Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Freesurfer default git clone branch
by Bignamini Christopher 08 May '19

08 May '19

External Email - Use Caution Dear list members, I would have a question about the naming of Freesurfer branches: I cloned the repository in order to build the code on my system and the default branch is the dev one. Should I switch to master in order to work with a stable code version or the dev one is fine? Thank you very much in advance for your attention. Best regards Christopher Bignamini

1 0

Cortex reconstruction using MRI with contrast
by Dengyu Wang 08 May '19

08 May '19

External Email - Use Caution Hello FreeSurfer developers, I am writing to ask about problem I met when reconstructing cortex from MRI with contrast? I had one subject that had only with contrast MRI images, and the recon-all can’t finish successfully. Is there any method or parameter setting that can solve the problem? Thank you! Best, Dengyu

2 3

White surface area and cortical surface area
by Ting Li 08 May '19

08 May '19

External Email - Use Caution Dear Freesurfer Experts, I have a very simple question. The white surface area we extract from the ?h.aparc.stats is the same area we used in the mri_surf2surf by parameter area? or the mri_surf2surf is the pial surface area? I am looking forward to your response. Thanks a lot! Best regards, Ting

1 0

Running multiple variables in mri_glmfit
by Erik Lindberg 08 May '19

08 May '19

External Email - Use Caution Dear Freesurfer experts, I am in the processing of running correlation with cortical thickness for almost 500 CSF variables. Thus I would like to use some sort of script. I previously used the common steps (mri_preproc, mri_glmfit and mri_glmfit-sim) but this procedure does not allow a .fsgd file with all the 500 CSF variables in it … correct? When running qdec many csf variables can be in the file … but then I cannot run it by script … right? So I wonder if there is a way to use one large file with the CSF data and then to make a script so that each variable is run iteratively until all is finished. Best case scenario I would also like to include snapshots from each correlation analysis. Is this possible to do? Thanks Olof Lindberg

1 0

skullstripping outside freesurfer
by Eric Cunningham 07 May '19

07 May '19

External Email - Use Caution Dear Freesurfer Experts, I have recently processed some data with the following 2 steps: 1) Perform skullstripping outside freesurfer to generate a nifti file (mostly using AFNI). 2) Run that through freesurfer using the -noskullstrip flag. Comparing the results from this with just running freesurfer alone, I found that the eTIV was significantly smaller, and not terribly well correlated (R^2 of .65). When looking at cortical volume measurements, it is generally considered a good idea to correct for eTIV. How would you recommend doing so in this case? Freesurfer version 5.3. Thanks, -Eric

1 0

funcroi-table-sess
by Nasiriavanaki, Zahra 07 May '19

07 May '19

Dear Freesurfer experts Hi I have a question about funcroi-table-sess, and I appreciate if you could please find a time to reply. Is there anyway that funcroi-sess-table can give out the activation values in each timepoint separately? Right now I can get the average of activation in each subject (in a specific region of interest and a specific contrast) by using the below commands, and I was wondering if I can get the values in each timepoint. funcroi-config -label ${lable}.label -roi ${subj}/${label_lh}.cfg -analysis loom.lh -force funcroi-sess -roi all_subjects/${subj}/${label}.cfg -s all_subjects/$subj -d . funcroi-table-sess -roi all_subjects/${subj}/${label}.cfg -s all_subjects/$subj -d . -o all_subjects/$subj/ROI_analysis/${label_lh}_${contrast}.txt -c $contrast -m cespct Thanks MOna

1 0

Conjunction analysis on the results of task-based fMRI
by Zhi Li 07 May '19

07 May '19

External Email - Use Caution Dear Freesurfer experts, I would like to investigate the overlap between two contrasts with conjunction analysis. May I know how should I use mri_glmfit-sim to correct the combined sig.nii.gz of contrast A and contrast B? Another question is if I want to do conjunction analysis on the corrected p maps of both contrasts, which file should I use, 'perm.th30.pos.sig.cluster.nii.gz' or 'perm.th30.neg.sig.voxel.nii.gz'? Besides, what is the difference between the p value in 'perm.th30.pos.sig.cluster.nii.gz' and 'perm.th30.neg.sig.voxel.nii.gz'? I tried to visualize the 'perm.th30.neg.sig.voxel.nii.gz', the figure was a little weird that the significant part in this file seemed to the the boundary of the uncorrected 'sig.nii.gz', is that correct? I asked a similar question before, maybe the post has been lost that I did not get answers. I am still confusing on the forming of the file 'perm.th30.pos.sig.cluster.nii.gz'. If the value in each cluster of this file is CWP, how does this p value generates (the CWP within a cluster is the same, but zero outside clusters)? Any suggestions would be much appreciated. Thanks and best wishes, Lizhi

1 0

dimensions swapped with head first-prone acquisition
by Caspar M. Schwiedrzik 07 May '19

07 May '19

External Email - Use Caution Hi! I have data acquired on a Siemens scanner with head first-prone. When I convert the dicom files to MGZ, left and right and superior and inferior, respectively, are swapped. The anterior-posterior dimension is ok. I am wondering what the correct way to correct this is? Following this entry in the wiki https://surfer.nmr.mgh.harvard.edu/fswiki/LeftRightReversal, it seems that I can use mri_convert with --in_orientation for that, and the images indeed look correct when I do this. I am however wondering whether I have to do the conversion to COR and fix the RAS coordinates as well? I found a 2007 entry on the mailing list about that https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2007-October/006250.h…, but it does not specify how to proceed. Your advice would be appreciated! Thanks, Caspar

2 2

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=…>

2 1

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

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer