Freesurfer

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30099 discussions

Determining problems for subjects using recon-all.log
by Vy Dinh 28 Jul '14

28 Jul '14

Dear Freesurfer develops, I'm having issues running recon-all -all on 2 of our subjects using the raw t1.nii file. According to their recon-all log, both subjects' recon-all -all command errs when encountering the mris_sphere step. I'm not sure how to address this problem, considering we have no known issues with these subject's data for our other data processing (VBM, etc). Any help will be much appreciated. Please not that I've attached recon-all.logs for both subjects. Thank you. Best, -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health

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preserve manual edits?
by Jason Tourville 28 Jul '14

28 Jul '14

Hi there, We have performed manual volume edits on a number of scans. Recently, we ran those scans through recon-all with a new Tal volume target. The seg and surfaces are improved using the new target but most of the manual edits performed on the earlier version would improve the surfaces. Is there an established means for porting the manually edited voxel values to the volumes of the new re-con? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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Cerebellum white matter mask {Disarmed}
by Alshikho, Mohamad J. 28 Jul '14

28 Jul '14

Hi Fs expers, What is the best way in Freesurfer to create a mask for the cerebellum white matter from the output of T1 segmentation? Thanks mohamad

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QDEC error and analysis termination during 'concatenating volumes'
by Isotalus, Hanna 28 Jul '14

28 Jul '14

Dear FreeSurfer gurus, I am using QDEC to run my analyses on a large data set. The analysis works fine with up to 1224 subjects but as soon as I add subject 1225 I get an error and the analysis stops. The error displays during 'concatenating volumes' and it just displays file names. When I try to run the analysis on the remaining subjects (around 360 of them) the analysis runs fine - so I am inclined to think there's nothing wrong with the data files. I've tried rotating the order of subjects and it just doesn't seem to allow me to run the analysis on all of them. Do you have any suggestions? Here's a link to a screenshot of the error I get: https://www.dropbox.com/s/08pqnmgep6crmr5/error%20message.gif I can't actually see all of the error message, here's it from the beginning of what I can see and it continues like that - displaying all file names I think. Thank you and best wishes, ?

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Converting volume to label
by Weiss, Sarah 28 Jul '14

28 Jul '14

Dear Freesurfer experts, We are trying to convert a volume created in SPM and saved as a .nii file into a label to overlay on a Freesurfer surface. We are using a template surface found online, colin (http://mindboggle.info/data.html) We are able to display our .nii in freeview successfully. The voxels that we wish to label have a value of 1, and elsewhere in the file the value is 0. The command that we are running is: mri_cor2label --i cluster3_roi.nii --l ./cluster3_roi.label --id 1 We do get a series of points as output. However, when we load the consequent label, it doesn't display correctly - the points are discontinuous, and don't correspond to the correct parts of the brain. Here are some of the error messages that we get: ltMNIreadEx: could not open file /Applications/freesurfer/subjects/rk/mri/transforms/talairach.xfm No such file or directory MRISreadVertexPosition(/Applications/freesurfer/subjects/rk/surf/rh.orig): could not open file /Applications/freesurfer/subjects/rk/surf/rh.orig No such file or directory MRISreadOriginalProperties: could not read surface file /Applications/freesurfer/subjects/rk/surf/rh.orig No such file or directory ******************** 0 nonzero vertices found ******************** label stat field identically zero - setting to 1 9389 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... Why does it say that 0 nonzero vertices have been found, yet it selects 9389 vertices? Is there an additional option that we should be utilizing? Is a label the correct way to create what we are looking for, or would an overlay be more appropriate? If the latter is the case, should we be using mri_vol2surf? Thank you in advance for your assistance! Best, Sarah Weiss and Robert Kim

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Permutation testing in freesurfer
by O'Shea,Andrew 28 Jul '14

28 Jul '14

Hello all, Does anyone know of a toolbox/script that would automate permutation testing in freesurfer? For example running x number of random permutations of a covariate and recording max sig levels similar to what the software SnPM does for SPM analyses? Thanks. -Andrew

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LocalGI error
by Sarina Iwabuchi 28 Jul '14

28 Jul '14

Hi all, I have been trying to run localGI and have been coming across errors. It creates the filled.mgz file and opens matlab (running 2012a) but crashes straight after with the below errors: >> reading filled volume... set: Variable name must begin with a letter. gunzip: Command not found. ERROR: problem reading fname set: Variable name must begin with a letter. rm: Command not found. SWITCH expression must be a scalar or string constant. Error in load_mgh (line 158) switch type Error in MRIread (line 87) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly); Error in make_outer_surface (line 24) vol=MRIread(filled_volume); Has anyone come across this? I do have gunzip on my system. Thanks very much, Sarina Iwabuchi Division of Psychiatry and Applied Psychology Room B07 Institute of Mental Health Triumph Road University of Nottingham Nottingham NG7 2TU This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Freesurfer ROI analysis
by Silas 28 Jul '14

