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
