Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

'mri_normalize' & 'mri_nu_correct', how do they work?
by Guido Orlando Pascariello 12 Nov '15

12 Nov '15

Hi FS Experts I'm bioengineering student and I'm working on my final project to get my degree. it's about process neuroimaging (IRM) in order to cuantific some parameter which could be helpful for medicine (clinical neurology). I'm using FreeSurfer to process my data. It works realy good. But it will be so much helpful to me if you can answer me a few question about it! *FIRST ONE*: I've been using 'mri_normalize' and I read the paper which describe it. But: 1. In step 4: Discard outliers from the array: You suppose variation in intensity due to magnetic field inhomogeneities is smooth across space. But, field inhomogeneities are corrected in 'NuCorrect' module using N3. 2. I understood the 1D normalization process. However the 3D normalization process works estimating a bias field like that which is corrected by 'NuCorrect' module. Could you tell me why did you that? and what are diferences with 'NuCorrect' module? *SECOND ONE*: It's abuou 'mri_nu_correct': I've read the description but I'm not sure about it. Does it use the N3 algorithm to work? In the description is written that "changing the number of iterations should be done carefully, because this can exacerbate artifacts". Could you tell me what are these artifact? and why is the default number of iteration four? I'll be grateful if you can help Being all for now, I await a reply Guido PASCARIELLO Facultad de Ingeniería - Universidad Nacional de Entre Ríos Argentina

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Downsampling the surface
by Ray Razlighi 12 Nov '15

12 Nov '15

Dear All, I can't find the mris_decimate command any more in the new freesurfer distribution. I assume there is substitute. Would someone direct me to the substitute. Also, I remember using mris_decimate changed the vertices coordinates. I was wondering if there is any way to downsample the surface in a way that the new vertices on the downsampled surface always fall on one of the original ones. I know this is not possible with exact downsample ratio; However I do not need exact downsampling ratio. -- Sincerely, Ray

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group mean greater than X
by Dace Apshvalka 12 Nov '15

12 Nov '15

Sorry, I was not very clear. I meant, how do I test whether the group mean is greater than 5, for example. The default is 0, but can I change it somehow? Dace --

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Computing Statistics with Custom ROI Masks
by Shady El Damaty 12 Nov '15

12 Nov '15

Hi FS-ers, I'm a bit stuck trying to compute cortical and subcortical statistics using the Buckner 2011 Cerebellum mask. I tried using mri_segstats to generate the .stats file for the provided image: mri_segstats --seg > Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --sum > test.summary --ctab-gca Buckner2011_7Networks_ColorLUT.txt --nonempty > $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ > cwd > cmdline mri_segstats --seg > Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --sum > test.summary --ctab-gca Buckner2011_7Networks_ColorLUT.txt --nonempty > sysname Darwin > hostname Apricot.local > machine x86_64 > user shady > UseRobust 0 > Loading > Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz > Segmentation fault: 11 Clearly I am doing something wrong. Can someone throw a pointer my way about how I can go about computing statistics on my subjects (or any arbitrary volume) using this mask? In the end I would like to be able to generate a .stats file for every subject in my SUBJECTS_DIR using any custom mask.. how can I make this possible? Your help would be very greatly appreciated!

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Re: [Freesurfer] Freesurfer@nmr.mgh.harvard.edu
by Douglas N Greve 12 Nov '15

