Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30063 discussions

Tracula / 0 slices processed in Bedpostx before queuing post processing stage
by Anna Mynick 28 Nov '17

28 Nov '17

Hi, I’m having difficulty making BedpostX work on non-tutorial data per the tutorial located here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula> The preprocessing has worked without errors, but now that I’m using BedpostX, the output is producing: subjectdir is {subject's directory}/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage 0 slices processed Queuing post processing stage Obviously, it shouldn’t be going straight from 0 slices processed to the post processing stage. I’m running the command directly (i.e. bedpostx {subject's directory}/dmri ), and when the process is done ( it ends in 25 seconds) the dmri folder has files that are in the format data_slice_00**.nii.gz and nodif_brain_mask_slice_00**.nii.gz. I’ve also tried running the command: trac-all -bedp -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial on a cluster, which produces the same output. Has anyone else had this issue? Thanks for any help, Anna

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ERROR: fast_sexavg3() failed\n
by Christina Pressl 28 Nov '17

28 Nov '17

Hi Freesurferteam, For some of my subjects I get an error when I try to perform my analyses, because the mcprextreg file is missing. It is not apparent to my why this file is missing for some of my subjects, while it is there for all the other subjects. Also, there is one subject for which the file is missing in one out of three bold runs. For the other two runs the file was perfectly generated. Could you please help me solving this issue? Thank you very much. Best regards, Christina

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neonatal brain
by Dijkshoorn, A.B.C. (Aicha) 28 Nov '17

28 Nov '17

Dear all, I want to build my own neonatal control reference template (n=35)to investigate cortical thickness measures and compare these to neonates with a rare type of bleeding. I read that freesurfer uses an adult reference atlas, but that a neonatal-infant (0-2y) is being made/has been made. Is this new pipeline yet available in freesurfer? And can I build my own reference template in FREESURFER without interference from an adult brain template? Kind regards, Aicha Dijkshoorn Stagiaire Onderzoek & Onderwijs | Divisie Vrouw en Baby, Neonatologie Universitair Medisch Centrum Utrecht | Flexruimte voor Verpleegkundigen & Medisch personeel, afdeling Neonatologie | 3508 AB UTRECHT

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Merging two groups
by Ramesh Babu 28 Nov '17

28 Nov '17

Hi, I have done recon-all -all processing for 2 groups in separate subjects directories. I want to put all subjects in one dkirectory. Should I copy paste all subject’s folders in one directory or is there any others steps to merge? Thanks in advance RB

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medial wall label in Freesurfer 6
by Sofia Rodriguez Penuela 28 Nov '17

28 Nov '17

Hello, when using "make_average_subject" in Freesurfer 6, we have noted that the medial wall label only contains 1 vertex leading, after applying "mri_glmfit, to significant results in regions of the medial wall. This problem didn't appear in Fresurfer 5.3 Is there something different with the command "make_average_subject" in Freesurfer 6 that prevent to correctly mask the cortical surface? We would like to include only cortical vertices in our analysis. Thank you in advance. Best, Sofia -- Sofía Rodríguez Peñuela, Técnico de Laboratorio. Laboratorio de Neurociencia Funcional Departamento de Fisiología, Anatomía y Biología Celular. Universidad Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - España - Movil: 627273085 Email: srodpen(a)upo.es http://www.upo.es/neuroaging/es/

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covariates in Qdec
by 박경일 28 Nov '17

28 Nov '17

Dear experts, I am trying to compare 2 groups with 2 covariates (age, sex) using qdec. After loading data, design tab displays "diagnosis" in discrete, "age" and "sex" in both continuous (covariates) and nuisance factor boxes. I just selected "diagnosis" and click "analyze". Is this a right way to remove effects by age and sex? Otherwise, do I need to check age and sex in nuisance factor box? Thank you so much. Park

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Recon-all -hires
by Hwee Ling Lee 28 Nov '17

28 Nov '17

Dear all, I have T1 images collected from the 7T MRI scanner. I downloaded the most recent freesurfer software, and followed all instructions to install the software before using it. I would like to segment the T1 data using its high resolution image, and also to segment the hippocampal subfields. For command, I use this: recon-all -all -s <subject name> -hires -i <subject dicom T1 image frame 1 location> However, I get an error message: cannot find $FREESURFER_HOME/average/RB_all_2008-03-26.gca I'm not sure what I did wrong. Also, how can I combine high resolution segmentation and hippocampal subfields segmentation? Could someone please help? Thanks. Best regards, Hweeling

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Re: [Freesurfer] make_average_subject label files
by M del Mar Velasco 28 Nov '17

28 Nov '17

I say I get only one vertex because lh or rh.Medial_wal.label has only one line. And lh or rh.cortex.label has 163841 lines. I send you the .label files that confirm it. I send you make_average log files too. Thanks you, M del Mar

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Skull-strip issues: commands not working
by Arsenije Subotic 27 Nov '17

27 Nov '17

Dear experts, I recently finished processing a subject for whom I had performed a skull-strip on the brainmask.mgz volume. I decreased the watershed parameter and re-examined the brainmask and the portion of the skull was gone, although some dura was left over. I did a recon-all using the following command as the troubleshooting tutorial suggested to regenerate the surfaces based on the new brainmask.mgz volume: recon-all -autorecon-pial -subjid <subject name> However, after the subject finished processing the surfaces were generated/outlined on the dura as well. I tried performing a g-cut command but it did not get rid of the dura. I also had issues with the subcortical segmentation as the ventricles were not completely segmented. Thank you for your help. Best, Arsenije

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error in make_average_subject
by Duran, Tugce 27 Nov '17

27 Nov '17

Dear FreeSurfer Experts, I’m getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: Loading aseg from /gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_DENOISED_DEOBLIQUE_FREESURFER60_DEFAULT_KARST_10092017_RES/fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop/mri/aseg.presurf.hypos.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; mghRead(mri/norm.mgz, -1): could not open file ------------------------- Labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from (null) Linux i1.karst.uits.iu.edu 2.6.32-696.13.2.el6.x86_64 #1 SMP Fri Sep 22 12:32:14 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s fsaverage_denoised-deoblique-default-nov-15-2017-ALL_DX_karstdesktop exited with ERRORS at Wed Nov 15 19:14:17 EST 2017 It appears that during the process it doesn’t create the norm.mgz file to read or open it in the later processes (I think?). What can I do to fix this error? Thanks, Tugce

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