Freesurfer February 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
143 discussions

Which FDG-PET file to use for PETSufer?
by Kate Marvel 24 Feb '20

24 Feb '20

External Email - Use Caution Hi FreeSurfer Users, I would like to perform PET analysis using PETSurfer and I have the following FDG-PET NIfTI files below: 1. TRANSAXIAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii 2. SAGITTAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii 3. CORONAL_BRAIN_3D_FDG_IR_CTAC+Time-TMGX.nii Which of the 3 NIfTI files above should one use for the PETSurfer? Thank you. -- kate

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Re: [Freesurfer] samseg permissions error
by Hoopes, Andrew 24 Feb '20

24 Feb '20

Hi Andrew, Thanks for pointing this out, it looks like the permissions of our fsaverage subjects have all changed since yesterday! Will fix this now Best, Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Russo, Andrew William" <AWRUSSO(a)mgh.harvard.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, February 24, 2020 at 10:51 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] samseg permissions error Hello Freesurfer Developers, I am trying to use the "samseg" function in /usr/local/freesurfer/dev but do not have permission to access the directory /usr/local/freesurfer/dev/subjects/fsaverage. Is this a restricted directory? ValueError: file /usr/local/freesurfer/dev/subjects/fsaverage/mri/orig.mgz does not exist ERROR: fs_time run_samseg I did not find any related issues with samseg on the archive and I have had it work in the past. Before running samseg I sourced the freesurfer environment: export FREESURFER_HOME=/usr/local/freesurfer/dev source $FREESURFER_HOME/SetUpFreeSurfer.sh (Using Freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) Thank you in advance, Andrew ____________ Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531

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Pre-release (beta) version of FreeSurfer v7 now available
by Douglas N. Greve 24 Feb '20

24 Feb '20

You can now download and install the beta version 7 of FreeSurfer. See this page https://surfer.nmr.mgh.harvard.edu/fswiki/dev7beta1 The purpose of this beta is for users to install and run FreeSurfer <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer> on some of their data sets using their computers and their commands and their post-processing to help us track down any errors prior to the full release scheduled for mid March. To that end, we would like for you to do several tests on a couple of subjects: * Do not use the beta version for any analyses that you want to publish. Only use full releases. * Run recon-all on the various computers (desktops, clusters, etc) that you use * Run recon-all with any special flags that you might use (eg, expert options) * Edit the recon and verify that the changes are taken and preserved * Run recon-all on problem data sets * Run recon-all on hires data (just add -hires flag), where hires is voxel size less than 1mm * Run recon-all with T2 or FLAIR input (1mm or hires) * Run longitudinal recon-all * Run the subfield analysis (hippcampal subfields, amygdalar and thalamic nuclei). You can do this by just adding -subfields to recon-all * Run samseg on a data set. We'll have more docs on samseg later, but for now SAMSEG = Sequence Adaptive Multimodal Segmentation can take any modality (or combination) and produce a volume segmentation (seg.mgz, like the aseg.mgz) -- it does not replace recon-all (samseg does not create surfaces, only volumetric segmentation). You can run it with something like "samseg --i inputvolume.mgz --o samsegdir". It should take about 45min. For now, we just want to make sure that it runs on your system. * Run any special post-processing to make sure that nothing breaks. We'll update the release notes with new features for the full release, but for now you should know that some features are not present in v7 (QDEC, GPU-capability, and recon-all -make). A new version of Tracula is in the works but probably will not be out until April or so; we'll have a minor release when it is ready. Let us know how it goes! The FreeSurfer Team

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Registration error
by Harrigan, Timothy P. 24 Feb '20

24 Feb '20

External Email - Use Caution Hi, I'm trying to learn to use Freesurfer to see if I can use it for some academic work on TBI. I downloaded it to a spare laptop at home, and filled out the registration form, and I got a message that stated "Registration Error: Spammer. Go Away." How could I address this? Thanks Tim Timothy P. Harrigan ScD Research and Exploratory Development Division Johns Hopkins University Applied Physics Laboratory Phone: 240-228-5943 Cell/Text: 240-280-9444

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how to convert the registered file (.lta) into NIfTI format in PETsurfer
by Kate Marvel 24 Feb '20

24 Feb '20

External Email - Use Caution Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks,

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skull stripping problem
by Marina Fernández 24 Feb '20

24 Feb '20

External Email - Use Caution Dear Freesurfeer experts, After running the recon-all, a part of the temporal lobe of one subject was removed. I used the watershed algorithm to be less agressive in the skull stripping step: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 And the problem was solved in the brainmask.mgz volume because I can see the temporal lobe completely, but the surfaces are still displaced. In order to correct the surfaces I used the white matter edit tool but there is no change after correcting WM and running the recon-all -autorecon2-wm -autorecon3. I also used control points and but the following error was shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3: recon-all -s sub_001 existed with errors I detected that there are very high values in the white matter of this part of the temporal lobe (even 132), maybe it has something to do. What can I do to solve the problem with this subject? Thank you very much in advance. Best regards, Marina.

