External Email - Use Caution Thanks Doug. Another question, how do i find the p-values for voxel-wise map corrected for multiple comparisons at a voxel (rather than cluster) level (perm.th40.abs.sig.voxel.mgh). There is no summary file for it. Best, Paul
On Wed, Aug 7, 2019 at 11:08 AM Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> wrote: > The 3 spaces is for left hemi, right hemi, and subcortical, so, if you > are using all three then correct for all 3 > > On 8/7/19 9:26 AM, miracle ozzoude wrote: > > > > External Email - Use Caution > > > > Got it. Thanks a lot doug. If i have to correct for multiple > > comparison in surface based pet analysis and mutlimodal analysis (pet > > and thickness), should i use --3spaces? > > Thank you. > > > > best, > > Paul > > > > On Mon, Aug 5, 2019 at 10:19 PM Greve, Douglas N.,Ph.D. > > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > > > I think there is still something not right. You should just have > > one mri_glmfit command for each hemisphere in which the input is > > ?h.thickness.15.mgh, the fsgdfile is project.fsgd, you then > > specify the pvrs for both groups (--pvr ?h.pvr_grp1_pet.nii.gz > > --pvr ?h.pvr_grp2_pet.niigz) and then use that first contrast. The > > second is the same as the first but with a reversed sign, but it > > is not necessary since we always use unsigned tests and show both > > signs (but you can still do it). > > > > On 8/5/2019 8:14 PM, miracle ozzoude wrote: > >> > >> External Email - Use Caution > >> > >> I think i got it now. Something like this: > >> > >> ## group1 comes first in my fsgd file. removing the effects of > >> age and education > >> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for group 2. > >> mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c > >> pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ > >> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > >> fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir > >> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c > >> pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ > >> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf fsaverage > >> lh --cortex --glmdir rh.pet.thickness.glmdir > >> > >> contrast = 0 0 0 0 0 0 1 -1 > >> > >> ##group 2 is second in my fsgd file. removing the effects of age > >> and education > >> ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for group2 > >> mri_glmfit --y lh.thickness.15.mgh --fsgd project.fsgd dods --c > >> pvr2.mtx --pvr allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > >> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir > >> rh.pet.thickness.glmdir > >> mri_glmfit --y rh.thickness.15.mgh --fsgd project.fsgd dods --c > >> pvr2.mtx --pvr allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > >> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex --glmdir > >> rh.pet.thickness.glmdir > >> > >> contrast = 0 0 0 0 0 0 -1 1 > >> > >> On Mon, Aug 5, 2019 at 6:47 PM Greve, Douglas N.,Ph.D. > >> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > >> > >> It still looks like you are using a group specific input > >> (--y). The input should be a simple file with both groups > >> (same input as you would use without pvr) > >> > >> On 8/5/2019 4:39 PM, miracooloz wrote: > >>> > >>> External Email - Use Caution > >>> > >>> Thanks Doug. How about the mri_glmfit commands? Since the > >>> contrasts are correct, I think the commands should be right. > >>> > >>> Best, > >>> Paul. > >>> > >>> > >>> > >>> Sent from my Samsung Galaxy smartphone. > >>> > >>> -------- Original message -------- > >>> From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu> > >>> <mailto:dgr...@mgh.harvard.edu> > >>> Date: 2019-08-05 15:52 (GMT-05:00) > >>> To: freesurfer@nmr.mgh.harvard.edu > >>> <mailto:freesurfer@nmr.mgh.harvard.edu> > >>> Subject: Re: [Freesurfer] Fwd: multimodal analysis (pet and > >>> cortical thickness relationship) using --pvr > >>> > >>> Yes, that contrast is correct. > >>> > >>> On 8/5/2019 3:11 PM, miracle ozzoude wrote: > >>>> > >>>> External Email - Use Caution > >>>> > >>>> Hello Doug, > >>>> > >>>> Thanks very much for your help. Your assumption was right > >>>> in that i want to run a group comparison (i.e. test for a > >>>> difference in amyloid-thickness slopes between the two > >>>> groups). However, I am having a hard time creating the > >>>> correct