Freesurfer April 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
217 discussions

Bits of dura being captured as GM ..
by Shane S 13 Apr '17

13 Apr '17

Hi Freesurfer Users, I am checking my data and there are many scans with a bit of dura being captured as GM. I have attached some screenshots below. This happens in more than 50% of my subjects. I am removing them manually them using Freeview, then running the autorecon-pial. But this will take a lot of time on 200+ subjects.. Does anyone have any tips to deal with these little inclusions? Thanks =) Best Wishes, Shane

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mri_watershed script not working
by Mario Rossi 13 Apr '17

13 Apr '17

Hello FreeSurfer Developers and experts, I am trying to run our FSPGR sequences using the -mri_watershed script, but I am not able to set and vary the -t threshold. The aim of my work is to calculate the BPF in order to quantify parenchymal atrophy in patients with Multiple Sclerosis. Instead of using the whole "-recon-all" command, I have tried to reduce the amount of datas (and the very long time needed to calculate them) performing this script: "-mri_watershed -atlas" The result of the extraction of the brain is good and fast, but I still could need to adjust the cut limits. I have tried to modify it into this new script: "-mri_watershed -atlas -t X" (where "X" stands for a variable between 0 and 50) but in this case, no matter what "X" I choose the results are all identical. Is it possible to set a -t threshold using -atlas? If not, can you suggest us how to change our approach? Is it possibile to use freesurfer with FLAIR sequences with the same aim (extract the BPF to evaluate brain atrophy)? Best regards, Mario Rossi 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: Linux Mint 1 Debian MATE 64-bit

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error from annot file : 7607 vertices did not have an annotation!
by Das S. 13 Apr '17

13 Apr '17

Dear FreeSurfer Developer, I have created my own atlas file and from the atlas file created the annot file. When I am trying to load my annot file on the sphere surface and view in tksurfer, I am getting below error: 7607 vertices did not have an annotation! I have the below steps in sequence: 1. I am creating my label files from matlab and keeping them in a folder. 2. From the labelled files I am creating the annot file using the below command: mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/MyColorLUTnew.txt --a eqnew40aparc --ldir 100307/label/eq_parcellation_label/ 3. When I am loading this lh.eqnew40aparc.annot file on sphere surface in tksurfer , it showing me all labels perfectly. tksurfer 100307 lh sphere 4. Then I am creating the .gcs file from the annot file using below command. The gcs files is being created without any error . mris_ca_train -t 100307/label/eq_parcellation_label/MyColorLUT.txt lh 100307/surf/lh.sphere.reg 100307/label/lh.left40aparc.annot 100307 100307/label/lh.reg40aparc.gcs 5. Then I am creating the .annot file using the my created atlas file using the below command: mris_ca_label -l 100307/label/lh.cortex.label -aseg 100307/mri/aseg.presurf.mgz 100307 lh 100307/surf/lh.sphere.reg 100307/label/lh.eqnew40aparc.gcs 100307/label/lh.aparc.annot using 100307/mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from 100307/label/lh.eqnew40aparc.gcs... reading color table from GCSA file.... average std = 0.2 using min determinant for regularization = 0.001 0 singular and 194 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 572 labels changed using aseg relabeling using gibbs priors... 000: 284 changed, 133181 examined... 001: 8 changed, 1741 examined... 002: 0 changed, 37 examined... 2 labels changed using aseg 000: 67 total segments, 24 labels (284 vertices) changed 001: 44 total segments, 1 labels (2 vertices) changed 002: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... 0 vertices marked for relabeling... 0 labels changed in reclassification. writing output to 100307/label/lh.aparc.annot... classification took 0 minutes and 6 seconds. koushik@koushik-DQ77MK:~/Parcellation$ 6. Now when I am trying to see this file in tksurfer loading as annot file on sphere surface I can see a big patch of gray color and showing me the message : 7607 vertices did not have an annotation! [X] I am attaching the .annot file , .gcs file and colortable .Plase help me to understand where the thing is going wrong,Any help will be much appreciated. Thanks & regards Sarbani

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mris_ca_label giving error CTABfindAnnotation: ct was NULL
by Das S. 13 Apr '17

13 Apr '17

Hi, I have created a color table, an annot file and a .gcs file( attached with the mail). But when I am trying to execute mris_ca_label with my own .gcs file I am getting the error : mris_ca_label -l 100307/label/lh.cortex.label -aseg 100307/mri/aseg.presurf.mgz 100307 lh lh.sphere.reg 100307/label/lh.eq40aparc.gcs lh.aparc.annot using 100307/mri/aseg.presurf.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ reading atlas from 100307/label/lh.eq40aparc.gcs... average std = 0.2 using min determinant for regularization = 0.001 0 singular and 185 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory ..... Before this I have used the below commands, to sucessfully create the .annot and .gcs file: 1. To create .annot file from label files and CTAB file-- mris_label2annot --s 100307 --h lh --no-unknown --ctab 100307/label/eq_parcellation_label/MyColorLUT.txt --a eq40aparc --ldir 100307/label/eq_parcellation_label 2. To crate .gcs file from annot file. mris_ca_train rh 100307/surf/rh.sphere 100307/label/rh.eq40aparc.annot 100307 100307/label/rh.eq40aparc.gcs I am not be able to understand where is the problem. Any help will be appreciated. Thanks Sarbani

