Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30084 discussions

LGI issue?
by Miguel Ángel Rivas Fernández 02 Dec '19

02 Dec '19

External Email - Use Caution Dear Freesurfer experts, I ran the LGI in several subjects and all of them have finished without errors. However when I opened the [lr]h.pial_lgi surfaces in tksurfer I noticed that some part of the brain are not overlayed. What could be the reason? Do you recommend to do some specific quality control on the LGI output? I send to you a screenshot in attachment. Best regards, [image: Screen Shot 2019-11-27 at 16.46.14.png] [image: Screen Shot 2019-11-27 at 16.45.25.png] -- *Miguel Ángel Rivas Fernández*

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about mri_vol2surf and mri_surf2surf
by 于倩倩 02 Dec '19

02 Dec '19

External Email - Use Caution Hello, I have some questions about the command of mri_vol2surf and mri_surf2surf 1. For fMRI data, I find previous paper reported that they used standard SPM8 preprocessing routines, no normalize to standard MNI152 template. The T-map images were translated to the individual cortical surface by using mri_vol2surf function, and then by using mri_sur2surf, all images were translated to the fsaverage space for intersubject comparison. But for me, I use the FsFAST to analysis our fMRI data and get each individual P-value result about sig.nii.gz. How do I use mri_surf2surf function, for translating to fsaverage space? Would I use the preprocessing with fsaverage directly? 2. For quantitative T1 and MTV data, the pervious paper reported that they used similar method (mri_vol2surf and mri_surf2surf). Where can I get the register.dat, when I use the mri_vol2surf function? May I understand it estimates the the relation fMRI and T1? Would I use the mri_vol2surf function and obtain an individual's surf data in fsaverage space directly? 3. For labels, can I make a mask about the BA44 area in which structure is simile with the file sig.nii.gz? How? Best wished! Qianqian Yu

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Problems about registration and tksurfer
by 朱青 02 Dec '19

02 Dec '19

External Email - Use Caution Dear madam or sir, I'm a student in China who use the Freesurfer to analyse my fMRI data and overlay some results on the surface. I met some problems about registration when I map my retinotopic results on the surface. I analysed the retinotopy by the analysePRF toolbox of Kendrick Kay, and the sulutions are matrix, the rows are voxels and the column is polar angle or eccentricity. So I replaced the BOLD values by the solutions in a volume image, for example, the polar angle solution, and I used it as overlay volume image, meanwhile I used the original volume image which is same but BOLD value didn't been changed as the template image to register, but whichever methods listed in the multimodal registration I used, the overlay volume image couldn't been overlaid in correct position on the inflated surface by freeview, just like the pic1.png in the attachment, at the same time the overlay volume image could been overlaid on the orig surface in correct position like the pic2.png in the attachment, so my first problem is why the inflated surface couldn't be overlaid correctly but the orig surface could be with the same registration data and what can I do to make the overlay volume image overlay on the inflated surface in correct position by freeview? Moreover I also used tksurfer to overlay, fortunately the overlay volume image could overlay on the inflated surface in correct position. But the overlay color scale couldn't be color wheel like the red-green-blue. Furthermore, the display in the tksurfer is upside down just like the pic3.png in the attachment. So my second problem is if there are some ways to make the tksurfer color scale like the freeview and how to make the tksurfer display correctly? Best regards, Qing Zhu

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fsfast no run directories
by Renew Andrade 02 Dec '19

02 Dec '19

External Email - Use Caution Dear FreeSurfer experts:I have some issues with "preproc-sess" because I cannot seem to get the setup of the directory structure or files to connect different things(the T1 subjects with functional bold or rest files). I have this output. root@andraderenew:/home/andraderenew/Downloads/barrios/project# preproc-sess -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.sess1.log -------------------------------------------------------------- $Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $ root setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR /usr/local/freesurfer/subjects Linux andraderenew 5.0.0-36-generic #39~18.04.1-Ubuntu SMP Tue Nov 12 11:09:50 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux /home/andraderenew/Downloads/barrios/project /usr/local/freesurfer/fsfast/bin/preproc-sess -s sess1 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run vie nov 29 07:33:28 CET 2019 instem f mc 1 f fmcpr stc 1 fmcpr fmcpr.up sm 0 mask 1 brain sess1 Template ----------------------------- mktemplate-sess -s sess1 -d /home/andraderenew/Downloads/barrios/project -fsd bold -update Session: /home/andraderenew/Downloads/barrios/project/sess1 ---------------- vie nov 29 07:33:28 CET 2019 ERROR: no run directories found my working directory is root@andraderenew:/home/andraderenew/Downloads/barrios/project# pwd /home/andraderenew/Downloads/barrios/project and root@andraderenew:/home/andraderenew/Downloads/barrios/project# ls copy.sh sess1 sess2 sess4 sess6 sess8 sessidlist log sess10 sess3 sess5 sess7 sess9 sessidlist~ root@andraderenew:/home/andraderenew/Downloads/barrios/project# cd sess1 root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1# ls bold rest subjectname root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1# cd bold root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# ls 1 root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold# cd 1 root@andraderenew:/home/andraderenew/Downloads/barrios/project/sess1/bold/1# ls sub-0030689_task-resthypnotic_bold.nii.gz And that is all. If I try with tutorial data there is no problem. One of the obvious differences is SUBJECTS_DIR is pointing not to subjects in freesurfer but to another folder where also is fsaverage. I don't know if this is required or I am missing another linking file. There you can see the files I have searched with terminal. Sincerely, Andrade.

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Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue 38
by Ferraro, Pilar 02 Dec '19

