Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

help with this error
by Manish Dalwani 03 Jun '13

03 Jun '13

Dear Freesurfer's I have been using (a slightly older version) Freesurfer on linux and it works fine. I just recently installed freesurfer on the mac workstation OS X 10.8.1. I get the following error: server:subjects manishdalwani$ cd anat_5214 server:anat_5214 manishdalwani$ recon-all -i MR1000200001.dcm -s 5214 ERROR: MR1000200001.dcm exists but is not readable Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s exited with ERRORS at Mon Jun 3 15:57:24 MDT 2013 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Kindly help! Regards, Manish

2 1

BrainSegNotVent
by Derek James Dean 03 Jun '13

03 Jun '13

2 1

image with Cerebellum
by Ray, Siddharth 03 Jun '13

03 Jun '13

Hi, I am new to freesurfer and just want to know can I just have skull-stripped image (with cerebellum) anywhere between stages in Freesurfer 5.3?? Please let me know. Thanks, Siddharth

2 1

possible to display data obtained through mri_segment as heatmap?
by Salil Soman 03 Jun '13

03 Jun '13

Dear Doug, Thank you for your recent advise with using freesurfer to extract mean values from non structural image data. Is there a way to generate an image (e.g. heat map) displaying those values in free view? Best wishes, Sal

2 7

freeview v5.3 reposition surface
by Adam Martersteck 03 Jun '13

03 Jun '13

Hi Freesurfer experts, I noticed that Freeview has gotten an upgrade from v5.1 to v5.3 and the reposition tool now has a GUI and it works! Dr. Fischl said in response to Dr. Pietro De Rossi on October 24th, 2012 that the pipeline for the reposition surface tool was not yet implemented and you still needed to rerun “mris_make_surface (including mris_thickness to regenerate the thickness map)”. [ https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2012-October/026209… I noticed that the freeview virtual representation of the surfaces are immediately regenerated. Should I be running the mris_make_surface command after saving the new surface(s)? Thanks, Adam Martersteck Cognitive Neurology and Alzheimer's Disease Center Northwestern University Feinberg School of Medicine 320 E. Superior Street, Searle 11 Chicago, IL 60611

2 1

correlation between resting state fmri and brain perfusion
by Chen, Yasheng 03 Jun '13

03 Jun '13

Hi all, Sorry to post a question not related to the brain surface analysis. I wonder why there are not many studies looking into the correlation between perfusion and resting state fmri. Perfusion should play an important role in modulating resting bold signal. Does any one have some experience using either ASL or perfusion measurement from PET to look into how these things are correlated? Is this an area worth pursuing? Thank you very much! Yasheng

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Fwd: Fwd: mir_convert produces a darkened file
by Erin Browning 03 Jun '13

03 Jun '13

It seems like it getting darker messes up the normalization later on; could this be the case? Here's what it looks like in AFNI (1029-afni.jpg), and here's what it looks like after we run motioncor (1029-orig.jpg). On Mon, Jun 3, 2013 at 1:33 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > that will not change the intensities at all. It is probably just a display > issue. Try changing the brightness/contrast. The artifact might cause > problems later on, but this is not an issue I think > doug > > > On 06/03/2013 02:20 PM, Erin Browning wrote: > >> We use: >> >> mri_convert N1029-anat+orig.BRIK freesurfer/mri/orig/001.mgz >> >> where freesurfer is our freesurfer subject folder. >> >> >> On Mon, Jun 3, 2013 at 1:18 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >> wrote: >> >> what is your mri_convert command line? >> >> On 06/03/2013 02:11 PM, Erin Browning wrote: >> > Hi everyone-- >> > >> > We have a series of scans with an hyperintense artifact cutting >> > through the temporal and frontal lobe. When we run mri_convert to >> > convert from AFNI .BRIK files to .mgz fles, the results look >> like the >> > attached image. >> > >> > How can I correct for this? We tried skullstripping in AFNI first to >> > remove some of the artifact, but that didn't seem to help very much. >> > >> > Thank you, >> > Erin Browning >> > >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >> > >> >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >> > >> >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** >> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >

3 7

Group Analysis Question
by Fotiadis, Panagiotis 03 Jun '13

03 Jun '13

Hey Doug, I have run a group analysis on my data with two different ways. (The input is cortical thickness.) In the first analysis, I specified 4 groups (Diseased_Male, Diseased_Female, Healthy_Male, and Healthy_Female) whereas in the second, just two groups (Diseased, Healthy). One of the comparisons that I did was the age slope between Diseased and Healthy. Therefore in the first analysis, I set the contrast vector to be [0 0 0 0 0.5 0.5 -0.5 -0.5] and in the second analysis I set it to [0 0 1 -1]. However, the results that came up were somewhat different. For instance there were clusters in the second analysis that were significant but were not significant in the first analysis. Shouldn't the results be the same? Thank you, Panos

3 8

Fwd: mir_convert produces a darkened file
by Erin Browning 03 Jun '13

03 Jun '13

Hi everyone-- We have a series of scans with an hyperintense artifact cutting through the temporal and frontal lobe. When we run mri_convert to convert from AFNI .BRIK files to .mgz fles, the results look like the attached image. How can I correct for this? We tried skullstripping in AFNI first to remove some of the artifact, but that didn't seem to help very much. Thank you, Erin Browning

2 3

Fwd: autorecon3 error
by Claudia Dacquino 03 Jun '13

03 Jun '13

Hi Freesurfers, I did autorecon3-cp and exited with errors. Ould anyone help me to understand what's the roblem? You can find the recon-all.log attached. Thanks in advance. Claudia

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Freesurfer June 2013