Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

Re: [Freesurfer] white matter edits not incorporated.
by Octavian Lie 10 Apr '17

10 Apr '17

Dear All, I wanted to know if there is any take on the issue of white matter edits (specifically deleting unwanted voxels from wm.mgz). I sent a subject a week ago for your review. It seems this is a problem that I had with several scans, and by the message list, I am not the only one. Recent users having the same issues have raised the possibility of editing orig.mgz by replacing wm intensity with gm intensity in the troubled areas as workaround to the wm.mgz issue. Please let me know, Thank you, octavian Dear Bruce, I just transferred subject r02.tar.gz. Again, wm.mgz edits (all deleted voxels, no additions) are not incorporated on reruns using any of the recon-all -autorecon-wm -aitorecon3 recon-all -autorecon2 -autorecon3 recon-all -make all FOr example, the complete command line for a rerun is recon-all -autorecon2-wm -autorecon3 -3T -bigventricles -cw256 -subjid r02 -parallel > output.txt & Here are some of the edited voxels which are not excluded from the wm on rerun: -40.14, -2.67, 116.29 coronal slice 132 12.73, -23.67, 126.16 coronal slice 171 14.05, 12.33, 11.61 coronal slice 147 I mention this is not the only subject where I have this problem. Thank you for your help.

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Re: [Freesurfer] A question regarding LUT/Freeview
by amir hosein 09 Apr '17

09 Apr '17

Dear Ruopeng, Thanks a lot for your reply. I am sorry, but I still could not fix this. Do you mean a command like this: freeview –v aparc+aseg.mgz:colormap=lut:isosurface=2032,2035 I could not perform what I have in mind using this command. I want to simultaneously show several different brain areas on a T1 image. The labels are so different; as examples, one is 14, one is 100, and one is 1250. Currently I am extracting labels, and using MATLAB I overlay them on a T1 image. I am sure Freesurfer should be able to nicely perform this, but this is not resolved for me yet :) Many thanks again, Amir

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-hemi flag
by Nillo, Ryan Michael R 09 Apr '17

09 Apr '17

Hi FreeSurfer users, I am using FreeSurfer v5.3 and have noticed that when -hemi is used as a flag in recon-all, the half I did not specify is not present in wm.mgz. The full command is recon-all -autorecon2 -autorecon3 -hemi (l or r)h -subjid subject_name -sd SUBJECTS_DIR. After running, white matter is missing in the half of wm.mgz not specified under the -hemi flag, but the surfaces and segmentation in aparc+aseg are unaffected. Is this a bug? Ryan Michael Nillo UCSF Center for Radiology and Biomedical Imaging Staff Research Associate

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QA Tool error when identifying aseg outliers
by Ladan Shahshahani 09 Apr '17

09 Apr '17

Dear all, I'm using QA_tools v1.2 to check the recon-all processes for my subjects. I'm getting the following lines in my terminal window while performing QA on some subjects: Processing each subcortical label ... (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error (standard_in) 1: syntax error summary log says that there are 0 outliers for this subject. Is this because of the syntax error I get that no outliers are identified or there are really no outliers in my data? In the [Subject id]/scripts/recon_checker.log I see lines like the following: checking subcortical label: Epidermis, 0 +/- 0 checking subcortical label: Conn-Tissue, 0 +/- 0 checking subcortical label: SC-Fat/Muscle, 0 +/- 0 checking subcortical label: CSF-SA, 0 +/- 0 My question is what is "0 +/-0" telling me? What does it represent? Thanks in advance. Bests, Ladan

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Freeview
by N Saf 08 Apr '17

08 Apr '17

Dear FreeSurfer experts, I have two questions please. 1- I cannot understand the concept of "existing labels". Why few labels (such as #19) do exist in the LUT, but they cannot be overlaid on the brain? What should I do if I need to map one of those labels on the brain that disappear when I press the button of "existing labels"? 2- I can see that the 11115 label is named as ctx-lh-G-front-middle, and the 1109 label is named as ctx-lh-G-frontal-middle. Is there any difference between these two? If yes, what is the difference? If no, why their name is different? (The 1109 label disappears when pressing the existing labels button) Sincerely yours, Nazanin

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withdrawing from the mailing list.
by kjunji＠med.kanazawa-u.ac.jp 08 Apr '17

08 Apr '17

Dear Secretariat of Freesurfer mailing list I want to stop receiving emails from the Freesurfer mailing list. Please teach me to withdraw from the mailing list. Sincerely yours. Junji Komatsu in Kanazawa university hospital.