02 Dec '19

External Email - Use Caution Hi, I apologize if I did not explain my issue properly. I'm interested in looking at age-related thickness reductions in 1 group (patients), but I'd like to also account for the effect of disease duration. We can say that in my case disease duration is the nuisance factor. Briefly, I have the same issue reported in here (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32860.html) but with only one group. How would you recommend to proceed? Many thanks, Pilar ________________________________ Message: 2 Date: Wed, 27 Nov 2019 16:56:20 +0000 From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue 36 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <fbb77a97-61b5-fac5-e2b3-0ee327e29ce3(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" what is the difference between and independent variable and a covariate? On 11/27/2019 6:57 AM, Ferraro, Pilar wrote: > External Email - Use Caution > > Yes, I did. > But in this case I have two factors, not only one. In particular, I have an independent variable X and a covariate I?d like to include in the model. > How would you suggest to proceed? > > > Thanks, > > Pilar > >> Message: 5 >> Date: Tue, 26 Nov 2019 21:22:34 +0000 >> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >> Subject: Re: [Freesurfer] Regression analysis correcting for 1 >> variable >> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >> Message-ID: <9ac0cfa1-6e63-7d67-695e-ee607f889655(a)mgh.harvard.edu> >> Content-Type: text/plain; charset="utf-8" >> >> did you look at the one group, one variable example here? >> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V >> >> >> On 11/25/2019 6:42 AM, Ferraro, Pilar wrote: >>> External Email - Use Caution >>> >>> Hi Freesurfer experts, >>> >>> I?ve received your last response concerning the cortical thickness comparison between patients and HC correcting for disease duration and I?ve successfully completed the procedure. >>> Thanks again! >>> Now I?m contacting you cause I?m running a different analysis and I?m struggling to understand how to proceed. >>> In particular I would like to complete a regression analysis (only in patients, therefore only one group) looking at the effect of Variable X on cortical thickness (which I assume being higher X values corresponding to lower CT values), correcting for the effect of Variable Y (disease duration). >>> When I?ve looked at the Freesurfer Wiki for finding good examples I?ve thought I can use the one group, two covariates example. >>> However, in this case I?m not sure how the FSGD file and the matrix should be organized. >>> I suppose the FSGD file can simply list the Input subjects, Variable X and Variable Y. >>> Then the matrix should be 0 -1 0. >>> Am I correct? >>> >>> Thanks for any help! >>> >>> Pilar Ferraro >>> >>> >>> >>>> ------------------------------ >>>> >>>> Message: 3 >>>> Date: Wed, 20 Nov 2019 22:40:29 +0000 >>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>> Subject: Re: [Freesurfer] Fwd: surface group analysis with qdec >>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>> Message-ID: <70fa9541-d854-4530-9180-d001cf008f04(a)mgh.harvard.edu> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> I responded to this a few days ago. Below is what I said >>>> >>>> The problem is that all of your class=0 subjects have a 0 duration >>>> meaning that you cannot compute a duration slope for this class. In this >>>> special case, you can run a different-offset, same-slope analysis with >>>> --fsgd dur.fsgd doss >>>> Change your contrast matrix to 1 -1 0 >>>> >>>> >>>> On 11/19/19 5:00 AM, Ferraro, Pilar wrote: >>>>> ????????External Email - Use Caution >>>>> >>>>> Hi, >>>>> >>>>> I?ve never got a response to my last email (you can find it below). >>>>> >>>>> Would you be able to let me know so I can proceed with the analyses? >>>>> >>>>> Many thanks, >>>>> >>>>> Pilar >>>>> >>>>>> Inizio messaggio inoltrato: >>>>>> >>>>>> *Da: *"Ferraro, Pilar" <FerraroP(a)pennmedicine.upenn.edu >>>>>> <mailto:FerraroP@pennmedicine.upenn.edu>> >>>>>> *Oggetto: **Fw: surface group analysis with qdec* >>>>>> *Data: *14 novembre 2019 3:47:42 PM CET >>>>>> *A: *"freesurfer(a)nmr.mgh.harvard.edu >>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>" >>>>>> <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>>>>> >>>>>> Hi, >>>>>> >>>>>> I'm trying to run a surface based group analysis comparing patients >>>>>> and HC, correcting for disease duration. >>>>>> I enclose here the fsgd file and the design matrix. >>>>>> I've followed all the steps of the tutorial >>>>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0)?with >>>>>> no errors. >>>>>> However, when I try to run the glm analysis with the following command: >>>>>> >>>>>> mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C >>>>>> lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir >>>>>> lh.dur.glmdir >>>>>> >>>>>> I get the error: >>>>>> >>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >>>>>> -------------------------------- >>>>>> Possible problem with experimental design: >>>>>> Check for duplicate entries and/or lack of range of >>>>>> continuous variables within a class. >>>>>> >>>>>> Of course there is no range for the continuous variable (disease >>>>>> duration) in the control group, so I'm wondering how to overcome >>>>>> this?limit and proceed correctly with the glm analysis. >>>>>> >>>>>> Many thanks in advance for any help you will provide, >>>>>> >>>>>> Pilar >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------ >>>>>> *From:*Ferraro, Pilar >>>>>> *Sent:*Monday, November 11, 2019 7:07 AM >>>>>> *To:*freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>>> <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>>>>> *Subject:*surface group analysis with qdec >>>>>> Hi! >>>>>> >>>>>> I've previously run a comparison between patients and HC using qdec, >>>>>> but now I'd like to correct the analysis for disease duration. >>>>>> I've therefore generated a second qdec.table.dat file inserting the >>>>>> disease duration column with the following structure: >>>>>> fsid group duration >>>>>> Input subj1 1 13 >>>>>> Input subj2 0 >>>>>> >>>>>> (For healthy controls group (group 0) I've tried both options, >>>>>> leaving the duration column blank or inserting 0 as a value). >>>>>> I've also left the group.level file the same of the previous analysis. >>>>>> However, when i open the new qdec.table.dat file with qdec I get >>>>>> problems in correctly uploading the data. >>>>>> In particular, I get the following error: >>>>>> >>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >>>>>> 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: >>>>>> ?This is the command line: >>>>>> ?mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh >>>>>> --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods >>>>>> --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage >>>>>> lh --label >>>>>> /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C >>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat >>>>>> --C >>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat >>>>>> >>>>>> Of course there is no range for the continuous variable (disease >>>>>> duration) in the control group, so I'm wondering how to overcome this >>>>>> and generate a?correct qdec.table.dat file. >>>>>> >>>>>> Thanks in advance for any help! >>>>>> >>>>>> Pilar >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 4 >>>> Date: Wed, 20 Nov 2019 22:45:18 +0000 >>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>> Subject: Re: [Freesurfer] Question about the input for longitudinal >>>> processing pipeline >>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>> Message-ID: <8be29ed9-8627-d005-fd9b-ca3ec56f8a5b(a)mgh.harvard.edu> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> I have not run images with contrast, but I think it should? work. Some >>>> people have tried to use the mp2rage UNI scan, but it often fails >>>> because of very bright voxels outside of the brain. If you can remove >>>> those (eg, skull stripping), then it might work. Alternatively, if you >>>> have a quantitative T1 that comes out of the mp2rage if you have the >>>> license, then you can simulate an mp1rage that will then work in FS (but >>>> it will have bias fields). If you don't have a qT1, it is not too hard >>>> to convert the UNI to qT1. Is this at 3T or 7t? >>>> >>>> On 11/19/19 5:35 AM, Darko Komneni? wrote: >>>>> ????????External Email - Use Caution >>>>> >>>>> Hi Douglas, >>>>> thanks for your reply. Indeed, in this particular data set they don't >>>>> all have contrast, which is unfortunate. But my question was also >>>>> general, if we assume that they all have contrast, would it be OK to >>>>> use those images as inputs in the longitudinal pipeline? And the same >>>>> question for mp2rage images, are they OK to use as well, or are they >>>>> not suitable for this pipeline? >>>>> Best, >>>>> Darko >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> Message: 11 >>>>> Date: Mon, 18 Nov 2019 18:41:37 +0000 >>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu >>>>> <mailto:DGREVE@mgh.harvard.edu>> >>>>> Subject: Re: [Freesurfer] Question about the input for longitudinal >>>>> ? ? ? ? processing pipeline >>>>> To: "freesurfer(a)nmr.mgh.harvard.edu >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>" >>>>> <freesurfer(a)nmr.mgh.harvard.edu >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>>>> Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa42e4(a)mgh.harvard.edu >>>>> <mailto:d5205fe6-329a-f9b4-252a-8f1857aa42e4@mgh.harvard.edu>> >>>>> Content-Type: text/plain; charset="utf-8" >>>>> >>>>> Do all images and time points have contrast? If some do and some >>>>> don't, >>>>> then I don't think you can properly do the analysis? >>>>> >>>>> On 11/15/19 10:06 AM, Darko Komneni? wrote: >>>>>> ????????External Email - Use Caution >>>>>> >>>>>> Dear Freesurfer experts, >>>>>> I wanted to run the Freesurfer's longitudinal processing pipeline >>>>>> (described here >>>>>> >>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) >>>>> on a >>>>>> series of MRI scans from a single patient. However, after >>>>> looking at >>>>>> the scans, i realized that for most time points, the patient >>>>> doesn't >>>>>> have a "simple/normal" T1 MPRAGE sequence available. Instead, they >>>>>> have a T1 sequence with a contrast agent, as well as T1 mp2rage >>>>>> sequences. >>>>>> >>>>>> Is it possible/advisable to run recon-all in general or this >>>>> pipeline >>>>>> in particular on T1 MPRAGE scans that have a contrast agent, or >>>>> that >>>>>> are mp2rage instead of MPRAGE? >>>>>> >>>>>> Thanks in advance! >>>>>> Best, >>>>>> Darko >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 5 >>>> Date: Wed, 20 Nov 2019 22:46:22 +0000 >>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>> Subject: Re: [Freesurfer] Local Gyrification Index: freesurfer version >>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>> Message-ID: <2601bc80-e87a-74b3-9227-24ca60dafd97(a)mgh.harvard.edu> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> It has not changed (and is no longer supported) >>>> >>>> On 11/19/19 6:48 AM, Steve Petersen wrote: >>>>> ????????External Email - Use Caution >>>>> >>>>> Dear Freesurfer experts, >>>>> >>>>> What freesurfer version do you recommend to perform the local >>>>> gyrification index, version 6 or 6 development version? >>>>> >>>>> >>>>> Thanks in advance. >>>>> >>>>> Best regards, >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 6 >>>> Date: Wed, 20 Nov 2019 22:51:21 +0000 >>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>> Subject: Re: [Freesurfer] Recon-all Error >>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>> Message-ID: <13cb3ba0-0342-6f84-2029-2d4ac0eb914e(a)mgh.harvard.edu> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> This is something that is being triggered by use -3T. Is there a reason >>>> you are using that option? >>>> >>>> On 11/19/19 5:15 PM, Meena M. Makary wrote: >>>>> ????????External Email - Use Caution >>>>> >>>>> Hi, >>>>> >>>>> I have been getting this error with one of my subjects Recon-all. I am >>>>> attaching the recon-all log file. any help would be appreciated! >>>>> >>>>> Meena >>>>> >>>>> -- >>>>> ? >>>>> *Meena M. Makary, Ph.D.* >>>>> Assistant Professor|Cairo University <http://bmes.cufe.edu.eg/> >>>>> Postdoctoral Fellow|Radiology, Harvard?Medical School >>>>> <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> >>>>> Postdoctoral Fellow| Athinoula A. Martinos Center, MGH >>>>> <https://www.nmr.mgh.harvard.edu/user/4550386> >>>>> Career Development and Mentoring Manager | OHBM Student and Postdoc >>>>> SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 7 >>>> Date: Wed, 20 Nov 2019 22:54:30 +0000 >>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>> Subject: Re: [Freesurfer] mask for cortical thickness >>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>> Message-ID: <f95d9228-9445-09c0-90d9-48f16e5a41f1(a)mgh.harvard.edu> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Pass the mask you want to mri_glmfit with either --label or --mask >>>> (depending on your format). You can convert the aparc to labels using >>>> mri_annotation2label , then pick the label you want. In this case, you >>>> cannot use --cache as that has been computed using whole hemi. You can >>>> generate your own MC simulation, but the better way to do this is with >>>> permutation. see >>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.… >>>> >>>> On 11/20/19 4:47 PM, Gwang-Won Kim wrote: >>>>> ????????External Email - Use Caution >>>>> >>>>> Hi there, >>>>> I would like to analyze clusterwise correction for multiple >>>>> comparisons using masks (exsample; superior frontal cortex and?middle >>>>> frontal cortex). >>>>> I know that "2spaces" means adjust p-values for two hemispheres as >>>>> follow; mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 2 abs >>>>> --2spaces. >>>>> If I use the masks such as the superior frontal cortex and?middle >>>>> frontal cortex,?how do I do? >>>>> Thanks, >>>>> Gwang-Won >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 8 >>>> Date: Wed, 20 Nov 2019 22:58:17 +0000 >>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>> Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue >>>> 26 >>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>> Message-ID: <453c8556-e0de-cf0e-f84b-65c5273e186e(a)mgh.harvard.edu> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Sorry, I don't have your fsgd file anymore. It will be computing >>>> FirstClass-SecondClass, so red means FirstClass>SecondClass >>>> >>>> On 11/19/19 6:05 AM, Ferraro, Pilar wrote: >>>>> External Email - Use Caution >>>>> >>>>> Thank you very much for your helpful reply! >>>>> I?ve kept the same fsgd file, and just edited the contrast matrix to 1 -1 0 and added the doss option to the command line, as you suggested. >>>>> I?m just a little bit confused cause now I get by default blue and red regions when I visualize the results in Freeview. Am I correct assuming that blue regions are the ones where cortical thickness is reduced in patients relative to HC correcting for disease duration? >>>>> I just wanted to ask for a confirmation since in my fsgd file class 1 (patients) comes first and then class 0 (hc). >>>>> >>>>> Many thanks, >>>>> >>>>> Pilar >>>>> >>>>> >>>>> >>>>> >>>>>> ------------------------------ >>>>>> >>>>>> Message: 6 >>>>>> Date: Mon, 18 Nov 2019 18:28:58 +0000 >>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] Fw: surface group analysis with qdec >>>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Message-ID: <b967bd8b-5fb9-0c00-7207-3944fad5c09a(a)mgh.harvard.edu> >>>>>> Content-Type: text/plain; charset="Windows-1252" >>>>>> >>>>>> The problem is that all of your class=0 subjects have a 0 duration >>>>>> meaning that you cannot compute a duration slope for this class. In this >>>>>> special case, you can run a different-offset, same-slope analysis with >>>>>> --fsgd dur.fsgd doss >>>>>> Change your contrast matrix to 1 -1 0 >>>>>> >>>>>> >>>>>> On 11/14/19 9:47 AM, Ferraro, Pilar wrote: >>>>>>> ????????External Email - Use Caution >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I'm trying to run a surface based group analysis comparing patients >>>>>>> and HC, correcting for disease duration. >>>>>>> I enclose here the fsgd file and the design matrix. >>>>>>> I've followed all the steps of the tutorial >>>>>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0)?with >>>>>>> no errors. >>>>>>> However, when I try to run the glm analysis with the following command: >>>>>>> >>>>>>> mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C >>>>>>> lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir >>>>>>> lh.dur.glmdir >>>>>>> >>>>>>> I get the error: >>>>>>> >>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >>>>>>> -------------------------------- >>>>>>> Possible problem with experimental design: >>>>>>> Check for duplicate entries and/or lack of range of >>>>>>> continuous variables within a class. >>>>>>> >>>>>>> Of course there is no range for the continuous variable (disease >>>>>>> duration) in the control group, so I'm wondering how to overcome >>>>>>> this?limit and proceed correctly with the glm analysis. >>>>>>> >>>>>>> Many thanks in advance for any help you will provide, >>>>>>> >>>>>>> Pilar >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------ >>>>>>> *From:* Ferraro, Pilar >>>>>>> *Sent:* Monday, November 11, 2019 7:07 AM >>>>>>> *To:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>> *Subject:* surface group analysis with qdec >>>>>>> Hi! >>>>>>> >>>>>>> I've previously run a comparison between patients and HC using qdec, >>>>>>> but now I'd like to correct the analysis for disease duration. >>>>>>> I've therefore generated a second qdec.table.dat file inserting the >>>>>>> disease duration column with the following structure: >>>>>>> fsid group duration >>>>>>> Input subj1 1 13 >>>>>>> Input subj2 0 >>>>>>> >>>>>>> (For healthy controls group (group 0) I've tried both options, leaving >>>>>>> the duration column blank or inserting 0 as a value). >>>>>>> I've also left the group.level file the same of the previous analysis. >>>>>>> However, when i open the new qdec.table.dat file with qdec I get >>>>>>> problems in correctly uploading the data. >>>>>>> In particular, I get the following error: >>>>>>> >>>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >>>>>>> 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: >>>>>>> ?This is the command line: >>>>>>> ?mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh >>>>>>> --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods >>>>>>> --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage >>>>>>> lh --label >>>>>>> /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C >>>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat >>>>>>> --C >>>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat >>>>>>> >>>>>>> Of course there is no range for the continuous variable (disease >>>>>>> duration) in the control group, so I'm wondering how to overcome this >>>>>>> and generate a?correct qdec.table.dat file. >>>>>>> >>>>>>> Thanks in advance for any help! >>>>>>> >>>>>>> Pilar >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> Message: 7 >>>>>> Date: Mon, 18 Nov 2019 18:30:46 +0000 >>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation >>>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Message-ID: <ff691f12-1e79-1b2d-463b-3ae47ace83c2(a)mgh.harvard.edu> >>>>>> Content-Type: text/plain; charset="utf-8" >>>>>> >>>>>> I don't understand what you are trying to do. I'm very confused by your >>>>>> mentioning of bert. What does bert have to do with any of your data? >>>>>> >>>>>> On 11/14/19 10:47 AM, An wrote: >>>>>>> ????????External Email - Use Caution >>>>>>> >>>>>>> Oops sorry for the mistakenly?reply. I will pay more attention in the >>>>>>> future. >>>>>>> >>>>>>> Bert is the folder with the anatomical data. I tried the following >>>>>>> steps with the 4D volume but failed. Then I checked the registration >>>>>>> result after bbregister and found that the volume was not registered. >>>>>>> After that I tried another 4D volume to do the steps and successfully >>>>>>> got the sampled intensity onto the surface. >>>>>>> >>>>>>> The difference between the new 4D volume I used and the previous one >>>>>>> is that there are two transformation matrices between them. The 4D >>>>>>> dataset that I previously used but failed is the volume already >>>>>>> registered to its anatomical volume(by using others tools). The new 4D >>>>>>> volume that I tried and succeed is the volume not registered. >>>>>>> >>>>>>> I have no idea why the 4D volume after the transformation would cause >>>>>>> a failed result. Could you please let me know that? >>>>>>> >>>>>>> Many thanks. >>>>>>> >>>>>>> Best, >>>>>>> An >>>>>>> >>>>>>> Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu >>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?13??? ??12:20??? >>>>>>> >>>>>>> If you have an anatomical MR that you have run through recon-all, >>>>>>> then >>>>>>> just use that one instead of bert in your steps below >>>>>>> ps. Please remember to post to the FS list and not to us personally >>>>>>> >>>>>>> On 11/12/19 8:41 PM, an wrote: >>>>>>>> ????????External Email - Use Caution >>>>>>>> >>>>>>>> Many thanks. >>>>>>>> >>>>>>>> I got the 4D fMRI dataset from others and it is not raw data. In >>>>>>> order >>>>>>>> to run mri_vol2surf, I need to calculate the register.dat for the >>>>>>>> required flag --srcreg so I tried in this way. >>>>>>>> >>>>>>>> FYI, the 4D fMRI dataset should have been registered with its >>>>>>>> anatomical MR volume by using other tools. >>>>>>>> >>>>>>>> For now I only ran the recon-all on its anatomical MR volume >>>>>>> without >>>>>>>> running the functional stream as I don't have the raw data. >>>>>>>> >>>>>>>> Should I also run the raw fMRI data from scratch by using >>>>>>> functional >>>>>>>> stream? Or if I can run mri_vol2surf independently, which command >>>>>>>> should I use to get a register.dat file? >>>>>>>> In addition, the intensity of the 4D fMRI dataset I have is between >>>>>>>> [-1, 1] and not integers, would this cause any problem? >>>>>>>> >>>>>>>> Best, >>>>>>>> An >>>>>>>> >>>>>>>> >>>>>>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote: >>>>>>>>> Don't do the 1st step. >>>>>>>>> Why are you registering it to bert? I'm pretty sure bert did not >>>>>>>>> participate in your fmri study >>>>>>>>> When you run mri_vol2surf, it will probably work better with >>>>>>>>> --projfrac 0.5 >>>>>>>>> >>>>>>>>> On 11/11/2019 1:32 PM, An wrote: >>>>>>>>>> ????????External Email - Use Caution >>>>>>>>>> >>>>>>>>>> Hi Prof. Greve, >>>>>>>>>> >>>>>>>>>> Thanks for your reply and sorry for the confusion. >>>>>>>>>> >>>>>>>>>> I have a 4D fMRI dataset with 10 time frames, where the >>>>>>> intensity of >>>>>>>>>> each voxel is between [-1,1] and not integers. I want to map the >>>>>>>>>> intensities of the volumes on its corresponding surface in >>>>>>> order to >>>>>>>>>> get the functional values on each vertex in each frame. I have >>>>>>>>>> already run its corresponding anatomical image in freesurfer. >>>>>>>>>> >>>>>>>>>> To achieve it, I tried the following steps: >>>>>>>>>> 1. conform the fmri series by using mri_convert >>>>>>>>>> 2. register the fmri series with the anatomy image by using >>>>>>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg >>>>>>> register.dat >>>>>>>>>> 3. assign values from volumes to each vertex by using >>>>>>> mri_vol2surf: >>>>>>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg >>>>>>>>>> register.dat --hemi lh >>>>>>>>>> ? ? I also tried the -regheader in mri_vol2surf: mri_vol2surf >>>>>>> --src >>>>>>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in >>>>>>> freeview. But >>>>>>>>>> after step2, the registered volume looks wrong. I am wondering >>>>>>> could >>>>>>>>>> I use bbregister to register multi-frame fMRI series to a single >>>>>>>>>> volume? >>>>>>>>>> I also tried to use --regheader to replace the --srcreg file in >>>>>>>>>> mri_vol2surf as the output register.dat in step2 is wrong. But >>>>>>> the >>>>>>>>>> output is still wrong. >>>>>>>>>> >>>>>>>>>> Many thanks. >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> An >>>>>>>>>> >>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu >>>>>>> <mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu >>>>>>> <mailto:DGREVE@mgh.harvard.edu>>> ?2019?11?11??? ??12:16??? >>>>>>>>>> ? ? ?When you say it is 4D, what do you mean? That each label >>>>>>> has its >>>>>>>>>> ? ? ?own frame? >>>>>>>>>> >>>>>>>>>> ? ? ?On 11/6/19 5:59 PM, ?? wrote: >>>>>>>>>> ? ? ?