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manual edits
by John Anderson 13 Apr '17

13 Apr '17

Dear Freesurfer experts, I am not an expert in manual edits, so I highly appreciate any feedback regarding the issues in my questions below. I ran the following command line “recon-all -s subjid -all” on T1 image for one of the subjects. when reviewing the output images (i.e. wm.mgz, brainmask.mgz) I found issues as attached. Attached is an output of the command: "Freeveiw orig.mgz wmparc.mgz wm.mgz" 1. When I reviewed “wm.mgz” I see interactions between the white matter (wm), and the cortex (yellow arrows). To fix this, I edited “wm.mgz” by removing the wm voxels from the cortex, and the data was saved in the file “wm.seg.mgz” 2. I found many holes in many slices similar to the (black arrow). I filled all these holes. The data saved in “wm.seg.mgz” 3. I fixed some issues related to dura and bad skullstipping Then I ran the command: “recon-all -autorecon2-wm -autorecon3 -subjid <subject>” which output the file “brain.finalsurfs.mgz” and the command “recon-all -autorecon-pial -subjid <subject>” Now, I want to understand where Freesurfer implement the new edits? Which files will be used as the main files that include the new edits. Logically, the edits must be implemented in "wm.mgz" and "brainmask.mgz". What confuses me is when I open orig.mgz wm.mgz and brainmask.mgz in freesview. I see the original non-edited files. I am not sure what I am doing wrong so I highly appreciate any help. John

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Longitudinal Pipeline
by Arman Eshaghi 13 Apr '17

13 Apr '17

Hi, I wonder if there is a way for mri_robust_template to perform iterative registration with 9 DOF rather than 6-7 default. The rational is to allow for a bit of scaling to adjust for potential scanner drifts in a longitudinal study over years. Thanks, Arman

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Reminder: FSurf webinar tomorrow
by Suchandra Thapa 12 Apr '17

12 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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Survey on inputs for surface-based analysis pipelines
by Christopher Markiewicz 12 Apr '17

12 Apr '17

Hi list, We're working on FMRIPREP <https://fmriprep.readthedocs.io/en/stable/>, a pipeline aimed at performing baseline preprocessing, and producing cleaned structural and functional data which can be fed into any of a number of analysis pipelines. We've recently begun incorporating surface reconstruction and surface-mapped functionals, and we'd like to get feedback on what outputs would be most valuable to people, in terms of formats, spaces and sampling strategies. 1) What surfaces do you use for sampling functional data and visualization? If you use down-sampled surfaces, do you have a preferred down-sampling strategy or target mesh? 2) What statistical analyses and model-fitting tools do you use for surface-based analyses? And are there any particular considerations you have for preparing your data for use by these tools? I appreciate your time and any input you may have to help us build a tool that fits the needs of the community. Thanks, -- Chris Markiewicz Center for Reproducible Neuroscience Stanford University

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correlation coefficient R
by tom parker 12 Apr '17

12 Apr '17

Dear Freesurfers, I made some correlations between cortical thickness and age in qdec. Is it possible to get the correlation coefficient value of this analysis? I just need to put it in a table with the significant results. Thank you so much!

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Fwd: wm edits not incorporated
by Octavian Lie 12 Apr '17

12 Apr '17

Dear All, Regarding wm.mgz edits not incorporated into wm surface, which seems to have been reported on by several of us with FS 6.00. I followed Antonin's idea of editing 001.mgz by switching wm-intensity voxels clearly not wm (mostly in the subtemporal regions, at times close to bright dural portions in the crown) to gm intensities and ran recon-all -all, and this time all was OK. So it seems that the problem is that on re-initializing during -autorecon2-wm rerun, the routine does not edit out high intensity voxels even if manually excluded in wm.mgz. This seems to be different to some extent with how FS 5.3 was reacting, although I did not look at this systematically. There may be a reason that manual editing is just part of the story during rerun and does not automatically override the recon stream, but I do not know it. Octavian ---------- Forwarded message ---------- From: Octavian Lie <octavian.lie(a)gmail.com> Date: Sun, Apr 2, 2017 at 7:59 PM Subject: wm edits not incorporated To: octavian lie <octavian.lie(a)gmail.com> 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. Octavian

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Freesurfer April 2017