Freesurfer

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30132 discussions

Issue with freeview display in ubuntu/Xming on windows 10: failed to get the current screen resources
by josua.zimmermann＠bli.uzh.ch 18 Jan '21

18 Jan '21

External Email - Use Caution Dear freesurfer experts, I installed freesurfer on ubuntu 18.04 (Windows 10), that uses Xming. Freesurfer seems to work fine. However, I have troubles with freeview. Freeview opens but I cannot display images. I get the following error message when I open freeview: failed to get the current screen resources QStandardPaths: XDG_RUNTIME_DIR not set, defaulting to '/tmp/runtime-joszim' QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20 QXcbConnection: XCB error: 170 (Unknown), sequence: 174, resource id: 90, major code: 146 (Unknown), minor code: 20 I have previously also installed FSL on ubuntu, and fsleyes that uses Xming works fine, so I guess Xming installation is not the issue. Any help is appreciated. Best wishes, Josua

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Recon-all error: CTABWriteFileASCII; could not open file for writing
by Loreto, Flavia 18 Jan '21

18 Jan '21

External Email - Use Caution Dear FreeSurfer Experts, Version: FreeSurfer 7.0 Platform: Bash remotely through High Performance Computing (HPC) on a MacOS Mojave We are trying to run recon-all on T1 images but the job stops with the following error: Reading annotation /rds/general/project/imperialapc/live/freesurfer/APC001/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 error: Permission denied error: CTABwriteFileASCII(/tmp/mri_segstats.tmp.APC001.lh.176.ctab): could not open for writing Could you please help us figuring out where is the problem? I am attaching the script we are running and the recon-all log for one of our analysed subjects. Thank you for your help. Kind regards, Flavia

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Holes in my ROIs
by Alberto Del Cerro Leon 18 Jan '21

18 Jan '21

External Email - Use Caution Hello Freesurfers, I created surface image based on AAL with mri_vol2surf. However i see that in some regions there are a lot of holes, i thought that probably is for the presence of subcortical regions in the AAL.ni. There is some workflow to select the regions from my volume to do mri_vol2sur? Can I create another volume from my AAL.nii selecting only the surface regions?

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Changes to lh.pial and rh.pial between FreeSurfer versions 6 and 7
by Mike Schmidt 17 Jan '21

17 Jan '21

External Email - Use Caution I have written a script that reads the binary representations of the vertices and faces from FreeSurfer's surf/{l,r}h.pial files and saves them out unchanged to stl and obj file formats for 3D rendering. I have used it with FreeSurfer 6 and several MRI images, everything working fine. Processing the identical input, a single T1-weighted MPRAGE MRI, FreeSurfer 7 works great and finishes faster than FreeSurfer 6, but we see strange aliasing on the 3D objects. I've spent a lot of time messing with different materials and textures, generating vertex normals at different stages, but I can't find anything that makes any difference except the FreeSurfer version. I have seen several items in the release notes ( https://secure-web.cisco.com/10e4A8ivZBudPVZzB2fSu2TWQAh7jeSCsKiZetlyqyRe4b…) that may be related, but I'm not sure how to go about investigating them. Left cortex images are included, with links if they don't show up in the email, of the same brain processed with FS6 and FS7. FreeSurfer 6.0.0 works well with a smooth surface and working transparency ( https://secure-web.cisco.com/1UQ6aOrt2bryipWe-PkobeSr25YVlze0fFJ35x4ZMQJwBf…) This image is of surf/lh.pial with 149,968 vertices and 299,932 faces. [image: rh_pial_oblique_from_fs6.png] FreeSurfer 7.1.1 results in the same size and shape cortex, but renders strangely with mottled shading of triangles. ( https://secure-web.cisco.com/1VT57uMXFOHM4VZNouJmVogT7JK7OwLFJy5l6ByvUoIQfw…) This image is from the same T1 image as above, but processed with FS7, resulting in 147,292 vertices and 294,580 faces. [image: rh_pial_oblique_from_fs7.png] I'm out of ideas, and the only difference I can find is FreeSurfer version, so thank you to anyone who can point me in the right direction to fix this issue. Mike Schmidt

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3dClustSim
by Meike Hettwer 17 Jan '21

17 Jan '21

External Email - Use Caution Dear Freesurfer experts, I ran a glm analysis a while back and corrected for MC using the glm-fit_sim --cache option / Monte Carlo simulation. I now saw that the AlphaSim algorithm this is based on is not recommended anymore (https://secure-web.cisco.com/1A4g1vq2U_gugbf-mlVAUZcEyLmp9YkEcL2Vw_tFG_wyrN…) Instead, it suggests using 3DClustSim. 1. Does that mean the Monte Carlo simulation as it is implemented in FreeSurfer does not allow for valid analyses / MC corrections anymore? 2. Is 3DClustSim implemented in Freesurfer? And if not, would I need to export the FreeSurfer files as a volume (i.e. 3D) file and analyse it externally? What would you recommend? (My analysis is a regression analysis for one group, so the design matrix is not really suitable for a permutation). Thanks in advance, Meike

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recon-all , fsaverage ?
by Fatemeh Ahmadi 15 Jan '21

