Freesurfer October 2015

freesurfer@nmr.mgh.harvard.edu

142 participants
214 discussions

Re: [Freesurfer] Calculate the cortical thickness in patients with brain tumor
by Bruce Fischl 06 Oct '15

06 Oct '15

Hi Feng it depends on where the tumor is cheers Bruce On Wed, 30 Sep 2015, chenhf_uestc wrote: > Hi, freesurfer experts, > > If my data came from the patients with brain tumors, could I perform > recon-all analyses to calculate cortical thickness, surface area and so on. > If not, could I mask the brain region with tumor and then conduct such > analyses? I think the tumor might lead to the inaccuracy of cortical > reconstruction > > Best, > Feng > >

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Re: [Freesurfer] Lost toolbar in freeview
by Antonin Skoch 06 Oct '15

06 Oct '15

Dear Ruopeng, I am using Ubuntu 12.04. LTS 32bits. There is no directory ~/Library/Preferences in my home directory. There is only "GNUstep" directory containing subdirectories "Defaults" and "Library". "Library" dir is empty and "Defaults" contains .GNUstepDefaults file, which is very short file containing only NSGlobalDomain entry. Regards, Antonin

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mris_surf2vol
by Kevin Aquino 06 Oct '15

06 Oct '15

Hi all, I am trying to "voxelize" the cortical surfaces generated in freesurfer and I am a little stuck. I have been using mris_surf2vol with the --mask option however this generates a very speckled representation of the cortical surface on the voxels. What I would prefer would be the level sets of the cortical surface interpolated onto voxels, even if they are at a different resolution that could be enough. Is this possible with any of the available commands? I also went down the route of mris_volmask however, this generates the cortical ribbon, which is something that I don't need. Cheers, *Dr Kevin Aquino* Research fellow, Sir Peter Mansfield Magnetic Imaging Center, School of Physics & astronomy, The University of Nottingham. Honorary Research Fellow School of Physics, Faculty of Science, University of Sydney. *E* Kevin.aquino(a)nottingham.ac.uk, aquino(a)physics.usyd.edu.au | *W* www.physics.usyd.edu.au/~aquino/ ---------------------------------------------- The brain is a wonderful organ. It starts working the moment you get up and does not stop until you get into the office. - Robert Frost CRICOS 00026A This email plus any attachments to it are confidential. Any unauthorised use is strictly prohibited. If you receive this email in error, please delete it and any attachments. Please think of our environment and only print this e-mail if necessary.

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Re: [Freesurfer] Question about the volume conversion in freesurfer
by chenhf_uestc 05 Oct '15

05 Oct '15

Yes, my data have been normalized to the MNI space. So, in my case, what should I do if I want to use the mri_surf2vol function? Best, Feng 发件人：Douglas Greve <greve(a)nmr.mgh.harvard.edu> 发送时间：2015-09-29 00:00 主题：Re: [Freesurfer] Question about the volume conversion in freesurfer 收件人："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> 抄送： This is not an easy thing to do. First of all, did you apply a nonlinear registration to get the fMRI to the normalized MNI space? If so, then you can not do what you want with the data you have pre-processed. On 9/24/15 2:26 AM, chenhf_uestc wrote: Dear freesurfer experts, I want to compute functional connectivity based on the region with significantly different cortical thickness of two groups. The fMRI data have been preprocessed by using SPM software and normalized to the MNI space. However, I do not how to use the function mri_surf2vol. The required flagged arguments include --surfva, --hemi and --volreg (i.e., volume registration file). How can I set up the --volreg argument? What is the third arguments --volreg? The online manual states that contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. The format of this file is that as output by tkregister2 and includes the name of the subject. It will be assumed that the input surface values are sampled on the surface of this subject. Where could I find the volume registration file? Any help would be greatly appreciately. Best, Feng _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] mri_vol2surf
by Douglas Greve 05 Oct '15

