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ATTACHMENT REMOVED--asegstats2table
by John Absher 15 Jul '22

15 Jul '22

Please be advised, This message contained one or more of the following prohibited file types: (.zip,.bat,.exe,.pif,.scr). The file(s) have been automatically removed from the message, in order to protect the privacy of our patients and employees, and to protect the integrity of our systems and data. As a security measure to prevent potential viruses and malware, Partners prohibits the receipt of attached files that have the potential to execute malicious code. You should contact the sender, and if you are sure that the original attached file(s) are safe, please use the Partners Secure File Transfer system, https://transfer.partners.org <https://transfer.partners.org> to work with the sender to securely transfer the removed attachment(s). If you do not have an account on the Partners Secure File Transfer System, please register for an account by using the following steps: 1. Go to https://transfer.partners.org <https://transfer.partners.org> 2. Click on "I don't have an account yet" 3. Enter your email address and click Register 4. You will receive an email with final instructions More information can be found at http://rc.partners.org/sFTP <http://rc.partners.org/sFTP> (Partners login required) If you have any questions or issues please enter a ticket in ServiceNow or call your Service Desk. **** Original message follows **** External Email - Use Caution Hi, We run freesurfer 6 on an HPC environment. We received this error when trying to run an asegstats2table script: [jabsher@node0130 results]$ ./asegstats2table_scr File "/zfs/hpcnirc/usr/bin/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/zfs/hpcnirc/usr/bin/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax [jabsher@node0130 results]$ We are running this version: You are running this version of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Here are the loaded modules: Currently Loaded Modules: 1) libxml2/2.9.10-gcc/8.3.1 2) openblas/0.3.10-gcc/8.3.1 3) matlab/2021b 4) anaconda3/5.1.0-gcc/8.3.1 5) openmpi/3.1.6-gcc/8.3.1-cuda10_2-ucx 6) cuda/10.2.89-gcc/8.4.1 The script is attached. We've gone to the wiki page (asegstats2table - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1eU_J79ltbqe0p9Duk2YmurJuRaHFOpDSqizGlzIClXlSH…> and tried essentially all permutations, including specifying the aseg.stats files by name for each subject. The "use -subjects" error comes up every time, and we tried this as specified, with -subjects followed by all the directory/subject names, with a \ at the end of each line for readability. I know this must be something very straightforward, but hoping you can help. Thanks, Warm Regards, John R. Absher, MD, FAAN Associate Professor, University of South Carolina School of Medicine Greenville Department of Internal Medicine, Division of Neurology Clinical Assistant Professor, Clemson University School of Health Research (CUSHR) Graduate Faculty, Clemson University School of Public Health Sciences Prisma Health-Upstate 200 Patewood Drive, Suite 350B Greenville, SC 29615 John.Absher(a)prismahealth.org<mailto:John.Absher@prismahealth.org> or absher(a)mailbox.sc.edu<mailto:absher@mailbox.sc.edu> or jabsher(a)clemson.edu<mailto:jabsher@clemson.edu> 864-454-4500 (office) 864-350-6655 (mobile) 864-454-4505 (fax) [cid:image001.jpg@01D89871.8F9C2110] Inspire health. Serve with compassion. Be the difference. ---------------------------------------------------------------------- CONFIDENTIALITY NOTICE This message is intended only for the use of the individual or entity to which it is addressed and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is strictly prohibited by law. If you have received this communication in error, please notify me immediately. A MIME attachment of type <application/octet-stream> was removed here by a drop-attachments-by-name filter rule on the host <esa8.hc4087-85.iphmx.com>.

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FSLOUTPUTTYPE=NIFTI_PAIR: Command not found
by Deanna Aghbashian 15 Jul '22

15 Jul '22

External Email - Use Caution Hello FreeSurfer Developers, I have set up with terminal in tcsh, and it was working without error. However, when I logged on late last week I got an error in setting up environment for FreeSurfer on Mac OS Monterey Version 12.4 -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSLOUTPUTTYPE=NIFTI_PAIR: Command not found. export: Command not found. FSL_DIR /usr/local/fsl [MacBook-Pro:~] deanna% nano ~/.cshrc Within my tcsh profile, I do not have anything to indicate to have FSLOUTPUTTYPE to be NIFTI_PAIR, nor do I have a line to export. I have also checked the SetUpFreeSurfer.csh, FreeSurferEnv.csh. I have tried clearing out my profile and recreating it, deleting and reinstalling FSL and FreeSurfer. When I use echo $FSLOUTPUTTYPE it comes back as NIFTI_GZ. My profile is below: # auto-inserted by @update.afni.binaries : setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace # set up tab completion for AFNI programs if ( -f $HOME/.afni/help/all_progs.COMP ) then source $HOME/.afni/help/all_progs.COMP endif if ( $?DYLD_LIBRARY_PATH ) then setenv DYLD_LIBRARY_PATH ${DYLD_LIBRARY_PATH}:/opt/X11/lib/flat_namespace else setenv DYLD_LIBRARY_PATH /opt/X11/lib/flat_namespace endif set path = ( $path $HOME/abin ) # include directories for FSL setenv FSLDIR /usr/local/fsl source ${FSLDIR}/etc/fslconf/fsl.csh setenv PATH ${FSLDIR}/bin:${PATH} setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh Does anyone have any suggestions? Thanks, Deanna

