Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

Qdec: regression with different numbers of variables
by ye tian 03 Sep '13

03 Sep '13

Dear Freesurfers, I am studying cortical thickness as a function of age (continuous) and meditation practice (categorical, level1=Normal, level2=TM). I have three separate cases of qdec, regression1, regression2 and regression3. Regression1: Discrete (Fixed Factor) = meditation; Continuous (Covariate) = age Regression2: Discrete (Fixed Factor) = meditation; Regression3: Discrete (Fixed Factor) = meditation; Nuisance Factor = age For the question "Does the average thickness differ between Normal and TM?", Regression1 and Regression3 have identical result, which is different from Regression2, i.e., (1 = 3 !=2 ). May I infer from this result the following about qdec: 1) Regression1 and Regression3 both fit cortical thickness,y, to the model y = b0 + age*b1 + meditation*b2 + err = y_hat + err Regression2 fits: y = b0 + b2*meditation + err = y_hat + err 2) Some function of y_hat goes into the "average thickness", hence the difference between 2 and the others. However, what role does "Nuisance Factor" play in this case? Thank you very much! Sincerely, Ye

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what is the minimum information needed to create a custom template?
by David Romano 03 Sep '13

03 Sep '13

Hi everyone, If I only have lh.sphere and lh.sulc files for each of collection of subjects, would this be enough information to generate a template for registering further subjects? I was thinking of trying to follow the workflow described on the page: https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates (in the section titled "Creating a registration template from scratch (GW)"), but wasn't sure whether more than just native spherical coordinates and convexity information would be implicitly required by the mris_make_template command. (The "Positional Arguments" table that appears on the page: https://surfer.nmr.mgh.harvard.edu/fswiki/mris_make_template only asks explicitly for references to the hemisphere data for a collection of subjects.) Thanks in advance for you help, David Romano (P.S. There's also appers to be a typo in the "Positional Arguments" table I mentioned above: In the description section for position 2, the {hemi} and {sphere_name} values seem to be reversed.)

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Qdec: does the average thickness differ from zero?
by ye tian 03 Sep '13

03 Sep '13

Dear freesurfers, When I look at the statistical map for the average thickness, there are regions where thickness is "statistically zero" (null hypothesis kept). Does this indicate error in manual editing? Thank you very much! Sincerely, Ye

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Fwd: How to smoothing area with mri_surf2surf?
by fatma zribi 03 Sep '13

03 Sep '13

---------- Forwarded message ---------- From: fatma zribi <zribi.fatma(a)gmail.com> Date: 2013/9/3 Subject: How to smoothing area with mri_surf2surf? To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Dear Bruce, Would you mind help me. I would like to smooth area surface with the command mri_surf2surf. I have done this instruction: mri_surf2surf --hemi lh --s s089_open_brain_sanlm_+TIR_normlalized --sval-area area --fwhm 15 --trgsubject avg_surfacique_all_database_SD --tval lh.area.15.mgh --cortex srcsubject = s089_open_brain_sanlm_+TIR_normlalized srcval = (null) srctype = trgsubject = avg_surfacique_all_database_SD trgval = lh.area.15.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 15 label-src = (null) label-trg = lh.cortex.label OKToRevFaceOrder = 1 Reading source surface reg /Copie5/s089_open_brain_sanlm_+TIR_normlalized/surf/lh.sphere.reg Loading source data Reading surface file /Copie5/s089_open_brain_sanlm_+TIR_normlalized/surf/lh.area nquads=4718596, nvertices=513 ERROR: MRISread: file '/Copie5/s089_open_brain_sanlm_+TIR_normlalized/surf/lh.area' has many more faces than vertices! Probably trying to use a scalar data file as a surface! No such file or directory. With best regards, Fatma

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Extracting Brodmann Area LGI values
by Alan Francis 03 Sep '13

03 Sep '13

Hi FreeSurfer folks: I am trying to extract LGI values from Brodmann Areas 44 and 45. I am using the following script. Unfortunately it gives me an error message. Could you please help me. aparcstats2table --skip -s /HM0403 /HM0503 /HM0603 /HM0703 /HM0903 /HM1003 /HM1103 /HM1203 /HM1303 /HM1403 /HM1703 /HM1903 /HM2003 /HM2103 /HM2203 /HM2303 /HM2403 /HM2503 /HM2803 /HM2903 /HM3003 /HM3103 /HM3202 /HM3203 /HM3303 /HM3403 /HM3503 /HM3603 /HM3703 /HM3903 /HM4003 /HM4203 /HM4303 /HM4403 /HM4503 /HM4603 /HM4703 /HM4803 /HM4903 /HM5103 /HM5203 /HM5303 /HM5403 /HM5503 /HM5603 /HM5703 /HM5903 /HM6003 /HM6103 /HM6203 /HM6303 /HM6403 /HM6503 /HM6603 /HM6703 /HM6803 /HM6903 /HM7003 /HM7103 /HM7203 /HM7303 /HM7403 /HM7503 /HM7603 /HM7703 /HM7903 /HM8003 /HM8103 /HM8203 /HM8303 /HM8403 /HM8503 /HM8603 /HM8703 /HM8803 /HM8903 /HM9003 --hemi lh --parc=BA --meas foldind --tablefile BA44 BA45 -lh.BA.stats --subjectsfile=BA_LGI.txt thanks so much, Alan Francis

