Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

130 participants
204 discussions

Re: [Freesurfer] epidewarp.fsl for FSL 5.x
by Douglas Greve 22 Mar '16

22 Mar '16

It is there again. I don't know what the status if it is in terms of the version. Try it and let me know doug On 11/25/14 4:34 PM, Morgan Hough wrote: > Hi Doug, > > Could you put the epidewarp.fsl script back on your ftp site? I don’t > see it at the link in the archives: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl > > BTW, is the script updated in some way for 5.x or can I can the old > script just be changed to accept 5.x version numbers. > > Cheers, > > -Morgan

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Re: [Freesurfer] 3_group_comparison
by Lee Tirrell 15 Mar '16

15 Mar '16

Hi Dusan, setenv is used when you are using tcsh. since you are using bash, you can run this command to set your language: export LANG=en_US.UTF-8 Hope this helps. Best, Lee On Tue, 29 Sep 2015, Dusan Hirjak wrote: > Thank you very much for your suggestion. Now it has worked well. > However, I am having trouble running the simulation via: > > mri_glmfit-sim --glmdir NSS_3_GR.glmdir --cache 4 abs --cwp 0.05 --2spaces > > ERROR: thresh = 4,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 > > > Where can I set up the EN language with "setenv LANG en_US.UTF-8"? > > > I am getting this message: > > > bash-3.2$ setenv LANG en_US.UTF-8 > > bash: setenv: command not found > > > How can I change the language? > > > Many thanks! > > Dusan > > ___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ > From: rpwang(a)nmr.mgh.harvard.edu > Date: Mon, 28 Sep 2015 19:35:12 -0400 > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] 3_group_comparison > > Was the path of the overlay file correct? It looks like it can’t find the file. Try providing the full path of the overlay file in the freeview command. > > Best, > Ruopeng > > On Sep 28, 2015, at 6:46 PM, Dusan Hirjak <dusanhirjak(a)hotmail.com> wrote: > > Many thanks!!!, yes, freeview has opened, but I am still not seeing any results, just the "lh.inflated" > It says: "Failed to load surface overlay" > > and than I got the following message: > > bash-3.2$ freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d > 2015-09-29 00:41:53.887 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.889 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.905 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.906 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.921 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.922 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable > 2015-09-29 00:41:53.939 Freeview[22049:303] invalid drawable > Did not find any volume geometry information in the surface > ø;C 8Íÿ¿ø;C È+’Àá > > reading colortable from annotation file... > colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, -1): could not open file > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, -1): could not open file > could not read overlay data from /users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh > mghRead(/users/dhirjak/MRI/Freesurfer_2/NSS_LGI/fsaverage/surf/lh.NSS_3_GR.glmdir/AvG-thickness-Cor/sig.mgh, -1): could not open file > 2015-09-29 00:42:02.445 Freeview[22049:303] modalSession has been exited prematurely - check for a reentrant call to endModalSession: > > I dont understand the problem. Do you have any ideas??? > > Thank you! > > Dusan > > > > > To: freesurfer(a)nmr.mgh.harvard.edu > > From: greve(a)nmr.mgh.harvard.edu > > Date: Mon, 28 Sep 2015 18:33:50 -0400 > > Subject: Re: [Freesurfer] 3_group_comparison > > > > I think it needs a -f before the surface > > > > On 09/28/2015 06:27 PM, Dusan Hirjak wrote: > > > Many thanks, yes, it did work well. > > > > > > But, than I ran "freeview > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 > > > -viewport 3d" > > > > > > and got the following message: > > > > > > bash-3.2$ freeview > > > $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:overlay=lh.NSS_3_GR.glmdir/AvG-thickness-NSS-Cor/sig.mgh:overlay_threshold=4,5 > > > -viewport 3d > > > > > > 2015-09-29 00:23:47.366 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.367 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.385 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.386 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.399 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.400 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.420 Freeview[22019:303] invalid drawable > > > > > > 2015-09-29 00:23:47.421 Freeview[22019:303] invalid drawable > > > > > > Unrecognized sub-option flag 'annot=aparc.annot'. > > > > > > > > > Freeview has opened, but it showed no results at all:-( > > > > > > > > > What should I do? I read that one has to upgrade the newest > > > freeview-version? Is it possible to get the newest version without > > > installing freesurfer again? > > > > > > Many thanks! > > > > > > Dusan > > > > > > > > > ------------------------------------------------------------------------ > > > Date: Mon, 28 Sep 2015 11:35:50 -0400 > > > From: greve(a)nmr.mgh.harvard.edu > > > To: freesurfer(a)nmr.mgh.harvard.edu > > > Subject: Re: [Freesurfer] 3_group_comparison > > > > > > Did you include the back slashes in your command? If so, remove them > > > and retry. > > > > > > On 9/25/15 7:11 PM, Dusan Hirjak wrote: > > > > > > Dear Freesurfer experts, > > > > > > I am trying to compare 3 groups (aut, sch, ges) according to > > > thickness, area and LGI at once (omnibus test). > > > > > > I did run the following command: > > > > > > mris_preproc --fsgd NSS_3_GR.fsgd \ --cache-in > > > thickness.fwhm15.fsaverage \ --target fsaverage --hemi lh \ --out > > > lh.NSS_3_GR.thickness.15.mgh > > > > > > > > > This step did work properly:-) > > > > > > > > > > > > Now, Im trying to run the following command, but it does not work: > > > > > > > > > mri_glmfit \ --y lh.NSS_3_GR.thickness.15.mgh \ --fsgd > > > NSS_3_GR.fsgd dods\ --C contrasts.mtx \ --surf fsaverage lh \ > > > --cortex \ --glmdir NSS_3_GR.glmdir > > > > > > > > > I got this message: "ERROR: Option--y unknown" > > > > > > > > > What am I doing wrong? > > > > > > > > > Thank you for your help! > > > > > > > > > > > > Best regards > > > > > > > > > Dusan > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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 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. > > > > > > > > > _______________________________________________ > > > 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 > _______________________________________________ > 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 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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Reading values from overlays with PETcoreg
by Benjamin Spurny 03 Mar '16

