Freesurfer

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30065 discussions

Freeview displaying images in the wrong orientation
by Nathan Kindred (PGR) 27 Feb '23

27 Feb '23

External Email - Use Caution Hi, When I am displaying certain images in freeview the orientation does not match what is displayed in both orient_mri and SPM. The coronal and horizontal views seems to be okay but the midsagittal view is often wrong with the front of the brain tilted up. How do I get freeview to display the images in the correct orientation? Thanks, Nathan

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What's the difference between pc1 and spc (glmfit)
by KennethSPrice 27 Feb '23

27 Feb '23

External Email - Use Caution Hey Freesurfers, I'm running a longitudinal study and have multiple outputs in my results. What's the difference between the "pc1" files and the "spc" files? Also what do the "rate" and "avg" files represent? Any response would be greatly appreciated! Thanks, Ken Sent with [Proton Mail](https://secure-web.cisco.com/1boPq8uQ-9H8Gy1fAGjjCB35J45SPTFBfkpwoo3x… secure email.

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different clusters in mri_surfcluster output versus viewing in Freeview
by Smith, Christine 26 Feb '23

26 Feb '23

External Email - Use Caution Hello, I am getting a mismatch of clusters when we view cluster results in freeview versus ask for a table of the significant clusters. I am performing a GLM analysis on Freesurfer to analyze cortical thickness (mri_glmfit). When viewing the significance map with freeview, we set the minimum threshold to 2 for the sig.mgh file. We also used the same threshold when creating a summary table of the clusters using mri_surfcluster. mri_surfcluster --in {$dir}/visuospatial_MCI_correlation/sig.mgh --hemi left --thmin 2 --thsign pos --minarea 10 --subject fsaverage --surf inflated --annot BN_Atlas --sum {$dir}/visuospatial_MCI_correlation/left.thickness.clustersummary_BN.txt We were hoping to use the summary text file to identify the clusters on freeview and their characteristics (e.g., size, x, y, z ccordinates). Unfortunately, the regions that we see for both methods don’t match as there are some clusters that we see on the summary text file that we don’t see on freeview and vice versa. How can we make the output of these two methods match up? Note that the issue is not the minimum cluster size in the summary table. When we put that to 1 we still get a mismatch. Please note that in the mri_surfcluster program we can indicate that we only want positive results. We don't see a way to do this in freeview or a way for that to affect the p value in freeview. Is this possibly the issue? If so, how can we make a picture in freeview that matches our summary table? Regards, Christine -- Christine N. Smith, Ph.D. Research Service, VA San Diego Healthcare System Department of Psychiatry, University of California San Diego VA San Diego Healthcare System VMRF Building 13 3350 La Jolla Village Drive (151A) San Diego, CA 92161 T: (858) 552-8585; then press *7128

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Re: [Freesurfer] Failing to execute QDEC
by fsbuild 24 Feb '23

24 Feb '23

External Email - Use Caution Hello Vittal, Just FYI, the qdec program is deprecated in 7.X releases and is no longer maintained.  In the 7.X releases, you can try using freeview for images and from the command line there are the mri* commands (mris_surf2surf, mri_glmfit, mri_glmfit-sim, etc.) for stream processing. The license files from older versions of freesrufer, e.g., version 6, are not guaranteed to work on newer versions of linux OS’s because of changes to the crypt libraries.  But a new license should work with a 7.X release. Please in the future do not post any license files or content from them to the public mailing list.  We can instruct you how to otherwise upload files for us to view. - R. On Feb 24, 2023, at 12:15, Wighton, Paul <PWIGHTON(a)mgh.harvard.edu> wrote:Hi Vittal,I tested your license file and it's fine.  Are you sure it's in the right place?  What's the output of `cat /usr/local/freesurfer/license.txt`?It also looks like QDEC is trying to write to `/usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh` do you have permissions to write there?  I'd suggest creating a FreeSurfer subjects directory under your home and setting the SUBJECTS_DIR environment variable accordingly, e.g.mkdir ~/fs-subjectsexport SUBJECTS_DIR="${HOME}/fs-subjects"-Paul________________________________________From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of vittal korann <vittalkorann(a)gmail.com>Sent: Friday, February 24, 2023 11:56 AMTo: Freesurfer support listSubject: Re: [Freesurfer] Failing to execute QDEC       External Email - Use CautionHi Freesurfer experts,I am looking forward to resolve this issue.Any help would be greatly appreciated!With regards,VittalOn Wed, Feb 22, 2023 at 3:13 PM vittal korann <vittalkorann@gmail.com<mailto:vittalkorann@gmail.com>> wrote:Hi Freesurfer experts,I am trying to run Qdec on schizophrenia pre and post intervention scans.I created .dat and .levels  files within the qdec folders and loaded the .dat file into qdec gui.It is suddenly crashing when I select my design and hit the Analyze button.And the same error message copied below from the terminal.Writing to /usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh--------------------------------------------------------------------------ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1nLzKBZWbv5Bmrf0Y03boA8pp7LUIugSlf4PhO_BVoRF79s… to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.Even though I renewed my license file, the issue still persists.FYI I did use qdec in the past and am quite comfortable with it.Also, I attached my license file if anything is missing.Any help would be appreciated!With regardsVittal_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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7.3.2-patch issues - thalamic segmentation
by Katie Rose Jobson 24 Feb '23