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FSurf Webinar Announcement
by Suchandra Thapa 07 Apr '17

07 Apr '17

Dear FreeSurfer Community, The Open Science Grid consortium (http://www.opensciencegrid.org) offers a service “FSurf” which allows large scale batch processing of MRI scans using FreeSurfer. FSurf supports the standard FreeSurfer workflow (autorecon-all) or workflows with arbitrary FreeSurfer options. FSurf currently uses FreeSurfer 5.3 but support for FreeSurfer 6.0 will be added in the near future. Note that no proposal for an allocation is required to use the service. We are hosting a 30 minute webinar on Thursday, April 13th, 2pm CDT to cover the basics of batch processing using FSurf. The webinar will be accessible from a PC, Mac, Linux, iOS, or Android device at https://IU.zoom.us/j/644966220. Instructions for getting started with FSurf can be found here: http://bit.ly/freesurferopensciencegrid. We hope to see you there, and best regards. The OSG FSurf support team Suchandra Thapa sthapa(a)ci.uchicago.edu Computation Institute Searle Chemistry Laboratory #201A 5735 South Ellis Avenue Chicago, IL 60637

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PETsurfer output error
by miracle ozzoude 07 Apr '17

07 Apr '17

Hello Freesurfer, I am trying to concat my surface pet file using mris_preproc but I get this error with no output folder or files " mris_preproc --fsgd Pet.fsgd --target fsaverage --hemi lh --is C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --is C6_01_003_140908/lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --o all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz nsubjects = 2 INFO: output detected as nifti, turning on reshaping tmpdir is ./tmp.mris_preproc.20623 /net/synapse/nt/mozzoude/Analysis Log file is all.lh.mgx.ctxgm.fsaverage.sm00.mris_preproc.log Fri Apr 7 10:03:48 UTC 2017 setenv SUBJECTS_DIR /net/synapse/nt/mozzoude/Analysis cd /net/synapse/nt/mozzoude/Analysis /opt/freesurfer-6.0.0/freesurfer/bin/mris_preproc --fsgd Pet.fsgd --target fsaverage --hemi lh --is C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --is C6_01_003_140908/lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --o all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz Linux neuron2.sri.utoronto.ca 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.76.2.1 2016/08/12 17:55:45 zkaufman Exp $ freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.20623 Src lh sphere.reg Trg lh sphere.reg --------------------------------------------------- #@# 1/2 C6_01_001_140813 Fri Apr 7 10:03:48 UTC 2017 -------------- ----------------------- mri_surf2surf --srcsubject C6_01_001_140813 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.20623/C6_01_001_140813.1.mgh --sval C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --reshape --cortex ERROR: dimension inconsistency in source data Number of surface vertices = 125993 Number of value vertices = 163842 Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /net/synapse/nt/mozzoude/Analysis cd /net/synapse/nt/mozzoude/Analysis mri_surf2surf --srcsubject C6_01_001_140813 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.20623/C6_01_001_140813.1.mgh --sval C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --reshape --cortex sysname Linux hostname neuron2.sri.utoronto.ca machine x86_64 user mozzoude srcsubject = C6_01_001_140813 srcval = C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz srctype = trgsubject = fsaverage trgval = ./tmp.mris_preproc.20623/C6_01_001_140813.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /net/synapse/nt/mozzoude/Analysis/C6_01_001_140813/surf/lh.sphere.reg Loading source data" Below are the scripts i ran prior to mris_preproc and the mris_preproc command line: 1) mri_vol2surf --mov C6_01_001_140813.gtmpvc.output/mgx.ctxgm.nii.gz --reg C6_01_001_140813.gtmpvc.output/aux/bbpet2anat.lta --hemi lh --projfrac 0.5 --o lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --cortex --trgsubject fsaverage 2) mri_vol2surf --mov C6_01_003_140908.gtmpvc.output/mgx.ctxgm.nii.gz --reg C6_01_003_140908.gtmpvc.output/aux/bbpet2anat.lta --hemi lh --projfrac 0.5 --o lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --cortex --trgsubject fsaverage 3) mris_preproc --fsgd Pet.fsgd --target fsaverage --hemi lh --is C6_01_001_140813/lh.mgx.ctxgm.C601001140813.fsaverage.sm00.nii.gz --is C6_01_003_140908/lh.mgx.ctxgm.C601003140908.fsaverage.sm00.nii.gz --o all.lh.mgx.ctxgm.fsaverage.sm00.nii.gz Thanks. Best, Paul

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help
by Dilip Puri 07 Apr '17

07 Apr '17

Hi everyone, I am working on Hippocampus segmentation using Neural Networks for that I need labeled images of Hippocampus corresponding to original images. I am using OASIS Dataset for this. I want to generate labeled images using FREESURFER. Is there any way to label each 3D co-ordinate HippoCampus -1 Otherwise - 0 Here are sample files link <https://drive.google.com/drive/folders/0B6rH1c6LupG_b3I4WUJ1RWZCbnM?usp=sha…> Kindly help me! Dilip Puri <http://dilippuri.github.io> IIIT Vadodara <http://www.iiitvadodara.ac.in>

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QDEC-Cortical Thickness
by Limachia, Gaurang (NIH/NINDS) [F] 07 Apr '17

07 Apr '17

Hello Freesurfer Experts, I want to compare the cortical thickness between the groups (HC & Patients), and wanted to know where qdec shows this information. Once the design tab is loaded, I am seeing the question in the analysis results – does the correlation between thickness and Age differ from zero? Do I need to a run the command for GLM in order to see if there is a cortical difference between the two populations? I would greatly appreciate your help. Thanks, Gaurang

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Freesurfer April 2017