Freesurfer

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30061 discussions

Issue with mri_glmfit-sim
by O'Neill, Alexandra Grace 12 Jan '24

12 Jan '24

Hello FS community, To correct for multiple comparisons for the results of a parametric modulation GLM analysis, I have run mri_glmfit-sim using Freesurfer version 6.0 with the following command: mri_glmfit-sim \ --debug --glmdir /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepSec/OSGM/osgm \ --perm 1000 2.0 abs \ --cwp 0.05 \ --2spaces \ --bg 1 The code completes without errors, however none of the output files mentioned in this tutorial<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.…> are created. Below are the contents of the mriglm-fit.log file in case that is helpful. $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago cmdline mri_glmfit.bin --y /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz --wls /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz --fsgd /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd --osgm --glmdir /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM --surf fsaverage rh --fwhm 6 sysname Linux hostname tempest.nmr.mgh.harvard.edu machine x86_64 user ago5 FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 fwhm 6.000000 niters 26.000000 OneSampleGroupMean 1 y /autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz logyflag 0 usedti 0 FSGD /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd labelmask /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/fsaverage/label/rh.cortex.label maskinv 0 glmdir /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM IllCondOK 0 ReScaleX 1 DoFFx 0 wFile /cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz weightinv 1 weightsqrt 1 ResidualFWHM 12.847434 SearchSpace 74490.844410 anattype surface Do you have any idea how to fix this problem? Thanks so much in advance! Alexandra Alexandra G. O'Neill (she/her) Clinical Research Coordinator Massachusetts General Hospital Department of Psychiatry Division of Neuropsychiatry and Neuromodulation 149 13th Street, Charlestown, MA 02129 T: (617) 726-8753 | E: agoneill(a)mgh.harvard.edu<mailto:agoneill@mgh.harvard.edu>

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Tksurfer and freeview
by JAEHYUN KIM 12 Jan '24

12 Jan '24

External Email - Use Caution Hello, I attempted to switch tksurfer to freeview in the script, but it seems like I need to change arguments "tcl" to something that can be applied to freeview. Option 'tcl' not recognized. What argument could possibly be used to replace *tcl* in the script such as *tmp.tcl* and *lh pial -tcl*?? Best, Ed

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modify intensity normalization pipeline
by Carlos Alcocer 12 Jan '24

12 Jan '24

External Email - Use Caution Hello, Is there a way to modify intensity normalization pipeline in recon-all script? The temporal lobe is being very poorly segmented because white matter is being segmented as gray matter and therefore gray matter does not reach outer boundary of pial surface. Thank you, Carlos

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Re: [Freesurfer] Freesurfer Digest, Vol 239, Issue 1
by Spapens, Jeltje (NP) 12 Jan '24

12 Jan '24

External Email - Use Caution Hi Douglas, I hope you had some nice holidays and a happy beginning of 2024. Thank you for your suggestion. I have added the intermediate picture and changed the MRI_vol2vol target volume from the original scan to the MRI/T1 recon_all output. The latter one seemed to prevent the orientation shift. However, the registration still does not seem of very good quality. I have tried init-fsl, header and spm, but the first one gave the best results. Do you have another advice for me? bbregister --s MRS_200_recon_all --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.nii --t2 --int /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/presurf_MPRAGEise/MRS_200_UNI_MPRAGEised_stripped.nii --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat --init-fsl mri_vol2vol --mov /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.nii --targ /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_recon_all/mri/T1.mgz --o /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_regt1.nii.gz --reg /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat --cubic Kind regards, Jeltje Spapens ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Message: 15 Date: Mon, 1 Jan 2024 16:07:00 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] FW: Boundary based registration To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <e31f2342-e539-4ecc-b146-2b059dab1b6c(a)mgh.harvard.edu <mailto:e31f2342-e539-4ecc-b146-2b059dab1b6c@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Have you tried using the "intermediate" option (--int) in bbregister? The intermediate volume should be a whole brain volume and it should share a RAS space with the slab volume (eg, if they were acquired in the same session; load both the slab and the intermediate in freeview to see if they are aligned). You can run bbregister with --help to get more info On 12/13/2023 2:48 AM, Spapens, Jeltje (NP) wrote: > > ????????External Email - Use Caution > > Hello Freesurfer developers, > > I want to register an MRI slap to a full FoV UNI scan of the same > subject, but I get a false reorientation with my code (see attached > image). I have tried multiple input and tried the script on different > subjects. > > I also changed som flags such as -init-header and --cubic, but all > seem to give the same results. > > bbregister --s MRS_200_recon_all --mov > /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz > --reg > /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat > --t2 --init-fsl > > mri_vol2vol--mov > /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_stripped.mgz--targ > /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_acpc_upsamp.nii > --o > /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_MT_tfl_regt1.nii.gz > --reg > /Users/robspapens/Desktop/Thesis/Subjects/MRS_200/MRS_200_NM2mp2rage.dat > ?trilin > > I would appreciate to hear your thoughts on this problem. > > Have a nice weekend and kind regards, > > Jeltje Spapens >

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FLAIR vs. T1 question
by aliyasuri＠yahoo.com 12 Jan '24

12 Jan '24

External Email - Use Caution Dear FS mailing list, My apologies if this is a naive question. I have FLAIR images that were acquired with much higher resolution than the T1 images for the same subject. Does it make sense to run recon-all using FLAIR as the input image? I tried it, and my segmentations look reasonable. I am mainly interested in volumetric WM segmentations. Am I missing something basic, or is there something else I can try that leverages the FLAIR (other than using it to refine the pial surfaces)? Thank you.

