Freesurfer January 2012

freesurfer@nmr.mgh.harvard.edu

97 participants
171 discussions

Tracula - bedpost failure
by Kiely Donnelly 10 Feb '12

10 Feb '12

Hi Everyone -- I've been having difficulty getting Tracula to run smoothly on our cluster. Similar to others on the listserv, the bedpost step was not creating the necessary files causing an error during the -path step. Based on previous posts, I ran bedpostx on the dmri directory. This initially seemed to work (I no longer received the message "1 slice processed" over and over), but for some reason the merged_ph1samples.nii.gz file is still not being created and I continue to run into an error when I run -path. It does create a merged_ph2samples.nii.gz output file. Any help would be greatly appreciated. Thanks, Kiely

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Verifying ICV in FS5
by Jeff Sadino 08 Feb '12

08 Feb '12

Hello, Thank you Nick, Martin, and Doug for your previous feedback about ICV. I have a couple more questions that I am hoping you could clarify for me. To verify my ICV value, some pages on the mailing list and wiki say to use this command: tkregister2 --s subject --fstal --surf Other places say to use this: tkregister2 --xfm talairach.xfm --targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca --mov ../nu_noneck.mgz --reg junk However, on this wiki page (http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV) it says that post fs4.2.0, the template is this file: 711-2C_as_mni_average_305.4dfp.img. In the first tkregister2 command above, doesn't the --fstal flag use the talairach template? But shouldn't it be using the 711 template? And since I am using fs5.0.0, does that mean that I should not be using the RB template? Ultimately, what is the correct way to verify the ICV in fs 5.0.0? Thank you very much, Jeff Sadino On Mon, Mar 1, 2010 at 7:57 AM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: > It's hard to tell from the coronal, but it looks ok. The problem is more > visible in the sagittal. > > doug > > Jeff Sadino wrote: >> >> Hello Doug, >> >> I loaded up the tkregister2 program and I think I see some poor >> transformations. I've never really used it before though. Am I just >> looking at whether or not the green line lines up with the target image wm? >> Can you look at my pictures real quick? 040002_S04_test is from fs4 that >> is having problems. 040002_S04 is from fs3 and has a good icv value. Some >> of the blank spots are from my graphics drivers and unrelated to fs. >> tkregister2 also said the determinant of 040002_S04_test was 1.49544. >> >> Martin, >> >> Thank you for the idea. I did this, and got a much better icv. On fs3, >> where the icv was good, the number was 1,767,481. On fs4, it was 1,302,696. >> Using your idea on fs4, it was 1,819,485. >> >> Thank you so much to everyone for your help! >> Jeff >> >> On Thu, Feb 25, 2010 at 8:53 PM, Martin Kavec <martin.kavec(a)gmail.com >> <mailto:martin.kavec@gmail.com>> wrote: >> >> Hi Jeff, >> >> I see this relatively often. Eventhough the talairach registration >> is fine, the >> ICV is underestimated. In this case I take old ICV, which helps. >> >> mri_segstats --subject $MYSUBJECT --old-etiv-only >> >> This is in 99% of these cases a cure. This is not just a blind >> attempt. In >> these cases I then compare each ICV normalized aseg volume against >> an age >> matched group and only if the old-etiv-only ICV gives better >> estimates I use >> it. >> >> Cheers, >> >> Martin >> >> On Thursday 25 February 2010 23:05:10 Jeff Sadino wrote: >> > Thanks Doug. That is very good news to hear! >> > >> > Maybe I spoke too soon about fixing the problem. I looked at 4 more >> > subjects, and even though the icv value is unique, its magnitude >> seems >> > wrong. Often times, it is smaller than the BrainSegVol, which >> doesn't make >> > much sense and it is also low overall. >> > >> > >> > # subjectname 090167_F01 >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1639959, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1639959.000000, mm^3 >> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >> Segmentation Volume >> > Without Ventricles, 1289194.000000, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1299686, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1299686.000000, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1105595.114652, mm^3 >> > >> > # subjectname 090182_S01 >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1599981, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1599981.000000, mm^3 >> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >> Segmentation Volume >> > Without Ventricles, 1199694.000000, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1205382, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1205382.000000, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1114008.197334, mm^3 >> > >> > # subjectname 090187_F01 >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1826694, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1826694.000000, mm^3 >> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >> Segmentation Volume >> > Without Ventricles, 1381871.000000, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1388801, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1388801.000000, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1307759.303915, mm^3 >> > >> > # subjectname 100014_F01 >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1948121, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1948121.000000, mm^3 >> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >> Segmentation Volume >> > Without Ventricles, 1467582.000000, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1488088, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1488088.000000, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1637915.031593, mm^3 >> > >> > # subjectname 040002_S04_test >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1774481, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1774481.000000, mm^3 >> > # Measure BrainSegNotVent, BrainSegVolNotVent, Brain >> Segmentation Volume >> > Without Ventricles, 1288022.000000, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1312132, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1312132.000000, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1302696.178406, mm^3 >> > >> > I had also done 040002_S04 in fs 3.0.5, and this is the result: >> > # subjectname 040002_S04 >> > # BrainMaskFile mri/brainmask.mgz >> > # BrainMaskFileTimeStamp 2008/29/08 15:44:46 >> > # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, >> 1753272, >> > unitless >> > # Measure BrainMask, BrainMaskVol, Brain Mask Volume, >> 1753272.000000, mm^3 >> > # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation >> Voxels, >> > 1310474, unitless >> > # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, >> 1310474.000000, >> > mm^3 >> > # Measure IntraCranialVol, ICV, Intracranial Volume, >> 1767481.547316, mm^3 >> > >> > All of the values are similar except the icv. Do you guys have >> any ideas >> > where I can look for the answer? >> > >> > Thank you very much, >> > Jeff >> > >> >> > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >

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Re: [Freesurfer] persistent bvecs error
by Alexander Lebedev 04 Feb '12

04 Feb '12

Hello Anastasia! Thank you very much for your response! My bvecs and bvals were created by saving excel spreadsheet as a tab delimited file on mac. I reformated my bvecs manually using "nano" and reran the preprocessing. Unfortunately, it exited with the same error. I'm providing you my reformated bvecs... I believe that the problem is not in reading of decimals, because running this step with "fake" bvecs of 1s and 0s (test_bvecs.txt) produces the same output with zeros, and everything seems to be ok with the tutorial dataset... What would you suggest? --- Best Regards, Alex

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Re: [Freesurfer] vertex extraction
by Douglas N Greve 04 Feb '12

04 Feb '12

Hi Alex, we don't have an elegant solution to this, but you can do it in matlab easily enough. If your data D are in a N-by-327684 matrix (I assume that this is left and right hemis), then a.vol = permute(D(:,1:163842),[2 3 4 1]); MRIwrite(a,'lh.yourdata.mgh'); b.vol = permute(D(:,163843:end),[2 3 4 1]); MRIwrite(b,'rh.yourdata.mgh'); doug Alexander Lebedev wrote: > Excuse me for disturbing Douglas, > > The matter is that I have the coefficients for each vertex and I would > like to find the easiest way to display them into the brain space, > showing their importance for the classification. My original ascii > file contains N-by-327684 matrix (N subjects, 327 684 vertices - 163 > 842 for each hemisphere). But I can easily change it if necessary... > I'm just wondering if there is a way to do this... I'm asking because > it seems like "y.mgh -> y.asc" (mri_convert y.mgh y.ascii --ascii) > conversion is available only one-way. > --- > Regards, > Alex > > > * Alexander Lebedev <awlman(a)rambler.ru> [Fri, 27 Jan 2012 10:07:11 > +0400]: >> Yes, sorry... >> --- >> Alex >> >> > Hi Alex, I'm not sure I understand what you mean. Do you mean that > you >> > have a coefficient for each vertex and you want to display your >> results >> > on a surface and need to get them into a format that FS can read? >> > doug >> > >> > Alexander Lebedev wrote: >> > > Yes, thanks a lot Douglas! That's what I was looking for. And it's >> > > much easier than my approach... I needed to extract the vertices > in >> > > order to perform a multivariate analysis in R. May I also ask >> another >> > > question then? I have performed pls-regression and would like to > map >> > > the coefficients into the brain space... Is there such an >> opportunity >> > > (at least theoretically speaking) ? >> > > --- >> > > Regards, >> > > Alex >> > > >> > > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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showedits bug
by Michael Harms 01 Feb '12

