yes, that is correct On 12/4/2019 5:30 AM, Ferraro, Pilar wrote: > External Email - Use Caution > > Yes, absolutely, this should work! Many Thanks! > I have just one last question concerning the colors in FreeView. > I have a fsgd file with class 1 (patients) coming first and then class 0 (hc) > after. > The contrast matrix is 1 -1 0. > Among the results I see blue and red regions 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. > > Many thanks, > > Pilar > > >>> Message: 2 >>> Date: Mon, 2 Dec 2019 16:06:54 +0000 >>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Fw: Regression Analysis accounting for one >>> variable >>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <c8973136-8b3d-801a-9e88-2d6b8fd39...@mgh.harvard.edu> >>> Content-Type: text/plain; charset="windows-1252" >>> >>> It sounds like it would be a one-group, two-variable situation, like this >>> https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf1G2V >>> Is that not correct? >>> >>> >>> On 11/28/2019 5:24 AM, Ferraro, Pilar wrote: >>> >>> 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." >>> <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu> >>> Subject: Re: [Freesurfer] [External] Freesurfer Digest, Vol 189, Issue >>> 36 >>> To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> >>> <freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: >>> <fbb77a97-61b5-fac5-e2b3-0ee327e29...@mgh.harvard.edu><mailto:fbb77a97-61b5-fac5-e2b3-0ee327e29...@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 >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191202/cec9033a/attachment-0001.html >>> >>> ------------------------------ >>> >>> Message: 3 >>> Date: Mon, 2 Dec 2019 16:08:08 +0000 >>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> >>> Subject: Re: [Freesurfer] fsfast no run directories >>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <41b08316-678f-ff4e-aa09-86993b0c7...@mgh.harvard.edu> >>> Content-Type: text/plain; charset="utf-8" >>> >>> In the bold directory, it looks like you have one run directory called "1". >>> Change this to "001" >>> >>> On 11/29/2019 1:48 AM, Renew Andrade wrote: >>> >>> 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. >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191202/eab43314/attachment-0001.html >>> >>> ------------------------------ >>> >>> Message: 4 >>> Date: Mon, 2 Dec 2019 16:10:20 +0000 >>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Problems about registration and tksurfer >>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <edc3d070-848e-d108-7fc1-df9243447...@mgh.harvard.edu> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Try using mri_vol2surf to sample your fMRI onto the surface, then load it >>> as a surface overlay in freeview >>> >>> On 11/29/2019 3:35 AM, ?? wrote: >>> >>> 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 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191202/d7963e03/attachment-0001.html >>> >>> ------------------------------ >>> >>> Message: 5 >>> Date: Mon, 2 Dec 2019 16:12:42 +0000 >>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> >>> Subject: Re: [Freesurfer] about mri_vol2surf and mri_surf2surf >>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <d49f91cf-9b15-0645-28a7-a9a557d60...@mgh.harvard.edu> >>> Content-Type: text/plain; charset="utf-8" >>> >>> >>> >>> On 11/29/2019 4:27 AM, ??? wrote: >>> >>> 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? >>> >>> It might already be on fsaverage, depending upon how you did the analysis. >>> What was your mkanalysis-sess command? >>> >>> >>> 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? >>> >>> Use bbregister >>> >>> >>> 3. For labels, can I make a mask about the BA44 area in which structure is >>> simile with the file sig.nii.gz? How? >>> Again, it depends on what space your sig.nii.gz is in. If it is in >>> fsaverage space, then you don't need to do anything more >>> >>> Best wished! >>> Qianqian Yu >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191202/0d882836/attachment-0001.html >>> >>> ------------------------------ >>> >>> Message: 6 >>> Date: Mon, 2 Dec 2019 16:18:49 +0000 >>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Multiple comparison using Monte Carlo >>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <c8beebe3-c9dc-6523-1b6d-dee753689...