mri_glmfit and contrasts in this case. Based on > >>>> your advice and searching through the forum > >>>> ( > https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2019-January/060029.html > ), i > >>>> need 2 PVRs for each hemisphere in the mri_glmfit command. > >>>> I gave it another shot below. Please let me know if i am > >>>> correct. > >>>> > >>>> Thank you. > >>>> Paul. > >>>> > >>>> ## group1 comes first in my fsgd file. removing the effects > >>>> of age and education > >>>> ##amyloid-thickness. first pet pvr = 1 for group1 and 0 for > >>>> group 2. > >>>> mri_glmfit --y lh_pvr_grp1_thickness.mgh --fsgd > >>>> project.fsgd dods --c pvr1.mtx --pvr lh.pvr_grp1_pet.nii.gz \ > >>>> --pvr allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz -surf > >>>> fsaverage lh --cortex --glmdir lh.pet.thickness.glmdir > >>>> mri_glmfit --y rh_pvr_grp1_thickness.mgh --fsgd > >>>> project.fsgd dods --c pvr1.mtx --pvr rh.pvr_grp1_pet.nii.gz \ > >>>> --pvr allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz -surf > >>>> fsaverage lh --cortex --glmdir rh.pet.thickness.glmdir > >>>> > >>>> contrast = 0 0 0 0 0 0 1 -1 > >>>> > >>>> ##group 2 is second in my fsgd file. removing the effects > >>>> of age and education > >>>> ##amyloid-thickness. first pet pvr = 0 for group1 and 1 for > >>>> group2 > >>>> mri_glmfit --y lh_pvr_grp2_thickness.mgh --fsgd > >>>> project.fsgd dods --c pvr2.mtx --pvr > >>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz \ > >>>> --pvr lh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex > >>>> --glmdir rh.pet.thickness.glmdir > >>>> mri_glmfit --y rh_pvr_grp2_thickness.mgh --fsgd > >>>> project.fsgd dods --c pvr2.mtx --pvr > >>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz \ > >>>> --pvr rh.pvr_grp2_pet.nii.gz -surf fsaverage lh --cortex > >>>> --glmdir rh.pet.thickness.glmdir > >>>> > >>>> contrast = 0 0 0 0 0 0 -1 1 > >>>> > >>>> > >>>> On Mon, Aug 5, 2019 at 12:26 PM Greve, Douglas N.,Ph.D. > >>>> <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> > wrote: > >>>> > >>>> That mostly looks good. > >>>> > >>>> I would suggest is to change your smoothing command to > >>>> something like > >>>> mris_fwhm --smooth-only --s fsaverage --hemi lh --fwhm > >>>> 5 --cortex --prune --i > >>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz > >>>> allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > >>>> The only difference will be that any vertices that are > >>>> 0 in the input will be excluded (pruned) from the > >>>> smoothing mask. > >>>> > >>>> The mri_glmfit command is not right. That command looks > >>>> like it is for analyzing each group separately and > >>>> independently. If that is what you want to do, then you > >>>> don't need to go through all the extra stuff of > >>>> creating zero files, etc. I had assumed that you wanted > >>>> to do some kind of comparison between groups. If so, > >>>> then you would use a single file with all your data in > >>>> it (probably what you were using before), and your fsgd > >>>> file would have both groups. > >>>> > >>>> 1) will my fsgd file contain both groups? > >>>> yes, see above > >>>> 2) If the answer from question is yes, i should have 2 > >>>> contrasts (pvr1.mtx for group1 and pvr2.mtx for > >>>> group2). yes/no? > >>>> Again, if all you want to do is to test the pvr for > >>>> each group separately, then you don't need to go > >>>> through the processes of creating zero files, etc. In > >>>> any event, if you want to test a pvr, then you need a > >>>> contrast for it. > >>>> 3) below is a sample of my fsgd file. are the > >>>> constrasts correct? > >>>> hard to say without resolving the questions above. You > >>>> will need to have a value in the contrast for each pvr. > >>>> > >>>> > >>>> > >>>> On 8/2/2019 3:56 PM, miracle ozzoude wrote: > >>>>> > >>>>> External Email - Use Caution > >>>>> > >>>>> Hello Doug, > >>>>> > >>>>> Thanks for answering. Based on your explanation, i > >>>>> wrote out a series of command needed to execute this. > >>>>> Please let me know if i made any mistakes/correct. > >>>>> ##step1 concatenating the 10 amyloid pet volumes files > >>>>> projected to surface using mri_vol2surf for group1 > >>>>> mri_concat --f grp1.lhmgxctx --o > >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --prune > >>>>> mri_concat --f grp2.rhmgxctx --o > >>>>> allgrp1.rhmgxctx.fsaverage.sm00.nii.gz --prune > >>>>> > >>>>> ##step2 concatenating the 20 amyloid pet volumes files > >>>>> projected to surface using mri_vol2surf for group2 > >>>>> mri_concat --f grp2.lhmgxctx --o > >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --prune > >>>>> mri_concat --f grp2.rhmgxctx --o > >>>>> allgrp2.rhmgxctx.fsaverage.sm00.nii.gz --prune > >>>>> > >>>>> ##step3 smooth on the surface for each hemisphere for > >>>>> group1 > >>>>> mri_surf2surf --hemi lh --s fsaverage --sval > >>>>> allgrp1.