Freesurfer January 2019

freesurfer@nmr.mgh.harvard.edu

119 participants
167 discussions

MRI sequence parameter difference and effect on cortical thickness values
by Arsenije Subotic 10 Jan '19

10 Jan '19

External Email - Use Caution Dear experts, For our study, we are planning on combining two different datasets to examine cortical thickness. There is a slight difference in the inversion time (400 vs 650) and flip angle ( 8 vs 11) between the two datasets. I know that free surfer measurements are fairly consistent across different scanner types and strengths, but do you know if slight differences in mri sequence parameters have an affect on cortical thickness? I was planning on adding it as a covariate in our analysis just in case. Thank you! Arsenije

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Subcortical divide parcellation
by WANG Huifang 10 Jan '19

10 Jan '19

External Email - Use Caution Dear freesurfer experts, I would like to do subcortical divide parcellation, such as the hippocampus. By my understanding in freesurfer, the cortical parcellation can be saved as vertices but subcortical parcellation is only saved as volumes. There are a few ways I can do the cortical divide parcellation, seems do not fit for subcortical parcellation, such as: mris_divide_parcellation. Can this function also do for the subcortical regions? Is any other suggestion for this-subcortical divide parcellation? Thank you so much, Huifang

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Pial surface error (failing dura removal)
by Rusche, Johann 10 Jan '19

10 Jan '19

Dear Freesurfers, I have been processing my T1 dataset through the longitudinal pipeline with the -3T flag (scanned at Martinos). Unfortunately in 50% of all subjects large areas of dura are being included in the pial surface. Both gcut and adjustment of watershed parameters (down to 5) did not bring significant improvements. I understand intensity characteristics are very similar for GM and dura. However, I wonder whether you can recommend a more elegant solution than painfully recon-editing all brainmasks by hand. Attached is a screenshot depicting the issue with and without gcut. I am using stable v6.0. Thanks for your time! Best, Johann __________________ Johann Rusche Graduate Research Student, Lazar Lab Department of Psychiatry – Neurosciences Massachusetts General Hospital

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Help with Reviewer Comment
by Shane Schofield 10 Jan '19

10 Jan '19

External Email - Use Caution Hi Freesurfer A reviewer asked whether there are concerns about whether Freesurfer may obtain accurate cortical thickness data in people with developmental conditions - the main focus in my study. I did a search and could not find any validation studies in these cohorts. Any idea? Thanks a lot. Regards,Shane

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segmentation problem
by Manuela Costa 10 Jan '19

10 Jan '19

External Email - Use Caution Dear all, We have a subject for whom we would like to do hippocampal subfield and amygdalar nuclei segmentation. Unfortunately, this subject has a large lesion in the right hemisphere. Looking at the aseg, the segmentation of the bilateral amygdala are fine, but the right hippocampus becomes incorrectly segmented towards the posterior end (shown in the attached images). Is there any way that this can be corrected, manually or otherwise? Will there be further problems down the line when we proceed with the subfield segmentation? We are running freesurfer-linux-centos6_x86_64-dev-20181121-910b841. Thanks in advance! Regards, Manuela -- Manuela Costa, PhD Cognitive Neuroscientist Lab. for Clinical Neuroscience,CTB, Madrid <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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problem with contrast in 1st-level analysis
by xi star 10 Jan '19

10 Jan '19

External Email - Use Caution Hi! FS Experts! In the fMRI experiment, there are 2 conditions: 1# 3D picture 2# zero disparity picture interleaved with fixation block (0). To compare 3D-vs-zero disparity, I used command: mkcontrast-sess -a 1 -c 2 -nosumconds but the results showed more activation then expected. To find the problem, I compared 3D-vs-fix (-a 1 -c 0), the result shows the same as 3D-vs-zero disparity. My question is: why the two contrast ( [1 0; 0 -1] and [1 0] ) came to the same result? How can I compared the two conditions? Thanks a lot ! Yours, Star

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freeview.bin: Fatal IO error: client killed
by 이충섭 10 Jan '19

10 Jan '19

External Email - Use Caution Hello Freesurfer developers, First, the recon-all command was completed without errors. However, the following command results in the same error as the mail subject . freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red If i enter only freeview, it runs without error.. Can you tell me what's wrong? Thank you. 1) Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 2) platform: Ubuntu 16.04.5 LTS 3)uname -a: Linux eclgpu4 4.4.0-135-generic #161-Ubuntu SMP Mon Aug 27 10:45:01 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached

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Yeo labels
by Tosun, Duygu 09 Jan '19

09 Jan '19

External Email - Use Caution Is there a recon-all flag similar to -label_v1 or -ba-labels to automatically create label and stat files for Yeo network parcellations?

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Talairach Transform failure
by Daniel Ferreira 09 Jan '19

09 Jan '19

External Email - Use Caution Dear experts, I am processing some data and one of my cases failed. I checked the recon-all.log and found the following: *#@# Talairach Failure Detection tis 11 dec 2018 11:32:31 CET* */home/daniel/FreeSurfer/0e63e2e7-d1e1-4e78-9106-150994a32c44/mri* * talairach_afd -T 0.005 -xfm transforms/talairach.xfm * *ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)* *Manual Talairach alignment may be necessary, or* *include the -notal-check flag to skip this test,* *making sure the -notal-check flag follows -all* *or -autorecon1 in the command string.* *See:* *http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach>* *ERROR: Talairach failed!* *Linux siv 4.4.0-140-generic #166-Ubuntu SMP Wed Nov 14 20:09:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux* *recon-all -s 0e63e2e7-d1e1-4e78-9106-150994a32c44 exited with ERRORS at tis 11 dec 2018 11:32:31 CET* Next, I tried to fix the issue by using tkregister: tkregister2 --mgz --s tal_before --fstal However, the Talairach volume does not load as a MOVEABLE volume. When I check the available recon-all output I only have: orig/001 --> looks good rawavg --> looks good orig --> its awful (it looks like millions of white tiny voxels on a black background) nu --> it is empty transforms/talairach.xfm --> is available I was wondering if you would know about any way to fix this? Thank you in advance, Dani -- *Daniel Ferreira, PhD, Assistant Professor* Division of Clinical Geriatrics; Department of Neurobiology, Care Sciences and Society Karolinska Institutet (Sweden) *Address: **Blickagången 16, 141 52 Huddinge | phone: +46 720128047 | email: daniel.ferreira.padilla(a)ki.se <daniel.ferreira.padilla(a)ki.se>*

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field of view mis-displacement complication
by Nasiriavanaki, Zahra 09 Jan '19

09 Jan '19

Dear Freesurfers Hi I have a bunch of data which have field of view mis-displacement at the time of data aquisition, so when I overlay the functional data on the structural image, the top part of the brain is cut off. Below I have copied one of the subject's functional image overlaid on his structural image on the right and the result of first level analysis (single subject map) in two different thresholds on the left. I have also copied one of the registration slices on the bottom. My question is why there is activation on parts of the brain which doesn't really have a functional data? Should I preprocess these data in a different way than the usual way? Thanks a lot Mona [cid:f6b8ef2d-9ae4-4ef4-b29e-a124467450ff] [cid:38d232c1-8e53-4f08-aa06-07e13e52789d] Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Freesurfer January 2019