01 Feb '12

Hi Nick, I found a small bug in recon-all that prevents the -showedits flag from working in conjunction with expert-options: Line 785 in recon-all of v5.1 currently has an extraneous closing parenthesis: if (-e $XOptsFile)) then but should be: if (-e $XOptsFile) then Also, I'm puzzled how the resulting edits.mgz gets translated when you load it as a segmentation -- e.g., areas with an addition to wm.mgz appear to be assigned the value 2 in edits.mgz, and are labeled as "wm- ON" if you load edits.mgz as a segmentation, but I don't see any entry for "wm-ON" in FreeSurferColorLUT.txt itself. Where is the full "key" for the values in edits.mgz? thanks, -MH

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WG: Save segmentation results as nifi files
by Fellhauer, Iven 01 Feb '12

01 Feb '12

Hi Bruce And thank you for your hint, but where are the files for GM, WM and CFS stored in the Freesurfer output directory structur? Best regards, Iven -----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Montag, 30. Januar 2012 15:20 An: Fellhauer, Iven Cc: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Save segmentation results as nifi files Hi Ivan you can convert any volume to any supported output type using mri_convert. It will figure out the format from the extension, so: mri_convert aseg.mgz aseg.nii.gz or mri_convert aseg.mgz aseg.nii should do the trick cheers Bruce On Mon, 30 Jan 2012, Fellhauer, Iven wrote: > > Dear all, > > > > I run recon-all with the ?autorecon1 and ?autorecon2 options. Now I > want to store the segmentation results in a spm like way. One nifti > file for each matter. Can I do this with freesurfer? And how can I do > this with freesurfer? > > > > Best regards, > > > > Iven Fellhauer > > > > ---------------------------------------------------------------- > > Universitätsklinikum Heidelberg > > Zentrum für Psychosoziale Medizin > > Klinik für Allgemeine Psychiatrie > > Sektion für Gerontopsychiatrie > > Voßstr. 4 > > 69115 Heidelberg > > Tel.: +49 (0) 6221 - 56 7578 > > Email: iven.fellhauer(a)med.uni-heidelberg.de > > > > > 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] Dura too bright/thick: brain extraction
by octavian lie 31 Jan '12

31 Jan '12

Thank you. Unfortunately, we use a Phillips scanner for 3T scans: MPRAGE T1 TR 9.89; TE 4.60. If you have any suggestions, including which of the protocols comes closest, let mw know. Best, Octavian On 1/31/12, Andre van der Kouwe <andre(a)nmr.mgh.harvard.edu> wrote: > Do you have a Siemens scanner? > > You can compare your protocols with the examples at > www.nmr.mgh.harvard.edu/~andre. > > On Tue, 31 Jan 2012, Bruce Fischl wrote: > >> Hi Octavian >> >> what kind of scanner are you using? Andre van der Kouwe and Dylan Tisdall >> (ccd) have developed a multi-echo mprage that allows one to identify dura >> by >> it's short T2*. They might be able to give it to you depending on your >> scanner and relationship with Siemens. Otherwise it can be difficult, as >> lenghtening your TE to reduce the dura signal also reduced gray/white >> contrast. >> >> cheers >> Bruce >> On Tue, 31 Jan 2012, octavian lie wrote: >> >>> Dear All, >>> >>> I am trying to perform brain extraction on T1 3D images, however the >>> dura appears too bright and thick compared to the underlying gray >>> matter. It seems that I have a hard time stripping the dura away. Do >>> you have any suggestions in terms of optimizing freesurfer parameters >>> to help with this problem, or alternatively, do you suggest a specific >>> T1 protocol (TE/TR) to dim the dura a bit? >>> Thank you, >>> >>> >>> Octavian Lie. >>> _______________________________________________ >>> 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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Dura too bright/thick: brain extraction
by octavian lie 31 Jan '12