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Pass code
by Ulysses Bernardet 15 Jul '22

15 Jul '22

External Email - Use Caution Hi, I would like to request the pass code for the FreeSurfer Virtual VM image. Cheers, Ulysses Dr Ulysses Bernardet Assistant Professor of Computer Science cybernetic human lab cs.aston.ac.uk/chl College of Engineering and Physical Sciences Aston University, Birmingham, UK

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[TRACULA] Auto-BIDS Config Variables Question
by Steven Meisler 15 Jul '22

15 Jul '22

External Email - Use Caution Hello, I am trying out the development dmri-bids-config script <https://secure-web.cisco.com/1w--1vLn2hIhDzN_sQmBI1_PGZkHehc5IsuQS_9ZRqntOo…> to set up my BIDS-formatted data for TRACULA. It runs fine without error, but I have some concerns about the automatically generated protocol variables. 1) For “echospacing”, should we be using the echo spacing as found in the scanner protocol, or effective echo spacing (as parsed from the BIDS json sidecar)? These values are fairly different from each other. It is also not clear what units the config file expects (I assume “ms” based on some of the examples and protocols I have looked at). 2) “epifactor” seems to be generated by a mathematical operation on the total readout time as parsed from the BIDS json file. The value I get from this operation is off by a few orders of magnitude. In my case, the predicted value from the BIDS json file is 127001, while the protocol epifactor is 128. What I imagine is happening here is that the script assumes the TotalReadoutTime is in different units, because it does some division by (0.001) and then adds 1 to the result. So if the units matched mine, then I would have ended up with 127+1 = 128 (which matches the protocol). In either case, I am happy to see this being configured for BIDS and am excited to see it deployed in 7.3! Best, Steven

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Password for unzipping .7z file of virtual image
by Weilguny, Nicolas 14 Jul '22

14 Jul '22

External Email - Use Caution Hi FreeSurfer-Team, I hereby request the password for unzipping the FS_7_2_0_Ubuntu_18_04_06.ova.7z file. Thank you in advance! Best regards, Nicolas Weilguny

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Freesurfer .7z password
by Kerezoudis, Panagiotis, M.D., M.S. 14 Jul '22

14 Jul '22

External Email - Use Caution Greetings, I would like to ask for the password to open and install the .7z file for Freesurfer on Windows. Thank you, Panos Panagiotis Kerezoudis, M.D., M.S. Resident | Department of Neurologic Surgery Mayo Clinic | Rochester, Minnesota<https://secure-web.cisco.com/1KQqKOxG8FySe-tB4is7yhyIC304BnfpZzLZiSpSYcMNmv…> 200 First Street SW, Rochester, MN, 55905 email: Kerezoudis.Panagiotis(a)mayo.edu<mailto:Kerezoudis.Panagiotis@mayo.edu> |phone: 5-6037<tel:5-6037> | pager: 17872<tel:17872>

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Re: [Freesurfer] SynthSR: Illegal Hardware Instruction
by fsbuild 12 Jul '22

12 Jul '22

External Email - Use Caution Hello Ahmed, This can result from how the code was compiled and/or optimized for older versions of MacOS - which may not translate well to running on newer versions of MacOS.  In your case, the the Mac is also running the Rosetta environment to translate the Intel binary instructions to run on the arm M1 chip.   The code would probably have to be complied differently to address this. If you have an example command and file input you could share, you could send it along and we could try and reproduce it. - R.  environment to translate instructions compiled  On Jul 12, 2022, at 09:28, Abdelkarim, Ahmed <a.karam(a)ucl.ac.uk> wrote:        External Email - Use Caution        Hello I have an issue getting SynthSR working with FreeSurfer dev.I have MacBook Pro with apple M1 chip and MacOS Monterey. In bash terminal, after setting up FreeSurfer, and running the SynthSR command, I get this error ‘’Illegal instruction: 4’’. Have you had a similar issue before? Any advice? Many thanks in advance. RegardsAhmed  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- This is a copy of a message which has been originally sent to: "To" field: freesurfer(a)nmr.mgh.harvard.edu "Copy" field: a..karam(a)ucl.ac.uk The message has been sent by https://secure-web.cisco.com/148oNXnm75KGvFGK5eicU0d_xOxYGERfT6ffGsller2qhI… and the used account name was: SSL

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Freesurfer July 2022