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > >>>>> --cortex --tval allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > >>>>> mri_surf2surf --hemi rh --s fsaverage --sval > >>>>> allgrp1.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > >>>>> --cortex --tval allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > >>>>> > >>>>> ##step4 smooth on the surface for each hemisphere for > >>>>> group2 > >>>>> mri_surf2surf --hemi lh --s fsaverage --sval > >>>>> allgrp2.lhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > >>>>> --cortex --tval allgrp2.lhmgxctx.fsaverage.sm05.nii.gz > >>>>> mri_surf2surf --hemi rh --s fsaverage --sval > >>>>> allgrp2.rlhmgxctx.fsaverage.sm00.nii.gz --fwhm 5 > >>>>> --cortex --tval allgrp2.rhmgxctx.fsaverage.sm05.nii.gz > >>>>> > >>>>> ##step5 create files of zeros for group1 for each > >>>>> hemisphere > >>>>> fscalc allgrp1.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > >>>>> allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > >>>>> fscalc allgrp1.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > >>>>> allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > >>>>> > >>>>> ##step6 create files of zeros for group2 for each > >>>>> hemisphere > >>>>> fscalc allgrp2.lhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz > >>>>> fscalc allgrp2.rhmgxctx.fsaverage.sm05.nii.gz mul 0 -o > >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz > >>>>> > >>>>> ##step7 create pvr files for group1 for each hemisphere > >>>>> mri_concat allgrp1.lhmgxctx.fsaverage.sm05.nii.gz > >>>>> allgrp2.lhmgxctx.fsaverage.sm05.zero.nii.gz --o > >>>>> lh.pvr_grp1_pet.nii.gz > >>>>> mri_concat allgrp1.rhmgxctx.fsaverage.sm05.nii.gz > >>>>> allgrp2.rhmgxctx.fsaverage.sm05.zero.nii.gz --o > >>>>> rh.pvr_grp1_pet.nii.gz > >>>>> > >>>>> ##step8 create pvr files for group2 for each hemisphere > >>>>> mri_concat allgrp1.lhmgxctx.fsaverage.sm05.zero.nii.gz > >>>>> allgrp2.lhmgxctx.fsaverage.sm05.nii.gz --o > >>>>> lh.pvr_grp2_pet.nii.gz > >>>>> mri_concat allgrp1.rhmgxctx.fsaverage.sm05.zero.nii.gz > >>>>> allgrp2.rhmgxctx.fsaverage.sm05.nii.gz --o > >>>>> rh.pvr_grp2_pet.nii.gz > >>>>> > >>>>> ###-----repeat steps 1-8 for cortical thickness------- > >>>>> > >>>>> ###run glm-fit for group1 > >>>>> mri_glmfit --y lh.pvr_grp1_pet.nii.gz --fsgd > >>>>> project.fsgd dods --c pvr1.mtx --pvr > >>>>> lh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex > >>>>> --glmdir lh.grp1.pet.thickness.glmdir > >>>>> mri_glmfit --y rh.pvr_grp1_pet.nii.gz --fsgd > >>>>> project.fsgd dods --c pvr1.mtx --pvr > >>>>> rh_pvr_grp1_thickness.mgh --surf fsaverage lh --cortex > >>>>> --glmdir rh.grp1.pet.thickness.glmdir > >>>>> > >>>>> ###run glm-fit for group2 > >>>>> mri_glmfit --y lh.pvr_grp2_pet.nii.gz --fsgd > >>>>> project.fsgd dods --c pvr2.mtx --pvr > >>>>> lh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex > >>>>> --glmdir lh.grp2.pet.thickness.glmdir > >>>>> mri_glmfit --y rh.pvr_grp2_pet.nii.gz --fsgd > >>>>> project.fsgd dods --c pvr2.mtx --pvr > >>>>> rh_pvr_grp2_thickness.mgh --surf fsaverage lh --cortex > >>>>> --glmdir rh.grp2.pet.thickness.glmdir > >>>>> > >>>>> My questions. > >>>>> 1) will my fsgd file contain both groups? > >>>>> 2) If the answer from question is yes, i should have 2 > >>>>> contrasts (pvr1.mtx for group1 and pvr2.mtx for > >>>>> group2). yes/no? > >>>>> 3) below is a sample of my fsgd file. are the > >>>>> constrasts correct? > >>>>> > >>>>> Thank you very much. > >>>>> Paul. > >>>>> The fsgd file lists: > >>>>> > ------------------------------------------------------------- > >>>>> GroupDescriptorFile 1 > >>>>> Title Relationship Amy-thick reg out age and education > >>>>> Class g1 > >>>>> Class g2 > >>>>> Variable Age Education > >>>>> Input XX1 g1 60 16 > >>>>> Input YY1 g2 62 20 > >>>>> > ------------------------------------------------------------- > >>>>> matrix for group1: > >>>>> pvr1.mtx= 1 0 0 0 0 0 0 > >>>>> is there a relationship between amyloid-thickness in > group1 regressing out age > >>>>> and education? > >>>>> matrix for group2: > >>>>> pvr2.mtx= 0 1 0 0 0 0 0 > >>>>> is there a relationship between amyloid-thickness in > group2 regressing out age > >>>>> and education? > >>>>> > >>>>> On Thu, Aug 1, 2019 at 9:44 PM Greve, Douglas N.,Ph.D. > >>>>> <dgr...