05 Oct '15

On 9/29/15 3:36 PM, Martin Tisdall wrote: > I am trying to produce a scalar overlay from PET data to overlay onto the pial surface. > I have coregistered the pet with T1.mgz and then used the transform from mri_info --scanner2tkr to co-localise with orig.mgz. What does that mean? You'll need to run bbregister to get the registration file > I then do: > mri_vol2surf --src <coregistered pet> --out <output file.w> --out_type paint --regheader <subject> --hemi lh --surf pial --projfrac 0.5. If you want it on the pial surface use --projfrac 0.0. The way you have it now, it will sample a distance of half the thickness beyond the pial surface. Also, I would recommend using .mgh as the output format as not many tools work the paint files. > > The output doesn't seem quite right as seems to be some areas of signal drop out. > Can anyone tell me if my options look right or am I missing something. > Thank you > Martin > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Re: [Freesurfer] problem fast_selxavg3b
by Douglas Greve 05 Oct '15

05 Oct '15

It is never good to mix versions, so I would re-do it. On 9/29/15 1:45 PM, Desiree Thielemann wrote: > Thanks Doug! > > I have another question: We did the fsfast analysis some time ago before > we updated freesurfer version with fast_selxavg3. Now we want to analyse > additional persons. Do you think it is comparable or is it better to > re-do the analysis for all persons with fast_selxavg3b instead of 13 > persons with fast_selxavg3 and 2 persons with fast_selxavg3b? > > Thanks in advance, > Desiree > > Am 29.09.2015 um 15:34 schrieb Douglas Greve: >> oops, sorry, that did not make it into the distribution. You can get it here >> >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fast_selxavg3… >> >> thanks >> doug >> >> >> On 9/29/15 9:15 AM, Silvia Désirée Thielemann wrote: >>> Dear members of the freesurfer mailing list, >>> >>> I'm using freesurfer-Linux-centos7_x86_64-dev-20150728. I started to >>> analyse mri data with fs-fast. I did the preprocessing and used the >>> function mkanalysis-sess and mkcontrast-sess without any problems. I >>> tried to run the function selxavg3-sess next and it stopped with the >>> error message: >>> >>>>>>>>>>> /opt/freesurfer/fsfast/toolbox/fast_selxavg3.m >>>>> /opt/freesurfer/fsfast/toolbox/fast_ldanaflac.m >>>>> /opt/freesurfer/matlab/MRIread.m >>>>>>>>> ??? Undefined function or method 'fast_selxavg3b' for input >>>>> arguments of type >>> 'char'. >>> >>>>> ------------------------------------------ >>> ERROR: fast_selxavg3() failed\n >>> >>> I looked for the function fast_selxavg3b in matlab. Unfortunatly only >>> the function fast_selxavg3 is included in the fsfast/toolbox. By >>> trying to use the function fast_selxavg3, it recommand me to use >>> fast_selxavg3b. I could not find the function in the internet. >>> >>> Do you have any suggestions what to do? >>> >>> Best regards, >>> Desiree >>> >>> _______________________________________________ >>> 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. >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Re: [Freesurfer] selxavg3-sess outputs
by Douglas Greve 05 Oct '15

05 Oct '15

Yes, they do. There is also a pcc.nii.gz which is the partial correlation coefficient. On 9/30/15 1:14 PM, Jiahe Zhang wrote: > Dear Freesurfer experts, > > The freesurfer command 'selxavg3-sess' outputs many files in the > contrast folder in addition to the three documented on the Wiki (ces, > cesvar, sig). Is there more detailed documentation on what each output > is and how they're computed? In particular, I was wondering if the > t.nii.gz and z.nii.gz maps contain standard t and standard z scores. > > Thanks, > Jiahe > > > -- > Jiahe Zhang > Ph.D. Candidate > Department of Psychology > Northeastern University > 617-373-4789 <tel:617-373-4789> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] percent difference adjust to results {Disarmed}
by pablo najt 05 Oct '15

