Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

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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Re: [Freesurfer] Problem in final analysis
by Douglas N Greve 21 Oct '13

21 Oct '13

fsaverage is already part of the distribution. I don't understand from your email what the problem is. doug On 10/21/2013 10:03 AM, carina(a)van-vlodrop.de wrote: > > Hi Doug, > > > I have already run: > > > recon-all -s subject -qcache -target avgsubject for each subject > > > Is it the same file? > > I am not sure if the brain is really created or if there is a problem > in uploading the brain in qdec. > > Is it possible to get the fsaverage brain from freesurfer to check the > cause of the problem? > > > Thank you > > Carina > > > > > >> ----- Ursprüngliche Nachricht ----- >> Von: Douglas Greve >> Gesendet: 28.09.13 17:46 Uhr >> An: freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: [Freesurfer] Problem in final analysis >> >> Hi Carina, run >> >> recon-all -s subject -qcache >> >> for each subject and this will create the file >> >> doug >> >> >> >> >> >> On 9/28/13 5:37 AM, carina(a)van-vlodrop.de wrote: >> >> Dear freesurfer community, we are conducting cortical-thickness >> analysis using freesurfer-4.4.0 and have been experiencing some >> problems with the final analysis steps. We are using the qdec. >> Uploading of the data table has been successful. When we try to >> use the “Analyze” command (design) in the qdec, we get the >> following error message: Error in Analyze: Couldn’t open file >> /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thickness.fwhm10.fsaverage.mgh >> Obviously, the file was never created during preprocessing. We >> wonder, how to create dir/lh.thickness.fwhm10.fsaverage.mgh and >> would be very grateful for your comments. Yours sincerely, Carina >> $ bugr FREESURFER_HOME: /apps/prod/i486/freesurfer-4.4.0 Build >> stamp: freesurfer-Linux-centos4-stable-pub-v4.4.0 Debian version: >> 5.0.6 Kernel info: Linux 2.6.27.39- 1 –ql-beowulf i686 $ which >> surfer -> /apps/prod/i486/freesurfer-4.4.0/bin/freesurfer Used >> command: qdec/design/Analyze Error message: Error in Analyze: >> Couldn’t open file >> /data/projects/oertelmatura/Neurodegeneration/AJ83/surf/lh.thikness.fwhm10.fsaverage.mgh >> >> >> >> _______________________________________________ Freesurfer >> mailing list Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > > _______________________________________________ > 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/

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Tcsh-error with Freesurfer
by Philippe Blaes 21 Oct '13

21 Oct '13

Dear Sir / madam, I'm a last year student of Medical Imaging (from Hoge school Universiteit Brussel, HUB). In January i'm defending my thesis. My subject is MRI and Alzheimer's disease. With volumetry I want to show that the Hippocampi have a smaller volume then normal patients. I used the program: SPM, VBM and IBASPM previous year, but I got weird results from those software. My supervisors said that it's probably the best to use a new software, so i'm trying to use Freesurfer. I'm not used to programming with Linux (Xbuntu), so it's a bit difficult for me personally. Also the physicist (who i colaborate with) isn't used to programming. This is my problem: When i open Virtualbox (installed with freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full) I go to file-system -> usr -> local -> freesurfer -> subjects (the map where also the subject"Bert" is in it). In the subject-folder is paste a folder with only T1-Dicom images. After i copied & pasted the DICOM-files in the subjects folder, i go to the "terminal". There I type: "tcsh" to setup freesurfer (I read it on the Freesurfer wiki site). After that I type: recon-all -s <new folder where the new made files are putted in> \ -i $SUBJECTS_DIR/<name of the folder where my DICOM-files are in (here i made an archive of the DICOM-files, extented with .mgz) > \ -autorecon1 When i hit Enter, i get a message that says: "tcsh v6.17.06 has an exit code bug! Please update tcsh!" There is also a new folder created, with some subfolders (BEM, label, scripts , MRI ,etc.). But there is nothing to see in those folders. My question is how can I update tcsh so I can do the recon-all procedure? Hopefully you can help me, Thank you in advance, Kind regards, Philippe Blaes (3rd year Medical Imaging)

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Maybe wrong registration
by Vicente Cutanda 21 Oct '13

21 Oct '13

Hello to everybody, I made a script to extract some structures from a T1 image. The code extract precentral and paracentral gyrus, putamen, nucleus caudate and accumbens. First of all convert from annotation to label, after that I used tkregister (maybe this can be the focus of the problem) to get the coordenates of my T1, finally extract areas with mri_label2vol, mri_convert and fslmaths. I paste the script below: mri_annotation2label --subject ${suje} --hemi lh --outdir $FREESURFER_HOME/subjects/${suje}/annot_labels/ mri_annotation2label --subject ${suje} --hemi rh --outdir $FREESURFER_HOME/subjects/${suje}/annot_labels/ #despues tenemos q calcular la matriz para pasar de freesurfer a espacio .nii tkregister2 --mov ${pathT1}${t1} --noedit --s ${suje} --regheader --reg ${path}register.dat cd ${path} #extraemos aqui precentral i paracentral mri_label2vol --label $FREESURFER_HOME/subjects/${suje}/annot_labels/lh.precentral.label --reg ${path}register.dat --temp ${pathT1}${t1} --subject ${suje} --hemi lh --o l_precent.nii --proj frac 0 1 .1 --fillthresh 0 mri_label2vol --label $FREESURFER_HOME/subjects/${suje}/annot_labels/rh.precentral.label --reg ${path}register.dat --temp ${pathT1}${t1} --subject ${suje} --hemi rh --o r_precent.nii --proj frac 0 1 .1 --fillthresh 0 mri_label2vol --label $FREESURFER_HOME/subjects/${suje}/annot_labels/lh.paracentral.label --reg ${path}register.dat --temp ${pathT1}${t1} --subject ${suje} --hemi lh --o l_paracent.nii --proj frac 0 1 .1 --fillthresh 0 mri_label2vol --label $FREESURFER_HOME/subjects/${suje}/annot_labels/rh.paracentral.label --reg ${path}register.dat --temp ${pathT1}${t1} --subject ${suje} --hemi rh --o r_paracent.nii --proj frac 0 1 .1 --fillthresh 0 mri_convert -rl $FREESURFER_HOME/subjects/${suje}/mri/rawavg.mgz -rt nearest $FREESURFER_HOME/subjects/${suje}/mri/aseg.mgz ${path}aseg.nii #we need to know the codes, caudate is 11 y 50; fslmaths aseg.nii -uthr 11 -thr 11 l_caud.nii fslmaths aseg.nii -uthr 50 -thr 50 r_caud.nii Thanks Vic

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Accuracy
by Vicente Cutanda 21 Oct '13

21 Oct '13

Hello, After run the recon-all instruction, I wanted to extract the paracentral and precentral gyrus in a accurate way. Does anyone knows how can I get extract these areas? Thank you Vicente

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