Freesurfer October 2017

freesurfer@nmr.mgh.harvard.edu

119 participants
179 discussions

16 Oct '17

Hello Freesurfer experts, After I run preproc-sess with this command ( preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run -s Sess01 -s Sess02 ), I get an error saying that the register.dof6.dat file is missing and I should run register-sess to create it. When I run this with the debug option (register-sess -s Sess01 -s Sess02 -d . -fsd bold -per-run -debug) the system again fails to create the register file and gives pretty much the same error preproc-sess spit out: MinCost: tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta regio_read_register(): No such file or directory Could not open bold/002/register.dof6.dat tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ERROR: reading bold/002/register.dof6.dat Cleaning up I thought of manually creating it with bbregister command but I am not sure about which scan I should use for "volume used for motion correction," and I would rather prefer to fix this with preproc-sess command. Also I attached a portion from file "register.dof6.dat.log" file I could get for my each run. I hope these excerpts help. I would deeply appreciate any help. Best, Idil COREGpreproc() done Testing if mov and target overlap Numerical result out of range mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg bold/002/tmp.bbregister.12926/reg.init.dat --out-reg bold/002/tmp.bbregister.12926/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open bold/002/tmp.bbregister.12926/reg.init.dat mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg bold/002/tmp.bbregister.12926/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/002/tmp.bbregister.12926/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open bold/002/tmp.bbregister.12926/bbr.pass1.dat MinCost: tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ERROR: reading bold/002/register.dof6.dat Cleaning up Started at Sun Oct 15 15:32:07 EDT 2017 Ended at Sun Oct 15 15:32:41 EDT 2017 BBR-Run-Time-Sec 34 bbregister Done To check results, run: tkregisterfv --mov bold/002/template.nii.gz --reg bold/002/register.dof6.lta --surfs

2 3

PETSURFER: MRTM2 volumes?
by Elijah Mak 16 Oct '17

16 Oct '17

Hi Doug, Referring to the PETSURFER tutorial for dynamic PET data, I am wondering if it is possible to obtain a volume-based equivalent of mrtm2.lh.sm05/bp.nii.gz? As I understand, bp.nii.gz is the partial-volumed corrected output that has been sampled onto the fsaverage surface. Thanks for your time again. Best Wishes, Elijah

2 5

mri_aparc2aseg output file values
by Sims, Sara A 16 Oct '17

16 Oct '17

Freesurfer people, I have a label file that I want to make into a volume file only in the white matter to use in diffusion tractography. I was told to use mri_aparc2aseg to put the labels onto the WM surface and make them into a volume. I made the label files into annotation files using the following commands: mris_label2annot --ctab clut.2lhV1.ctab --s 100206 --h lh --l /data/user/snolin/subjects_reconall/100206/label/2_LH_V1.label --a 2V1 mris_label2annot --ctab clut.2rhV1.ctab --s 100206 --h rh --l /data/user/snolin/subjects_reconall/100206/label/2_RH_V1.label --a 2V1 These ran with no errors and made annotation files. Then I ran mri_aparc2aseg using the following command: mri_aparc2aseg --s 100206 --annot 2V1 --new-ribbon This is my log file: SUBJECTS_DIR /data/user/snolin/subjects_reconall subject 100206 outvol /data/user/snolin/subjects_reconall/100206/mri/2V1+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /data/user/snolin/subjects_reconall/100206/surf/lh.white Reading lh pial surface /data/user/snolin/subjects_reconall/100206/surf/lh.pial Loading lh annotations from /data/user/snolin/subjects_reconall/100206/label/lh.2V1.annot reading colortable from annotation file... colortable with 2 entries read (originally clut.2lhV1.ctab) Reading rh white surface /data/user/snolin/subjects_reconall/100206/surf/rh.white Reading rh pial surface /data/user/snolin/subjects_reconall/100206/surf/rh.pial Loading rh annotations from /data/user/snolin/subjects_reconall/100206/label/rh.2V1.annot reading colortable from annotation file... colortable with 2 entries read (originally clut.2rhV1.ctab) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /data/user/snolin/subjects_reconall/100206/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /data/user/snolin/subjects_reconall/100206/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1764 Used brute-force search on 0 voxels Writing output aseg to /data/user/snolin/subjects_reconall/100206/mri/2V1+aseg.mgz It creates the 2V1+aseg.mgz file and I tried opening it in freeview with the color lookup table that I used when I made it into an annotation file and its all black. Without the color lookup table it is all white. Clicking around the values are 41, 0, or 2000 etc., but I can’t visually see anything. What have I done wrong here? As I mentioned before, I just want to use these label file for diffusion tractography, so if I am heading down the wrong path, I would appreciate advice. Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: linux based cluster Thank you! Sara Sims