31 Jan '12

Dear All, I am trying to perform brain extraction on T1 3D images, however the dura appears too bright and thick compared to the underlying gray matter. It seems that I have a hard time stripping the dura away. Do you have any suggestions in terms of optimizing freesurfer parameters to help with this problem, or alternatively, do you suggest a specific T1 protocol (TE/TR) to dim the dura a bit? Thank you, Octavian Lie.

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Installation
by Nooshin Zadeh 31 Jan '12

31 Jan '12

Hi, I am trying to install FS on the mini Mac. I downloaded the darwin leopard version of FS and it went to "Application". For setup configuration step, in tcsh terminal I wrote "setenv FREESURFER_HOME /Application/freesurfer " and then "source $FREESURFER_HOME/SetUpFreeSurfer.csh". It says no such file or directory, but I see SetUpFreeSurfer.csh in the FS folder on the "Application". Once I copied the FS on the desktop and then wrote "setenv" and "source" again. It worked temporarily but when I was done with all installation steps, it did not recognize tkmedit and tksurfer. Can you please guide me how can I fix the problem. Thanks, -- Best Regards --------------------------------------------------- Nooshin N. Zadeh Graduate Assistant Departments of Electrical Engineering and Neurology University of Miami ** * * * *

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Re: [Freesurfer] re-running mri_glmfit-sim
by Douglas N Greve 31 Jan '12

31 Jan '12

That is a slight bug in that there is no default (you have to specify). Below is the text from running it with --help. If you have an apriori hypothesis that group1 > group2, then choose positive. If you don't know the sign, then use abs. Choosing a sign will yield stronger results (ie, smaller p-values), but you will lose the other sign. doug This is the sign of the threshold used to create the clusters for cluster-wise correction of multiple comparisons. Antonella Kis wrote: > Dear Doug, > > Thank you so much for your help. I still have one more question > please: WHEN i WAS TRYING TO RUN THE: > > mri_glmfit-sim \ > --glmdir Group_Analysis.glmdir \ > --sim neg perm 10000 3 permcsd\ > --cwpvalthresh .05 > > > as you recommended me so withouth --sim-sign I got the error that I > must specify the sign so I choose neg. I believe the default should be > abs but can you please shortly explain what exactly the --sim-sign means? > > Thank you very much. > Antonella > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* Antonella Kis <atorok9(a)yahoo.com> > *Cc:* "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > *Sent:* Tuesday, January 31, 2012 12:39 PM > *Subject:* Re: [Freesurfer] re-running mri_glmfit-sim > > You have to re-run > doug > > Antonella Kis wrote: > > dear All, > > > > I would like to know if I am running the > > mri_glmfit-sim \ > > --glmdir Group_Analysis.glmdir \ > > --sim perm 10000 3 permcsd \ > > --sim-sign neg \ > > --cwpvalthresh .05 > > > > and I want to change the --sim-sign from neg to positive if I need > to run again the whole simulation or I can just run: > > > > mri_glmfit-sim --glmdir Group_Analysis.glmdir \ --no-sim --sim-sign > pos or how exactly to edit the mri_glmfit in this case? > > > > Also if I need to add one more subject do I need to re-run the whole > simulation or for multiple comparison I can just use the --no-sim option? > > > > Thank you very much! > > Antonella > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Freesurfer January 2012