> >>>>>>>>>> ? ? ?> ????????External Email - Use Caution >>>>>>>>>> ? ? ?> >>>>>>>>>> ? ? ?> Hi there, >>>>>>>>>> ? ? ?> >>>>>>>>>> ? ? ?> I am working with creating a surface parcellation from a >>>>>>>>>> ? ? ?volumetric >>>>>>>>>> ? ? ?> parcellation and have some questions as follows: >>>>>>>>>> ? ? ?> >>>>>>>>>> ? ? ?> 1. If the volumetric parcellation is a labeled 4D >>>>>>> multi-frame >>>>>>>>>> ? ? ?dataset, >>>>>>>>>> ? ? ?> could I still use the mris_sample_parc? Or could >>>>>>> mri_vol2surf >>>>>>>>>> ? ? ?get the >>>>>>>>>> ? ? ?> sampled labels for every vertex? >>>>>>>>>> ? ? ?> >>>>>>>>>> ? ? ?> 2. For the 4D multi-frame dataset and mri_vol2surf output >>>>>>>>>> ? ? ?results, >>>>>>>>>> ? ? ?> which GUI should I use to visualize it? I tried freeview >>>>>>> for 4D >>>>>>>>>> ? ? ?> multi-frame dataset but it looks weird. >>>>>>>>>> ? ? ?> >>>>>>>>>> ? ? ?> 3. Is there any command to separate?multi-frame volume to >>>>>>>>>> ? ? ?single frame >>>>>>>>>> ? ? ?> volumes? >>>>>>>>>> ? ? ?> >>>>>>>>>> ? ? ?> Many thanks! >>>>>>>>>> ? ? ?> >>>>>>>>>> ? ? ?> >>>>>>>>>> ? ? ?> Best, >>>>>>>>>> ? ? ?> An >>>>>>>>>> ? ? ?> >>>>>>>>>> ? ? ?> _______________________________________________ >>>>>>>>>> ? ? ?> Freesurfer mailing list >>>>>>>>>> ? ? ?> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> ? ? ?<mailto:Freesurfer@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 >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> ? ? ?<mailto:Freesurfer@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 >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> <mailto:Freesurfer@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 >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> Message: 8 >>>>>> Date: Mon, 18 Nov 2019 18:31:35 +0000 >>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] Multiple comparisons >>>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Message-ID: <745185b7-5ebb-43bf-6d2d-b7328622fe5f(a)mgh.harvard.edu> >>>>>> Content-Type: text/plain; charset="utf-8" >>>>>> >>>>>> My preferred method is to use permutation >>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.… >>>>>> >>>>>> On 11/14/19 12:29 PM, Juan Rivas wrote: >>>>>>> ????????External Email - Use Caution >>>>>>> >>>>>>> I would like to know how the correction is made for multiple >>>>>>> comparisons in the statistical analysis? We are using QDEC, with False >>>>>>> Discovery Rate or Montecarlo Null-Z. Is there a better way to do that? >>>>>>> Best, >>>>>>> JC. >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> Message: 9 >>>>>> Date: Mon, 18 Nov 2019 18:38:43 +0000 >>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] Questions for PetSurfer >>>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Message-ID: <f98e29f6-3532-91ed-021f-1e947468f57f(a)mgh.harvard.edu> >>>>>> Content-Type: text/plain; charset="utf-8" >>>>>> >>>>>> >>>>>> >>>>>> On 11/15/19 4:19 AM, Soo-Jong Kim wrote: >>>>>>> ????????External Email - Use Caution >>>>>>> >>>>>>> Dear FreeSurfer experts, >>>>>>> >>>>>>> I am a student in neuroimaging using FreeSurfer. >>>>>>> I have some questions and I don't know where to send questions. >>>>>>> That's why I found this mail and writing. >>>>>>> >>>>>>> I've studied PetSurfer for partial volume correction of PET. >>>>>>> I saw the tutorial in website. >>>>>>> Originally, I want to use RBV method for pvcorrected PET for SUVR >>>>>>> analysis. >>>>>>> >>>>>>> After generating gtmseg and coregistration to make lta file, I >>>>>>> followed this code and changed some. >>>>>>> >>>>>>> *mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz * >>>>>>> *--default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov >>>>>>> --rbv --o output_pvc* >>>>>>> >>>>>>> After this, rbv.nii.gz file was generated. and SUVR analysis was >>>>>>> performed as reference region (cerebellar cortex).? But Compared to >>>>>>> original un-pvc PET, Cortex SUVR was reduced... >>>>>>> >>>>>>> In ideal pv-corrected PET, cortex SUVR was higher than?un-pvc PET. >>>>>>> >>>>>>> Is is okay if I use the output file as rbv.nii.gz ? >>>>>> Yes, it does work. Is your tracer one where you expect GM > WM? >>>>>>> in Thomas et al, 2011, >>>>>>> He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions. >>>>>>> Frontal, Temporal, Occipital and so on. (Only gray matter to correct >>>>>>> PET using RBV method) >>>>>>> >>>>>>> In that case, What are the regions to make rbv.nii.gz method in PetSurfer? >>>>>> Look in aux/seg.ctab (you can visualize the aux/seg.nii.gz) >>>>>>> Can I use the rbv.nii.gz as partial volume corrected PET from RBV method? >>>>>> Yes >>>>>>> If not, Please tell me what is the correct command of mri_gtmpvc. >>>>>>> I need only partial volume corrected PET using RBV method. >>>>>>> >>>>>>> Sincerely, >>>>>>> >>>>>>> Soo-Jong Kim >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> Message: 10 >>>>>> Date: Mon, 18 Nov 2019 18:39:32 +0000 >>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] Cortical thickness values on a vertex base >>>>>> level >>>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Message-ID: <b9a9830f-fe4d-0321-ede7-1e0a3ee82ca0(a)mgh.harvard.edu> >>>>>> Content-Type: text/plain; charset="Windows-1252" >>>>>> >>>>>> The sig file >>>>>> >>>>>> On 11/15/19 9:16 AM, Aicha Dijkshoorn wrote: >>>>>>> ????????External Email - Use Caution >>>>>>> >>>>>>> Thank you so much for your repsonse. >>>>>>> Could you maybe please tell us which input file we should use? >>>>>>> >>>>>>> Best wishes, >>>>>>> AIcha >>>>>>> ------------------------------------------------------------------------ >>>>>>> *Van:* freesurfer-bounces(a)nmr.mgh.harvard.edu >>>>>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> namens Greve, Douglas >>>>>>> N.,Ph.D. <DGREVE(a)mgh.harvard.edu> >>>>>>> *Verzonden:* donderdag 31 oktober 2019 19:16 >>>>>>> *Aan:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex >>>>>>> base level >>>>>>> You can run mri_surfcluster with your fdr threshold as the --thmin >>>>>>> value. This will output cluster number (ocn) map. This will assign the >>>>>>> cluster number to a vertex. You can then use mri_segstats with --seg >>>>>>> ocn.mgz --excludeid 0 and input being the mean thickness or area maps. >>>>>>> When you use area as thhe input, make sure to --accumulate to get the >>>>>>> total area. You can get an area map in the same way that you got the >>>>>>> thickness map, ie, mris_preproc, etc >>>>>>> >>>>>>> On 10/31/19 1:28 PM, Aicha Dijkshoorn wrote: >>>>>>>> ????????External Email - Use Caution >>>>>>>> >>>>>>>> Dear Greve, >>>>>>>> >>>>>>>> Thank you for your quick respons. >>>>>>>> >>>>>>>> Yes, I believe that is what I mean. Let me illustrate with some >>>>>>>> (fictive) data; >>>>>>>> We were able to prove these data for the entire hemisphere as can be >>>>>>>> seen below. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> *Group 1* >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> *Group 2* >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> *Difference* >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> */Sig./* >>>>>>>> >>>>>>>> Thickness >>>>>>>> >>>>>>>> (in mm) >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Left >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 1.48 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 1.46 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> .004 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> .19 >>>>>>>> >>>>>>>> Right >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 1.46 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 1.46 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> .003 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> .03 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> However, we would like to provide similar data in our vertex-base >>>>>>>> analyses: >>>>>>>> >>>>>>>> *Significantly different clusters between group 1 and group 2* >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> *Cortical thickness group 1* >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> *Cortical thickness group 2* >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> *Difference in mm2* >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> */Sig./* >>>>>>>> >>>>>>>> Left Cuneus >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 0.013 >>>>>>>> >>>>>>>> Left Fusiform gyrus >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 0.021 >>>>>>>> >>>>>>>> Right Paracentral lobule >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 0.001 >>>>>>>> >>>>>>>> Right parahippocampal gyrus >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 0.002 >>>>>>>> >>>>>>>> >>>>>>>> Does this clarify my question? >>>>>>>> >>>>>>>> Best wishes, >>>>>>>> Aicha >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------ >>>>>>>> *Van:* freesurfer-bounces(a)nmr.mgh.harvard.edu >>>>>>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> namens Greve, Douglas >>>>>>>> N.,Ph.D. <DGREVE(a)mgh.harvard.edu> >>>>>>>> *Verzonden:* donderdag 31 oktober 2019 16:25 >>>>>>>> *Aan:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex >>>>>>>> base level >>>>>>>> I'm not sure what you mean. Do you want the mean thickness of a cluster >>>>>>>> and/or its surface area? >>>>>>>> >>>>>>>> On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote: >>>>>>>>> ????????External Email - Use Caution >>>>>>>>> >>>>>>>>> Dear developers, >>>>>>>>> >>>>>>>>> For a case-control study we are comparing the cortical thickness and >>>>>>>>> cortical surface area on a vertex-base level, for which we found >>>>>>>>> significant differences throughout the brain. >>>>>>>>> >>>>>>>>> Is it possible that, in addition to the significance values (p < .05 >>>>>>>>> after FDR correction) on a vertex-base level, we can include the exact >>>>>>>>> thickness or surface area value (or difference) of the significant >>>>>>>>> clusters on a vertex base-level between the groups. In order words, to >>>>>>>>> provide some measures to highlight the size of the significant cluster >>>>>>>>> or the differences in cortical thickness / cortical surface area to >>>>>>>>> provide clinically useful context. For instance, a command comparable >>>>>>>>> to 'voxel size' in TBSS. >>>>>>>>> >>>>>>>>> As this is my first time using Freesurfer any help that you could >>>>>>>>> offer on this matter would be highly appreciated. >>>>>>>>> >>>>>>>>> Best wishes, >>>>>>>>> Brigitte Dijkshoorn >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> 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 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> Message: 11 >>>>>> Date: Mon, 18 Nov 2019 18:41:37 +0000 >>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] Question about the input for longitudinal >>>>>> processing pipeline >>>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa42e4(a)mgh.harvard.edu> >>>>>> Content-Type: text/plain; charset="utf-8" >>>>>> >>>>>> Do all images and time points have contrast? If some do and some don't, >>>>>> then I don't think you can properly do the analysis? >>>>>> >>>>>> On 11/15/19 10:06 AM, Darko Komneni? wrote: >>>>>>> ????????External Email - Use Caution >>>>>>> >>>>>>> Dear Freesurfer experts, >>>>>>> I wanted to run the Freesurfer's longitudinal processing pipeline >>>>>>> (described here >>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) on a >>>>>>> series of MRI scans from a single patient. However, after looking at >>>>>>> the scans, i realized that for most time points, the patient doesn't >>>>>>> have a "simple/normal" T1 MPRAGE sequence available. Instead, they >>>>>>> have a T1 sequence with a contrast agent, as well as T1 mp2rage >>>>>>> sequences. >>>>>>> >>>>>>> Is it possible/advisable to run recon-all in general or this pipeline >>>>>>> in particular on T1 MPRAGE scans that have a contrast agent, or that >>>>>>> are mp2rage instead of MPRAGE? >>>>>>> >>>>>>> Thanks in advance! >>>>>>> Best, >>>>>>> Darko >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> Message: 12 >>>>>> Date: Mon, 18 Nov 2019 18:45:17 +0000 >>>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>>> Subject: Re: [Freesurfer] Brain lobules pooling- request >>>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Message-ID: <a457c4e8-913e-706e-c7ef-8925c7eaad3d(a)mgh.harvard.edu> >>>>>> Content-Type: text/plain; charset="Windows-1252" >>>>>> >>>>>> sorry, it is not clear to me what is going wrong here. Did the >>>>>> mri_annotation2label command fail? or mris_anatomical_stats command? >>>>>> >>>>>> On 11/17/19 9:55 PM, Samson Nivins wrote: >>>>>>> ????????External Email - Use Caution >>>>>>> >>>>>>> Hi FreeSurfer Team, >>>>>>> >>>>>>> ????? I am interested in individual lobular volume and thickness. So I >>>>>>> have extracted based on the Q and A I created few script to run and >>>>>>> extract the data. >>>>>>> >>>>>>> However, I got few questions regarding thickness and WM >>>>>>> >>>>>>> For extracting lobular GM I used >>>>>>> >>>>>>> mri_annotation2label --subject 1014? --hemi lh --lobesStrict >>>>>>> lh.lobesStrict.annot >>>>>>> >>>>>>> mri_annotation2label --subject 1014? --hemi lh --annotation >>>>>>> lobesStrict --outdir >>>>>>> '/home/samson/Volume/freesurfer/subjects/recon-all_working/lh' >>>>>>> >>>>>>> for computing stats I used >>>>>>> >>>>>>> mris_anatomical_stats -l >>>>>>> '/home/samson/Volume/freesurfer/subjects/recon-all_working/lh/lh.occipital.label' >>>>>>> -b 1014 lh >>>>>>> >>>>>>> I am not sure, whether any command is there to export the data. >>>>>>> >>>>>>> And, the average cortical thickness which we obtain in the terminal >>>>>>> window during individual extraction, does it correspond to the lobular >>>>>>> thickness or as whole >>>>>>> >>>>>>> For example >>>>>>> >>>>>>> I extracted stats for left frontal cortex: >>>>>>> >>>>>>> I got the following details in Terminal window >>>>>>> >>>>>>> Number of vertices, Total surface area, total gray matter, average >>>>>>> cortical thickness ?. >>>>>>> >>>>>>> In this average cortical thickness ? correspond to the ROI specifc are >>>>>>> as a whole? >>>>>>> >>>>>>> Thanks for you help. >>>>>>> >>>>>>> Looking forward to hearing from you >>>>>>> >>>>>>> Cheers >>>>>>> >>>>>>> Best regards, >>>>>>> >>>>>>> Sam >>>>>>> >>>>>>> *Samson Nivins? |**PhD Student* >>>>>>> >>>>>>> ** >>>>>>> >>>>>>> *A*The University of Auckland, Liggins Institute >>>>>>> >>>>>>> Building 505, Level 2, 85 Park Road, Auckland >>>>>>> >>>>>>> *Ph *+(64) 21 256 5964 >>>>>>> >>>>>>> *E*samson.nivins(a)gmail.com <mailto:samson.nivins@gmail.com> >>>>>>> >>>>>>> *//* >>>>>>> >>>>>>> cid:image001.png@01D4C1F6.9273DF90 >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> Message: 13 >>>>>> Date: Mon, 18 Nov 2019 13:48:58 -0500 >>>>>> From: An <annaqu1024(a)gmail.com> >>>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation >>>>>> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Message-ID: >>>>>> <CAJVCUNcDB0ggDRvgbBVYBzftLTdQ42jvUhGhO0+UKe+tkniRoA(a)mail.gmail.com> >>>>>> Content-Type: text/plain; charset="utf-8" >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> I want to map the intensities of the volumes on its corresponding surface >>>>>> in order to get the functional values on each vertex in each frame. I ran >>>>>> recon-all for the anatomical volume and saved all outputs(mri,labels,surf >>>>>> and etc.) in the bert folder. I use it because I need to specify the >>>>>> required flag -s in bbregister in order to register the functional volume >>>>>> to its anatomical volume. >>>>>> >>>>>> Many thanks. >>>>>> >>>>>> Best, >>>>>> An >>>>>> >>>>>> Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> ?2019?11?18??? ??1:31??? >>>>>> >>>>>>> I don't understand what you are trying to do. I'm very confused by your >>>>>>> mentioning of bert. What does bert have to do with any of your data? >>>>>>> >>>>>>> On 11/14/19 10:47 AM, An wrote: >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> Oops sorry for the mistakenly reply. I will pay more attention in the >>>>>>>> future. >>>>>>>> >>>>>>>> Bert is the folder with the anatomical data. I tried the following >>>>>>>> steps with the 4D volume but failed. Then I checked the registration >>>>>>>> result after bbregister and found that the volume was not registered. >>>>>>>> After that I tried another 4D volume to do the steps and successfully >>>>>>>> got the sampled intensity onto the surface. >>>>>>>> >>>>>>>> The difference between the new 4D volume I used and the previous one >>>>>>>> is that there are two transformation matrices between them. The 4D >>>>>>>> dataset that I previously used but failed is the volume already >>>>>>>> registered to its anatomical volume(by using others tools). The new 4D >>>>>>>> volume that I tried and succeed is the volume not registered. >>>>>>>> >>>>>>>> I have no idea why the 4D volume after the transformation would cause >>>>>>>> a failed result. Could you please let me know that? >>>>>>>> >>>>>>>> Many thanks. >>>>>>>> >>>>>>>> Best, >>>>>>>> An >>>>>>>> >>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu >>>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?13??? ??12:20??? >>>>>>>> >>>>>>>> If you have an anatomical MR that you have run through recon-all, >>>>>>>> then >>>>>>>> just use that one instead of bert in your steps below >>>>>>>> ps. Please remember to post to the FS list and not to us personally >>>>>>>> >>>>>>>> On 11/12/19 8:41 PM, an wrote: >>>>>>>>> External Email - Use Caution >>>>>>>>> >>>>>>>>> Many thanks. >>>>>>>>> >>>>>>>>> I got the 4D fMRI dataset from others and it is not raw data. In >>>>>>>> order >>>>>>>>> to run mri_vol2surf, I need to calculate the register.dat for the >>>>>>>>> required flag --srcreg so I tried in this way. >>>>>>>>> >>>>>>>>> FYI, the 4D fMRI dataset should have been registered with its >>>>>>>>> anatomical MR volume by using other tools. >>>>>>>>> >>>>>>>>> For now I only ran the recon-all on its anatomical MR volume >>>>>>>> without >>>>>>>>> running the functional stream as I don't have the raw data. >>>>>>>>> >>>>>>>>> Should I also run the raw fMRI data from scratch by using >>>>>>>> functional >>>>>>>>> stream? Or if I can run mri_vol2surf independently, which command >>>>>>>>> should I use to get a register.dat file? >>>>>>>>> In addition, the intensity of the 4D fMRI dataset I have is between >>>>>>>>> [-1, 1] and not integers, would this cause any problem? >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> An >>>>>>>>> >>>>>>>>> >>>>>>>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote: >>>>>>>>>> Don't do the 1st step. >>>>>>>>>> Why are you registering it to bert? I'm pretty sure bert did not >>>>>>>>>> participate in your fmri study >>>>>>>>>> When you run mri_vol2surf, it will probably work better with >>>>>>>>>> --projfrac 0.5 >>>>>>>>>> >>>>>>>>>> On 11/11/2019 1:32 PM, An wrote: >>>>>>>>>>> External Email - Use Caution >>>>>>>>>>> >>>>>>>>>>> Hi Prof. Greve, >>>>>>>>>>> >>>>>>>>>>> Thanks for your reply and sorry for the confusion. >>>>>>>>>>> >>>>>>>>>>> I have a 4D fMRI dataset with 10 time frames, where the >>>>>>>> intensity of >>>>>>>>>>> each voxel is between [-1,1] and not integers. I want to map the >>>>>>>>>>> intensities of the volumes on its corresponding surface in >>>>>>>> order to >>>>>>>>>>> get the functional values on each vertex in each frame. I have >>>>>>>>>>> already run its corresponding anatomical image in freesurfer. >>>>>>>>>>> >>>>>>>>>>> To achieve it, I tried the following steps: >>>>>>>>>>> 1. conform the fmri series by using mri_convert >>>>>>>>>>> 2. register the fmri series with the anatomy image by using >>>>>>>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg >>>>>>>> register.dat >>>>>>>>>>> 3. assign values from volumes to each vertex by using >>>>>>>> mri_vol2surf: >>>>>>>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg >>>>>>>>>>> register.dat --hemi lh >>>>>>>>>>> I also tried the -regheader in mri_vol2surf: mri_vol2surf >>>>>>>> --src >>>>>>>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in >>>>>>>> freeview. But >>>>>>>>>>> after step2, the registered volume looks wrong. I am wondering >>>>>>>> could >>>>>>>>>>> I use bbregister to register multi-frame fMRI series to a single >>>>>>>>>>> volume? >>>>>>>>>>> I also tried to use --regheader to replace the --srcreg file in >>>>>>>>>>> mri_vol2surf as the output register.dat in step2 is wrong. But >>>>>>>> the >>>>>>>>>>> output is still wrong. >>>>>>>>>>> >>>>>>>>>>> Many thanks. >>>>>>>>>>> >>>>>>>>>>> Best, >>>>>>>>>>> An >>>>>>>>>>> >>>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu >>>>>>>> <mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu >>>>>>>> <mailto:DGREVE@mgh.harvard.edu>>> ?2019?11?11??? ??12:16??? >>>>>>>>>>> When you say it is 4D, what do you mean? That each label >>>>>>>> has its >>>>>>>>>>> own frame? >>>>>>>>>>> >>>>>>>>>>> On 11/6/19 5:59 PM, ?? wrote: >>>>>>>>>>>> External Email - Use Caution >>>>>>>>>>>> >>>>>>>>>>>> Hi there, >>>>>>>>>>>> >>>>>>>>>>>> I am working with creating a surface parcellation from a >>>>>>>>>>> volumetric >>>>>>>>>>>> parcellation and have some questions as follows: >>>>>>>>>>>> >>>>>>>>>>>> 1. If the volumetric parcellation is a labeled 4D >>>>>>>> multi-frame >>>>>>>>>>> dataset, >>>>>>>>>>>> could I still use the mris_sample_parc? Or could >>>>>>>> mri_vol2surf >>>>>>>>>>> get the >>>>>>>>>>>> sampled labels for every vertex? >>>>>>>>>>>> >>>>>>>>>>>> 2. For the 4D multi-frame dataset and mri_vol2surf output >>>>>>>>>>> results, >>>>>>>>>>>> which GUI should I use to visualize it? I tried freeview >>>>>>>> for 4D >>>>>>>>>>>> multi-frame dataset but it looks weird. >>>>>>>>>>>> >>>>>>>>>>>> 3. Is there any command to separate multi-frame volume to >>>>>>>>>>> single frame >>>>>>>>>>>> volumes? >>>>>>>>>>>> >>>>>>>>>>>> Many thanks! >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> Best, >>>>>>>>>>>> An >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>> <mailto:Freesurfer@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 >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>> <mailto:Freesurfer@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 >>>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>> _______________________________________________ >>>>>>>>>> Freesurfer mailing list >>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>> <mailto:Freesurfer@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 >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>