@mgh.harvard.edu> >>> Content-Type: text/plain; charset="utf-8" >>> >>> That will use the pre-computed ("cached") CSD files distributed with >>> FreeSurfer. This used 10,000 iterations. >>> >>> On 12/1/2019 11:34 PM, Ting Li wrote: >>> >>> External Email - Use Caution >>> >>> Dear Freesurfer Expert: >>> >>> I have used the simulation code as show below: >>> >>> >>> mri_glmfit-sim \ >>> --glmdir lh.gender_age.glmdir \ >>> --cache 4 neg \ >>> --cwp 0.05\ >>> --2spaces >>> >>> My question is how many iterations are done during this simulation? I >>> didn?t specify the iteration number. >>> >>> Why I didn?t have the csd file? >>> >>> Thanks a lot for your response! >>> >>> Best regards, >>> Ting >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191202/99d6a01e/attachment-0001.html >>> >>> ------------------------------ >>> >>> Message: 7 >>> Date: Mon, 2 Dec 2019 16:17:37 +0000 >>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> >>> Subject: Re: [Freesurfer] Question on GLM - correlation >>> To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> >>> Message-ID: <2fb25ca2-dfd3-e49e-684a-8cf439c10...@mgh.harvard.edu> >>> Content-Type: text/plain; charset="windows-1252" >>> >>> I'm not sure what you are doing here. You say that you have two continuous >>> variables, but there is only one in the fsgd file. The contrast has 3 >>> items, but it would test for the offset, not the slope. Also, why do you >>> have --no-prune? >>> >>> On 11/29/2019 3:08 PM, Barletta, Valeria wrote: >>> Dear Freesurfers, >>> I am running glmfit to assess for correlation between y and another >>> continue variable across the cortex (ficvf), correcting for the effect of >>> age, using the command: >>> >>> mri_glmfit \ >>> --y {surfname_cme}.mgh \ >>> --fsgd {contrast}.fsgd \ >>> --C {contrast}.mat \ >>> --pvr ${hemi}.ficvf.mgh" \ >>> --surf fsaverage $hemi \ >>> --glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_cme} \ >>> --no-prune >>> >>> This is my matrix: >>> 1 0 0 >>> >>> And my fsgd file: >>> >>> Title CME >>> Class MS >>> Variable age >>> Input MS069_R01_01 MS 29 >>> Input MS070_R01_02_R1year MS 44 >>> Input MS072_R01_04 MS 38 >>> Input MS073_R01_05 MS 47 >>> Input MS075_R01_07_R1year MS 34 >>> Input MS076_R01_08 MS 25 >>> Input MS077_R01_09 MS 30 >>> Input MS078_R01_10 MS 22 >>> Input MS080_R01_12 MS 52 >>> Input MS081_R01_13 MS 31 >>> Input MS082_R01_14 MS 37 >>> Input MS084_R01_16 MS 42 >>> Input MS086_R01_18 MS 28 >>> Input MS087_R01_19_R1year MS 39 >>> Input MS088_R01_20 MS 44 >>> Input MS089_R01_29 MS 44 >>> Input MS090_R01_21 MS 32 >>> Input MS091_R01_22 MS 32 >>> Input MS092_R01_23 MS 36 >>> Input MS094_R01_25 MS 47 >>> Input MS104_R01_36 MS 52 >>> >>> >>> This is the result: >>> [cid:part1.9EE9F34D.23B9DFF4@mgh.harvard.edu][cid:part2.A1889CBE.3AAE2CA4@mgh.harvard.edu] >>> >>> Am I proceeding correctly? >>> >>> Thank you, >>> Valeria >>> >>> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -------------- next part -------------- >>> An HTML attachment was scrubbed... >>> URL: >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191202/fc43917e/attachment.html >>> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: Screenshot at 2019-11-29 15-07-35.png >>> Type: image/png >>> Size: 490626 bytes >>> Desc: Screenshot at 2019-11-29 15-07-35.png >>> Url : >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191202/fc43917e/attachment.png >>> -------------- next part -------------- >>> A non-text attachment was scrubbed... >>> Name: Screenshot at 2019-11-29 15-07-41.png >>> Type: image/png >>> Size: 468240 bytes >>> Desc: Screenshot at 2019-11-29 15-07-41.png >>> Url : >>> http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20191202/fc43917e/attachment-0001.png >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> End of Freesurfer Digest, Vol 190, Issue 3 >>> ****************************************** > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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