03 Mar '16

Dear Freesurfer experts! I am currently working on PET analysis using FS I coregistered my PET with the processed MR using bbregister, transfered it to a surface using mri_vol2surf and now createt an overlay in freeview with the lh.inflated and used the labels from the lh.aparc.a2009s.annot file. In freeview i get the corresponding BP value for each vertex now but is there a way to get a list of vertices with the corresponding BP value and the corresponding ROI this vertex belongs to? Or is there a better to do this analyis? Many thanks in advance! Benjamin

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Statistical analyses with QDEC
by Francesco Cardinale 18 Feb '16

18 Feb '16

Dear Freesurfer experts, I have some questions about statistical analyses. How to adjust for sex and age? I use the precompiled Freesurfer 5.3.0 MacOSX version, and its tool QDEC to compare cortical thickness between two groups. I would like to use age and sex as nuisance factors. No problem with the age, but I don’t see the sex in the list of usable variables if I code it as a categorical variable (male / female). On the opposite, If I code it as numbers (male = 1, female = 2) I can use it, but how can I declare that it is a factor and not a continuous numerical variable? I don’t want that “female” affects the fitting of the GLM with a value that means “male” * 2. What about the use of other morphometric properties as nuisance factors? For example, how could I use sulcality or LGI as nuisance factors? Is it possible to use more than one scalar simultaneously? Similarly to question 2, is it possible to use home-made *.mgh scalars as a nuisance factors? How? Do the command-line tools allow such analyses better than QDEC? Related to my questions, which features do they add? In this field of interest, are there any major advantages coming with Freesurfer 6.0? Thanks a lot and best regards Cico

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MNI coords in GLM cluster
by Bronwyn Overs 16 Feb '16

16 Feb '16

Hi Freesurfer mailing list, Is there a way to determine if a specific MNI location is included in any of the clusters that are significant in a freesurfer GLM analysis (after monte-carlo)? We have a specific coordinate of interested from a previous analysis (e.g. -21, 11, -17) and wish to know if this is included in any of the significant clusters from an alternate GLM in freesurfer. -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 neura.edu.au <http://neura.edu.au> Follow @neuraustralia on twitter <https://twitter.com/neuraustralia>Follow NeuRA on facebook <https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>

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Longitudinal analysis--mass univariate
by John Anderson 12 Feb '16