2 1

Constrain smoothing to GM for PET data
by Elijah Mak 16 Oct '17

16 Oct '17

Hi Doug, I have used PETSURFER to derive MGX GM volumes from PET data. Now, I would like to constrain the smoothing to the GM. Is it advisable to use the PVF in the aux folder for this purpose? If not, what is the best approach do this? Thanks! Best Wishes, Elijah

3 10

R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance
by stdp82＠virgilio.it 16 Oct '17

16 Oct '17

I have applied the contrasts that we discussed in the previous mails but they produce doubt results. In summary, I aim to look at: A- Difference between groups without considerer the covariate effect (I suppose that the maps will be in the intercept folder) ---> ANOVA between 4 groups B- Clusters in which the fMRI (dependent variable) is associated to the structural data (covariate), taking in account the groups (I suppose that the maps will be in the slope folder) ---> MANOVA between 4 groups Please could you check the contrast reported below? I suspect that there are some errors because, looking at results: The slope map is the inverse in color of the intercept map and the intercept did not correspond to the results which I obtain by using G4V0 C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 C13) gr1+gr2-vs-gr3+gr4.intercept 0.25 0.25 0.25 0.25 0 0 0 0 C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.25 0.25 0.25 0.25 C15) group.effect.intercept 1 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 1 0 0 -1 0 0 0 0 C16) group.effect.slope 0 0 0 0 1 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 1 0 0 -1 Best regards Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 11-ott-2017 17.28 >A: <stdp82(a)virgilio.it>, <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: R: Re: R: Re: Map of covariance > >the rational is to make them sum to 1.0 so that the gamma.mgh file has >units of mm (or whatever the input units are). It is unimportant for >p-values. > > >On 10/10/2017 01:54 PM, stdp82(a)virgilio.it wrote: >> Thanks >> >> In which contrast I must change "1" with "0.25"? >> What is the rationale to use 0.25? >> >> >> Sent from Virgilio Mobile >> ________________________________ >> >> Il 10/10/2017, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> ha scritto: >> >> I don't understand what you mean by "where I should use" >> >> I thought I looked through all those contrasts a few weeks ago, no? >> >> >> On 10/10/2017 04:22 AM, stdp82(a)virgilio.it wrote: >>> You have suggested to use >>> 0 0 0 0 .25 .25 .25 .25 >>> to look the map where, considering the group differences, the covariate >>> predicts the dependent variable (functional connectivity) in 4GV1. >>> >>> Below I'm reporting the contrast that I have used. >>> Please could you check it and suggest correction? >>> Could you explain where I should use 0 0 0 0 .25 .25 .25 .25, please? >>> >>> Thanks >>> >>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>> C15) group.effect.intercept >>> 1 -1 0 0 0 0 0 0 >>> 1 0 -1 0 0 0 0 0 >>> 1 0 0 -1 0 0 0 0 >>> C16) group.effect.slope >>>> 0 0 0 0 1 -1 0 0 >>>> 0 0 0 0 1 0 -1 0 >>>> 0 0 0 0 1 0 0 -1 >>> >>> >>> >>> >>> >>> >>> On 10/6/17 9:24 AM, stdp82(a)virgilio.it wrote: >>>> Thank you very much. >>>> Where I should put 0 0 0 0 .25 .25 .25 .25? >>>> Which are the contrast reported below that I should modify? >>>> >>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>> C15) group.effect.intercept >>>> 1 -1 0 0 0 0 0 0 >>>> 1 0 -1 0 0 0 0 0 >>>> 1 0 0 -1 0 0 0 0 >>>> C16) group.effect.slope >>>> 0 0 0 0 1 -1 0 0 >>>> 0 0 0 0 1 0 -1 0 >>>> 0 0 0 0 1 0 0 -1 >>>> ----Messaggio originale---- >>>> Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >>>> Data: 9-ott-2017 22.56 >>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: R: Re: Map of covariance >>>> >>>> I don't know what you are asking >>>> >>>> >>>> On 10/6/17 9:24 AM, stdp82(a)virgilio.it wrote: >>>>> Thank you very much. >>>>> Where I should put 0 0 0 0 .25 .25 .25 .25? >>>>> Which are the contrast reported below that I should modify? >>>>> >>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 0 -1 >>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>>> C15) group.effect.intercept >>>>> 1 -1 0 0 0 0 0 0 >>>>> 1 0 -1 0 0 0 0 0 >>>>> 1 0 0 -1 0 0 0 0 >>>>> C16) group.effect.slope >>>>> 0 0 0 0 1 -1 0 0 >>>>> 0 0 0 0 1 0 -1 0 >>>>> 0 0 0 0 1 0 0 -1 >>>>> >>>>> >>>>>> ----Messaggio originale---- >>>>>> Da: "Douglas Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>> Data: 3-ott-2017 16.19 >>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: R: Re: Map of covariance >>>>>> >>>>>> probably you want 0 0 0 0 .25 .25 .25 .25 >>>>>> >>>>>> >>>>>> >>>>>> On 10/3/17 10:10 AM, stdp82(a)virgilio.it wrote: >>>>>>> Many thank for your response. >>>>>>> Claryfing my question on point 3, >>>>>>> When I look in group.effect.slope, the map show the group difference >>>>> removing >>>>>>> the effect of the covariate. >>>>>>> Conversely, I would to obtain the map reporting only the effect of >>>>> covariate >>>>>>> on dependent variable (functional connectivity). >>>>>>> Is possible to look on it? >>>>>>> Regards >>>>>>> Stefano >>>>>>> >>>>>>> >>>>>>>> ----Messaggio originale---- >>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>> Data: 2-ott-2017 16.58 >>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>> Ogg: Re: [Freesurfer] R: Re: R: Re: Map of covariance >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 10/01/2017 05:08 PM, stdp82(a)virgilio.it wrote: >>>>>>>>> Hi, >>>>>>>>> on 4 groups, 1 covariate (4GV1) >>>>>>>>> >>>>>>>>> I run mri_glmfit using the following .mtx >>>>>>>>> >>>>>>>>> C1) gr1-gr2_intercept 1 -1 0 0 0 0 0 0 >>>>>>>>> C2 )gr1-gr2_slope 0 0 0 0 1 -1 0 0 >>>>>>>>> C3) gr1-gr3_intercept 1 0 -1 0 0 0 0 0 >>>>>>>>> C4) gr1-gr3_slope 0 0 0 0 1 0 -1 0 >>>>>>>>> C5) gr1-gr4_intercept 1 0 0 -1 0 0 0 0 >>>>>>>>> C6) gr1-gr4_slope 0 0 0 0 1 0 -1 0 >>>>>>>> should be >>>>>>>> >>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>> >>>>>>>>> C7) gr2-gr3_intercept 0 1 -1 0 0 0 0 0 >>>>>>>>> C8) gr2-gr3_slope 0 0 0 0 0 1 -1 0 >>>>>>>>> C9) gr2-gr4_intercept 0 1 0 -1 0 0 0 0 >>>>>>>>> C10) gr2-gr4_slope 0 0 0 0 0 1 0 -1 >>>>>>>>> C11) gr3-gr4_intercept 0 0 1 -1 0 0 0 0 >>>>>>>>> C12) gr3-gr4_slope 0 0 0 0 0 0 1 -1 >>>>>>>>> C13) gr1+gr2-vs-gr3+gr4.intercept 0.5 0.5 -0.5 -0.5 0 0 0 0 >>>>>>>>> C14) gr1+gr2-vs-gr3+gr4.slope 0 0 0 0 0.5 0.5 -0.5 -0.5 >>>>>>>>> C15) group.effect.intercept >>>>>>>>> 1 -1 0 0 0 0 0 0 >>>>>>>>> 1 0 -1 0 0 0 0 0 >>>>>>>>> 1 0 0 -1 0 0 0 0 >>>>>>>>> C16) group.effect.slope >>>>>>>>> 0 0 0 0 1 -1 0 0 >>>>>>>>> 0 0 0 0 1 0 -1 0 >>>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>>> >>>>>>>>> Please: >>>>>>>>> 1) Could you check whether the all .mtx are complete and corrected, in >>>>>>>>> particular the gr1+gr2-vs-gr3+gr4.intercept and the gr1+gr2-vs- gr3+gr4. >>>>>>> slope? >>>>>>>> they look correct, except for the one i noted >>>>>>>>> 2) Could you explain the meaning of: >>>>>>>>> gr1+gr2-vs-gr3+gr4.slope - does the average slope of grp1 and grp2 >>> differ >>>>>>> from that of grp3 and 4 >>>>>>>>> gr1+gr2-vs-gr3+gr4.intercept - same >>>>>>>>> group.effect.slope - interaction between group and covariate >>>>>>>>> group.effect.intercept - is there an effect of group on the inercept >>>>>>>>> 3) Which is the contrast identifying the effect of covariate on group >>>>>>>>> differences? >>>>>>>> not sure what you mean >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> Best regards >>>>>>>>> >>>>>>>>> >>>>>>>>> Stefano >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> ----Messaggio originale---- >>>>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>> Data: 5-set-2017 22.59 >>>>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>>> Ogg: Re: [Freesurfer] R: Re: Map of