Re: [Freesurfer] Monte Carlo simulation: Talairach coordinates - Freesurfer

2 Jul 2013


      It is hard to say, since 4.5 came out 3 years ago:). It is ok to do 
group analysis in a different version of FS.
doug
ps. Please remember to copy the list instead of sending emails directly 
to us. thanks!
On 07/02/2013 01:53 PM, Emily Boeke wrote:
...
Strange, I have run simulations before in 4.5 and gotten talairach coords. Are you sure there isn't any other reason the coordinates are in this format in this simulation?
Is it generally ok to do a group analysis in a later version of freesurfer if the first level analyses have been done in 4.5? Or would you recommend redoing the individual analyses as well?
Thanks!
Emily
On Jul 2, 2013, at 12:18 PM, Douglas N Greve wrote:
...
OK, in later versions it will give you the talairach coords. I would
download 5.3 and run your group analysis in that, just be careful not to
run recon-all using 5.3 (unless you want to upgrade all your subjects).
doug
On 07/02/2013 11:48 AM, Emily Boeke wrote:
...
4.5
Emily
On Jul 2, 2013, at 11:45 AM, Douglas N Greve wrote:
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Hi Emily, what version of FS are you using?
doug
On 07/02/2013 11:41 AM, Emily Boeke wrote:
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Hi Doug,
Sorry to be overly persistent, but I just wanted to make sure you saw this email!
Thanks,
Emily
On Jul 1, 2013, at 9:20 AM, Emily Boeke wrote:
...
This was the command I ran:
mri_glmfit-sim --glmdir tal.sm.wls.pct.rfx --sim mc-z 10000 2 HvL.SBQ.2.10000.pos  --stim-sign pos
On Jun 28, 2013, at 3:29 PM, Douglas N Greve wrote:
> Hi Emily, what > doug > > > On 06/28/2013 >> Any thoughts >> >> Thanks! >> Emily >> >> On Jun 26, >> >>> Sure, here it is: >>> >>> # Cluster >>> # $Id: >>> # cwd >>> # cmdline >>> # sysname  Linux >>> # hostname compute-0-114 >>> # machine  x86_64 >>> # user     eboeke01 >>> # Input Volume: >>> # Frame Number:      0 >>> # Minimum Threshold: 2 >>> # Maximum >>> # Threshold Sign:    pos >>> # AdjustThreshWhenOneTail >>> # Size Threshold: >>> # Size Threshold: >>> # Voxel Size: >>> # Registration: >>> # Mask Vol: >>> # Mask Thresh: >>> # Mask Sign:         abs >>> # Mask Invert:       0 >>> # AllowDiag:         0 >>> # NClusters          192 >>> # CSD thresh  2.000000 >>> # CSD nreps    10000 >>> # CSD simtype  mc-z >>> # CSD contrast group >>> # CSD confint  90.000000 >>> # >>> # Reporting >>> # Cluster >>>   1 >>>   2 >>>   3        1124 >>>   4 >>>   5 >>>   6 >>>   7 >>>   8 >>>   9 >>> 10         150 >>> 11         298 >>> 12         343 >>> 13         467 >>> 14         276 >>> 15         134 >>> 16          75 >>> 17          74 >>> 18          45 >>> 19          15 >>> 20          55 >>> 21          79 >>> 22          35 >>> 23          44 >>> 24          14 >>> 25          71 >>> 26           5 >>> 27         130 >>> 28          81 >>> 29          73 >>> 30          16 >>> 31          28 >>> 32          11 >>> 33           5 >>> 34          16 >>> 35          23 >>> 36          28 >>> 37          23 >>> 38           7 >>> 39          49 >>> 40          42 >>> 41          37 >>> 42          21 >>> 43          32 >>> 44          12 >>> 45          50 >>> 46          22 >>> 47          12 >>> 48          27 >>> 49          16 >>> 50          37 >>> 51          22 >>> 52          39 >>> 53           7 >>> 54           6 >>> 55          10 >>> 56          13 >>> 57           6 >>> 58          15 >>> 59          16 >>> 60           4 >>> 61          37 >>> 62          10 >>> 63          20 >>> 64           2 >>> 65           9 >>> 66           