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Announcing Release of PySurfer 0.4
by Eric Larson 03 Sep '13

03 Sep '13

Dear All, We are pleased to announce the 0.4 release of PySurfer, a Python-based package for visualizing Freesurfer data. This release includes bugfixes and multiple enhancements, including: - Displaying data from both hemispheres simultaneously - Displaying multiple views simultaneously - Toggling Mayavi toolbars - Using nibabel for IO functions - A variety of minor improvements here and there Please see our website (http://pysurfer.github.com/) for information on installation, documentation, and the example gallery. We hope you find it useful in your research! Eric Larson, Michael Waskom, Alexandre Gramfort, and the Nipy team

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Re: [Freesurfer] error in MRI processing
by Boric, Katica A. 03 Sep '13

03 Sep '13

this: drwxr-xr-x. 7 root root 4096 Oct 23 2012 /usr/local/freesurfer/subjects/fsaverage ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Friday, August 30, 2013 11:15 AM To: Boric, Katica A. Subject: Re: [Freesurfer] error in MRI processing how about: ls -ald $FREESURFER_HOME/subjects/fsaverage On Fri, 30 Aug 2013, Boric, Katica A. wrote: > This comes out: > drwxrwxrwx. 1 root root 0 Aug 29 11:10 /mnt/hgfs/Linux_Share/subjects > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Friday, August 30, 2013 11:11 AM > To: Boric, Katica A. > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] error in MRI processing > > that probably means you don't have write access to the subject directory. > Can you run: > > ls -ald /mnt/hgfs/Linux_Share/subjects > > On Fri, 30 Aug 2013, Boric, Katica A. > wrote: > >> It says: >> $ ln -s /usr/local/freesurfer/subjects/fsaverage >> ln: failed to create symbolic link `./fsaverage': Operation not supported >> >> ________________________________________ >> From: freesurfer-bounces(a)nmr.mgh.harvard.edu >> [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Bruce Fischl >> [fischl(a)nmr.mgh.harvard.edu] >> Sent: Friday, August 30, 2013 11:04 AM >> To: Boric, Katica A. >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] error in MRI processing >> >> can you run: >> >> cd /mnt/hgfs/Linux_Share/subjects >> ln -s /usr/local/freesurfer/subjects/fsaverage >> >> and tell us what it says? >> Bruce >> On Fri, 30 Aug 2013, Boric, >> Katica A. >> wrote: >> >>> Hi Bruce! >>> Thanks for your fast response. >>> /usr/local/freesurfer/subjects/fsaverage does exists! >>> >>> Thanks again, >>> Katica >>> ________________________________________ >>> From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] >>> Sent: Friday, August 30, 2013 10:51 AM >>> To: Boric, Katica A. >>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] error in MRI processing >>> >>> Hi Katica >>> >>> does /usr/local/freesurfer/subjects/fsaverage exist? Do you have write >>> access to /mnt/hgfs/Linux_Share/subjects? >>> >>> cheers >>> Bruce >>> >>> On Fri, 30 Aug 2013, Boric, Katica A. wrote: >>> >>>> Hi everyone! >>>> I am new to freesurfer, and I was processing and MRI using "recon-all >>>> -autorecon1 -autorecon2 -autorecon3" command and I have a message that >> the >>>> processing was exited with ERRORS. When checking the recon-all. log it >>>> appears that these are the error (highlighted in yellow): >>>> >>>> #@# BA Labels lh Thu Aug 29 22:14:42 PDT 2013 >>>> INFO: fsaverage subject does not exist in SUBJECTS_DIR >>>> INFO: Creating symlink to fsaverage subject... >>>> >>>> cd /mnt/hgfs/Linux_Share/subjects; ln -s >>>> /usr/local/freesurfer/subjects/fsaverage; cd - >>>> >>>> ln: failed to create symbolic link `./fsaverage': Operation not supported >>>> >>>> mri_label2label --srcsubject fsaverage --srclabel >>>> /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label --trgsubject >>>> MGH013_SurferOutput --trglabel ./lh.BA1.label --hemi lh --regmethod >> surface >>>> >>>> No such file or directory >>>> mri_label2label: could not open label file >>>> /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label >>>> >>>> srclabel = /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label >>>> srcsubject = fsaverage >>>> trgsubject = MGH013_SurferOutput >>>> trglabel = ./lh.BA1.label >>>> regmethod = surface >>>> >>>> srchemi = lh >>>> trghemi = lh >>>> trgsurface = white >>>> srcsurfreg = sphere.reg >>>> trgsurfreg = sphere.reg >>>> usehash = 1 >>>> Use ProjAbs = 0, 0 >>>> Use ProjFrac = 0, 0 >>>> DoPaint 0 >>>> >>>> SUBJECTS_DIR /mnt/hgfs/Linux_Share/subjects >>>> FREESURFER_HOME /usr/local/freesurfer >>>> Loading source label. >>>> Invalid argument >>>> ERROR reading /mnt/hgfs/Linux_Share/subjects/fsaverage/label/lh.BA1.label >>>> Linux localhost.localdomain 3.6.11-4.fc16.x86_64 #1 SMP Tue Jan 8 >> 20:57:42 >>>> UTC 2013 x86_64 x86_64 x86_64 GNU/Linux >>>> >>>> recon-all -s MGH013_SurferOutput exited with ERRORS at Thu Aug 29 >> 22:14:43 >>>> PDT 2013 >>>> >>>> If any of you could give us any advice on how to fix this we would really >>>> appreciate it! >>>> Thank you very much, >>>> >>>> Cheers, >>>> Katica >>>> >>>> >>>> >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Fixing incorrect segmentation and pial surface
by Brenna Day 03 Sep '13