15 Jan '21

External Email - Use Caution Hi Dear Dr., I run recon -all and get an ERROR reading /media/sf_shared/fsaverage/label/lh.BA1.label I saw that you answered similar questions as follows: It should be symlinked from you $SUBJECTS_DIR to $FREESUFER_HOME/subjects/fsaverage. How do I do this? Thank you in advance, --------------------- Fatemeh Ahmadi,PhD Student in Computer Science,Department of Mathematics and Computer Science,Amirkabir University of Technology, Tehran, IranEmail: f.ahmadi(a)aut.ac.ir

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almost empty mask.mgh with glmfit
by Julie Ottoy 15 Jan '21

15 Jan '21

External Email - Use Caution Dear Doug, I was wondering why the flag --prune is recommended (petsurfer website) when creating a stacked pet file and during surface-smoothing. If I understood correctly, this would set all vertices that are 0 in at least one subject to 0 ("set vox to 0 unless all frames are non-zero")? In my non-pvc data, it seems as though a lot of the surface-projected values are 0. Hence, when I perform a surface-based regression between PET and a regressor and I use the --prune flag during mri_concat, I don't get any results. Thank you! best regards Julie

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FW: Missing transformation files in longitudinal pipeline
by Nederpelt, D. van (David) 15 Jan '21

15 Jan '21

External Email - Use Caution Hi FS-team, I ran a longitudinal recon-all stream(FS version 7.1.1) and trying to convert the aseg.mgz back to native space. However, in the transform file the <tpid>_to_<tpid>.long.<baseid>.lta is missing. This is the case for every subject I ran, while the recon-all.log showed freesurfer finished without errors. I've attached the .log file. The base dir does have the needed transform files. How can I resolve this and transform ROI to native space? Thank you in advance, Kind regards, David ______________________________________________________ VUmc disclaimer : http://secure-web.cisco.com/17Hm37rdmQA7fExuo50mOppILpRbNMLA_qrH6JxGVW_f9CA… AMC disclaimer : http://secure-web.cisco.com/1ebdk9doSyywTxkQ7Inu7GvhMGGJLlbd6W1lSNC3xIcWP8s…

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Group Analysis Question
by Swanson,Clayton 15 Jan '21

15 Jan '21

External Email - Use Caution Hi Freesurfer Team, I am performing an analysis on 23 HC and 26 people with MS and I would like to perform the stats appropriately. I would like to control for (or regress out) age and sex. Therefore, I created my FSGD file which has 4 classes (HC_Male, HC_Female, MS_Male, MS_Female) with age being the only variable. My contrast for this analysis is: 0.5 -0.5 0.5 -0.5 0 0 0 0. Lastly, I want to run a permutation analysis, so I set it up like this: #!/bin/tcsh setenv study $argv[1] foreach meas (thickness volume) foreach hemi (lh rh) foreach smoothness (10) foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir) mri_glmfit-sim \ --glmdir {$dir} \ --perm 1000 1.3 pos \ --cwp 0.05 \ --2spaces \ --overwrite end end end end After running the permutation, my next steps were to view the results in Freeview with the command [ freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=perm.th13.pos.sig.cluster.mgh ] because it’s my understanding that would overlay the cluster-wise corrected map and the view I get is an entirely yellow hemisphere. However, there are no significant clusters when viewing the perm.th13.pos.sig.cluster.summary, so I am a bit confused. Also, when I look at the uncorrected results with the sig.mgh file there are a number of spots on the hemisphere. Does this result mean that there are no cortical thickness differences between HC and MS when controlling for Age and Sex? Or does this result mean something different? What could be the next analysis steps I could perform? My goals are to assess cortical thickness differences between HC and MS. Thanks for any help you can provide, Clayton ________________________________ Clayton Swanson MS Graduate Research Assistant & PhD Candidate Sensorimotor Neuroimaging Laboratory Colorado State University Office: (970) 491-6160 Clayton.Swanson(a)colostate.edu<mailto:Clayton.Swanson@colostate.edu> (He/Him)

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Qdec crash while analysis almost finished
by chenbh35＠mail.sysu.edu.cn 15 Jan '21

15 Jan '21

External Email - Use Caution Hi, dear Freesurfer experts, I recently came across an invalid Freesurfer license key error while using v5.3, and I tried apply for another license key, it just sent me the same license key as I have apply before. Then I put the licence file to /usr/local/freesurfer and has changed the name to .license as well. But it still doesn't work. Owing to the version I used last time was v6.0, so I reinstall a v6.0 and use the same license file. But here comes the new problem, when the analysis almost finished, qdec just crash and disappear, parts of the contents in the command window are: """""""""""""""""""""" Writing results lh-Avg-Intercept-thickness maxvox sig=1e+10 F=3846.45 at index 14 0 0 seed=1611502349 lh-Diff-PCE-CON-Intercept-thickness maxvox sig=3.52355 F=15.3058 at index 11472 0 0 seed=1611502349 mri_glmfit done ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Writing to /media/lava/DATA/ESSAY/FirstWave/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/1l89yx4rr6CbgxQdMiHeY9D8oLAHswLvN7Y1eaaby-Qvn6B… to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. """"""""""""""""""""""" I wonder what was the question? Appreciate for any suggestions.

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