Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

Avoid interaction term in qdec?
by Yang, Daniel 06 Sep '13

06 Sep '13

Dear FS Experts, My model has two categorical variable: Diagnosis and Sex. I am interested in the effect of Diagnosis but I want to control the Sex effect. Toward this goal, I want to model two main effects and want to avoid modeling their interaction term. Is this something feasible in FreeSurfer group analysis? Would using DOSS help with the solution? Thanks! Daniel

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tool to compare surface files (along the lines of diff)?
by David Romano 06 Sep '13

06 Sep '13

Hi everyone, I'm trying to figure out whether two surfaces which appear identical in freeview are indeed identical. Using diff shows the files are not, but since they're binary, I can't tell whether this difference is simply due to header information that might be embedded in the files, or whether the surfaces do indeed differ. Is there a FreeSurfer command that can be used to determine this? Thanks in advance for your help, David Romano

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Difference between QDEC and glm results
by ye tian 05 Sep '13

05 Sep '13

Dear Freesurfers, I compared my QDEC and glm (command line) results, using the same contrast and threshold, but the size of the red cluster (barely visible on glm) is quite different. Is this a problem? Thank you very much! Sincerely, Ye

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Estimated Total Intra Cranial Vol
by stdp82＠virgilio.it 05 Sep '13

05 Sep '13

Hi list. I'm looking mailing list to find responce to this question. "Estimated Total Intra Cranial Vol" obtained by asegstats2table also included ventricles volume? I'd like to assess the volumetric changes of a subcortical structures. Do you advise me to consider "Estimated Total Intra Cranial Vol" (with or without ventricles?) or, alternatively, subcortical brain volume? Thank you very much, Stefano

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Tracula error - unknown queue "long.q", "short.q"
by Joana Braga Pereira 05 Sep '13

05 Sep '13

Dear Anastasia and FreeSurfers, I was preprocessing some data using tracula and found this error after running trac-all -bedp -c dmrirc: INFO: SUBJECTS_DIR is /data-02/joana/Last INFO: Diffusion root is /data-02/joana/tracula/ Actual FREESURFER_HOME /usr/local/freesurfer-5.3 WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /data-02/joana/tracula//XXX/dmri subjectdir is /data-02/joana/tracula/XXX/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue "short.q". Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue "long.q". Exiting. Queuing post processing stage Unable to run job: denied: "60" is not a valid object name (cannot start with a digit) Job was rejected because job requests unknown queue "long.q". Exiting. Type /data-02/joana/tracula/3119/dmri.bedpostX/monitor to show progress. Type /data-02/joana/tracula/3119/dmri.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. So far no slices have been processed. Does anyone know how to solve it? Thanks!

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using mris_make_surfaces for nonstandard input
by David Romano 05 Sep '13

05 Sep '13

Hi everyone, I would like to produce lh.white, lh.area, and lh.curv files of the type produced by mris_make_surfaces, but where the input is a mask of the left hemisphere white matter alone. Specifically, suppose I start with the file lh.wm-mask.nii and use mri_convert to make lh.wm-mask.mgz. I can then follow the -tessellate and -fix steps of the -autorecon2 section on the webpage http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable to produce the file lh.orig, one of the required inputs to mris_make_surfaces. The only other files required to have mris_make_surfaces produce lh.white, lh.area, and lh.curv files, seem to be the files filled.mgz, brain.mgz, and wm.mgz. Since wm.mgz is the output of a call to mri_pretess from the -segmentation step of the -autorecon2 section, I can create wm.mgz by using the command mri_pretess lh.wm-mask.mgz 1 wm.mgz. My inclination at this point is to create copies of wm.mgz that are given the names filled.mgz and brain.mgz. I can then run mris_make_surfaces -whiteonly -noaparc -mgz subjectID lh and the desired files are produced, but I'm not sure what the effect of using wm.mgz as both filled.mgz and brain.mgz would have on the output. Given this setting, my question is: what are the roles played by filled.mgz an brain.mgz in creating the output of mris_make_surfaces? Thanks in advance for your help, David Romano

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Output mris_anatomical_stats into table for spreadsheet
by Tara Ann Miskovich 05 Sep '13

05 Sep '13

Hello everyone, I am trying to gather the curvature (of a frontal ROI created through mri_mergelabels) through mris_anatomical_stats using the following mris_anatomical_stats -l 1220/label/lh.frontalmerge.label -f frontal_table 1220 lh pial The table produced doesn't upload well into a spreadsheet (measurements all in one cell). Does anyone know how to make a table that can be uploaded into a spreadsheet? Thanks! Tara

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lh.orig.nofix vs. lh.white
by David Romano 05 Sep '13

05 Sep '13

Hi everyone, I've been trying to go through the various steps described on the page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable and I'm trying to understand part of the -autorecon2 section, and in particular, 1) how the lh.orig.nofix file that is produced by the end of the -tessellate subsection is different from the the lh.white file that is produced by the -white subsection, and 2) whether the area and curvature files produced by the command

