Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

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

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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

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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

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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

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niiRead: error opening file, through mri_convert
by Andrew 02 Aug '21

02 Aug '21

External Email - Use Caution Hello, I’m trying to reconstruct an old pipeline that I don’t completely understand (so sorry if this is very elementary or out of date), and one step is to convert the freesurfer T1 segmentation ribbon.mgz to .nii format using mri_convert. Through freesurfer interface I see the T1 and the segmentation are fine; but mri_convert seems to fail on looking for the T1: The command (from inside Matlab) is: mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii Output looks like: mri_convert --reslice_like /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii -rt nearest /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz /Users/amhaun01/Documents/HERIdata/anatomy/ah2/t1_class_test2.nii reading from /Applications/freesurfer/7.1.1/subjects/ah2/mri/ribbon.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) reading template info from volume /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii... error: niiRead(): error opening file /Users/amhaun01/Documents/HERIdata/anatomy/AX_FSPGR_BRAVO_NEW_acpc.nii***** It is failing to read the T1 and then it does not save the output file. But the input files (T1.nii and ribbon.mgz) are all where they should be. What could I be doing wrong? thanks, -Andrew

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SAMstats2table option
by AJ 02 Aug '21

02 Aug '21

External Email - Use Caution Hi, I was wondering if there is a simple command for generating a table from all the SamsegOutput/stats files across all subjects. When I use the asegstats2table, I get index error: list index out of range. I guess this has to do with the structure of files in the samsegOutput/stats versus the aseg.stats file? Thank you. AJ

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Correct Contrast to use; Permutation running for 2 days
by Avi Gharehgazlou 02 Aug '21

02 Aug '21

External Email - Use Caution Hi, I want to investigate lGI differences between 4 groups (n=449) while controlling for sex, age and surface area using DODS design matrix on the command line stream of FreeSurfer. Will you please tell me which of the below two contrasts are correct for this purpose? I have ran both contrasts (separately) and although all steps have completed successfully, the permutation tests have been running for the past 2 days (now on poll ~14616) – I think this is normal given my previous experience with how long permutation tests take to complete with large numbers of participants such as this case. However, I’d really appreciate it if you’d please inform me which contrast (1 or 2 below) is correct, and if I should just wait for the permutation tests to complete or if you think something may be wrong? I have provided below information regarding my regressors: *In my data here, I have: * - 2 discrete factors: Diagnosis, sex - 8 groups/levels/classes: TD M, TD F, NDD M, NDD F, ASD M, ASD F, ADHD M, ADHD F - 2 continuous covariates: age, SA - Number of classes: 8 - Number of variables: 2 - NregressorsDODS= Nclasses*(Nvariables+1)= 8*(2+1)= 24 - 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: ones for ASDM subjects, 0 otherwise. Codes intercept for ASDM - Regressor 6: ones for ASDF subjects, 0 otherwise. Codes intercept for ASDF - Regressor 7: ones for ADHDM subjects, 0 otherwise. Codes intercept for ADHDM - Regressor 8: ones for ADHDF subjects, 0 otherwise. Codes intercept for ADHDF - Regressor 9: age for TDM subjects, 0 othersie. Codes for TDM - Regressor 10: age for TDF subjects, 0 otherwise. Codes for TDF - Regressor 11: age for NDDM subjects, 0 otherwise. Codes for NDDM - Regressor 12: age for NDDF subjects, 0 otherwise. Codes for NDDF - Regressor 13: age for ASDM subjects, 0 othersie. Codes for ASDM - Regressor 14: age for ASDF subjects, 0 otherwise. Codes for ASDF - Regressor 15: age for ADHDM subjects, 0 othersie. Codes for ADHDM - Regressor 16: age for ADHDF subjects, 0 otherwise. Codes for ADHDF - Regressor 17: SA for TDM subjects, 0 otherwise. Codes for TDM - Regressor 18: SA for TDF subjects, 0 otherwise. Codes for TDF - Regressor 19: SA for NDDM subjects, 0 otherwise. Codes for NDDM - Regressor 20: SA for NDDF subjects, 0 otherwise. Codes for NDDF - Regressor 21: SA for ASDM subjects, 0 otherwise. Codes for ASDM - Regressor 22: SA for ASDF subjects, 0 otherwise. Codes for ASDF - Regressor 23: SA for ADHDM subjects, 0 otherwise. Codes for ADHDM - Regressor 24: SA for ADHDF subjects, 0 otherwise. Codes for ADHDF *Contrast 1:* Null hypothesis: is there a difference in lGI between TD and any of the other 3 groups (NDD or ASD or ADHD groups) regressing out the effects of sex, age and SA? 0.5 0.5 -0.5 -0.5 -0.5 -0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 OR *Contrast 2:* Null hypothesis: is there a difference in lGI between TD and NDD or ASD or ADHD groups regressing out the effects of sex, age and SA? 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0 0 0 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1st line tests for a difference between TD and NDD 2nd line tests for a difference between TD and ASD 3rd line tests for a difference between TD and ADHD *The permutation command line I used:* mri_glmfit-sim --glmdir lh.lgi.TD_NDD_ASD_ADHD_age_sex_SA_FWHM0.glmdir --perm 1000 1.3 abs --perm-resid --cwp 0.05 --2spaces --bg 1 I’d appreciate your soon reply, Thank you, Avi

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vol2subfield: which file to use?
by Shane Schofield 02 Aug '21

02 Aug '21

External Email - Use Caution Hi Freesurfer Tema, I am trying to use vol2subfield to extract DTI measurements like FA and MD. For this purpose, should I be using the rh.hippoAmygLabels-T1.v21.CA.FSvoxelSpace.mgz or rh.hippoAmygLabels-T1.v21.CA.mgz ? Thank you!

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Problem with images captured through quicksnaps.tiff in Qdec
by Koustav Chatterjee 02 Aug '21

02 Aug '21

External Email - Use Caution Dear Forum members, In 'qdec' I was trying to use quicksnaps.tiff and as a result of which 4 images (different view) automatically saved into specific destinations. However, the images are completely black, nothing can be visible. Can you please tell what I did wrong? [image: image.png] Thank you for your time and help. Regards, KC

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Re: [Freesurfer] (no subject)
by Stephanie K 02 Aug '21

02 Aug '21

External Email - Use Caution Hello, Can you please clarify the following: Do we use subcortical QC rating for all subcortical measures such as accumbens as well measures such as total white matter volume. We do not use it for estimated total intracranial volume as this is accurately measured? Do we use cortical QC rating for all regional cortical measures but not the global measures (e.g. mean thickness/total surface area) as these are accurately parcellated? Sorry for my very basic questions. I am using already processed data and only using the statistics for brain MRI data Thanks, Stephanie

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