05 Oct '15

Hi my message was lost in the long correspondences. Would anyone advice about below, please?Thank you.Pablo From: pablonajt(a)hotmail.com To: freesurfer(a)nmr.mgh.harvard.edu Date: Thu, 1 Oct 2015 11:47:10 +0000 Subject: [Freesurfer] percent difference adjust to results {Disarmed} Dear FS expertsI have a query about how can I make that the percent difference results matches the same clusters of my output from my main glm analysis.I run a glm analysis g4v1 (Male_Pt, Male_HC, Fem_Pt, Fem_HC) with Age and sex as covariates.My contrasts are as follow -0.5 0.5 -0.5 0.5 0 0 0 0This contrast is meant to test "is there a difference between HC and PT controlling for age and sex. I separately run contrast of PT agains "0" 0.5 0 0.5 0 0 0 0 0and HC against "0"0 0.5 0 0.5 0 0 0 0 calculated percent difference as follows fscalc Pt_group/gamma.mgh add HCgroup/gamma.mgh div 2 -o group.mean.mgh Then computed the percent difference: fscalc HCgroup/gamma.mgh sub Pt_group/gamma.mgh div group.mean.mgh mul 100 -o pctdiff.mgh Now when I open my results from the first contrast above and the pctdiff.mgh separately, I am not quite sure they match. How could I adjust the min and saturation values to make them match and show how much percent difference is between the groups in the cluster shown in the main contrast. I have embedded the two results and parameters to give you an idea of how I am setting this up and if there is anything I can tune to improve visualisation.Thank you very much in advance.Pablo results from main contrast pctdiff _______________________________________________ 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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Re: [Freesurfer] Error using selexavg3-sess
by Morenikeji Adebayo 05 Oct '15

05 Oct '15

Just following up on this - thanks! > On Sep 29, 2015, at 1:29 PM, Morenikeji Adebayo <keji(a)nmr.mgh.harvard.edu> wrote: > > Hi there, > > I’m running into difficulty executing the “selexavg3-sess” command for a few participants. For example, when I run the command: > > foreach c(lh rh mni305) > selxavg3-sess -analysis analysis_encoding_stimXmem.$c -s nmasa_045_130621 -d . -no-preproc > end > > > I get the following error: > > > Error using svd > Input to SVD must not contain NaN or Inf. > > Error in cond (line 36) > s = svd(A); > > Error in fast_selxavg3 (line 279) > XCond = cond(XtX); > > Any help on this error would be much appreciated! > > Thanks, > Keji > > --- > Morenikeji Adebayo > Clinical Research Coordinator > Department of Psychiatric Neuroscience > Massachusetts General Hospital > (p) 617.643.6347 > keji(a)nmr.mgh.harvard.edu <mailto:keji@nmr.mgh.harvard.edu> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- Morenikeji Adebayo Clinical Research Coordinator Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 keji(a)nmr.mgh.harvard.edu

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Re: [Freesurfer] Longitudinal_analysis_results
by Lee Tirrell 05 Oct '15

05 Oct '15

Hi Dusan, On the RepeatedMeasuresAnova page you sent, the last command doesn't include the --surface flag. You can try running your command without that part: mri_glmfit --glmdir lh.rmanova --y lh.thickness.sm15.mgh --fsgd long.table.fsgd doss --C contrast.mtx --C contrast2.mtx --C mean.mtx Best, Lee On Tue, 29 Sep 2015, Dusan Hirjak wrote: > Dear Freesurfer Experts, > I am trying to run a longitudinal analysis. I have done the first three steps of the analysis. > Now, I am trying to visualize my results. > > However, I am having trouble doing the last step of the analysis: https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova > > bash-3.2$ mri_glmfit --glmdir lh.rmanova --y lh.thickness.sm15.mgh --fsgd long.table.fsgd doss --surface lh.thickness.sm15.mgh --C contrast.mtx --C contrast2.mtx --C mean.mtx > > gdfReadHeader: reading long.table.fsgd > > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. > > Continuous Variable Means (all subjects) > > 0 TP1-vs-TP2 0 1 > > Class Means of each Continuous Variable > > 1 Subject1 0.0000 > > 2 Subject2 0.0000 > > 3 Subject3 0.0000 > > 4 Subject4 0.0000 > > 5 Subject5 0.0000 > > 6 Subject6 0.0000 > > 7 Subject7 0.0000 > > 8 Subject8 0.0000 > > 9 Subject9 0.0000 > > 10 Subject10 0.0000 > > 11 Subject11 0.0000 > > INFO: gd2mtx_method is doss > > Reading source surface /users/dusan/MRI/Ch_Sport/lh.thickness.sm15.mgh/surf/--C.contrast.mtx > > MRISread(/users/dusan/MRI/Ch_Sport/lh.thickness.sm15.mgh/surf/--C.contrast.mtx): could not open file > > Not a directory > > mri_glmfit: could not read surface /users/dusan/MRI/Ch_Sport/lh.thickness.sm15.mgh/surf/--C.contrast.mtx > > Not a directory > > > Any suggestions what I should do??? I dont understand what/which surface shoul I use? > > Many thanks! > > > Dusan > >

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Freesurfer October 2015