Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

Freesurfer installation
by pablo najt 17 Jul '13

17 Jul '13

Dear Freesurfer experts, I have a question regarding the installation/running of FreeSurfer. I have been trying to install freesurfer in a macbook pro (snow leopard) but no success. I followed the webpage from freesurfer (link below). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PersonalLaptopSetup But after the installations when I open the terminal nothing happens. I also tried to launch freesurfer this way: export FREESURFER_HOME=/Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.sh If I do this I get: command not found command not found command not found Any advice on how to finally set up the software would be great help. Thank you in anticipation.Pablo

2 2

Re: [Freesurfer] Button Press Regressor
by Douglas N Greve 17 Jul '13

17 Jul '13

It looks like it is the 1st regressor. Although there appears to be a period of time where this is no button press. If the button press is the only event, then it is definitely the 1st regressor. Note that all runs are concatenated together. doug On 07/16/2013 12:17 PM, Nicholas Paul Denisuk wrote: > Freesurfer Users, > > Here is the X.mat file. Thank you! > > Nick Denisuk > > On 7/16/13, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: >> can you send the X.mat file? >> >> >> On 07/16/2013 12:04 PM, Nicholas Paul Denisuk wrote: >>> Dear Freesurfer Users, >>> >>> I have opened up the X.mat file from the analysis. I think that the >>> button regressor is the third column in the file, but I am not 100% >>> sure. Do you know which column the button regressor is? Below is the >>> background info to this question. >>> >>> >>>>> I am trying to regress out the activity associated with button presses >>> in my GLM analysis. How do I generate a nuisance regressor file >>> analogous to a white matter regressor generated in functional >>> connectivity (a one column time course file)? >>> >>> Thanks you, >>> >>> Nick >>> >>> >>>>> Hi Nick, please remember to post to the list and not to us personally. >>> To answer your question, you could create an run an analysis with just >>> the button press. Go into the analysis and get the button press >>> regressor from X.mat, then save it as a text file in the run folder. >>> Then make your analysis and specify this as a task regressor. I >>> *think* that should work. >>> >>> doug >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

2 2

Gray matter missed in the pial layer after mri_segment
by Erin Browning 17 Jul '13

17 Jul '13

Hello-- We have a set of scans with bad artifact throughout the temporal lobe and the superior cortex. We've had to do the normalization steps (n3 correction, normalization) manually on most of these scans to preserve the gm/wm boundary. Now, when we run mri_segment, it leaves out some gray matter along the pial border. Is there a correction for this? Mri_segment has wlo and whi and ghi, but no glo, and it doesn't look like there's a method to add gray matter to the pial boundary like there is to remove it. Thank you, Erin Browning

2 1

Q) Medial_wall.label
by Yune Lee 17 Jul '13

17 Jul '13

Hello freesurfer experts, For visualization purpose (i.e., displaying group maps), I applied a mask for medial wall regions using the files (e.g., rh.Medial_wall.label or lh.Medial.wall.label), which I found in fsaverage/label/ directory. However, I noticed a somewhat imperfect medial wall masking in both hemispheres, such that transversing lines are seen in unthresholded t maps for both hemispheres (see attached ). Those lines eventually disappear when I increased threshold, but I wonder why this happened. Any ideas? best, yune

2 1

Crash in mri_register_ca during recon-all -base id -tp id1 -tp id2 -all
by Knut J Bjuland 17 Jul '13

17 Jul '13

Hi, I have some trouble running recon-all longitudinal pipelines. When recon-all comes to mri_register_ca it crashes without giving a message, even tough 8g ram was available. I have run the program with -debug. Is there any other option I may use? The system is running Rocks 6.0 (Mamba), and it uses Slurm queue system. Can I use the FreeSurfer 5.3 longitudinal process with data processed with FreeSurfer 5.1? I wish to use the new Longitudinal linear mixed effects model MATLAB tools. Knut J

1 0

Re: [Freesurfer] SWI acquisition question
by Fotiadis, Panagiotis 17 Jul '13

17 Jul '13

Hi Bruce, Don't worry about it! In addition, I was wondering about something else as well. I've been using MRIcron to analyze some of my Susceptibility Clinical Scans and even though they used to open fine, some of them (like the one I have attached in this email) appear distorted in a way. In the images I attached the "Original" one is how the Susceptibility clinical image should appear like, and the "Distorted" is how it appears for some of my subjects. Would you happen to know why is this happening? Thanks again for your time and help! Best, Panos ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Wednesday, July 17, 2013 11:54 AM To: Fotiadis, Panagiotis Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] SWI acquisition question Hi Panos sorry, I think this is pretty far outside our expertise, and it would be hard in any case to try to figure out what happened to give you these strange looking results. I certainly don't have any insight sorry, Bruce On Wed, 17 Jul 2013, Fotiadis, Panagiotis wrote: > Hi FS Community, > > I was wondering whether anyone had a chance to look into this. Thanks again for your time! > > Best, > Panos > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis > Sent: Tuesday, July 16, 2013 2:00 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: [Freesurfer] SWI acquisition question > > Hi FreeSurfer community, > > I am analyzing some SWI scans of some old subjects. For most of my subjects when a SWI was acquired, the resulting files that I would get would be a Magnitude image, a Phase image, a mIP image, and the SWI image. However, I have a couple of subjects for whom I get only the mIP and the SWI images, and the SWI image looks more blurry than it's supposed to be. I was wondering: > > 1) Why do I get only the mIP and the SWI images for those subjects and not the magnitude and phase images as well, > 2) Is it normal for the mIP to look like that? Usually it looks different, and > 3) Why is the final SWI image more blurry than usual? By looking at the image, I believe that maybe the head coil was not properly connected to the scanner at the time of the acquisition but I don't know whether that would be a sufficient explanation. > > I have attached two attachments: One of the resulting mIP and one of the equivalent blurry SWI of the same subject. > > Thank you in advance for your help and time! > > Best, > Panos >