24 Feb '23

External Email - Use Caution Hi FS experts, I am attempting to implement the patch on version 7.3.2 for issues with thalamic segmentation. I followed the instructions found here: https://secure-web.cisco.com/1JULaWPox6hiL5oNotdoE4us3D1hhs0HqpeHRUYFRvLuHP… and placed the scripts in their designated directories. However, I received the same error as before. The output indicates that the core.py script is located in the '$FREESURFER/python/packages/freesurfer/subregions/' directory, as opposed to the directory I was instructed to put the core.py script in ('$FREESURFER/python/packages/gems/subregions/'). Should I replace the core.py script within '$FREESURFER/python/packages/freesurfer/subregions/'? Or is there another course of action that I can do that may solve this issue? Here is the exact error, if that is at all helpful: Step 2: aligning atlas to reference segmentation Traceback (most recent call last): File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions", line 99, in <module> subregions.run_cross_sectional(args.structure, parameters) File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py", line 52, in run_cross_sectional model.align_atlas_to_seg() File "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py", line 240, in align_atlas_to_seg mask = mask.resize(1, interp='nearest') TypeError: resize() got an unexpected keyword argument 'interp' Thank you in advance for your help! Best Wishes, Katie -- Katie Jobson, M.S. | Personal Website<https://secure-web.cisco.com/1pn78j_bRtnBgT0xpSoaIHzF2FCTjom5RSQL5Coy-3athV…> Ph.D. Student | Cognitive Neuroscience Lab<https://secure-web.cisco.com/13fFt8PE3xjBFNhyYO17_fs-djBanSzBziNRRKhkYNAIjV…> Department of Psychology and Neuroscience | Temple University

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Failing to execute QDEC
by vittal korann 24 Feb '23

24 Feb '23

External Email - Use Caution Hi Freesurfer experts, I am trying to run Qdec on schizophrenia pre and post intervention scans. I created .dat and .levels files within the qdec folders and loaded the .dat file into qdec gui. It is suddenly crashing when I select my design and hit the Analyze button. And the same error message copied below from the terminal. Writing to /usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://secure-web.cisco.com/15DaQ_a1o5YqT7dopqDTQDqaw-6K4jw9WyiYPYFheSvTtpu… to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. Even though I renewed my license file, the issue still persists. FYI I did use qdec in the past and am quite comfortable with it. Also, I attached my license file if anything is missing. Any help would be appreciated! With regards Vittal

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Re: [Freesurfer] FreeSurfer installation in a Code Ocean Capsule
by fsbuild 24 Feb '23

24 Feb '23

External Email - Use Caution Hello Chiara, It reads like Code Ocean wants to be a solution for someone to host all their research files for published articles, scripts, applications and binaries to run - in 1 place.  But it’s not clear to me applications/scripts/binaries can be run from there in real-time.  It looks more like another form of source control, e.g., GitHub, to enable sharing and managing of files (including disaster recovery).  The text at the bottom of this page, https://secure-web.cisco.com/1aH9sOdWmoRBiry1WokL4RYzdttBbVqc-sC…, indicates they use Amazon AWS servers.  So maybe a code capsule would connect with and run software via an AWS server image with the needed software installed.  That server would in turn need to run a flavor of linux that would allow installing one of the freesurfer distribution packages from https://secure-web.cisco.com/17phn5CctlPx0-cSxitH_2EOSCGyEjytacc8… For scientific clusters, you usually file a ticket to request installation of a software package not already available to run on the cluster.  I would ask Code Ocean tech support how a code capsule currently runs python scripts and/or linux binaries in real-time from a users account.  If that already works to run python scripts or some programs installed on linux servers, then you could ask tech support how 3rd party software packages (like freesurfer) could be managed and installed to run from a users account. - R. On Feb 24, 2023, at 03:50, Chiara Marzi - UniFI <chiara.marzi(a)unifi.it> wrote:        External Email - Use Caution        Dear Freesurfer, I am trying to use some FreeSurfer tools inside a Code Ocean capsule (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-WWfxxHb5KgsxJyNmbX2M5iZmuUeIU8z2QsbW… cloud-based computational reproducibility platform that provides researchers and developers an easy way to share, discover, and run code published in academic journals and conferences. Specifically, I set up my capsule environment including a Python package (freely available at Github: XXX) that requires FreeSurfer for full functionality. Is it possible to install FreeSurfer on such a platform? Do you have any suggestions?Thanks!Have a nice day,Chiara_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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FreeSurfer installation in a Code Ocean Capsule
by Chiara Marzi - UniFI 24 Feb '23

24 Feb '23

External Email - Use Caution Dear Freesurfer, I am trying to use some FreeSurfer tools inside a Code Ocean capsule (https://secure-web.cisco.com/1F1n6n0E7KQZBogoJ-y7cciJe_z3d-WxxhEPHp2zwkasIm…) a cloud-based computational reproducibility platform that provides researchers and developers an easy way to share, discover, and run code published in academic journals and conferences. Specifically, I set up my capsule environment including a Python package (freely available at Github: XXX) that requires FreeSurfer for full functionality. Is it possible to install FreeSurfer on such a platform? Do you have any suggestions? Thanks! Have a nice day, Chiara

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[FreeSurfer] recon-all exited with error
by Krystal Xiwing Yau 23 Feb '23

23 Feb '23

External Email - Use Caution Dear FreeSurfer experts, I ran the command "recon-all -s Sub-139 -i 139.nii -all -qcache -parallel -openmp 6" successfully in the first few hours, and exited with error before generating all the output files. It happened to other subjects, too. The attached file contains the whole processing steps and ended with error. I have set SUBJECTS_DIR to the shared folder, which was mounted in FreeSurfer beforehand. Then, the data for analysis was copied to the Desktop. I typed in the command and it exited with error in the end, though. Would somebody kindly advise how to fix it, please? Your help would be highly appreciated! OS: Windows 11 VM: ubuntu 18 Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Tracula 6.0 - : Command not found. set: Variable name must begin with a letter. does not exist.DIR
by Thorn, Kathryn 23 Feb '23

23 Feb '23

External Email - Use Caution Hi Freesurfer Experts, I’m attempting to run Tracula and receiving the same error for both Tracula 6.0. Note: I have also tried updating to Freesurfer 7.2 and running recon-all (which runs without issue) and then Tracula (which returns the same error as 6.0), so I don’t think version is my issue. I have gotten Tracula 6.0 to run in the past on the machine I’m using now and I have not made any major modifications or updates since then. Here is the set of commands I am passing to Tracula: export FREESURFER_HOME=/Applications/freesurfer/6.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh export TUTORIAL_DATA=/Users/kayti/Desktop/Projects/MIND/Freesurfer6 export SUBJECTS_DIR=$TUTORIAL_DATA/02_Data/01_recon_all cd $SUBJECTS_DIR trac-all -prep -c $TUTORIAL_DATA/01_Protocols/dmrirc.mind95 And here is the full text of my config file: setenv SUBJECTS_DIR $SUBJECTS_DIR set subjlist = (A201) set dcmlist = (/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all/A201/dwi_preprocessed.nii) set bveclist = (/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all/A201/dwi_preprocessed.bvec) set bvallist = (/Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all/A201/dwi_preprocessed.bval) set dob0 = 0 set doeddy = 0 set intrareg = 2 set interreg = 2 And here is the full text of the error message: domainname: Command not found. : Command not found. set: Variable name must begin with a letter. does not exist.DIR /Users/kayti/Desktop/Projects/MIND/Freesurfer6/02_Data/01_recon_all I have ensured that the directory above DOES exist. I have seen other posts in these forums with this issue and I have tried all of the fixes I’ve found: removing trailing/extraneous spaces, correcting my paths, etc. Does anyone have any ideas why this is happening? Thank you! Ryn Thorn (she/her) Lab Manager Medical University of South Carolina Department of Neurology Center for Biomedical Imaging 135 Cannon St. CS101 Charleston, SC 29425

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