2 2

Editing a subcortical segmentation and updating aseg.stat accordingly?
by Mohammad Rashid 29 Nov '19

29 Nov '19

External Email - Use Caution Hello all, I've got a scan with an abnormally high Left-Hippocampus volume (based on the measurement in the aseg.stats file). Loading aparc+aseg.mgz and brainmask.mgz into freeview confirms that far too much matter has been labelled as Left-Hippocampus. I'd like to replace the extra Left-Hippocampus with Left-Cerebral-White-Matter. Is it sufficient to simply draw Left-Cerebral-White-Matter directly on top of the Left-Hippocampus voxels I want to replace (using the Voxel edit tool)? I also need the Left-Hippocampus volume measurement in the aseg.stats file to be updated after my edits. Presumably I need to rerun recon-all from a certain point to achieve this, but I'm not sure from which point. Also, is editing aparc+aseg.mgz is the correct way to go about this? There are many other files (such as lh.hippoSfLabels-T1.v10.mgz) that also visualize the hippocampus and also show the excessive left hippocampus labeling, so maybe I need to edit those instead. I suppose this question boils down to which file aseg.stats bases its measurements off of. Summary: -To erase voxels of one structure, is it proper to simply overwrite it with voxels of whatever other structure I want in its place? -Which file should I edit if I want the volume measurements in aseg.stats to be updated? -After I make my edit, from what point should I rerun recon-all to have aseg.stats updated accordingly? Any help is greatly appreciated.

