Freesurfer

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30132 discussions

Make_average_subject
by Jürgen Hänggi 22 Oct '13

22 Oct '13

Dear FS experts When using make_average_subject the resulting volume files (T1.mgz, orig.mgz, brain.mgz, etc.) are cut off superiorly (see attachment). Any idea? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Strange behavior of the dods option
by Jürgen Hänggi 22 Oct '13

22 Oct '13

Dear FS experts I compared two groups wrt cortical thickness using total grey matter volume as a covariate. The results obtained without the covariate (first row in the attached figure) and with the covariate modeled across both groups (doss option, second row in the figure) differed only in quantity (clusters are smaller with the covariate). However, when using the covariate with dods, the results changed completely (third row in figure) compared to doss and compared without the covariate. Then I tested (using dods) the covariates itself (using 0 0 1 -1) and get almost identical clusters (although in the opposite direction, forth row in the figure) as found in the group comparison with the covariate (dods, third row). In my opinion, this is puzzling! Any idea? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Re: [Freesurfer] medial wall crossing the surface: repost
by silver47＠gmx.com 21 Oct '13

21 Oct '13

Thanks Bruce for your response, I'll fix aseg where it is incorrect, but what about the instances where the aseg is correct and the pial surfaces cross? Other than needing to update aseg.stats, are there any other concerns with the 'hemisphere' approach I described below? Thanks again, Paul > ----- Original Message ----- > From: Bruce Fischl > Sent: 10/22/13 09:46 AM > To: silver47(a)gmx.com > Subject: Re: [Freesurfer] medial wall crossing the surface: repost > > Try fixing the aseg and rerunning > Cheers > Bruce > > > On Oct 21, 2013, at 6:23 PM, "silver47(a)gmx.com" <silver47(a)gmx.com> wrote: > > > > Not always, but yes, in some instances the aseg crosses. > > > > > >> ----- Original Message ----- > >> From: Bruce Fischl > >> Sent: 10/18/13 01:22 PM > >> To: silver47(a)gmx.com > >> Subject: Re: [Freesurfer] medial wall crossing the surface > >> > >> Does the aseg cross as well? > >> > >> > >> > >>> On Oct 17, 2013, at 10:07 PM, "silver47(a)gmx.com" <silver47(a)gmx.com> wrote: > >>> > >>> Dear All, > >>> > >>> I too am seeing the medial pial surfaces crossing hemispheres in some subjects. > >>> > >>> The approach that appears to be working for me involves making copies of brainmask.mgz and aseg.mgz > >>> For the left hemisphere crossing into the right, edit brainmask.mgz and aseg.mgz to delete voxels at the crossing belonging to the right hemisphere. > >>> I then run recon-all -autorecon-pial -hemi lh -subjid subject > >>> followed by returning the brainmask.mgz and aseg.mgz back to their original copy. > >>> > >>> This is similarly repeated for the right hemisphere crossing into the left. > >>> > >>> Are there any issues or concerns with this approach particularly in regard to thickness or the segmentations? > >>> > >>> Thanks, > >>> > >>> Paul > >>> _______________________________________________ > >>> 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. > > > >

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Re: [Freesurfer] medial wall crossing the surface: repost
by silver47＠gmx.com 21 Oct '13

21 Oct '13

Not always, but yes, in some instances the aseg crosses. > ----- Original Message ----- > From: Bruce Fischl > Sent: 10/18/13 01:22 PM > To: silver47(a)gmx.com > Subject: Re: [Freesurfer] medial wall crossing the surface > > Does the aseg cross as well? > > > > On Oct 17, 2013, at 10:07 PM, "silver47(a)gmx.com" <silver47(a)gmx.com> wrote: > > > Dear All, > > > > I too am seeing the medial pial surfaces crossing hemispheres in some subjects. > > > > The approach that appears to be working for me involves making copies of brainmask.mgz and aseg.mgz > > For the left hemisphere crossing into the right, edit brainmask.mgz and aseg.mgz to delete voxels at the crossing belonging to the right hemisphere. > > I then run recon-all -autorecon-pial -hemi lh -subjid subject > > followed by returning the brainmask.mgz and aseg.mgz back to their original copy. > > > > This is similarly repeated for the right hemisphere crossing into the left. > > > > Are there any issues or concerns with this approach particularly in regard to thickness or the segmentations? > > > > Thanks, > > > > Paul > > _______________________________________________ > > 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.

