Freesurfer September 2013

freesurfer@nmr.mgh.harvard.edu

124 participants
243 discussions

recon-all -aseg.stats doubt
by Anupa AV 04 Sep '13

04 Sep '13

Dear FS experts, I'm using freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0 for my analysis. After recon-all with hippo-subfield, only 45 brain volumes were genreated in aseg.stats file. Freesurfer v.5.1 analysis were able to generate cortical structure's volumes also. Where v.5.2 mainly generated subcortical volumes like caudate. putamen, amygdala and so on. MAy I knw, is there any way to generate cortical structures also using recon-all command.. Any help 'll be greatly appreciated.

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QDEC for subcortical segmentation
by ye tian 03 Sep '13

03 Sep '13

Dear freesurfers, Is there a way to visualize glm for volume segments in qdec, i.e., instead of analyzing and visualizing vertices on the surface we analyze and visualize voxels on the volume? For example, I would like to ask whether or not regions of posterior/anterior cingulate shrink/expand with age? Thank you very much! Sincerely, Ye

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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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Freesurfer September 2013