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cluster size threshold
by Elisa Castaldi 24 Feb '20

24 Feb '20

External Email - Use Caution Dear experts, To perform a Monte Carlo based cluster correction, I have run the following line: mri_glmfit-sim --glmdir glmdir --mczsim 3 abs --cwp 0.05 --2spaces --a2009s I need to figure out which is the minimum number of voxels required for a cluster to be considered significant. In other words, which is the cluster *size* threshold in this case? Where can I find this information? Thanks Elisa

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Version Beta 7.0
by Victor Montal Blancafort 24 Feb '20

24 Feb '20

External Email - Use Caution Freesurfer developers, I have seen from the download webpage, that there is already a v7.0 beta version. Since we were planing to re-run a lot of individuals 1000+ with Freesurfer6, I was wondering if you could provide timings regarding the release of stabe 7.0. Also, could you briefly explain the main changes in this version? We are mainly interested on cortical thickness analysis, so... there will be big differences in the recon-all pipeline? Thank you in advance! V.

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Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary
by CiRong Liu 24 Feb '20

24 Feb '20

External Email - Use Caution Dear experts of the freesurfer, I was trying to create the white matter and pial surfaces of the cerebellum of the marmoset, based on ultra-high (80um) resolution ex-vivo images. I manually segment the cerebellum into the white matter and the gray matter and change the header information to 1mm. Based on the manual segmented files, I created white matter surfaces (rh.orig). I tried to use the mris_make_surfaces to expand the white matter to create the matched pial surface. However, the *mris_make_surfaces* failed to push the surface enough. See the attached files and screenshots. I tried smoothing the segmentation, enhancing the contrasts, and tested different expert option (for example: -max_csf 0.1 -min_gray_at_csf_border 1) This was this best I got, but still cannot get an optimal result (not pushed enough): *mris_mask_surfaces -max_csf 0.1 -min_gray_at_csf_border 1 -orig_wm orig -orig_pial orig -noaseg -noaparc -T1 ceb_sm marmosetceb rh * Since I have already manually segmented the cerebellum, *is there a way to force the mris_make_surfaces to expand to the boundary of the image?* The files can be download to replicate what I did: https://pitt.box.com/s/6269a9mnwbs6zi0azn08dn55u47yfa7i Thank you very much! Best Regards, CiRong Liu

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Optseq2 help needed
by Gergely Darnai 24 Feb '20

24 Feb '20

External Email - Use Caution Dear Developers, I am planning to run PVT (psychomotor vigilance task) in fMRI using event related design. This is an extremely simple reaction time task: participant has to respond to the appeared geometric shape as quickly as possible. The key feature of this paradigm is that we will have fluctuating and quite rapid event presentation times (ranging between 300 and 500 msec). Another important information is that we will use FSL FEAT for the evaluation. We decided to use opseq2 to optimize the design with the following parameters: optseq2 --ntp 150 --tr 2 --psdwin 0 20 --ev evt1 1 45 --nkeep 3 --o exp --nsearch 10000 --tnullmin 3 --tnullmax 11 --repvar 10 Although with this design I get quite satisfying efficiency and VRF scores I do not understand that if I decrease dPSD why does it have significant negative effect on efficiency and VRF. Could you explain this? If I understand well, this is the only option to shift the onset of the event from the scanning points, and I would assume that if there is fluctuation in time between scanning points and stimuli presentation, it would help to "catch" the hemodynamic response easier (if the stimulus onset always goes together with the scans, we can always catch the same timepoints of the HRF). Did I misunderstand something? If I use FSL that is based on HRF estimation (and not on FIR), do these parameters (dPSD) and scores (efficiency & VRF) have meaning and function at all? My last question is related to event duration. Although I have fluctuating and short events, as you can see I chose 1 sec (because it has to be the integer multiple of the dPSD). Is it problematic? Thank you for your suggestions, Gergely ----------------------------------------- Gergely Darnai PhD Department of Behavioural Sciences Medical School, University of Pécs Phone: +36/72/536-256 Fax: +36/72/536-257 H-7624 Szigeti u. 12, Pécs, Hungary

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Freesurfer February 2020