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Pial surface interhemispheric overlap
by Jon Wieser 21 Oct '13

21 Oct '13

Hi Freesurfer experts I recently created surfaces with recon-all, and found that in the straight gyrus in the medial inferior frontal lobe, the pial surfaces are overlaping between the hemispheres. I have attached a picture to show the problem. You can see from the picture that the pial surface from the Right hemisphere (in Blue) and the pial surface from the left hemisphere ( in Red) are overlapping (crossing over) to the other hemisphere. how can I fix this? Thanks Jon -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

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"command not found" - unable to set up freesurfer
by Laura Taylor 21 Oct '13

21 Oct '13

Hi, I have just downloaded and I thought installed freesurfer on a Debian system (Debian 3.2.51-1 x86_64 GNU/Linux). However when I go to test the install by typing in freeview (or any other command) in the terminal window I get the following: % freeview freeview: Command not found. Before doing this, I added my license key to a .license file in the freesurfer directory. I had also previously set up the environment as follows: % setenv FREESURFER_HOME /Data/freesurfer % source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Data/freesurfer FSFAST_HOME /Data/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Data/freesurfer/subjects MNI_DIR /Data/freesurfer/mni When I type freesurfer in the terminal window I am told that: You are running this version of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 _____ Can you help me figure out why I can't get freesurfer to run?? I have previously been able to install and use freesurfer on a different computer running Unbuntu. Many Thanks, Laura

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Manually drawing surfaces
by Jonathan Holt 21 Oct '13

21 Oct '13

Is this possible? jon

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Re: [Freesurfer] running recon-all for FSL-based ROIs
by Douglas N Greve 21 Oct '13

21 Oct '13

It is not done with recon-all. Use mri_label2vol to map your ROIs to fsaverage space using the registration below doug On 10/21/2013 11:54 AM, Paul Beach wrote: > Hi Doug, > > Thank you for the response. > > You'll have to pardon my ignorance here, but how would I integrate > this into the actual recon-all command? What kind of flag would I utilize? > > The setup is that I have a folder named "anterior_Salience" in my > subjects directory - this folder has the NIFTI file > anterior_Salience.nii.gz: > > /recon-all -s anterior_Salience \/ > /-i > /extern/research/PI/training/beachpau/Beach_FreeSurfer_data/anterior_Salience/anterior_Salience.nii.gz > *-flag?? */*/$FREESURFER_HOME//average/mni152.register.dat/* > */ > /* > */ > /* > Thanks > > > On Mon, Oct 21, 2013 at 11:19 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > If you are trying to get them into fsaverage/mni305 space, then use > $FREESURFER_HOME//average/mni152.register.dat > > doug > > On 10/21/2013 10:58 AM, Paul Beach wrote: > > Hello FS experts, > > > > I am interested in utilizing the functional ROIs made by the > Greicius > > lab out of Stanford (found here > > <http://findlab.stanford.edu/functional_ROIs.html>). However, these > > ROIs were made using FSL and the coordinate system for them is not > > responding to simple resampling commands (such as mri_convert or > > 3dresample). The resulting file from utilizing these commands > "works" > > in the sense that it puts them in the proper orientation, but > the ROIs > > are still way out of whack, somehow. > > > > Thus, I would like to try utilizing recon-all to get these ROIs > (which > > correspond to MNI152-2mm) into the standard space I'm utilizing > > (Freesurfer-defined MNI305, based on the subjects' talairach.m3z > > file). However, I have no idea how to do this. Could I have some > > general guidance on the steps and options for recon-all that would > > accomplish this? > > > > I have some additional information about the ROIs below. > > > > *_This is the 3dinfo output for the ROIs (in this case, > > anterior-salience)_* > > Template Space: TLRC > > Dataset Type: Anat Bucket (-abuc) > > Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST] > > Storage Mode: NIFTI > > Storage Space: 3,610,516 (3.6 million [mega]) bytes > > Geometry String: "MATRIX(2,0,0,-90,0,-2,0,126,0,0,2,-72):91,109,91" > > Data Axes Tilt: Plumb > > Data Axes Orientation: > > first (x) = Right-to-Left > > second (y) = Posterior-to-Anterior > > third (z) = Inferior-to-Superior [-orient RPI] > > R-to-L extent: -90.000 [R] -to- 90.000 [L] -step- 2.000 > mm [ > > 91 voxels] > > A-to-P extent: -90.000 [A] -to- 126.000 [P] -step- 2.000 mm > > [109 voxels] > > I-to-S extent: -72.000 [I] -to- 108.000 [S] -step- 2.000 > mm [ > > 91 voxels] > > > > > > Thanks! > > -- > > Paul Beach > > DO/PhD candidate - Year VI > > Michigan State University > > - College of Osteopathic Medicine > > - Neuroscience Program > > - Bozoki Lab: Neurology/Radiology > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel: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 > 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/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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. > > > > > -- > Paul Beach > DO/PhD candidate - Year VI > Michigan State University > - College of Osteopathic Medicine > - Neuroscience Program > - Bozoki Lab: Neurology/Radiology -- 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/