covariance >>>>>>>>>> >>>>>>>>>> you would need to create a contrast to look for the interaction. If >>> you >>>>>>>>>> have four gruops and 1 covariate, then it would be >>>>>>>>>> >>>>>>>>>> 0 0 0 0 1 -1 0 0 >>>>>>>>>> >>>>>>>>>> 0 0 0 0 1 0 -1 0 >>>>>>>>>> >>>>>>>>>> 0 0 0 0 1 0 0 -1 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 09/05/2017 04:32 PM, stdp82(a)virgilio.it wrote: >>>>>>>>>>> Hi, >>>>>>>>>>> e.g., by considering two or more groups, I would like to map the >>>>> clusters >>>>>>>>>>> reporting the covariance between the functional connectivity or >>>>> cortical >>>>>>>>>>> thickness (dependent variable) and age, tacking in account the group >>>>>>>>>>> differences. >>>>>>>>>>> Instead, I'm not interested to map the group differences, taking in >>>>>>> account >>>>>>>>>>> the nuisance factors. >>>>>>>>>>> Thanks, >>>>>>>>>>> Stefano >>>>>>>>>>> >>>>>>>>>>>> ----Messaggio originale---- >>>>>>>>>>>> Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >>>>>>>>>>>> Data: 5-set-2017 18.12 >>>>>>>>>>>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>>>>>>>>>>> Ogg: Re: [Freesurfer] Map of covariance >>>>>>>>>>>> >>>>>>>>>>>> I don't understand what you are asking. can you elaborate? >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On 08/30/2017 12:50 PM, stdp82(a)virgilio.it wrote: >>>>>>>>>>>>> Hi list, >>>>>>>>>>>>> by applying a design e.g. 4GV1 in fsgd I could assess the >>> dependence >>>>>>>>>>>>> of group differences taking in account the effect of covariate. >>>>>>>>>>>>> Anyway, where I should look if I want assess the the map showing >>> the >>>>>>>>>>>>> clusters in which the dependent variable is associated to >>> covariate, >>>>>>>>>>>>> tacking in account the group difference? Please could you suggest >>> my >>>>>>>>>>>>> the path? >>>>>>>>>>>>> Thanks >>>>>>>>>>>>> >>>>>>>>>>>>> Stefano >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>> -- >>>>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>>>> MGH-NMR Center >>>>>>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>>>>> Fax: 617-726-7422 >>>>>>>>>>>> >>>>>>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >>>>> edu/transfer/outgoing/flat/greve/ >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> The information in this e-mail is intended only for the person to >>> whom >>>>>>> it >>>>>>>>> is >>>>>>>>>>>> addressed. If you believe this e-mail was sent to you in error and >>> the >>>>>>> e- >>>>>>>>> mail >>>>>>>>>>>> contains patient information, please contact the Partners Compliance >>>>>>>>> HelpLine >>>>>>>>>>> at >>>>>>>>>>>> http://www.partners.org/complianceline . If the e-mail was sent to >>> you >>>>>>> in >>>>>>>>>>> error >>>>>>>>>>>> but does not contain patient information, please contact the sender >>>>> and >>>>>>>>>>> properly >>>>>>>>>>>> dispose of the e-mail. >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Freesurfer mailing list >>>>>>>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>>>> MGH-NMR Center >>>>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>>>> Phone Number: 617-724-2358 >>>>>>>>>> Fax: 617-726-7422 >>>>>>>>>> >>>>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. >>> edu/transfer/outgoing/flat/greve/ >>>>>>>>>> _______________________________________________ >>>>>>>>>> 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 >>>>>>>>> >>>>>>>>> >>>>>>>> -- >>>>>>>> Douglas N. Greve, Ph.D. >>>>>>>> MGH-NMR Center >>>>>>>> greve(a)nmr.mgh.harvard.edu >>>>>>>> Phone Number: 617-724-2358 >>>>>>>> Fax: 617-726-7422 >>>>>>>> >>>>>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>>>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >>>>>>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>>>>> Outgoing: ftp://surfer.nmr.mgh.harvard. edu/transfer/outgoing/flat/greve/ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>> > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

