Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

Re: [Freesurfer] recon-all stops in CORRECTING DEFECT
by Marina Fernández 07 May '19

07 May '19

External Email - Use Caution Hi Bruce, Thank you very much for your reply. We try to do it in the way that you told me but we could see (when we loaded [r/l]h.orig.nofix inside the brainmask.mgz and wm.mgz) that in this subject there aren't yellow lines that delimitate the white matter in a lot of slices. On the other hand, we also could see that the posterior defect isn't caused by a bunch of skull/muscle not removed by the stripping. This part is brain but it seems like a defect because the other parts of the brain near this part aren't taken into account in the [r/l]h.inflated.nofix. You can see it in attached files. I also attach this problematic subject. We would be very grateful if you can check this subject and tell us your opinion, because we suspect that we will not solve this problem only with control points and the wm edit tool because there isn't lines in a lot of slices. Thank you in advance! Best wishes, Marina pre_030.zip <https://drive.google.com/file/d/17rQ9F-kUY_oo-CEblNJ916otWk-jy4Pv/view?usp=…>

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Creating mask using mri_label2vol
by Holmes, Emma 07 May '19

07 May '19

External Email - Use Caution Dear list, I'm new to freesurfer and would like to create a volumetric region of interest from the Destrieux atlas labels, to mask my spm12 results. All my images have been normalised so I just need the mask in avg305T1 space. I tried running the following command: mri_label2vol --label ctx-lh-S_intraparietal-and_Parietal_transverse.label --temp [MATLAB_PATH]/spm12/canonical/avg305T1.nii --o [PATH_TO_OUTPUT_DIR]/test.mgz --reg /usr/local/freesurfer/subjects/fsaverage/mri/brainmask.mgz I get the following print-out and error message: $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -------- -0.50000 -0.00000 -0.00000 45.50000; -0.00000 -0.00000 -0.50000 54.50000; -0.00000 0.50000 -0.00000 45.50000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 8 nHits Thresh: 0 Loading registration from /usr/local/freesurfer/subjects/fsaverage/mri/brainmask.mgz regio_read_register(): Success Error reading inplaneres from /usr/local/freesurfer/subjects/fsaverage/mri/brainmask.mgz As I'm new to freesurfer, I'm probably missing something simple. I've tried searching the archives (e.g., I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/018159.ht…) and notice that many use register.dat as the --reg input, and I assume this is where the problem arises here. However, I'm not sure how to go about generating this file, as I'm using the average brain: Do I need to run a full surface reconstruction on the avg305T1.nii file? Or is there a simpler way to get around this? I have mni152.register.dat in my freesurfer directory but no mni305.register.dat equivalent. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c uname -a: Linux localhost.localdomain 3.10.0-957.10.1.el7.x86_64 #1 SMP Mon Mar 18 15:06:45 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Platform: Windows 8.1, running through VirtualBox 6.0.6 Thanks in advance for your help with this, Emma

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How to get the difference between motion, NU intensity correction images and the originate image?
by chen 06 May '19

06 May '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set. According to my results, there exsit difference between ROIs. So, i want to check the difference between the originate image and the images after motion and NU intensity correction to confirm the most variation area. How can i get this information?I am looking forward to your kind suggestions.Best regards,Jiachen ------------------ 首都医科大学宣武医院杜佳晨

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trac-all -bedp error
by Daniel Callow 06 May '19

06 May '19

External Email - Use Caution Hello, When running the pre.job script created from /Volumes/DANIEL/trac-all -bedp -jobs job -c /Volumes/DANIEL/ dmrirc.long.example.sh which I am trying to submit by running setenv FREESURFER_HOME /Applications/freesurfer/ source $FREESURFER_HOME/SetUpFreeSurfer.csh foreach subj (AES101 AES102 AES104 AES107 AES108 AES109 AES110 AES111) bedpostx_preproc.sh /Volumes/DANIEL/dti_freesurf/trac/Ex.${subj}.long.base_${subj}/dmri bedpostx_preproc.sh /Volumes/DANIEL/dti_freesurf/trac/Rest.${subj}.long.base_${subj}/dmri end end I get the following error. [255a-280:/Volumes/DANIEL/dti_freesurf] amos% ./pre.job.sh Copying files to bedpost directory usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... target_directory /usr/local/fsl/bin/bedpostx_preproc.sh: line 79: [: -eq: unary operator expected Done Is this the incorrect way of trying to run trac-all -bedp in parallel? And if so how should I go about running the job scripts? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Volume computation from Surface and Thickness
by Daniela Vecchio 06 May '19