1 0

NordicNeuroLab is hiring!
by Stian Scisly Sagevik 29 Nov '19

29 Nov '19

External Email - Use Caution Are you a math or physics major with Good Programming Skills and have a desire to making a difference to People's Lives? We at NordicNeuroLab take pride in being a leading supplier of hardware and software for functional MRI, used for diagnosis of diseases and injuries related to brain function. Our customers include hospitals and research centres worldwide. Our employees have a diverse background from different disciplines, and we offer excellent academic and career opportunities in a young, dynamic environment. We are now searching for skilled programmers to strengthen our team: https://nordicneurolab.com/blog/ Best Regards Stian Scisly Sagevik EVP Engineering NordicNeuroLab AS www.nordicneurolab.com

1 0

Applying -qcache following manual edits
by Marisa Cathryn Ross 27 Nov '19

27 Nov '19

External Email - Use Caution Hello, We have a large set of images that have been processed in FS 6.0 (on linux) with manual edits for all stages of recon-all. We would like to utilize the QDEC package to do group analyses, but did not have the -qcache flag in our pipeline when we ran recon-all. Is it possible to create the necessary fsaverage files without losing the manual edits? We have never generated these files, as -qcache has not been designated previously in our pipeline. If this is possible, how should we go about re-running recon-all with -qcache so as to not lose the manual edits? Thank you, Marisa Ross -- Marisa C. Ross, MPA PhD Candidate Neuroscience and Public Policy Program University of Wisconsin-Madison mross9(a)wisc.edu<mailto:mross9@wisc.edu>

2 1

Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue 36
by Ferraro, Pilar 27 Nov '19