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Re: [Freesurfer] Improving the accuracy of average surfaces made from make_average_subject
by Bruce Fischl 05 Sep '13

05 Sep '13

Hi Miggy can you cc the list so that others can answer? The two atlases we provide are described in: https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl04-parcellation.pdf https://surfer.nmr.mgh.harvard.edu/ftp/articles/desikan06-parcellation.pdf http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937159/pdf/nihms213933.pdf and yes, I guess you could edit the ribbon.mgz and then convert it back to wm.mgz. You'll need to make sure that the "on" edits are turned to 255 and the "off" ones to 1 (not 0) for things to work properly cheers Bruce On Wed, 4 Sep 2013, Miggy Chuapoco wrote: > Hi Bruce, > Thanks for the help. To explain a bit more about the first issue, we convert > ribbon.mgz into a a nifti file using a script in matlab, which we then edit > in ITK-SNAP to fix the segmentation. Typically from there we use a program > called mrVista to create meshes and do other data analysis depending on what > we need to do. However, we are doing group averaging for the first time and > we would like to use these fixed segmentations that we have in the group > averaging, and not the raw segmentations from recon-all. I was curious to > know that if I were able to convert the nifti file that we have edited back > into an .mgz file, would we be able to theoretically obtain a new wm.mgz > file and run autorecon2-wm. Let me know if that makes sense. > > With regards to the second issue, which atlas is used in the > make_average_subject process and where would I be able to find a list of the > annotation files within each atlas? > > Thanks for your help! > Miggy > > > On Wed, Sep 4, 2013 at 1:45 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Miggy, > > not sure about your first issue as the ribbon is the gray matter > and the wm.mgz is white matter, so how would edits in one change > the other? > > For the second one, there is a flag in mris_register that allows > you to draw a label on an individual subject and indicate what > parcellation unit is should be in the average. The syntax is: > > > mris_register -l <label file> <gcsa file> <annotation name> ... > > where > > <label_file> is the label you draw on the individual (e.g. in > tksurfer) > <gcas_file> is one of our standard atlases, listed in > $FREESURFER_HOME/average/*.gcs > <annotation name> is the name of the annotation in the atlas > that the label should map to (e.g. S_central in the Destrieux > atlas) > > cheers > Bruce > > > On Wed, 4 Sep 2013, Miggy Chuapoco wrote: > > Hi all, > I'm trying to make a group average of a set of > subjects that we've collected > various functional data on and use anatomical > landmarks of the group average > surface to predict the locations of functional areas > that we've found to be > correlated to the anatomy of the ventral cortex. As > such, we'd like to get > as accurate of an average surface as possible. I've > come up on two problems > that I'd like to address and was wondering if anyone > could help come up with > a solution. > > I ran the recon-all command on all the subjects and > created a segmentation, > however we made edits to the segmentation using > ITK-SNAP, and not tkmedit. > Some of the changes were fairly drastic and we'd > like to use the fixed > segmentations in the averaging process. I've > considered perhaps running the > -autorecon2-wm flag, but unfortunately using > ITK-SNAP essentially makes > edits to ribbon.mgz, and not wm.mgz. I was wondering > if there was a way to > "extract" a new wm.mgz from an edited ribbon.mgz. > > My second problem involves trying to anchor a sulcus > on the ventral surface > during the averaging process (the mid-fusiform > sulcus) in hopes of getting a > more accurate representation of the sulcus on the > average surface. As it > stands there is a bit too much variability of the > average MFS location when > compared to the individual subjects' MFS location, > and we'd like to reduce > that if possible. Is there any way of using a label, > or something similar, > that can be considered as an "anchor" during the > averaging process? > > Thanks and regards, > Miggy Chuapoco > > > > > 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. > > > >

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license error with FS5.3
by S.V.Shepherd [work] 05 Sep '13

05 Sep '13

I wanted to bump this: I have license errors with FS 5.3 that don't appear for equivalently-configured FS 5.1 and FS 4.5 installations. How shall I troubleshoot? SYMPTOMS: $ mri_convert $FREESURFER_HOME/subjects/bert/mri/T1.mgz T1.mgz mri_convert /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/subjects/bert/mri/T1.mgz T1.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/subjects/bert/mri/T1.mgz... -------------------------------------------------------------------------- ERROR: Invalid FreeSurfer license key found in license file /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full/.license -------------------------------------------------------------------------- $ bugr FREESURFER_HOME: /space/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-full Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 RedHat release: Red Hat Enterprise Linux Server release 5.9 (Tikanga) Kernel info: Linux 2.6.18-308.4.1.el5 x86_64 LICENSE The license file is the same as we use for our other FS installations, which work. I've also tried copying it from .license to license, which didn't solve the problem. Please let me know if you have any leads or suggestions. *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620

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Freesurfer September 2013