12 Nov '15

/ really? So if you run ls -l /Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz/ what do you get? On 11/11/2015 07:59 PM, Heidi Foo wrote: > Hi Dr Greve, > > Yes it does, for all base templates, there > are lh(rh).long.thickness-avg(pc1, rate, and > spc).fwhm0(5,10,20,25).fsaverage.mgh files. > > I did the following steps in preprocessing: > > 1. recon-all -all -s <tpNid> -i path_to_tpN_dc m > 2. recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all > 3. recon-all -long <tpNid> <templateid> -all > 4. long_mris_slopes --qdec > /Users/nnidementia/Documents/PDFS/long.qdec.table.txt --meas thickness > --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label > --time years --qcache fsaverage --sd /Users/nnidementia/Documents/PDFS > 5. long_mris_slopes --qdec > /Users/nnidementia/Documents/PDFS/QDEC/long.qdec.table.txt --meas > thickness --hemi lh --sd /Users/nnidementia/Documents/PDFS --do-pc1 > --do-label --generic-time --fwhm 10 --qcache fsaverage --stack-pc1 > /Users/nnidementia/Documents/PDFS/QDEC/lh.cross.qdec.table.txt.thickness-pc1.stack.mgh > --isec-labels > /Users/nnidementia/Documents/PDFS/QDEC/lh.cross.qdec.table.txt.fsaverage.cortex.label > > Thanks. > > Regards, > Heidi Foo > > > > > On Wed, Nov 11, 2015 at 11:57 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > does that file exist? Did you run recon-all -qcache ? > > > On 11/11/15 7:54 AM, Heidi Foo wrote: >> Apologies, the error message should be /Error in >> analyze: couldn't open >> /Users/nnidementia/Documents/PDFS/FSVASE_002/surf/lh.thickness.fwhm10.fsaverage.mgz >> or .mgh file./ >> >> On Wed, Nov 11, 2015 at 8:48 PM, Heidi Foo <heidifoo92(a)gmail.com >> <mailto:heidifoo92@gmail.com>> wrote: >> >> Hi Dr Greve, >> >> Thank you for your advice, it is deeply appreciated. I >> removed the blank lines of wmh.levels and included a carriage >> return at the end of the long.qdec.table.txt. >> >> However, there is still /error in analyze: Couldn't open >> /Users/nnidementia/Documents/PDFS/FS_PD002_1.nii/surf/lh.thickness.fwhm10.fsaverage.mgz >> or .mgh file./ >> / >> / >> I checked my qdec.table.txt (both cross and long) but I did >> not see any fsaverage included in the list of subjects. Am I >> missing something? >> >> Thank you. >> >> Regards, >> Heidi Foo >> / >> / >> >> On Wed, Nov 11, 2015 at 12:28 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> Also, try removing the blank line at the end of >> wmh.levels, and make sure you have a carriage return at >> the end of long.qdec.table.txt. This may fix the 2nd error >> >> On 11/09/2015 10:38 PM, Heidi Foo wrote: >> >> Dear Dr Greve, >> >> Thanks for your reply. I have already linked >> fsaverage to my SUBJECTS_DIR but the error still >> persists. >> >> Attached is my qdec (long and cross) files. >> >> Thanks. >> >> Regards, >> Heidi Foo >> >> >> >> On Tue, Nov 10, 2015 at 6:36 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >> >> >> >> On 11/06/2015 09:35 PM, Heidi Foo wrote: >> >> Dear FreeSurfer experts, >> >> I am trying to compare between stable WMH >> group and rapid >> progressed WMH group in regards to the >> cortical thickness as >> well as volume changes in the gray matter. >> The nuisance >> variable in my case is age. I ran my analysis >> using QDEC but >> encountered a few problems: >> >> 1. There is error in analyze: couldn't open file >> >> It looks like it cannot find fsaverage. Link it >> to your >> SUBJECTS_DIR if you have not already. >> >> 2. If this error doesn't appear, another one >> does. >> QdecGlmDesign::Create: zero factors! >> (Attached the screenshot of the errors for >> your perusal) >> >> please send the qdec file >> >> >> I am hoping that you could give me a solution >> to my problems. >> >> Thank you so much. >> >> Regards, >> Heidi >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> >> 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 <mailto:greve@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> > > -- 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/

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Re: [Freesurfer] How to compute area of subcortical structures
by anirudh nihalani 12 Nov '15