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Re: [Freesurfer] Longitudinal Freesurfer & TRACULA quality control
by Anastasia Yendiki 21 Oct '13

21 Oct '13

Hi Vincent, 3. It's a pain, isn't it? I sympathize but looking at the data is always a good idea. Since you'll see all 3 views in fslview, the dark slices will look like dark lines in two of these views, so you don't have to scroll through slices. There's a couple of things you can do about motion, for example you can remove the DWI volumes that have the artifacts. But you'll have to make sure you're not doing this more for one group than the other. 2. What I usually look at is dlabel/diff/aparc+aseg.bbr.nii.gz, overlaid on dmri/dtifit_FA.nii.gz. And yes, I do this for all subjects and yes, it takes a while. Listening to music helps. Let me know if you have more questions! a.y On Mon, 14 Oct 2013, Vincent Brunsch wrote: > Hi Anastasia! > > I will go backwards with increasing difficulty to understand everything: > > 4. I see, yes this would not make sense. Thank you for the explanation! > > 3. With fslview I will have to run through 393,120 slices, then. (72 slices > in z-direction for our 70 DWI scans for tp1 and tp2 for each of our 39 > subjects) I will go dwi image by dwi image running through the 72 slices > rather fast. Just to make sure I am not wasting a lot of time: is this what I > should do? If I detect slices that are much darker than their neighbors, will > I need to exclude this subject for the analysis or can I do something about > it? > > 2. Yes, I use bbregister and I also use the anatomical T1 weighted scan to > extract the brain mask (usemaskanat=1). To make sure that everything is > alright, I would go slice by slice in tkmedit with > tkmedit [subject] brainmask.mgz -surfs -aparc+aseg where [subject] would be > the base AND both longitudinal runs. I understand that I need to check if > white matter is where it should be, if the cortical and pial surfaces are > where they should be and if the labelling is correct. Again, as this will > take probably even longer than 3. I would like to make sure this is the right > thing to do before starting the quality check. > > Thanks again! > Vincent > > > > Am 10/11/2013 2:13 PM, schrieb Anastasia Yendiki: >> >> Hi Vincent - I'll take on the tracula-related parts: >> >> 2. For tracula, the part of the recon-all output that matters is the >> aparc+aseg. The surfaces will play a role only the DWI-to-T1 registration >> (assuming you opt to use bbregister). >> >> 3. It's important to check your DWI data for obvious motion artifacts, >> (slices that are much darker than their neighbors). Right now this has to >> be done visually, but it's on my list to produce some motion metrics as >> part of the preprocessing. >> >> 4. The ball-and-stick model (that bedpostx fits to your data) is used by >> the tractography algorithm in tracula, but there are no stats produced on >> the parameters of that model currently. That's something that can be added >> in the future as well. Note though that it wouldn't make sense to just >> average f1 or f2 over the pathway, because compartment 1 in one voxel may >> correspond to compartment 2 in some other voxel. >> >> Hope this helps, >> a.y >> >> On Fri, 11 Oct 2013, vbrunsch(a)nmr.mgh.harvard.edu wrote: >> >>> Dear Freesurfer experts, >>> >>> I want to do a quality check on our imaging data. I used the longitudinal >>> stream for SBA and as the first step for the longitudinal white matter >>> analysis with TRACULA. >>> We had two time points in our study and thus, in the freesurfer output >>> directory there are 5 folders per subject (2 cross-sectional runs, 2 long >>> runs and the base). >>> >>> 1. Would you recommend to use (all of) the QA_TOOLS on all of these 5 >>> folders per subject for the SBA? >>> 2. Independent of the previous question, for the longitudinal version of >>> TRACULA would you recommend to use (all of) the QA_TOOLS on the freesurfer >>> base folder only / additional folders? >>> 3. In addition to the late visual check for well reconstructed pathways >>> with freeview, is there another automated possibility to check the quality >>> of the diffusion weighted images beforehand/do you think this is >>> necessary? >>> >>> 4. On another note: If I understand correctly, in TRACULA bedpostX is used >>> to reconstruct the pathways but then the mean over the voxels that were >>> hit (by the MCMC sampling of the paths) of measures from the tensor model >>> are taken as outputs. I wonder, is there also the possibility of using the >>> partial volumes f1, f2,.. as output measures? >>> >>> Best, >>> Vincent >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> > > >