1 0

kvlQuantifyHippocampalSubfieldSegmentations.sh empty text files
by Jasmeet Hayes 17 Jul '13

17 Jul '13

Dear Freesurfer experts, I tried running the kvlQuantifyHippocampalSubfieldSegmentations.sh script and get two text files (left & right stats) but the only information in the text files is the subject ID number. However, on my terminal window, I can see the volume output for each subfield and for each subject (see below for an example of 1 subject). And there were no errors after running the script. Every subject in the folder went through the hippocampal subfield recon procedure, and I have verified that there were no errors (each subject's folder has the left and right posterior_* files). We made a slight modification to the kvl script, only to change the Subject directory. Any ideas about what might be the problem? Thanks! -Jasmeet cd .. Quantifying subject er002_recon/ right Doing right side cd mri THIS IS THE COMPRESSION LOOKUP TABLE FILE /Applications/freesurfer/data/GEMS/compressionLookupTable.txt PWD before running KVLQuantifyPosteriorProb IS: /Volumes/VA_Imaging/Projects/jpannuhayes/emoreg/HIPPOCAMPAL_SUBFIELDS/er002_recon/mri kvlQuantifyPosteriorProbabilityImages /Applications/freesurfer/data/GEMS/compressionLookupTable.txt posterior_Right-Hippocampus.mgz posterior_right_presubiculum.mgz posterior_right_CA1.mgz posterior_right_CA2-3.mgz posterior_right_fimbria.mgz posterior_right_subiculum.mgz posterior_right_CA4-DG.mgz posterior_right_hippocampal_fissure.mgz > volumeStats_right.txt volumeInVoxels: Right-Hippocampus: 3094.49 right_presubiculum: 4373.15 right_CA1: 2483.23 right_CA2-3: 8192.11 right_fimbria: 740.934 right_subiculum: 5402.79 right_CA4-DG: 4688.93 right_hippocampal_fissure: 541.872 cd .. cd ..

2 4

Missing flirt.fsl file in bin folder
by Gundran, Andrew 17 Jul '13

17 Jul '13

Hello freesurfers, I’ve been trying to run tracula on freesurfer and it seems that when I get to the point where it uses FSL’s flirt I receive an error. I looked into it further and it seems I am missing a file to run flirt: $FREESURFER_HOME/bin/flirt.fsl It seems that I somehow do not have that file to complete tracula. I was hoping someone could help with this or perhaps send me the file? I am using freesurfer- Darwin-snowleopard-i686-stable-pub-v5.3.0- MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Hope to hear from someone soon, Andrew

2 1

Re: [Freesurfer] SWI acquisition question
by Fotiadis, Panagiotis 17 Jul '13

17 Jul '13

Hi FS Community, I was wondering whether anyone had a chance to look into this. Thanks again for your time! Best, Panos ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Fotiadis, Panagiotis Sent: Tuesday, July 16, 2013 2:00 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] SWI acquisition question Hi FreeSurfer community, I am analyzing some SWI scans of some old subjects. For most of my subjects when a SWI was acquired, the resulting files that I would get would be a Magnitude image, a Phase image, a mIP image, and the SWI image. However, I have a couple of subjects for whom I get only the mIP and the SWI images, and the SWI image looks more blurry than it's supposed to be. I was wondering: 1) Why do I get only the mIP and the SWI images for those subjects and not the magnitude and phase images as well, 2) Is it normal for the mIP to look like that? Usually it looks different, and 3) Why is the final SWI image more blurry than usual? By looking at the image, I believe that maybe the head coil was not properly connected to the scanner at the time of the acquisition but I don't know whether that would be a sufficient explanation. I have attached two attachments: One of the resulting mIP and one of the equivalent blurry SWI of the same subject. Thank you in advance for your help and time! Best, Panos

2 1

Propagating changes to segmentation
by Liane Hunter 17 Jul '13

17 Jul '13

Hello, I have a question about propagating changes to segmentation. Once I have saved my edits what is the appropriate command to propagate these changes for both cortical and subcortical changes that I have made. The workflow instructs that after segmentation edits are made to run -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3 to the wm. mgz file. However the instructions indicate to open brainmask.mgz to make edits. Should I make changes on the wm.mgz file? Any clarification on this topic would be much appreciated. -- Liane Hunter MD/Ph.D Candidate Albert Einstein College of Medicine

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