@mgh.harvard.edu > >>>>> <mailto:dgr...@mgh.harvard.edu>> wrote: > >>>>> > >>>>> Each PVR adds a single column to the design > >>>>> matrix. In a two group design, this can make it > >>>>> tricky to set up. Let's say you have 10 of group1 > >>>>> and 20 of group2. You will need to create two PVR > >>>>> files, each with 30=10+20 frames. In the first > >>>>> one, the first 10 frames will be cortical > >>>>> thickness (or amyloid sampled on the surface) of > >>>>> group1; the next 20 frames will be all zeros. For > >>>>> the 2nd PVR, the first 10 frames will be 0s and > >>>>> the next 20 frames will be the cortical thickness > >>>>> (or amyloid) for group2. I would start by running > >>>>> mris_preproc for the two groups separate (so 2 > >>>>> files, one with 10 frames the other 20 frames). > >>>>> Then create the file of zeros using > >>>>> fscalc group2.mgz mul 0 -o group2.zeros.mgz > >>>>> Then > >>>>> mri_concat group1.mgz group2.zeros.mgz --o pvr1.mgz > >>>>> Then create the contrast based on the FSGD, but > >>>>> then add two more numbers, one for PVR1 (which > >>>>> tests for the within group correlation), and one > >>>>> for PVR2 > >>>>> > >>>>> > >>>>> On 8/1/2019 3:14 PM, miracle ozzoude wrote: > >>>>>> > >>>>>> External Email - Use Caution > >>>>>> > >>>>>> Please, can anyone help me with this. > >>>>>> Thank you > >>>>>> > >>>>>> Paul > >>>>>> > >>>>>> ---------- Forwarded message --------- > >>>>>> From: *miracle ozzoude* <miracoo...@gmail.com > >>>>>> <mailto:miracoo...@gmail.com>> > >>>>>> Date: Wed, Jul 31, 2019 at 2:11 PM > >>>>>> Subject: multimodal analysis (pet and cortical > >>>>>> thickness relationship) using --pvr > >>>>>> To: Douglas N Greve > >>>>>> <freesurfer@nmr.mgh.harvard.edu > >>>>>> <mailto:freesurfer@nmr.mgh.harvard.edu>> > >>>>>> > >>>>>> > >>>>>> Hello Experts, > >>>>>> > >>>>>> I am performing an analysis looking at the > >>>>>> relationship between amyloid uptake and cortical > >>>>>> thickness using --pvr flag in mri_glmfit. I've 2 > >>>>>> groups and 2 variables (age and education). I > >>>>>> want to run a within group analysis while > >>>>>> regressing out age and education (i.e. Within > >>>>>> group 1, is there a negative relationship between > >>>>>> amyloid uptake and cortical thickness regressing > >>>>>> out the effects of age and education). > >>>>>> > >>>>>> However, i'm not sure how my pvr contrasts will > >>>>>> look like. Below are my fsgd and an attempt at > >>>>>> creating contrasts. Please, can you let me know > >>>>>> if my contrasts are correct based on my questions. > >>>>>> > >>>>>> Thank you. > >>>>>> > >>>>>> Best, > >>>>>> Paul > >>>>>> > >>>>>> The fsgd file lists: > >>>>>> > ------------------------------------------------------------- > >>>>>> GroupDescriptorFile 1 > >>>>>> Title Relationship Amy-thick reg out age and > education > >>>>>> Class g1 > >>>>>> Class g2 > >>>>>> Variable Age Education > >>>>>> Input XX1 g1 60 16 > >>>>>> Input XX2 g1 58 14 > >>>>>> Input YY1 g2 62 20 > >>>>>> Input YY1 g2 62 20 > >>>>>> > ------------------------------------------------------------- > >>>>>> matrix for group1: > >>>>>> pvrgroup1= 1 0 0 0 0 0 0 > >>>>>> is there a relationship between amyloid-thickness > in group1 regressing out age > >>>>>> and education? > >>>>>> matrix for group2: > >>>>>> pvrgroup2= 0 1 0 0 0 0 0 > >>>>>> is there a relationship between amyloid-thickness > in group2 regressing out age > >>>>>> and education? > >>>>>> > >>>>>> > >>>>>> > >>>>>> > >>>>>> _______________________________________________ > >>>>>> Freesurfer mailing list > >>>>>> Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > >>>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>> > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer@nmr.mgh.harvard.edu > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu > >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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