6 >>> 67          39 >>> 68          11 >>> 69           6 >>> 70           8 >>> 71           4 >>> 72           3 >>> 73           8 >>> 74          12 >>> 75           3 >>> 76           9 >>> 77          18 >>> 78           6 >>> 79           7 >>> 80           6 >>> 81          14 >>> 82          11 >>> 83           5 >>> 84          10 >>> 85           9 >>> 86           7 >>> 87          10 >>> 88           8 >>> 89           5 >>> 90           4 >>> 91          11 >>> 92           5 >>> 93           3 >>> 94           6 >>> 95           1 >>> 96           1 >>> 97           4 >>> 98           2 >>> 99           3 >>> 100 >>> 101 >>> 102 >>> 103 >>> 104 >>> 105 >>> 106 >>> 107 >>> 108 >>> 109           1 >>> 110 >>> 111 >>> 112 >>> 113 >>> 114           1 >>> 115 >>> 116 >>> 117 >>> 118 >>> 119 >>> 120 >>> 121 >>> 122 >>> 123 >>> 124 >>> 125 >>> 126 >>> 127           1 >>> 128           1 >>> 129           1 >>> 130           1 >>> 131 >>> 132 >>> 133           1 >>> 134           1 >>> 135 >>> 136           1 >>> 137           1 >>> 138           1 >>> 139 >>> 140 >>> 141           1 >>> 142 >>> 143           1 >>> 144           1 >>> 145 >>> 146           1 >>> 147           1 >>> 148           1 >>> 149           1 >>> 150           1 >>> 151           1 >>> 152           1 >>> 153           1 >>> 154           1 >>> 155 >>> 156           1 >>> 157           1 >>> 158           1 >>> 159           1 >>> 160           1 >>> 161 >>> 162 >>> 163           1 >>> 164           1 >>> 165           1 >>> 166 >>> 167 >>> 168 >>> 169 >>> 170           1 >>> 171           1 >>> 172           1 >>> 173 >>> 174           1 >>> 175           1 >>> 176           1 >>> 177           1 >>> 178           1 >>> 179           1 >>> 180           1 >>> 181           1 >>> 182           1 >>> 183           1 >>> 184           1 >>> 185           1 >>> 186           1 >>> 187           1 >>> 188           1 >>> 189           1 >>> 190           1 >>> 191           1 >>> 192           1 >>> >>> >>> Date: >>> From: >>> mailto:greve@nmr.mgh.harvard.edu> Re: [Freesurfer] Monte Carlo simulation: Talairach nmr.mgh.harvard.edu href="mailto:freesurfer@nmr.mgh.harvard.edu">mailto:freesurfer@nmr.mgh.harvard.edu <51C9C3BF.7000000@nmr.mgh.harvard.edu href="mailto:51C9C3BF.7000000@nmr.mgh.harvard.edu">mailto:51C9C3BF.7000000@nmr.mgh.harvard.edu> text/plain; charset=ISO-8859-1; format=flowed 10:08 AM, Emily Boeke wrote: running Monte Carlo simulations on functional data, and the information outputted in the cluster.summary file isn't sense. Usually the coordinates for the clusters listed are coordinates, but in the .summary files I'm getting, the are labeled "VoxX VoxY VoxZ" instead of "TalX TalY TalZ" the numbers are clearly not Talairach coordinates. Above the it says "Reporting Coordinates in Voxel Indices." I also that in the descriptive information above the table, it says None: Tal Coords invalid." the .nii files I'm seeing look like I would expect them too. using the same command line I've run before, so I have no idea the .summary file looks different. Does anyone know why this ____________________________ href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer rvard.edu/fswiki/BugReporting href="https://gate.nmr.mgh.harvard.edu/filedrop2">https://gate.nmr.mgh.harvard.edu/filedrop2 /facility/filedrop/index.html nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ________________________ href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___________________ href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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/