28 Jul '14

Hi Freesurfer, I'm currently making a structural analysis on about 60 Parkinson's Disease patients using freesurfer - and i would like to make a ROI analysis. I have two MR pictures of each subject; a picture where the patients are on medication and an off medication picture (the medication is levodopa: Precursor to catecholamines e.g. dopamin). I would like to investigate the morphological differences in specific areas of the brain such as Nucleus Accumbens bilat., Orbitofrontal cortex bilat. and Anterior Cingulate Cortex. How would you consider freesurfer's strength in investigating differences in such specific areas in the brain? I have another question regarding movement artefacts. In a structural analysis would you remove pictures with movement artefacts if the segmentation after manual editing seems alright? Best,Silas

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Re: [Freesurfer] wm.mgz
by Xiaomin Yue 25 Jul '14

25 Jul '14

Thanks. I will replace 0 with 1. Xiaomin ________________________________ From: Bruce Fischl<mailto:fischl@nmr.mgh.harvard.edu> Sent: ‎7/‎25/‎2014 9:43 PM To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] wm.mgz Yes, they won't be preserved unless they are 1 > On Jul 25, 2014, at 9:33 PM, Xiaomin Yue <yuexm(a)hotmail.com> wrote: > > It is 5.3. The voxels erased was set as 0. Is that the problem? If so, I can try to replace 0 with 1. > > Xiaomin > From: Bruce Fischl > Sent: ‎7/‎25/‎2014 9:22 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] wm.mgz > > What version? Check the voxels you erased and see if they were set to 1 instead of 0 > > On Jul 25, 2014, at 8:39 PM, Xiaomin Yue <yuexm(a)hotmail.com> wrote: > >> Hi Bruce, >> >> Thanks for your response. the editing was done in freeview. I saved the edited version as wm.edited.mgz, then copy the wm.edited.mgz to wm.mgz. is that the problem? Is it necessary to save the edited wm.mgz as wm.mgz in freeview? I hope it is clear what I did. >> >> Thanks, >> Xiaomin >> >> From: Bruce Fischl >> Sent: ‎Friday‎, ‎July‎ ‎25‎, ‎2014 ‎8‎:‎36‎ ‎PM >> To: Freesurfer support list >> >> Hi Xiaomin >> >> how did you edit wm.mgz? If within tkmedit (or "recon editing" in freeview) >> and you reran recon-all it should have preserved your edits, even though it >> regenerated the file. Have you checked? >> >> Bruce >> >> >> On Fri, 25 Jul 2014, Xiaomin Yue wrote: >> >> > Hi, >> > >> > My edited wm.mgz was saved as wm.edited.mgz, then it copied to wm.mgz. I re-run the anlysis using >> > recon-all -s cologna -autorecon2-wm. From some reason, the analysis regenerated wm.mgz from brain.mgz, >> > which of course replaced my edited wm.mgz. Did I do some wrong here? >> > >> > Thanks, >> > Xiaomin >> > >> > >> _______________________________________________ >> 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 _______________________________________________ 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] wm.mgz
by Xiaomin Yue 25 Jul '14

25 Jul '14

It is 5.3. The voxels erased was set as 0. Is that the problem? If so, I can try to replace 0 with 1. Xiaomin ________________________________ From: Bruce Fischl<mailto:fischl@nmr.mgh.harvard.edu> Sent: ‎7/‎25/‎2014 9:22 PM To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] wm.mgz What version? Check the voxels you erased and see if they were set to 1 instead of 0 > On Jul 25, 2014, at 8:39 PM, Xiaomin Yue <yuexm(a)hotmail.com> wrote: > > Hi Bruce, > > Thanks for your response. the editing was done in freeview. I saved the edited version as wm.edited.mgz, then copy the wm.edited.mgz to wm.mgz. is that the problem? Is it necessary to save the edited wm.mgz as wm.mgz in freeview? I hope it is clear what I did. > > Thanks, > Xiaomin > > From: Bruce Fischl > Sent: ‎Friday‎, ‎July‎ ‎25‎, ‎2014 ‎8‎:‎36‎ ‎PM > To: Freesurfer support list > > Hi Xiaomin > > how did you edit wm.mgz? If within tkmedit (or "recon editing" in freeview) > and you reran recon-all it should have preserved your edits, even though it > regenerated the file. Have you checked? > > Bruce > > > On Fri, 25 Jul 2014, Xiaomin Yue wrote: > > > Hi, > > > > My edited wm.mgz was saved as wm.edited.mgz, then it copied to wm.mgz. I re-run the anlysis using > > recon-all -s cologna -autorecon2-wm. From some reason, the analysis regenerated wm.mgz from brain.mgz, > > which of course replaced my edited wm.mgz. Did I do some wrong here? > > > > Thanks, > > Xiaomin > > > > > _______________________________________________ > 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.

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