06 May '19

External Email - Use Caution Dear all, referring to the lh.aparc.DKTatlas40.stats Freesurfer output, I would like to know how the GrayVol column is computed as just multiplying ThickAvg*SurfArea I obtained different values. Thanks in advance for helping! Dani

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Transforming Amygdala nuclei atlas to MNI space
by Dev vasu 04 May '19

04 May '19

External Email - Use Caution Dear all, I am having a difficulty in transforming the segmented subfields of Amygdala atlas from surface based .mgz to nifti format. I have extracted the labels using mri_extract_label lh.hippoAmygLabels-T1.v21.nii.gz 7009 Cortico_amygloid.mgz then i convert .mgz file to NIFTI using mri_convert Cortico_amygloid.mgz Cortico_amygloid.nii.gz. Later i tried to transform Cortico_amygloid.nii.gz to MNI space using FLIRT but i notice seed region Cortico_amygloid.nii.gz is oriented in different place. Kindly let me know what more i have to do , in order to transform .mgz label into MNI space. Thanks Vasudev

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Petsurfer: Motion Correction
by Shane Schofield 04 May '19

04 May '19

External Email - Use Caution Hi Freesurfer Team, How may I align 5 volumes of my PET data ( 5 min acquisitions each) to a mean image for motion correction across the acquisition? I can use mri_concat to get the the mean image, but I am not sure how to do the realignment after that. Thank you. Best Wishes,Shane

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[WARNING: UNSCANNABLE EXTRACTION FAILED]Transforming Amygdala nuclei atlas to MNI space
by Dev vasu 03 May '19

03 May '19

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applyMorph on talairach.m3z
by Peled, Noam 03 May '19

03 May '19

Dear group, How can I apply the talairach.m3z transformation on a list of points? I was trying to use applyMorph on one of my subjects: applyMorph --template $SUBJECTS_DIR/M1/mri/orig.mgz --transform $SUBJECTS_DIR/M1/mri/transforms/talairach.m3z point_list $SUBJECTS_DIR/M1/electrodes/electrodes_to_morph.txt tal.txt a but I got this error: Template name:/autofs/space/thibault_001/users/npeled/subjects//M1/mri/orig.mgz After loading template Template name:/autofs/space/thibault_001/users/npeled/subjects//M1/mri/orig.mgz After loading template extension = m3z terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Abort (core dumped) I'm using the FreeSurfer dev version (in martinos), and my SUBJECT_DIR is /autofs/space/thibault_001/users/npeled/subjects/ Thanks! Noam

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recon-all error
by 王梦星 03 May '19

03 May '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attampting to do a structural MRI analysis with the command "recon-all -i sub102.nii.gz -s bert -all", as described in the FreeSurfer Download and Install (http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) But I always met the error as recorded in the recon-all.log, " /home/share/test2/bert/surf mris_curvature -w lh.white.preaparc total integrated curvature = 10.012*4pi (125.809) --> -9 handles ICI = 164.9, FI = 1856.5, variation=28617.761 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H Linux wmx 2.6.32-754.12.1.el6.x86_64 #1 SMP Tue Apr 9 14:52:26 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Mon Apr 22 11:44:12 CST 2019 " And then I checked that, the '?.white.preaparc' had been created while the '?h.white.H/K' had not, so I did some steps described in http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0, The commands "mris_curvature -w ?h.white.preaparc " and " mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ?h.inflated " were done to generate some files successfully. Howevere, when I continue to use "mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm <subjid> ?h curv sulc ", there were errors below: " mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/?h.curv.stats -F smoothwm bert ?h curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/?h.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ bert/?h.smoothwm ] Reading surface...MRISread(/home/share/test2/bert/surf/?h.smoothwm): could not open file No such file or directory [ ok ] mris_curvature_stats: could not read surface file /home/share/test2/bert/surf/?h.smoothwm No such file or directory " In fact, the '?h.smoothwm' files exist and I can find it by 'ls' commond. Any help is greatly appreciated. Thanks. Mengxing Wang

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