12 Nov '15

Hi Bruce, Thank you very much for your quick reply. Sorry I hadn't been able to reply faster as I was trying to figure out the below mentioned issue from two days. I have computed surface area of left-hippocampus using the commands mri_tessellate and mris_info. However I found that in freeview by selecting Tools->show label stats, I am able to display area of any label (PFA a screenshot) but these area stats do not match with the areas obtained using mri_tessellate and mris_info. I have two queries regarding this: 1) Surface areas of labels displayed in freeview doesn't match with subcortical structures' areas obtained by running mri_tesselate and mris_info. For example the attached screenshot shows that area of left-hippocampus is 71 mm^2 where as mri_tessellate followed by mris_info found the area for left-hippocampus to be 3586 (PFA the output of mris_tessellate and mris_info). Why is there a mismatch? 2) Based on your reply I thought area stats are not calculated for subcortical structures during "recon-all". If that is the case, how is freeview displaying area stats for subcortical areas? Also which file does freeview use to display these stats? Is it stats/[l/r]h.aparc.stats? I ask because even cortical structures' areas displayed by freeview are not matching with what is stored in these files. Please let me know. Thank you. Regards, Anirudh

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dilating labels within a parcellation
by David Grayson 11 Nov '15

11 Nov '15

Hi all, Is there a tool to surface-dilate all the labels contained within an annotation file simultaneously, while preserving the non-overlapping nature of the labels? I saw there is a development version of mri_label2label that works for individual label files separately, but that gets me into the problem of overlap and arbitrary starting points. Thanks very much, David

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Re: [Freesurfer] Freesurfer Digest, Vol 141, Issue 22
by Gonzalo Rojas Costa 11 Nov '15

11 Nov '15

Hi Martin: But, between version 5.3 and 6.0 there are any differences in the algorithms for subcortical volume, cortical thickness, etc., or only additions to that, such as the hippocampus or brainstem subfields ?... and in general, if I segment for example the same healthy control in freesurfer 5.3 and 6.0 in the same operating system, there will be any difference in subcortical volumes and/or cortical thickness ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl On Wed, Nov 11, 2015 at 7:57 AM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > ------------------------------ > > Message: 24 > Date: Tue, 10 Nov 2015 16:57:43 -0500 > From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] 5.3 vs 6.0 volumetric differences... > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <56426857.3030804(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > Hi Gonzalo, > > of course. > > There is even a difference when running the same FS version with a > different operating system (due to differences in the numerical > libraries, optimizations etc). > > Are changes big or small? > In a single case they can be very big (it could be a case that failed in > 5.3 and works with 6.0 - or the other way) > > Are changes directional (significantly larger or smaller volumes/thickness)? > Hard to say and hard to detect if small, but it can happen due to a new > algorithm that measurements are consistently larger (/smaller) than in > another version. We try to avoid this, but it can theoretically happen. > > That is why it is so important to stick with the same version and > operating system when processing data. > > Best, Martin > > On 11/10/2015 04:48 PM, Gonzalo Rojas Costa wrote: >> Hi: >> >> There are any difference between subcortical structures volume, >> cortical thickness, supratentorial volume, gray matter volume, etc. >> computed with freesurfer 5.3 and 6.0 ?... >> >> Sincerely, >> >> >> Gonzalo Rojas Costa >> > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu

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Re: [Freesurfer] group mean greater than X
by Dace Apshvalka 11 Nov '15

11 Nov '15

That's what I will do. Just wanted to enquire whether there is an option to specify the value directly for the one-sample ttest. Thank you! Dace > Could you also just subtract 5 from all your input data? Then when you test > against zero (and only look at positive p values) you'll really be testing > whether the values are greater than 5? > > Kx > > On 11 November 2015 at 21:35, Douglas Greve <greve at nmr.mgh.harvard.edu> > wrote: > >> I guess you could subtract 5 from the gamma.mgh, then recompute the t = >> gamma-5.mgh/sqrt(gammavar.mgh). You'd then need to convert the t to a p >> or sig given the dof. >> doug >> >> ps. Please remember to include previous correspondences so we know the >> context of the question >> >> On 11/11/15 4:10 PM, Dace Apshvalka wrote: >> > Sorry, I was not very clear. >> > >> > I meant, how do I test whether the group mean is greater than 5, for >> > example. >> > >> > The default is 0, but can I change it somehow? >> > >> > >> > Dace >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer at 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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group mean greater than X
by Dace Apshvalka 11 Nov '15

11 Nov '15

Hi, How would I make a one sided t-test to see whether group mean is greater than X (any other number than 0)? Thanks, Dace

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Freesurfer