03 Sep '13

Hi, I have a file where the pial surface is excluding some of the gray matter. I edited wm.mgz and added control points to brainmask.mgz, this fixed some of the pial surface errors but not all. After looking at the aseg closer there is a section of incorrectly labeled wm near the pial surface errors. Voxels which look like they should be labeled at wm are labeled as left-putamen in the aseg. Is there a way to fix this other than manual edits to the aseg? I'm using v5.0.0 and the aim is to run mri_segstats with the segmented brain and a matched PIB scan, so I do need the segmentation and the pial surface to be quite correct. I've attached some screenshots of the problematic area, it runs through coronal slices 96-106 and 118-124. Thanks for any help you can give. Regards, Brenna [image: Inline image 1][image: Inline image 2][image: Inline image 3]

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FW: No brain tissue after recon-all all
by pablo najt 03 Sep '13

03 Sep '13

Hi Doug, Thank you very much for your output about my output files. Yes, I understand that these images are skull stripped. But since there are possibilities of error in the skull stripping process I was concern about extra no brain tissue being included in the output. I think the location of the tissue I was referring was mistaken. To make it clearer I have circled (in red) the specific area in the images attached I have concerns about not being brain tissue. I noticed that this repeats in several other of my subjects and I wanted to make sure it is fine. Best,Pablo > Date: Tue, 3 Sep 2013 09:50:06 -0400 > From: greve(a)nmr.mgh.harvard.edu > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] No brain tissue after recon-all all > > > Hi Pablo, this is a skull stripped image. In the human brain there is no > brain tissue ventral to the orbital frontal areaso any tissue there has > been stripped away. > doug > > > On 09/02/2013 12:49 AM, pablo najt wrote: > > > > Dear FS experts, > > I have a doubt about a potential registration problem after running > > recon-all -all. I noticed that one of the image outcome when opened > > with tkmedit shows no-brain tissue (perhaps eye tracts) ventral to > > orbitofrontal areas. I have attached snapshots to illustrate the image. > > I would greatly appreciate your output on this since I have no > > experience with FS and I am not sure what to expect. I would like to > > enquire whether I should be concerned about this image or if this is > > not a problem. > > > > Many thanks, > > Pablo > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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 > 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/ > > _______________________________________________ > 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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trying to understand mri_surf2surf
by David Romano 03 Sep '13

03 Sep '13

Hi everyone, In an earlier post, I had asked how to transform the white surface of one subject to the white surface of another subject, and Bruce Fischl suggested mri_surf2surf should be able to do this. After looking over the website material related to mri_surf2surf, I find I'm not sure how mri_surf2surf works, and so am still not sure how to proceed. As a starting point, suppose we have the file lh.sphere.reg for each of two subjects, A and B, and consider, say, vertex 1 of subject A. Here is what I understand: This vertex maps to a point P on the sphere that has coordinates given in subjects A's lh.sphere.reg file. The point P is contained in some closed triangle T from B's mesh, as that mesh appears in B's lh.sphere.reg file. This triangle is formed from three points on the sphere that correspond to three vertices that appear in B's lh.white file. These three vertices thus form a triangle T' in B's native volume space, and thus the point P contained in T corresponds to a point P' in B's native volume space that is contained in T'. So here is my question: How would I used mri_surf2surf to find the coordinates (in B's native volume space) of the point P'? Thanks in advance for you help in clarifying this for me. Best regards, David Romano

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