2 1

Normalize to mni
by Jan Willem Koten 16 Oct '17

16 Oct '17

3 2

Generating Mean thickness surface file for volume ROI mask
by Dev vasu 16 Oct '17

16 Oct '17

Dear all, I have a ROI mask volume file and i would like to generate Mean cortical thickness surface file (i.e lh.ROI.thickness.fsaverage.mgh and rh.ROI.thickness.fsaverage.mgh) , could some one guide me how i could obtain such file. I have 120 subjects and I have done recon-all for all subjects. Thanks Vasudev

2 1

How to obtain a label for Custom ROI mask
by Dev vasu 16 Oct '17

16 Oct '17

Dear all, I have custom ROI mask ( MNI Space ) that i have prepared from Jülich atlas , I would be like to obtain corresponding surface label file, Could you please guide me necessary the steps that i have to follow inorder to obtain corresponding label for my mask. Thanks Vasudev

2 1

Questions about the transformation of DKatlas from surface to volume
by Zhiqiang Sha 16 Oct '17

16 Oct '17

Hi, I have three questions about the transformation. (1) Is Desikan-Killiany Atlas in Talairach space? The volume was transposed onto the "inflated" cortical surface based on the image in freesurfer/average/mni305.cor.mgz ? (2) DK_atlas seems to be obtained from the inflation of interface of gray and white matter. Did you release the inflated surfaces based on the inner and outer surfaces ? (3) I have transformed this atlas from surface to volume using mri_aparc2aseg with default parameters (e.g. mri_aparc2aseg --s bert). Is this transformed volume in Talariach space ? Do I need transform it to MNI space again ? I am looking forward to your reply. Thank you very much ! Best Wishes, Zhiqiang Sha

3 3

New Openings for Postdoctoral Fellows
by Thomas Yeo 16 Oct '17

16 Oct '17

Dear Everyone, My lab has new openings for postdoctoral fellows. Please see job descriptions here: https://yeolab.weebly.com/jobs.html Thanks, Thomas

1 0

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Freesurfer October 2017