27 Nov '19

External Email - Use Caution Yes, I did. But in this case I have two factors, not only one. In particular, I have an independent variable X and a covariate I’d like to include in the model. How would you suggest to proceed? Thanks, Pilar > > Message: 5 > Date: Tue, 26 Nov 2019 21:22:34 +0000 > From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] Regression analysis correcting for 1 > variable > To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <9ac0cfa1-6e63-7d67-695e-ee607f889655(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > did you look at the one group, one variable example here? > https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G1V > > > On 11/25/2019 6:42 AM, Ferraro, Pilar wrote: >> External Email - Use Caution >> >> Hi Freesurfer experts, >> >> I?ve received your last response concerning the cortical thickness comparison between patients and HC correcting for disease duration and I?ve successfully completed the procedure. >> Thanks again! >> Now I?m contacting you cause I?m running a different analysis and I?m struggling to understand how to proceed. >> In particular I would like to complete a regression analysis (only in patients, therefore only one group) looking at the effect of Variable X on cortical thickness (which I assume being higher X values corresponding to lower CT values), correcting for the effect of Variable Y (disease duration). >> When I?ve looked at the Freesurfer Wiki for finding good examples I?ve thought I can use the one group, two covariates example. >> However, in this case I?m not sure how the FSGD file and the matrix should be organized. >> I suppose the FSGD file can simply list the Input subjects, Variable X and Variable Y. >> Then the matrix should be 0 -1 0. >> Am I correct? >> >> Thanks for any help! >> >> Pilar Ferraro >> >> >> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Wed, 20 Nov 2019 22:40:29 +0000 >>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Fwd: surface group analysis with qdec >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <70fa9541-d854-4530-9180-d001cf008f04(a)mgh.harvard.edu> >>> Content-Type: text/plain; charset="utf-8" >>> >>> I responded to this a few days ago. Below is what I said >>> >>> The problem is that all of your class=0 subjects have a 0 duration >>> meaning that you cannot compute a duration slope for this class. In this >>> special case, you can run a different-offset, same-slope analysis with >>> --fsgd dur.fsgd doss >>> Change your contrast matrix to 1 -1 0 >>> >>> >>> On 11/19/19 5:00 AM, Ferraro, Pilar wrote: >>>> ????????External Email - Use Caution >>>> >>>> Hi, >>>> >>>> I?ve never got a response to my last email (you can find it below). >>>> >>>> Would you be able to let me know so I can proceed with the analyses? >>>> >>>> Many thanks, >>>> >>>> Pilar >>>> >>>>> Inizio messaggio inoltrato: >>>>> >>>>> *Da: *"Ferraro, Pilar" <FerraroP(a)pennmedicine.upenn.edu >>>>> <mailto:FerraroP@pennmedicine.upenn.edu>> >>>>> *Oggetto: **Fw: surface group analysis with qdec* >>>>> *Data: *14 novembre 2019 3:47:42 PM CET >>>>> *A: *"freesurfer(a)nmr.mgh.harvard.edu >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>" >>>>> <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>>>> >>>>> Hi, >>>>> >>>>> I'm trying to run a surface based group analysis comparing patients >>>>> and HC, correcting for disease duration. >>>>> I enclose here the fsgd file and the design matrix. >>>>> I've followed all the steps of the tutorial >>>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0)?with >>>>> no errors. >>>>> However, when I try to run the glm analysis with the following command: >>>>> >>>>> mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C >>>>> lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir >>>>> lh.dur.glmdir >>>>> >>>>> I get the error: >>>>> >>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >>>>> -------------------------------- >>>>> Possible problem with experimental design: >>>>> Check for duplicate entries and/or lack of range of >>>>> continuous variables within a class. >>>>> >>>>> Of course there is no range for the continuous variable (disease >>>>> duration) in the control group, so I'm wondering how to overcome >>>>> this?limit and proceed correctly with the glm analysis. >>>>> >>>>> Many thanks in advance for any help you will provide, >>>>> >>>>> Pilar >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------ >>>>> *From:*Ferraro, Pilar >>>>> *Sent:*Monday, November 11, 2019 7:07 AM >>>>> *To:*freesurfer@nmr.mgh.harvard.edu >>>>> <mailto:freesurfer@nmr.mgh.harvard.edu> >>>>> <freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> >>>>> *Subject:*surface group analysis with qdec >>>>> Hi! >>>>> >>>>> I've previously run a comparison between patients and HC using qdec, >>>>> but now I'd like to correct the analysis for disease duration. >>>>> I've therefore generated a second qdec.table.dat file inserting the >>>>> disease duration column with the following structure: >>>>> fsid group duration >>>>> Input subj1 1 13 >>>>> Input subj2 0 >>>>> >>>>> (For healthy controls group (group 0) I've tried both options, >>>>> leaving the duration column blank or inserting 0 as a value). >>>>> I've also left the group.level file the same of the previous analysis. >>>>> However, when i open the new qdec.table.dat file with qdec I get >>>>> problems in correctly uploading the data. >>>>> In particular, I get the following error: >>>>> >>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >>>>> 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: >>>>> ?This is the command line: >>>>> ?mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh >>>>> --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods >>>>> --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage >>>>> lh --label >>>>> /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C >>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat >>>>> --C >>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat >>>>> >>>>> Of course there is no range for the continuous variable (disease >>>>> duration) in the control group, so I'm wondering how to overcome this >>>>> and generate a?correct qdec.table.dat file. >>>>> >>>>> Thanks in advance for any help! >>>>> >>>>> Pilar >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> ------------------------------ >>> >>> Message: 4 >>> Date: Wed, 20 Nov 2019 22:45:18 +0000 >>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Question about the input for longitudinal >>> processing pipeline >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <8be29ed9-8627-d005-fd9b-ca3ec56f8a5b(a)mgh.harvard.edu> >>> Content-Type: text/plain; charset="utf-8" >>> >>> I have not run images with contrast, but I think it should? work. Some >>> people have tried to use the mp2rage UNI scan, but it often fails >>> because of very bright voxels outside of the brain. If you can remove >>> those (eg, skull stripping), then it might work. Alternatively, if you >>> have a quantitative T1 that comes out of the mp2rage if you have the >>> license, then you can simulate an mp1rage that will then work in FS (but >>> it will have bias fields). If you don't have a qT1, it is not too hard >>> to convert the UNI to qT1. Is this at 3T or 7t? >>> >>> On 11/19/19 5:35 AM, Darko Komneni? wrote: >>>> ????????External Email - Use Caution >>>> >>>> Hi Douglas, >>>> thanks for your reply. Indeed, in this particular data set they don't >>>> all have contrast, which is unfortunate. But my question was also >>>> general, if we assume that they all have contrast, would it be OK to >>>> use those images as inputs in the longitudinal pipeline? And the same >>>> question for mp2rage images, are they OK to use as well, or are they >>>> not suitable for this pipeline? >>>> Best, >>>> Darko >>>> >>>> >>>> ------------------------------ >>>> >>>> Message: 11 >>>> Date: Mon, 18 Nov 2019 18:41:37 +0000 >>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu >>>> <mailto:DGREVE@mgh.harvard.edu>> >>>> Subject: Re: [Freesurfer] Question about the input for longitudinal >>>> ? ? ? ? processing pipeline >>>> To: "freesurfer(a)nmr.mgh.harvard.edu >>>> <mailto:freesurfer@nmr.mgh.harvard.edu>" >>>> <freesurfer(a)nmr.mgh.harvard.edu >>>> <mailto:freesurfer@nmr.mgh.harvard.edu>> >>>> Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa42e4(a)mgh.harvard.edu >>>> <mailto:d5205fe6-329a-f9b4-252a-8f1857aa42e4@mgh.harvard.edu>> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Do all images and time points have contrast? If some do and some >>>> don't, >>>> then I don't think you can properly do the analysis? >>>> >>>> On 11/15/19 10:06 AM, Darko Komneni? wrote: >>>>> ????????External Email - Use Caution >>>>> >>>>> Dear Freesurfer experts, >>>>> I wanted to run the Freesurfer's longitudinal processing pipeline >>>>> (described here >>>>> >>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) >>>> on a >>>>> series of MRI scans from a single patient. However, after >>>> looking at >>>>> the scans, i realized that for most time points, the patient >>>> doesn't >>>>> have a "simple/normal" T1 MPRAGE sequence available. Instead, they >>>>> have a T1 sequence with a contrast agent, as well as T1 mp2rage >>>>> sequences. >>>>> >>>>> Is it possible/advisable to run recon-all in general or this >>>> pipeline >>>>> in particular on T1 MPRAGE scans that have a contrast agent, or >>>> that >>>>> are mp2rage instead of MPRAGE? >>>>> >>>>> Thanks in advance! >>>>> Best, >>>>> Darko >>>>> >>>>> _______________________________________________ >>>>> 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 >>> >>> >>> >>> ------------------------------ >>> >>> Message: 5 >>> Date: Wed, 20 Nov 2019 22:46:22 +0000 >>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Local Gyrification Index: freesurfer version >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <2601bc80-e87a-74b3-9227-24ca60dafd97(a)mgh.harvard.edu> >>> Content-Type: text/plain; charset="utf-8" >>> >>> It has not changed (and is no longer supported) >>> >>> On 11/19/19 6:48 AM, Steve Petersen wrote: >>>> ????????External Email - Use Caution >>>> >>>> Dear Freesurfer experts, >>>> >>>> What freesurfer version do you recommend to perform the local >>>> gyrification index, version 6 or 6 development version? >>>> >>>> >>>> Thanks in advance. >>>> >>>> Best regards, >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> ------------------------------ >>> >>> Message: 6 >>> Date: Wed, 20 Nov 2019 22:51:21 +0000 >>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Recon-all Error >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <13cb3ba0-0342-6f84-2029-2d4ac0eb914e(a)mgh.harvard.edu> >>> Content-Type: text/plain; charset="utf-8" >>> >>> This is something that is being triggered by use -3T. Is there a reason >>> you are using that option? >>> >>> On 11/19/19 5:15 PM, Meena M. Makary wrote: >>>> ????????External Email - Use Caution >>>> >>>> Hi, >>>> >>>> I have been getting this error with one of my subjects Recon-all. I am >>>> attaching the recon-all log file. any help would be appreciated! >>>> >>>> Meena >>>> >>>> -- >>>> ? >>>> *Meena M. Makary, Ph.D.* >>>> Assistant Professor|Cairo University <http://bmes.cufe.edu.eg/> >>>> Postdoctoral Fellow|Radiology, Harvard?Medical School >>>> <https://connects.catalyst.harvard.edu/Profiles/display/Person/176550> >>>> Postdoctoral Fellow| Athinoula A. Martinos Center, MGH >>>> <https://www.nmr.mgh.harvard.edu/user/4550386> >>>> Career Development and Mentoring Manager | OHBM Student and Postdoc >>>> SIG <https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3449> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> ------------------------------ >>> >>> Message: 7 >>> Date: Wed, 20 Nov 2019 22:54:30 +0000 >>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] mask for cortical thickness >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <f95d9228-9445-09c0-90d9-48f16e5a41f1(a)mgh.harvard.edu> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Pass the mask you want to mri_glmfit with either --label or --mask >>> (depending on your format). You can convert the aparc to labels using >>> mri_annotation2label , then pick the label you want. In this case, you >>> cannot use --cache as that has been computed using whole hemi. You can >>> generate your own MC simulation, but the better way to do this is with >>> permutation. see >>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.… >>> >>> On 11/20/19 4:47 PM, Gwang-Won Kim wrote: >>>> ????????External Email - Use Caution >>>> >>>> Hi there, >>>> I would like to analyze clusterwise correction for multiple >>>> comparisons using masks (exsample; superior frontal cortex and?middle >>>> frontal cortex). >>>> I know that "2spaces" means adjust p-values for two hemispheres as >>>> follow; mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 2 abs >>>> --2spaces. >>>> If I use the masks such as the superior frontal cortex and?middle >>>> frontal cortex,?how do I do? >>>> Thanks, >>>> Gwang-Won >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> ------------------------------ >>> >>> Message: 8 >>> Date: Wed, 20 Nov 2019 22:58:17 +0000 >>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>> Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue >>> 26 >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Message-ID: <453c8556-e0de-cf0e-f84b-65c5273e186e(a)mgh.harvard.edu> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Sorry, I don't have your fsgd file anymore. It will be computing >>> FirstClass-SecondClass, so red means FirstClass>SecondClass >>> >>> On 11/19/19 6:05 AM, Ferraro, Pilar wrote: >>>> External Email - Use Caution >>>> >>>> Thank you very much for your helpful reply! >>>> I?ve kept the same fsgd file, and just edited the contrast matrix to 1 -1 0 and added the doss option to the command line, as you suggested. >>>> I?m just a little bit confused cause now I get by default blue and red regions when I visualize the results in Freeview. Am I correct assuming that blue regions are the ones where cortical thickness is reduced in patients relative to HC correcting for disease duration? >>>> I just wanted to ask for a confirmation since in my fsgd file class 1 (patients) comes first and then class 0 (hc). >>>> >>>> Many thanks, >>>> >>>> Pilar >>>> >>>> >>>> >>>> >>>>> ------------------------------ >>>>> >>>>> Message: 6 >>>>> Date: Mon, 18 Nov 2019 18:28:58 +0000 >>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>> Subject: Re: [Freesurfer] Fw: surface group analysis with qdec >>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Message-ID: <b967bd8b-5fb9-0c00-7207-3944fad5c09a(a)mgh.harvard.edu> >>>>> Content-Type: text/plain; charset="Windows-1252" >>>>> >>>>> The problem is that all of your class=0 subjects have a 0 duration >>>>> meaning that you cannot compute a duration slope for this class. In this >>>>> special case, you can run a different-offset, same-slope analysis with >>>>> --fsgd dur.fsgd doss >>>>> Change your contrast matrix to 1 -1 0 >>>>> >>>>> >>>>> On 11/14/19 9:47 AM, Ferraro, Pilar wrote: >>>>>> ????????External Email - Use Caution >>>>>> >>>>>> Hi, >>>>>> >>>>>> I'm trying to run a surface based group analysis comparing patients >>>>>> and HC, correcting for disease duration. >>>>>> I enclose here the fsgd file and the design matrix. >>>>>> I've followed all the steps of the tutorial >>>>>> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0)?with >>>>>> no errors. >>>>>> However, when I try