12 Feb '16

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Free surfer- correcting for head size
by Christina van den Brink 10 Feb '16

10 Feb '16

Hello, I have a question regarding volume-correction for the morphometry stats obtained via recon-all. I’ve noted that eTIV is derived using the atlas scaling factor in order to account for head size. I’m wondering whether the other volumes given, e.g. TotalGray or lhCorticalWhiteMatter, have also been corrected for head size? If not, is there a recommended method in which to do so so that regional volumes can be compared between participants? Many thanks for your help! Best, Christina

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Re: [Freesurfer] Tracula_weighted dti metrics values
by Anastasia Yendiki 09 Feb '16

09 Feb '16

Hi John - The values are weighted (multiplied) by the probability distribution (path.pd.nii.gz) at the same voxel. So they are the expected values, from a probabilistic standpoint. The distribution is thresholded at 20% of its maximum by default (this is a parameter in dmri_pathstats). Best, a.y On Wed, 16 Sep 2015, John Anderson wrote: > Hi Anastasia, > How the script "dmri_pathstats" compute the weighted FA, MD, AD, and RD > values? > I checked the command "dmri_pathstats" inside the file "trac-all.log" but I > was unable to figure out how this weighting is working. Is it by multiplying > the mean DTI metrics by the number of voxel? > > If my FA maps is "dtifit_FA.nii.gz" and my probabilistic distribution map > for the cortico spinal tract is "path.pd.nii.gz" and I want to compute FA > value using the command "fslstats" like: > > fslstats dtifit_FA.nii.gz -k path.pd.nii.gz -m ==== >This command will > output the mean FA for the probabilistic distribution map. How can I weight > this FA value using the previous command line? > > Bests, > John Anderson > > Senior Research Associate > Psychological and Brain Sciences Dept. > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 > Phone: +1 (603) 646-9834 > Fax: +1 (603) 646-1419 > >

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Gray matter intensity
by Sabrina Yu 08 Feb '16

08 Feb '16

Hello, I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html> And have successfully gotten the wm-gm signal intensity contrast, but now have a few questions regarding signal intensity for white matter and gray matter intensity. 1) Does the wmparc.stats contain mean white matter intensity values for each ROI? 2) Is it possible to extract these same mean intensity values for gray matter? There is no gmparc.stats file. We know that it's possible to calculate these from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more direct way to get this data. Thank you, Sabrina Yu

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matrix is ill-conditioned or badly scaled, condno = 27492.1
by Nabin Koirala 07 Feb '16

07 Feb '16

Dear Freesurfer forum, 'I am trying to run qdec analysis for a group of subjects to see if correlation exists but I am getting this error only for this particular set of data but could not figure out what is exactly wrong with it. Your suggestion would be greatly appreciated. Following is the terminal output for the process: .......... Saving design matrix to /g/f/h/s/freesurfer/subjects/qdec/Untitled/Xg.dat Normalized matrix condition is 27492.1 Design matrix ------------------ 1.000 0.408; 1.000 0.417; 1.000 0.417; 1.000 0.405; 1.000 0.412; 1.000 0.412; 1.000 0.411; 1.000 0.417; 1.000 0.405; 1.000 0.406; 1.000 0.402; 1.000 0.419; 1.000 0.413; 1.000 0.413; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 27492.1 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y /g/f/h/s/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /g/f/h/s/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /g/f/h/s/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label /g/f/h/s/freesurfer/subjects/fsaverage/label/lh.aparc.label --C /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-alpha1-Cor.mat 2. The FSGD file (if using one) 3. And the design matrix above Error in Analyze: command failed: mri_glmfit --y /g/f/h/s/freesurfer/subjects/qdec/Untitled/y.mgh --fsgd /g/f/h/s/freesurfer/subjects/qdec/Untitled/qdec.fsgd dods --glmdir /g/f/h/s/freesurfer/subjects/qdec/Untitled --surf fsaverage lh --label /g/f/h/s/freesurfer/subjects/fsaverage/label/lh.aparc.label --C /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /g/f/h/s/freesurfer/subjects/qdec/Untitled/contrasts/lh-Avg-thickness-alpha1-Cor.mat Many thanks in advance. Regards, Nabin

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Freesurfer January 2016