Freesurfer August 2013

freesurfer@nmr.mgh.harvard.edu

145 participants
268 discussions

make_average_subject without aparc and talairach.xfm
by Caspar M. Schwiedrzik 18 Sep '13

18 Sep '13

Hi Freesurfer experts, I am trying to make an average surface from several monkey surfaces, and I ran into a problem with make_average_subject. Specifically, I do not have an aparc file nor a talairach.xfm. It seems that these problems have come up on the list before ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15595.html) I tried to download make_average_surface.no-aparc, however, the link seems to be broken. Also, I couldn't find a solution to the missing talairach.xfm on the list. It would be great if you could provide me with a working link to make_average_surface.no-aparc; any suggestions regarding making an average surface without talairach.xfm would be appreciated. I already made a new template and aligned all individual surfaces to this template. Thanks! Caspar

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"Nuisance factors" in Qdec
by ye tian 17 Sep '13

17 Sep '13

Dear Freesurfers, I have a question concerning the "nuisance factors" in the qdec dialogue. Suppose I have two independent variables x1 (discrete) and x2 (continuous), and only one observable y. I choose "Discrete (Fixed factor) = x1", "Continuous (covariate) = x2". If I further chose "Nuisance factor = x2", does that imply that 1) my contrast matrix is (0 1) 2) null hypothesis: Y is independent of x2 Thank you very much! Sincerely, Ye

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Segmentation edits
by krista kelly 09 Sep '13

09 Sep '13

Hi all, I am doing cortical thickness and surface area analyses and had a few questions regarding editing the borders. 1) Is it reasonable to edit every (big and small) error that I find? Basically, how much a difference would it make in terms of the surface area and cortical thickness values if I did not edit the smaller errors? 2) If the skull hasn't been completely stripped, but is not designated as either white or gray matter, do I need to adjust the thresholding for extracting the brain and re-extract? The only situation in which I feel this would be a problem is when doing whole brain analyses. 3) Would it make a difference to the data if I initially ran recon-all using freesurfer version 5.0 and then, after editing the segmentations/labels/skullstripping, reran autorecon 2,or 3 using freesurfer version 5.1? If anyone could answer any or all of these questions that would be great! Krista

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Estimated Total Intra Cranial Vol
by stdp82＠virgilio.it 05 Sep '13

05 Sep '13

Hi list. I'm looking mailing list to find responce to this question. "Estimated Total Intra Cranial Vol" obtained by asegstats2table also included ventricles volume? I'd like to assess the volumetric changes of a subcortical structures. Do you advise me to consider "Estimated Total Intra Cranial Vol" (with or without ventricles?) or, alternatively, subcortical brain volume? Thank you very much, Stefano

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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: 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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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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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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Converting fsaveraged EPI to volume
by Marcel Falkiewicz 03 Sep '13

03 Sep '13

Hello, I would like to perform some Bayesian analyses implemented in SPM, but with the data normalized with FreeSurfer. I would like to merge together surface and subcortal normalized timeseries into a single 4d timeseries in volumetric space, which could be used as an input to spm. I tried using vlrmerge, but it produces only a single volume. One method would be splitting the timeseries for each space into single volumes, using vlrmerge on each triplet and then merging the results. However, this would take enourmous ammout of time. Do you know any quicker workarounds? Thanks in advance, Marcel

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mri_surf2surf to fsaverageX introduces offset
by Franz Liem 03 Sep '13

03 Sep '13

Dear Freesurfers, I tried to map a single subject surface to fsaverageX (for the sake of demonstration lets take fsaverage6). I did the following: mri_surf2surf --hemi lh --srcsubject $s --sval-xyz white --trgsubject fsaverage6 --tval-xyz --tval ./lh.white.ico6 This produces a surface that seems systematically shifted (see figure). Also the newly generated surface does not contain valid geomery information (see mris_info print of lh.white and lh.white.ico6). Is there a way to fix this? Another question: is there a reason why mris_decimate is not included in the freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 build Any help is very much appreciated. Best, Franz mris_info $s/surf/lh.white > SURFACE INFO ======================================== > type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE > num vertices: 118611 > num faces : 237218 > num strips : 0 > surface area: 77595.6 > AvgVtxArea 0.654202 > AvgVtxDist 0.885026 > StdVtxDist 0.251941 > ctr : (-33.3535, -11.9536, 42.7693) > vertex locs : surfaceRAS > talairch.xfm: > 1.045 -0.093 -0.014 1.081; > 0.099 1.095 0.070 -4.263; > 0.010 -0.083 1.290 -41.092; > 0.000 0.000 0.000 1.000; > surfaceRAS to talaraiched surfaceRAS: > 1.045 -0.093 -0.014 1.177; > 0.099 1.095 0.070 13.377; > 0.010 -0.083 1.290 -49.756; > 0.000 0.000 0.000 1.000; > talairached surfaceRAS to surfaceRAS: > 0.949 0.081 0.006 -1.900; > -0.085 0.902 -0.050 -14.449; > -0.013 0.058 0.772 37.650; > 0.000 0.000 0.000 1.000; > volume geometry: > extent : (256, 256, 256) > voxel : ( 1.0000, 1.0000, 1.0000) > x_(ras) : (-1.0000, -0.0000, 0.0000) > y_(ras) : (-0.0000, 0.0000, -1.0000) > z_(ras) : ( 0.0000, 1.0000, -0.0000) > c_(ras) : ( 0.0989, 0.9660, 0.9027) > ... mris_info lh.white.ico6 > SURFACE INFO ======================================== > type : MRIS_TRIANGULAR_SURFACE=MRIS_ICO_SURFACE > num vertices: 40962 > num faces : 81920 > num strips : 0 > surface area: 75477.4 > AvgVtxArea 1.842620 > AvgVtxDist 1.573724 > StdVtxDist 0.523314 > ctr : (-33.3983, -12.0872, 42.7743) > vertex locs : surfaceRAS > volume geometry info is either not contained or not valid. > ...

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Freesurfer August 2013