Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

the problem about XL defect detected...
by Abby tang 15 Apr '19

15 Apr '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon-all subjects but for some of my subjects I get the following error when I run recon-all command: CORRECTING DEFECT 0 (vertices=18460, convex hull=3400, v0=4) XL defect detected... Killed Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux I don't know how to check and amend ?h.orig.nofix. please give me some commands in detail. Thank you for your help.

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recon-all error after maual control points definition
by Boris Rauchmann 14 Apr '19

14 Apr '19

External Email - Use Caution reading input surface xyz/fs_all_subjects/0031/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.3220 (-4.6610) -vertex loglikelihood: -6.6151 (-3.3076) -normal dot loglikelihood: -3.5637 (-3.5637) -quad curv loglikelihood: -6.1122 (-3.0561) Total Loglikelihood : -25.6131 CORRECTING DEFECT 0 (vertices=16503, convex hull=4824, v0=77) mrisAddEdge: too many edges (255) XL defect detected... Large defect found - not a problem, but a curiousity No such file or directory Linux linuxrechner 4.15.0-47-generic #50~16.04.1-Ubuntu SMP Fri Mar 15 16:06:21 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 0031 exited with ERRORS at Sun Apr 14 16:45:47 CEST 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any idea what causes this problem? Thank you, Boris

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How to convert a functional FSL mask to an anatomical Freesurfer mask
by Jennifer Legault 12 Apr '19

12 Apr '19

External Email - Use Caution Hi Freesurfer experts, We ran a functional language localizer analysis in FSL and we want to apply the mask from this analysis to our SMRI analyses using the mri_glmfit command with the --mask option. Basically, we want to examine whether GMV within these language localizer regions is correlated with performance on various tasks. I previously used mri_convert to convert the .nii file to .mgh, and tried to run the mri_glmfit --mask command but received an error (ERROR: dimension mismatch 1 between y and mask) which I believe is linked to the fact that the previously run mris_preproc files are 4D, while our functional mask is still only 3D. When I use tksurfer and overlay the 3D mask file, it looks fine. So the question is how can we convert our 3D functional mask into a format that we can use for the mri_glmfit command (Nverteces x 1 x 1 x Nsubjects)? Thanks for all your help! Best, Jen -- Jennifer Legault PhD, Neuroscience Postdoctoral Scholar Language Acquisition and Brain Lab University of Delaware

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mri_segstats
by Nasiriavanaki, Zahra 12 Apr '19

12 Apr '19

Dear Freesurferers I was trying to do a connectivity analysis using subnuclei of Amygdala. I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf Amygdala) and I tried to use that in mri_segstats to extract the timeseries and then use it as a seed in my analysis. However when I looked at the results, the values are too high (around 800). Could you please let me know what I'm doing wrong? P.S: the segmentation was basically done in MNI152-1mm and I moved it to MNI305-2mm by mri_vol2vol. mri_vol2vol --mov MNI152template/MNI152_1/mri/reg.lh.HBT.mgz --targ $SUBJECTS_DIR/fsaverage/mri.2mm/mni305.cor.mgz --o $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --interp nearest --regheade mri_segstats --i $all_subjects/$subj/rest/009/fmcpr.sdf.sm5.mni305.2mm.nii.gz --seg $SUBJECTS_DIR/$subj/mri/reg.lh.HBT.mgz --id 7001 --avgwf lateral.txt Thanks a lot MOna

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Re: [Freesurfer] Hippocampal subfield version
by Iglesias Gonzalez, Eugenio 12 Apr '19

12 Apr '19

External Email - Use Caution Hi Emily, You need to download the dev version, but run the subfield/amygdala volume on cases reconned with FS6.0. Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Emily Schwartz <emily.schwartz(a)einstein.yu.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, 3 April 2019 at 15:44 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal subfield version External Email - Use Caution Hello FS experts, I was planning to use the hippocampal subfield segmentation module in FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei of the amygdala segmentation, but realized I need to download the development version in order to do that. Is there any reason why I shouldn't use the development version over the 6.0 release? Thank you in advance. Best, Emily

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Fwd: Fw: mriglmfit error
by Amrita Bedi 12 Apr '19

12 Apr '19

External Email - Use Caution ---------- Forwarded message ---------- From: *abedi000(a)citymail.cuny.edu <abedi000(a)citymail.cuny.edu>* < abedi000(a)citymail.cuny.edu> Date: Thursday, April 11, 2019 Subject: Fw: mriglmfit error To: Amrita Bedi <amibedi273(a)gmail.com> Amrita Bedi *Biomedical Engineering - Class of 2018* *The City College of New York - CUNY* ------------------------------ *From:* abedi000(a)citymail.cuny.edu *Sent:* Thursday, April 11, 2019 8:38 AM *To:* Freesurfer(a)nmr.mgh.harvard.edu *Subject:* mriglmfit error Good morning Freesurfer developers, While using the mri-glmfit command on 20 subjects. I got the following error- -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx --surf fsaverage lh --cortex --glmdir test.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.000000 (col 6), Max=228.790298 (col 3) The scale is much different between columns 6 and 3, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 6, all values are 0. 1. My command line used was- mri_glmfit --y test.10B.mgh --fsgd TEST.fsgd --C TEST.mtx --surf fsaverage lh --cortex --glmdir test.glmdir 2. My fsgd file and design matrix file are attached. Thank you for your help. Amrita Bedi

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Labels in nii files
by Vidal Maxime 12 Apr '19

12 Apr '19

External Email - Use Caution Hello, I have a t1w.nii file and a segmentation.nii file. For the latter, I was wondering how I could join labels together and create new labels. Best, Maxime

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Aparc stats files aren’t being generated
by Romella Durrani 12 Apr '19

12 Apr '19

External Email - Use Caution Hello, I am having problems generating the aparc stats files for all my scans. I have checked the surfaces for all scans and they were all generated correctly. However, when I go to generate the stats files, I am able to get all the aseg stats for all scans, but many of them are missing aparc stats, despite passing visual review of the surfaces. Is there a way to generate these files without having to reprocess all of them again? Thanks, Romella

2 1

Using Custom Atlas for Segmentation of Brain Surfaces
by Mina Shire 12 Apr '19

12 Apr '19

External Email - Use Caution Dear All, I would like to extract cortical envelop from my subjects T1 images to use later on for a source reconstruction in on their EEG data. I would like to use Power et al (2011)'s atlas with 264 regions. I am pretty new to Freesurfer and my search through the mailing list and tutorials confused me very much. So I would really appreciate if anyone could explain using a custom atlas to me or direct me to the sources that I can follow please. So I have 2 questions regarding that. 1. Is there any chance that you could direct me step by step how to do this with Freesurfer. 2. While I am running extraction with Freesurfer, should I be using ROI nifti files in MNI coordinate or should I be using ROI nifti files that were inverse normalised to subject's native space? I would really appreciate if you could help me with this please. Thank you very much in advance Kind regards Mina

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Quantify recon-all results from different scan protocols
by Weber, Wade A 11 Apr '19

11 Apr '19

External Email - Use Caution Hi all you Freesurfer users! I have scans on a person that are slightly different protocols (like 1mm voxels vs. 0.8mm voxels amongst other setting differences), and I ran them through recon-all. Is there a way to quantify which one came through with fewer errors to manually correct? I searched the archives as well as I could, but I really wasn't sure what to look for. Thanks! ---- Wade A. Weber, MS Psychiatry Research Program Coordinator Dell Medical School | The University of Texas at Austin o: 512-495-5217 | f: 512-495-5482 | dellmedschool.utexas.edu

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