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running recon-all for FSL-based ROIs
by Paul Beach 21 Oct '13

21 Oct '13

Hello FS experts, I am interested in utilizing the functional ROIs made by the Greicius lab out of Stanford (found here<http://findlab.stanford.edu/functional_ROIs.html>). However, these ROIs were made using FSL and the coordinate system for them is not responding to simple resampling commands (such as mri_convert or 3dresample). The resulting file from utilizing these commands "works" in the sense that it puts them in the proper orientation, but the ROIs are still way out of whack, somehow. Thus, I would like to try utilizing recon-all to get these ROIs (which correspond to MNI152-2mm) into the standard space I'm utilizing (Freesurfer-defined MNI305, based on the subjects' talairach.m3z file). However, I have no idea how to do this. Could I have some general guidance on the steps and options for recon-all that would accomplish this? I have some additional information about the ROIs below. *This is the 3dinfo output for the ROIs (in this case, anterior-salience)* Template Space: TLRC Dataset Type: Anat Bucket (-abuc) Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST] Storage Mode: NIFTI Storage Space: 3,610,516 (3.6 million [mega]) bytes Geometry String: "MATRIX(2,0,0,-90,0,-2,0,126,0,0,2,-72):91,109,91" Data Axes Tilt: Plumb Data Axes Orientation: first (x) = Right-to-Left second (y) = Posterior-to-Anterior third (z) = Inferior-to-Superior [-orient RPI] R-to-L extent: -90.000 [R] -to- 90.000 [L] -step- 2.000 mm [ 91 voxels] A-to-P extent: -90.000 [A] -to- 126.000 [P] -step- 2.000 mm [109 voxels] I-to-S extent: -72.000 [I] -to- 108.000 [S] -step- 2.000 mm [ 91 voxels] Thanks! -- Paul Beach DO/PhD candidate - Year VI Michigan State University - College of Osteopathic Medicine - Neuroscience Program - Bozoki Lab: Neurology/Radiology

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