to run the glm analysis with the following command: >>>>>> >>>>>> mri_glmfit.bin --y lh.dur.thickness.10.mgh --fsgd dur.fsgd dods --C >>>>>> lh-Avg-thickness-dur-Cor.mtx --surf fsaverage lh --cortex --glmdir >>>>>> lh.dur.glmdir >>>>>> >>>>>> I get the error: >>>>>> >>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >>>>>> -------------------------------- >>>>>> Possible problem with experimental design: >>>>>> Check for duplicate entries and/or lack of range of >>>>>> continuous variables within a class. >>>>>> >>>>>> Of course there is no range for the continuous variable (disease >>>>>> duration) in the control group, so I'm wondering how to overcome >>>>>> this?limit and proceed correctly with the glm analysis. >>>>>> >>>>>> Many thanks in advance for any help you will provide, >>>>>> >>>>>> Pilar >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------ >>>>>> *From:* Ferraro, Pilar >>>>>> *Sent:* Monday, November 11, 2019 7:07 AM >>>>>> *To:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> *Subject:* surface group analysis with qdec >>>>>> Hi! >>>>>> >>>>>> I've previously run a comparison between patients and HC using qdec, >>>>>> but now I'd like to correct the analysis for disease duration. >>>>>> I've therefore generated a second qdec.table.dat file inserting the >>>>>> disease duration column with the following structure: >>>>>> fsid group duration >>>>>> Input subj1 1 13 >>>>>> Input subj2 0 >>>>>> >>>>>> (For healthy controls group (group 0) I've tried both options, leaving >>>>>> the duration column blank or inserting 0 as a value). >>>>>> I've also left the group.level file the same of the previous analysis. >>>>>> However, when i open the new qdec.table.dat file with qdec I get >>>>>> problems in correctly uploading the data. >>>>>> In particular, I get the following error: >>>>>> >>>>>> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 >>>>>> 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: >>>>>> ?This is the command line: >>>>>> ?mri_glmfit.bin --y /home/ospite/Pilar/freesurfer/qdec/Untitled/y.mgh >>>>>> --fsgd /home/ospite/Pilar/freesurfer/qdec/Untitled/qdec.fsgd dods >>>>>> --glmdir /home/ospite/Pilar/freesurfer/qdec/Untitled --surf fsaverage >>>>>> lh --label >>>>>> /home/ospite/Pilar/freesurfer/fsaverage/label/lh.aparc.label --C >>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat >>>>>> --C >>>>>> /home/ospite/Pilar/freesurfer/qdec/Untitled/contrasts/lh-Diff-1-0-Intercept-thickness.mat >>>>>> >>>>>> Of course there is no range for the continuous variable (disease >>>>>> duration) in the control group, so I'm wondering how to overcome this >>>>>> and generate a?correct qdec.table.dat file. >>>>>> >>>>>> Thanks in advance for any help! >>>>>> >>>>>> Pilar >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> Message: 7 >>>>> Date: Mon, 18 Nov 2019 18:30:46 +0000 >>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation >>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Message-ID: <ff691f12-1e79-1b2d-463b-3ae47ace83c2(a)mgh.harvard.edu> >>>>> Content-Type: text/plain; charset="utf-8" >>>>> >>>>> I don't understand what you are trying to do. I'm very confused by your >>>>> mentioning of bert. What does bert have to do with any of your data? >>>>> >>>>> On 11/14/19 10:47 AM, An wrote: >>>>>> ????????External Email - Use Caution >>>>>> >>>>>> Oops sorry for the mistakenly?reply. I will pay more attention in the >>>>>> future. >>>>>> >>>>>> Bert is the folder with the anatomical data. I tried the following >>>>>> steps with the 4D volume but failed. Then I checked the registration >>>>>> result after bbregister and found that the volume was not registered. >>>>>> After that I tried another 4D volume to do the steps and successfully >>>>>> got the sampled intensity onto the surface. >>>>>> >>>>>> The difference between the new 4D volume I used and the previous one >>>>>> is that there are two transformation matrices between them. The 4D >>>>>> dataset that I previously used but failed is the volume already >>>>>> registered to its anatomical volume(by using others tools). The new 4D >>>>>> volume that I tried and succeed is the volume not registered. >>>>>> >>>>>> I have no idea why the 4D volume after the transformation would cause >>>>>> a failed result. Could you please let me know that? >>>>>> >>>>>> Many thanks. >>>>>> >>>>>> Best, >>>>>> An >>>>>> >>>>>> Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu >>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?13??? ??12:20??? >>>>>> >>>>>> If you have an anatomical MR that you have run through recon-all, >>>>>> then >>>>>> just use that one instead of bert in your steps below >>>>>> ps. Please remember to post to the FS list and not to us personally >>>>>> >>>>>> On 11/12/19 8:41 PM, an wrote: >>>>>>> ????????External Email - Use Caution >>>>>>> >>>>>>> Many thanks. >>>>>>> >>>>>>> I got the 4D fMRI dataset from others and it is not raw data. In >>>>>> order >>>>>>> to run mri_vol2surf, I need to calculate the register.dat for the >>>>>>> required flag --srcreg so I tried in this way. >>>>>>> >>>>>>> FYI, the 4D fMRI dataset should have been registered with its >>>>>>> anatomical MR volume by using other tools. >>>>>>> >>>>>>> For now I only ran the recon-all on its anatomical MR volume >>>>>> without >>>>>>> running the functional stream as I don't have the raw data. >>>>>>> >>>>>>> Should I also run the raw fMRI data from scratch by using >>>>>> functional >>>>>>> stream? Or if I can run mri_vol2surf independently, which command >>>>>>> should I use to get a register.dat file? >>>>>>> In addition, the intensity of the 4D fMRI dataset I have is between >>>>>>> [-1, 1] and not integers, would this cause any problem? >>>>>>> >>>>>>> Best, >>>>>>> An >>>>>>> >>>>>>> >>>>>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote: >>>>>>>> Don't do the 1st step. >>>>>>>> Why are you registering it to bert? I'm pretty sure bert did not >>>>>>>> participate in your fmri study >>>>>>>> When you run mri_vol2surf, it will probably work better with >>>>>>>> --projfrac 0.5 >>>>>>>> >>>>>>>> On 11/11/2019 1:32 PM, An wrote: >>>>>>>>> ????????External Email - Use Caution >>>>>>>>> >>>>>>>>> Hi Prof. Greve, >>>>>>>>> >>>>>>>>> Thanks for your reply and sorry for the confusion. >>>>>>>>> >>>>>>>>> I have a 4D fMRI dataset with 10 time frames, where the >>>>>> intensity of >>>>>>>>> each voxel is between [-1,1] and not integers. I want to map the >>>>>>>>> intensities of the volumes on its corresponding surface in >>>>>> order to >>>>>>>>> get the functional values on each vertex in each frame. I have >>>>>>>>> already run its corresponding anatomical image in freesurfer. >>>>>>>>> >>>>>>>>> To achieve it, I tried the following steps: >>>>>>>>> 1. conform the fmri series by using mri_convert >>>>>>>>> 2. register the fmri series with the anatomy image by using >>>>>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg >>>>>> register.dat >>>>>>>>> 3. assign values from volumes to each vertex by using >>>>>> mri_vol2surf: >>>>>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg >>>>>>>>> register.dat --hemi lh >>>>>>>>> ? ? I also tried the -regheader in mri_vol2surf: mri_vol2surf >>>>>> --src >>>>>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh >>>>>>>>> >>>>>>>>> >>>>>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in >>>>>> freeview. But >>>>>>>>> after step2, the registered volume looks wrong. I am wondering >>>>>> could >>>>>>>>> I use bbregister to register multi-frame fMRI series to a single >>>>>>>>> volume? >>>>>>>>> I also tried to use --regheader to replace the --srcreg file in >>>>>>>>> mri_vol2surf as the output register.dat in step2 is wrong. But >>>>>> the >>>>>>>>> output is still wrong. >>>>>>>>> >>>>>>>>> Many thanks. >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> An >>>>>>>>> >>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu >>>>>> <mailto:DGREVE@mgh.harvard.edu> >>>>>>>>> <mailto:DGREVE@mgh.harvard.edu >>>>>> <mailto:DGREVE@mgh.harvard.edu>>> ?2019?11?11??? ??12:16??? >>>>>>>>> ? ? ?When you say it is 4D, what do you mean? That each label >>>>>> has its >>>>>>>>> ? ? ?own frame? >>>>>>>>> >>>>>>>>> ? ? ?On 11/6/19 5:59 PM, ?? wrote: >>>>>>>>> ? ? ?> >>>>>>>>> ? ? ?> ????????External Email - Use Caution >>>>>>>>> ? ? ?> >>>>>>>>> ? ? ?> Hi there, >>>>>>>>> ? ? ?> >>>>>>>>> ? ? ?> I am working with creating a surface parcellation from a >>>>>>>>> ? ? ?volumetric >>>>>>>>> ? ? ?> parcellation and have some questions as follows: >>>>>>>>> ? ? ?> >>>>>>>>> ? ? ?> 1. If the volumetric parcellation is a labeled 4D >>>>>> multi-frame >>>>>>>>> ? ? ?dataset, >>>>>>>>> ? ? ?> could I still use the mris_sample_parc? Or could >>>>>> mri_vol2surf >>>>>>>>> ? ? ?get the >>>>>>>>> ? ? ?> sampled labels for every vertex? >>>>>>>>> ? ? ?> >>>>>>>>> ? ? ?> 2. For the 4D multi-frame dataset and mri_vol2surf output >>>>>>>>> ? ? ?results, >>>>>>>>> ? ? ?> which GUI should I use to visualize it? I tried freeview >>>>>> for 4D >>>>>>>>> ? ? ?> multi-frame dataset but it looks weird. >>>>>>>>> ? ? ?> >>>>>>>>> ? ? ?> 3. Is there any command to separate?multi-frame volume to >>>>>>>>> ? ? ?single frame >>>>>>>>> ? ? ?> volumes? >>>>>>>>> ? ? ?> >>>>>>>>> ? ? ?> Many thanks! >>>>>>>>> ? ? ?> >>>>>>>>> ? ? ?> >>>>>>>>> ? ? ?> Best, >>>>>>>>> ? ? ?> An >>>>>>>>> ? ? ?> >>>>>>>>> ? ? ?> _______________________________________________ >>>>>>>>> ? ? ?> Freesurfer mailing list >>>>>>>>> ? ? ?> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> ? ? ?<mailto:Freesurfer@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 >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> ? ? ?<mailto:Freesurfer@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 >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>> _______________________________________________ >>>>>>>> Freesurfer mailing list >>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@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 >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> Message: 8 >>>>> Date: Mon, 18 Nov 2019 18:31:35 +0000 >>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>> Subject: Re: [Freesurfer] Multiple comparisons >>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Message-ID: <745185b7-5ebb-43bf-6d2d-b7328622fe5f(a)mgh.harvard.edu> >>>>> Content-Type: text/plain; charset="utf-8" >>>>> >>>>> My preferred method is to use permutation >>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.… >>>>> >>>>> On 11/14/19 12:29 PM, Juan Rivas wrote: >>>>>> ????????External Email - Use Caution >>>>>> >>>>>> I would like to know how the correction is made for multiple >>>>>> comparisons in the statistical analysis? We are using QDEC, with False >>>>>> Discovery Rate or Montecarlo Null-Z. Is there a better way to do that? >>>>>> Best, >>>>>> JC. >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> Message: 9 >>>>> Date: Mon, 18 Nov 2019 18:38:43 +0000 >>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>> Subject: Re: [Freesurfer] Questions for PetSurfer >>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Message-ID: <f98e29f6-3532-91ed-021f-1e947468f57f(a)mgh.harvard.edu> >>>>> Content-Type: text/plain; charset="utf-8" >>>>> >>>>> >>>>> >>>>> On 11/15/19 4:19 AM, Soo-Jong Kim wrote: >>>>>> ????????External Email - Use Caution >>>>>> >>>>>> Dear FreeSurfer experts, >>>>>> >>>>>> I am a student in neuroimaging using FreeSurfer. >>>>>> I have some questions and I don't know where to send questions. >>>>>> That's why I found this mail and writing. >>>>>> >>>>>> I've studied PetSurfer for partial volume correction of PET. >>>>>> I saw the tutorial in website. >>>>>> Originally, I want to use RBV method for pvcorrected PET for SUVR >>>>>> analysis. >>>>>> >>>>>> After generating gtmseg and coregistration to make lta file, I >>>>>> followed this code and changed some. >>>>>> >>>>>> *mri_gtmpvc --i PET.nii --reg subj1.reg.lta --psf 5 --seg gtmseg.mgz * >>>>>> *--default-seg-merge --auto-mask PSF .01 --no-rescale --no-reduce-fov >>>>>> --rbv --o output_pvc* >>>>>> >>>>>> After this, rbv.nii.gz file was generated. and SUVR analysis was >>>>>> performed as reference region (cerebellar cortex).? But Compared to >>>>>> original un-pvc PET, Cortex SUVR was reduced... >>>>>> >>>>>> In ideal pv-corrected PET, cortex SUVR was higher than?un-pvc PET. >>>>>> >>>>>> Is is okay if I use the output file as rbv.nii.gz ? >>>>> Yes, it does work. Is your tracer one where you expect GM > WM? >>>>>> in Thomas et al, 2011, >>>>>> He used aparc+aseg.mgz file from FreeSurfer. and he merged some regions. >>>>>> Frontal, Temporal, Occipital and so on. (Only gray matter to correct >>>>>> PET using RBV method) >>>>>> >>>>>> In that case, What are the regions to make rbv.nii.gz method in PetSurfer? >>>>> Look in aux/seg.ctab (you can visualize the aux/seg.nii.gz) >>>>>> Can I use the rbv.nii.gz as partial volume corrected PET from RBV method? >>>>> Yes >>>>>> If not, Please tell me what is the correct command of mri_gtmpvc. >>>>>> I need only partial volume corrected PET using RBV method. >>>>>> >>>>>> Sincerely, >>>>>> >>>>>> Soo-Jong Kim >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> Message: 10 >>>>> Date: Mon, 18 Nov 2019 18:39:32 +0000 >>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>> Subject: Re: [Freesurfer] Cortical thickness values on a vertex base >>>>> level >>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Message-ID: <b9a9830f-fe4d-0321-ede7-1e0a3ee82ca0(a)mgh.harvard.edu> >>>>> Content-Type: text/plain; charset="Windows-1252" >>>>> >>>>> The sig file >>>>> >>>>> On 11/15/19 9:16 AM, Aicha Dijkshoorn wrote: >>>>>> ????????External Email - Use Caution >>>>>> >>>>>> Thank you so much for your repsonse. >>>>>> Could you maybe please tell us which input file we should use? >>>>>> >>>>>> Best wishes, >>>>>> AIcha >>>>>> ------------------------------------------------------------------------ >>>>>> *Van:* freesurfer-bounces(a)nmr.mgh.harvard.edu >>>>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> namens Greve, Douglas >>>>>> N.,Ph.D. <DGREVE(a)mgh.harvard.edu> >>>>>> *Verzonden:* donderdag 31 oktober 2019 19:16 >>>>>> *Aan:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex >>>>>> base level >>>>>> You can run mri_surfcluster with your fdr threshold as the --thmin >>>>>> value. This will output cluster number (ocn) map. This will assign the >>>>>> cluster number to a vertex. You can then use mri_segstats with --seg >>>>>> ocn.mgz --excludeid 0 and input being the mean thickness or area maps. >>>>>> When you use area as thhe input, make sure to --accumulate to get the >>>>>> total area. You can get an area map in the same way that you got the >>>>>> thickness map, ie, mris_preproc, etc >>>>>> >>>>>> On 10/31/19 1:28 PM, Aicha Dijkshoorn wrote: >>>>>>> ????????External Email - Use Caution >>>>>>> >>>>>>> Dear Greve, >>>>>>> >>>>>>> Thank you for your quick respons. >>>>>>> >>>>>>> Yes, I believe that is what I mean. Let me illustrate with some >>>>>>> (fictive) data; >>>>>>> We were able to prove these data for the entire hemisphere as can be >>>>>>> seen below. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> *Group 1* >>>>>>> >>>>>>> >>>>>>> >>>>>>> *Group 2* >>>>>>> >>>>>>> >>>>>>> >>>>>>> *Difference* >>>>>>> >>>>>>> >>>>>>> >>>>>>> */Sig./* >>>>>>> >>>>>>> Thickness >>>>>>> >>>>>>> (in mm) >>>>>>> >>>>>>> >>>>>>> >>>>>>> Left >>>>>>> >>>>>>> >>>>>>> >>>>>>> 1.48 >>>>>>> >>>>>>> >>>>>>> >>>>>>> 1.46 >>>>>>> >>>>>>> >>>>>>> >>>>>>> .004 >>>>>>> >>>>>>> >>>>>>> >>>>>>> .19 >>>>>>> >>>>>>> Right >>>>>>> >>>>>>> >>>>>>> >>>>>>> 1.46 >>>>>>> >>>>>>> >>>>>>> >>>>>>> 1.46 >>>>>>> >>>>>>> >>>>>>> >>>>>>> .003 >>>>>>> >>>>>>> >>>>>>> >>>>>>> .03 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> However, we would like to provide similar data in our vertex-base >>>>>>> analyses: >>>>>>> >>>>>>> *Significantly different clusters between group 1 and group 2* >>>>>>> >>>>>>> >>>>>>> >>>>>>> *Cortical thickness group 1* >>>>>>> >>>>>>> >>>>>>> >>>>>>> *Cortical thickness group 2* >>>>>>> >>>>>>> >>>>>>> >>>>>>> *Difference in mm2* >>>>>>> >>>>>>> >>>>>>> >>>>>>> */Sig./* >>>>>>> >>>>>>> Left Cuneus >>>>>>> >>>>>>> >>>>>>> >>>>>>> ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> 0.013 >>>>>>> >>>>>>> Left Fusiform gyrus >>>>>>> >>>>>>> >>>>>>> >>>>>>> ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> 0.021 >>>>>>> >>>>>>> Right Paracentral lobule >>>>>>> >>>>>>> >>>>>>> >>>>>>> ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> 0.001 >>>>>>> >>>>>>> Right parahippocampal gyrus >>>>>>> >>>>>>> >>>>>>> >>>>>>> ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> 0.002 >>>>>>> >>>>>>> >>>>>>> Does this clarify my question? >>>>>>> >>>>>>> Best wishes, >>>>>>> Aicha >>>>>>> >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------ >>>>>>> *Van:* freesurfer-bounces(a)nmr.mgh.harvard.edu >>>>>>> <freesurfer-bounces(a)nmr.mgh.harvard.edu> namens Greve, Douglas >>>>>>> N.,Ph.D. <DGREVE(a)mgh.harvard.edu> >>>>>>> *Verzonden:* donderdag 31 oktober 2019 16:25 >>>>>>> *Aan:* freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>> *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a vertex >>>>>>> base level >>>>>>> I'm not sure what you mean. Do you want the mean thickness of a cluster >>>>>>> and/or its surface area? >>>>>>> >>>>>>> On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote: >>>>>>>> ????????External Email - Use Caution >>>>>>>> >>>>>>>> Dear developers, >>>>>>>> >>>>>>>> For a case-control study we are comparing the cortical thickness and >>>>>>>> cortical surface area on a vertex-base level, for which we found >>>>>>>> significant differences throughout the brain. >>>>>>>> >>>>>>>> Is it possible that, in addition to the significance values (p < .05 >>>>>>>> after FDR correction) on a vertex-base level, we can include the exact >>>>>>>> thickness or surface area value (or difference) of the significant >>>>>>>> clusters on a vertex base-level between the groups. In order words, to >>>>>>>> provide some measures to highlight the size of the significant cluster >>>>>>>> or the differences in cortical thickness / cortical surface area to >>>>>>>> provide clinically useful context. For instance, a command comparable >>>>>>>> to 'voxel size' in TBSS. >>>>>>>> >>>>>>>> As this is my first time using Freesurfer any help that you could >>>>>>>> offer on this matter would be highly appreciated. >>>>>>>> >>>>>>>> Best wishes, >>>>>>>> Brigitte Dijkshoorn >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> Message: 11 >>>>> Date: Mon, 18 Nov 2019 18:41:37 +0000 >>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>> Subject: Re: [Freesurfer] Question about the input for longitudinal >>>>> processing pipeline >>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Message-ID: <d5205fe6-329a-f9b4-252a-8f1857aa42e4(a)mgh.harvard.edu> >>>>> Content-Type: text/plain; charset="utf-8" >>>>> >>>>> Do all images and time points have contrast? If some do and some don't, >>>>> then I don't think you can properly do the analysis? >>>>> >>>>> On 11/15/19 10:06 AM, Darko Komneni? wrote: >>>>>> ????????External Email - Use Caution >>>>>> >>>>>> Dear Freesurfer experts, >>>>>> I wanted to run the Freesurfer's longitudinal processing pipeline >>>>>> (described here >>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing) on a >>>>>> series of MRI scans from a single patient. However, after looking at >>>>>> the scans, i realized that for most time points, the patient doesn't >>>>>> have a "simple/normal" T1 MPRAGE sequence available. Instead, they >>>>>> have a T1 sequence with a contrast agent, as well as T1 mp2rage >>>>>> sequences. >>>>>> >>>>>> Is it possible/advisable to run recon-all in general or this pipeline >>>>>> in particular on T1 MPRAGE scans that have a contrast agent, or that >>>>>> are mp2rage instead of MPRAGE? >>>>>> >>>>>> Thanks in advance! >>>>>> Best, >>>>>> Darko >>>>>> > >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> Message: 12 >>>>> Date: Mon, 18 Nov 2019 18:45:17 +0000 >>>>> From: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu> >>>>> Subject: Re: [Freesurfer] Brain lobules pooling- request >>>>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Message-ID: <a457c4e8-913e-706e-c7ef-8925c7eaad3d(a)mgh.harvard.edu> >>>>> Content-Type: text/plain; charset="Windows-1252" >>>>> >>>>> sorry, it is not clear to me what is going wrong here. Did the >>>>> mri_annotation2label command fail? or mris_anatomical_stats command? >>>>> >>>>> On 11/17/19 9:55 PM, Samson Nivins wrote: >>>>>> ????????External Email - Use Caution >>>>>> >>>>>> Hi FreeSurfer Team, >>>>>> >>>>>> ????? I am interested in individual lobular volume and thickness. So I >>>>>> have extracted based on the Q and A I created few script to run and >>>>>> extract the data. >>>>>> >>>>>> However, I got few questions regarding thickness and WM >>>>>> >>>>>> For extracting lobular GM I used >>>>>> >>>>>> mri_annotation2label --subject 1014? --hemi lh --lobesStrict >>>>>> lh.lobesStrict.annot >>>>>> >>>>>> mri_annotation2label --subject 1014? --hemi lh --annotation >>>>>> lobesStrict --outdir >>>>>> '/home/samson/Volume/freesurfer/subjects/recon-all_working/lh' >>>>>> >>>>>> for computing stats I used >>>>>> >>>>>> mris_anatomical_stats -l >>>>>> '/home/samson/Volume/freesurfer/subjects/recon-all_working/lh/lh.occipital.label' >>>>>> -b 1014 lh >>>>>> >>>>>> I am not sure, whether any command is there to export the data. >>>>>> >>>>>> And, the average cortical thickness which we obtain in the terminal >>>>>> window during individual extraction, does it correspond to the lobular >>>>>> thickness or as whole >>>>>> >>>>>> For example >>>>>> >>>>>> I extracted stats for left frontal cortex: >>>>>> >>>>>> I got the following details in Terminal window >>>>>> >>>>>> Number of vertices, Total surface area, total gray matter, average >>>>>> cortical thickness ?. >>>>>> >>>>>> In this average cortical thickness ? correspond to the ROI specifc are >>>>>> as a whole? >>>>>> >>>>>> Thanks for you help. >>>>>> >>>>>> Looking forward to hearing from you >>>>>> >>>>>> Cheers >>>>>> >>>>>> Best regards, >>>>>> >>>>>> Sam >>>>>> >>>>>> *Samson Nivins? |**PhD Student* >>>>>> >>>>>> ** >>>>>> >>>>>> *A*The University of Auckland, Liggins Institute >>>>>> >>>>>> Building 505, Level 2, 85 Park Road, Auckland >>>>>> >>>>>> *Ph *+(64) 21 256 5964 >>>>>> >>>>>> *E*samson.nivins(a)gmail.com <mailto:samson.nivins@gmail.com> >>>>>> >>>>>> *//* >>>>>> >>>>>> cid:image001.png@01D4C1F6.9273DF90 >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> ------------------------------ >>>>> >>>>> Message: 13 >>>>> Date: Mon, 18 Nov 2019 13:48:58 -0500 >>>>> From: An <annaqu1024(a)gmail.com> >>>>> Subject: Re: [Freesurfer] 4D multi-frame parcellation >>>>> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >>>>> Message-ID: >>>>> <CAJVCUNcDB0ggDRvgbBVYBzftLTdQ42jvUhGhO0+UKe+tkniRoA(a)mail.gmail.com> >>>>> Content-Type: text/plain; charset="utf-8" >>>>> >>>>> External Email - Use Caution >>>>> >>>>> I want to map the intensities of the volumes on its corresponding surface >>>>> in order to get the functional values on each vertex in each frame. I ran >>>>> recon-all for the anatomical volume and saved all outputs(mri,labels,surf >>>>> and etc.) in the bert folder. I use it because I need to specify the >>>>> required flag -s in bbregister in order to register the functional volume >>>>> to its anatomical volume. >>>>> >>>>> Many thanks. >>>>> >>>>> Best, >>>>> An >>>>> >>>>> Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu> ?2019?11?18??? ??1:31??? >>>>> >>>>>> I don't understand what you are trying to do. I'm very confused by your >>>>>> mentioning of bert. What does bert have to do with any of your data? >>>>>> >>>>>> On 11/14/19 10:47 AM, An wrote: >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> Oops sorry for the mistakenly reply. I will pay more attention in the >>>>>>> future. >>>>>>> >>>>>>> Bert is the folder with the anatomical data. I tried the following >>>>>>> steps with the 4D volume but failed. Then I checked the registration >>>>>>> result after bbregister and found that the volume was not registered. >>>>>>> After that I tried another 4D volume to do the steps and successfully >>>>>>> got the sampled intensity onto the surface. >>>>>>> >>>>>>> The difference between the new 4D volume I used and the previous one >>>>>>> is that there are two transformation matrices between them. The 4D >>>>>>> dataset that I previously used but failed is the volume already >>>>>>> registered to its anatomical volume(by using others tools). The new 4D >>>>>>> volume that I tried and succeed is the volume not registered. >>>>>>> >>>>>>> I have no idea why the 4D volume after the transformation would cause >>>>>>> a failed result. Could you please let me know that? >>>>>>> >>>>>>> Many thanks. >>>>>>> >>>>>>> Best, >>>>>>> An >>>>>>> >>>>>>> Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu >>>>>>> <mailto:DGREVE@mgh.harvard.edu>> ?2019?11?13??? ??12:20??? >>>>>>> >>>>>>> If you have an anatomical MR that you have run through recon-all, >>>>>>> then >>>>>>> just use that one instead of bert in your steps below >>>>>>> ps. Please remember to post to the FS list and not to us personally >>>>>>> >>>>>>> On 11/12/19 8:41 PM, an wrote: >>>>>>>> External Email - Use Caution >>>>>>>> >>>>>>>> Many thanks. >>>>>>>> >>>>>>>> I got the 4D fMRI dataset from others and it is not raw data. In >>>>>>> order >>>>>>>> to run mri_vol2surf, I need to calculate the register.dat for the >>>>>>>> required flag --srcreg so I tried in this way. >>>>>>>> >>>>>>>> FYI, the 4D fMRI dataset should have been registered with its >>>>>>>> anatomical MR volume by using other tools. >>>>>>>> >>>>>>>> For now I only ran the recon-all on its anatomical MR volume >>>>>>> without >>>>>>>> running the functional stream as I don't have the raw data. >>>>>>>> >>>>>>>> Should I also run the raw fMRI data from scratch by using >>>>>>> functional >>>>>>>> stream? Or if I can run mri_vol2surf independently, which command >>>>>>>> should I use to get a register.dat file? >>>>>>>> In addition, the intensity of the 4D fMRI dataset I have is between >>>>>>>> [-1, 1] and not integers, would this cause any problem? >>>>>>>> >>>>>>>> Best, >>>>>>>> An >>>>>>>> >>>>>>>> >>>>>>>> On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrote: >>>>>>>>> Don't do the 1st step. >>>>>>>>> Why are you registering it to bert? I'm pretty sure bert did not >>>>>>>>> participate in your fmri study >>>>>>>>> When you run mri_vol2surf, it will probably work better with >>>>>>>>> --projfrac 0.5 >>>>>>>>> >>>>>>>>> On 11/11/2019 1:32 PM, An wrote: >>>>>>>>>> External Email - Use Caution >>>>>>>>>> >>>>>>>>>> Hi Prof. Greve, >>>>>>>>>> >>>>>>>>>> Thanks for your reply and sorry for the confusion. >>>>>>>>>> >>>>>>>>>> I have a 4D fMRI dataset with 10 time frames, where the >>>>>>> intensity of >>>>>>>>>> each voxel is between [-1,1] and not integers. I want to map the >>>>>>>>>> intensities of the volumes on its corresponding surface in >>>>>>> order to >>>>>>>>>> get the functional values on each vertex in each frame. I have >>>>>>>>>> already run its corresponding anatomical image in freesurfer. >>>>>>>>>> >>>>>>>>>> To achieve it, I tried the following steps: >>>>>>>>>> 1. conform the fmri series by using mri_convert >>>>>>>>>> 2. register the fmri series with the anatomy image by using >>>>>>>>>> bbregister: bbregister --mov /4Dvol.nii/ --s bert --reg >>>>>>> register.dat >>>>>>>>>> 3. assign values from volumes to each vertex by using >>>>>>> mri_vol2surf: >>>>>>>>>> mri_vol2surf --src /4Dvol.nii /--out/lhtest.mgz/ --srcreg >>>>>>>>>> register.dat --hemi lh >>>>>>>>>> I also tried the -regheader in mri_vol2surf: mri_vol2surf >>>>>>> --src >>>>>>>>>> /4Dvol.nii /--out/lhtest.mgz/ --regheader bert --hemi lh >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> The /4Dvol.nii /aligns very well with the orig.mgz in >>>>>>> freeview. But >>>>>>>>>> after step2, the registered volume looks wrong. I am wondering >>>>>>> could >>>>>>>>>> I use bbregister to register multi-frame fMRI series to a single >>>>>>>>>> volume? >>>>>>>>>> I also tried to use --regheader to replace the --srcreg file in >>>>>>>>>> mri_vol2surf as the output register.dat in step2 is wrong. But >>>>>>> the >>>>>>>>>> output is still wrong. >>>>>>>>>> >>>>>>>>>> Many thanks. >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> An >>>>>>>>>> >>>>>>>>>> Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu >>>>>>> <mailto:DGREVE@mgh.harvard.edu> >>>>>>>>>> <mailto:DGREVE@mgh.harvard.edu >>>>>>> <mailto:DGREVE@mgh.harvard.edu>>> ?2019?11?11??? ??12:16??? >>>>>>>>>> When you say it is 4D, what do you mean? That each label >>>>>>> has its >>>>>>>>>> own frame? >>>>>>>>>> >>>>>>>>>> On 11/6/19 5:59 PM, ?? wrote: >>>>>>>>>>> External Email - Use Caution >>>>>>>>>>> >>>>>>>>>>> Hi there, >>>>>>>>>>> >>>>>>>>>>> I am working with creating a surface parcellation from a >>>>>>>>>> volumetric >>>>>>>>>>> parcellation and have some questions as follows: >>>>>>>>>>> >>>>>>>>>>> 1. If the volumetric parcellation is a labeled 4D >>>>>>> multi-frame >>>>>>>>>> dataset, >>>>>>>>>>> could I still use the mris_sample_parc? Or could >>>>>>> mri_vol2surf >>>>>>>>>> get the >>>>>>>>>>> sampled labels for every vertex? >>>>>>>>>>> >>>>>>>>>>> 2. For the 4D multi-frame dataset and mri_vol2surf output >>>>>>>>>> results, >>>>>>>>>>> which GUI should I use to visualize it? I tried freeview >>>>>>> for 4D >>>>>>>>>>> multi-frame dataset but it looks weird. >>>>>>>>>>> >>>>>>>>>>> 3. Is there any command to separate multi-frame volume to >>>>>>>>>> single frame >>>>>>>>>>> volumes? >>>>>>>>>>> >>>>>>>>>>> Many thanks! >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Best, >>>>>>>>>>> An >>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:Freesurfer@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 >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> <mailto:Freesurfer@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 >>>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>> _______________________________________________ >>>>>>>>> Freesurfer mailing list >>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>> <mailto:Freesurfer@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 >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>

2 1

Using individual atlas in PETSurfer
by Boris Rauchmann 27 Nov '19

27 Nov '19

External Email - Use Caution Dear all, I have a LUT, a gca file for subcortical segmentation and two gcs files for parcellation available. How can I get SUVRs for both the cortical and subcortical structures? I tried using xcerebralseg to create a individual segmentation to replace the apas+head.mgz but when I'm using gtmseg I only managed it to get results for the cortical parcellation using a annot created from the two gcs files (--ctx-annot atlas --ctab LUT). Can someone help me with this? Best, Boris

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