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Bug in FSFAST functional connectivity analysis
by Douglas N. Greve 12 Jan '24

12 Jan '24

There is a bug in the FSFAST <https://surfer.nmr.mgh.harvard.edu/fswiki/FsFast> functional connectivity seed-based analysis (current version and all previous versions). The amplitude of the seed waveforms are not rescaled in any way. This can affect the amplitude of the regression coefficient with the rest of the image (which is rescaled). This will not have any effect under several circumstances: (1) it will have no impact on the sig.nii.gz (p-value) or the Pearson correlation (pcc) at the individual level, (2) the seed uses a pca/svd, (3) if the intensity scale in each image/subject is the same (or close to it), or (4) if you are passing up the Pearson correlation (pcc) to the higher level. Note that the typical FSFAST analysis passes up the contrast effect size (ces) to the higher level which will be affected by this bug. The problem will manifest itself as extra variability at the group level due to the variability of the mean intensity at the individual level (so your group results should probably improve when fixed). This has been fixed in the dev version of FS and will be in the next release. The change will require that you specify the type of rescaling you want. If you run the new fcseed-sess on an old configuration that does not have a scaling method specified, it will exit with a error message (this can be overridden by adding -no-require-rescale-type). Please reach out with any questions and sorry about the inconvenience. doug

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Freeview crashes when trying to load volumes
by Ford, Jamie K 12 Jan '24

12 Jan '24

External Email - Use Caution Hello, Please could I get some advice on my installation? I've downloaded version 7.4.0 using the same steps described in the installation video https://secure-web.cisco.com/1f3eoE6wiYWgcSSn4HiWKsg1DLQo_L2RuFn8xDGE0ZoFRi… Everything seems fine until I try to load any sort of volume, e.g., a Bert MRI file (like on the video). Freeview then crashes. This is the same for any volume. Could someone please advice? Any guidance would be greatly appreciated. Many Thanks, Jamie

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Longitudinal TRACULA Thalamic segmentation failure
by Brendan Angelo 11 Jan '24

11 Jan '24

External Email - Use Caution Hi experts, I have been attempting to analyze a group of subjects through the longitudinal TRACULA pipeline and have run into many issues regarding the preprocessing step making use of the thalamic segmentation. I've combed through the archives on this topic and have found many different threads relating to issues with the necessary files for the thalamic segmentation not being created, particularly the aparc+aseg+thalnuc.nii.gz file during the trac-all -prep step. I am attempting these analyses on a newer Mac Studio computer and cannot make use of the MATLAB 2014b runtime to segment the thalamus with the old script. Using the suggestions from this<https://secure-web.cisco.com/1t4cK7l09VEg6fqBR20KopNrVyhT0Q4mm45aUdJMiOcUDS…> previous question, I ran the segment_subregions thalamus python script and renamed all the outputs to match the MATLAB outputs (ThalamicNuclei.v12.T1.FSvoxelSpace.mgz, ThalamicNuclei.v12.T1.mgz, ThalamicNuclei.v12.T1.volumes.txt), but still ran into errors with the prep script and creation of the aparc+aseg+thalnuc.nii.gz file mentioned above. It seems like all the previous threads on this issue result in no permanent solution, are there any suggestions on ways to fix this, at least temporarily? Any discussion on this topic would be appreciated. I've also attached the log files from one of my failed runs, as well as the TRACULA configuration file. This was all done on Freesurfer 7.4.1. Thanks, Brendan Brendan Angelo, MS BRANCH Lab USC

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Trouble with ssh tunneling & Freeview
by Dong, Yilei 11 Jan '24

11 Jan '24

External Email - Use Caution Hi Freesurfer team, I have Freesurfer installed on UCSD's Expanse HPC, which uses the Rocky Linux 8 operating system. Whenever we try to do ssh tunneling and more specifically, logging into our HPC via ssh -X to open up Freeview's GUI, it always aborts. Prior to logging into my HPC from my Mac laptop's terminal, I always open up XQuartz. Another colleague of mine has also encountered similar issues, where they have managed to get X11 and Xeyes to run, but also Freeview's window keeps aborting. We have also tried to follow instructions from the following links when it comes to getting ssh tunneling to work correctly in hopes of making Freeview's GUI pop up: https://secure-web.cisco.com/1R4ZWuowqG86V3YyoRGTRpJOHdknCViNdSnswxzgoNUJh-… https://secure-web.cisco.com/1n_nrksVR91kPB04lGzr6COj_EYtJE9nZ9kVxcDWeDscsO… If we operate from a Mac computer, is it better to use a VNC or XQuartz for ssh tunneling? In addition, can we find an error log in Freesurfer's directory to find out exactly why Freeview keeps aborting in our circumstance? Thank you. Sincerely, Yilei

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Infant_recon_all generated surface does not align well with the provided aseg file
by Yanbin Niu 11 Jan '24

11 Jan '24

External Email - Use Caution Hi Freesurfers, I'm currently working on running infant_recon_all with our edited aseg.nii.gz for newborn data. However, we've encountered an issue where the generated surface does not align well with the provided aseg file. I have attached some screenshots as an example, in which a fold that infant_recon_all is failing to fully recognize. This problem seems consistent across the brain and subjects. I'm reaching out to inquire if anyone has experience with this issue and if there are specific parameters that we can adjust to address this issue. Here is the command we've been using: infant_recon_all --s sub-1041 --age 1 --inputfile ${SUBJECTS_DIR}/sub-1041/mprage.nii.gz --segfile ${SUBJECTS_DIR}/sub-1041/aseg.nii --masked ${SUBJECTS_DIR}/sub-1041/brain_mask.nii.gz Thank you, Yanbin Niu

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